Research

Jump to: Review

Open AccessArticle Knockout of RNA Binding Protein MSI2 Impairs Follicle Development in the Mouse Ovary: Characterization of MSI1 and MSI2 during Folliculogenesis

by Jessie M. Sutherland, Alexander P. Sobinoff, Kara M. Gunter, Barbara A. Fraser, Victoria Pye, Ilana R. Bernstein, Evan Boon, Nicole A. Siddall, Luisa I. De Andres, Gary R. Hime, Janet E. Holt, Thomas Graf and Eileen A. McLaughlin

Biomolecules 2015, 5(3), 1228-1244; doi:10.3390/biom5031228

Received: 11 March 2015 / Revised: 29 May 2015 / Accepted: 9 June 2015 / Published: 26 June 2015

PDF Full-text (3815 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Characterizing the mechanisms underlying follicle development in the ovary is crucial to understanding female fertility and is an area of increasing research interest. The RNA binding protein Musashi is essential for post-transcriptional regulation of oocyte maturation in Xenopus and is expressed during ovarian

[...] Read more.

Characterizing the mechanisms underlying follicle development in the ovary is crucial to understanding female fertility and is an area of increasing research interest. The RNA binding protein Musashi is essential for post-transcriptional regulation of oocyte maturation in Xenopus and is expressed during ovarian development in Drosophila. In mammals Musashi is important for spermatogenesis and male fertility, but its role in the ovary has yet to be characterized. In this study we determined the expression of mammalian Musashi proteins MSI1 and MSI2 during mouse folliculogenesis, and through the use of a MSI2-specific knockout mouse model we identified that MSI2 is essential for normal follicle development. Time-course characterization of MSI1 and MSI2 revealed distinct differences in steady-state mRNA levels and protein expression/localization at important developmental time-points during folliculogenesis. Using a gene-trap mouse model that inactivates Msi2, we observed a significant decrease in ovarian mass, and change in follicle-stage composition due to developmental blocking of antral stage follicles and pre-antral follicle loss through atresia. We also confirmed that hormonally stimulated Msi2-deficient mice produce significantly fewer MII oocytes (60.9% less than controls, p < 0.05). Furthermore, the majority of these oocytes are of poor viability (62.2% non-viable/apoptotic, p < 0.05), which causes a reduction in female fertility evidenced by decreased litter size in Msi2-deficient animals (33.1% reduction to controls, p < 0.05). Our findings indicate that MSI1 and MSI2 display distinct expression profiles during mammalian folliculogenesis and that MSI2 is required for pre-antral follicle development. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

Open AccessArticle Study of Protein Phosphatase 2A (PP2A) Activity in LPS-Induced Tolerance Using Fluorescence-Based and Immunoprecipitation-Aided Methodology

by Lei Sun, Adlai L. Pappy, II, Tiffany T. Pham and Thomas P. Shanley

Biomolecules 2015, 5(3), 1284-1301; doi:10.3390/biom5031284

Received: 29 April 2015 / Revised: 3 June 2015 / Accepted: 4 June 2015 / Published: 29 June 2015

PDF Full-text (3584 KB) | HTML Full-text | XML Full-text

Abstract

Protein phosphatase 2A (PP2A) is one of the most abundant intracellular serine/threonine (Ser/Thr) phosphatases accounting for 1% of the total cellular protein content. PP2A is comprised of a heterodimeric core enzyme and a substrate-specific regulatory subunit. Potentially, at least seventy different compositions of

[...] Read more.

Protein phosphatase 2A (PP2A) is one of the most abundant intracellular serine/threonine (Ser/Thr) phosphatases accounting for 1% of the total cellular protein content. PP2A is comprised of a heterodimeric core enzyme and a substrate-specific regulatory subunit. Potentially, at least seventy different compositions of PP2A exist because of variable regulatory subunit binding that accounts for various activity modulating numerous cell functions. Due to the constitutive phosphatase activity present inside cells, a sensitive assay is required to detect the changes of PP2A activity under various experimental conditions. We optimized a fluorescence assay (DIFMU assay) by combining it with prior anti-PP2A immunoprecipitation to quantify PP2A-specific phosphatase activity. It is also known that prior exposure to lipopolysaccharides (LPS) induces “immune tolerance” of the cells to subsequent stimulation. Herein we report that PP2A activity is upregulated in tolerized peritoneal macrophages, corresponding to decreased TNF-α secretion upon second LPS stimulation. We further examined the role of PP2A in the tolerance effect by using PP2ACα^l°^xl°^x;lyM-Cre conditional knockout macrophages. We found that PP2A phosphatase activity cannot be further increased by tolerance. TNF-α secretion from tolerized PP2ACα^l°^xl°^x;lyM-Cre macrophages is higher than tolerized control macrophages. Furthermore, we showed that the increased TNF-α secretion may be due to an epigenetic transcriptionally active signature on the promoter of TNF-α gene rather than regulation of the NFκB/IκB signaling pathway. These results suggest a role for increased PP2A activity in the regulation of immune tolerance. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessArticle High-Resolution Respirometry for Simultaneous Measurement of Oxygen and Hydrogen Peroxide Fluxes in Permeabilized Cells, Tissue Homogenate and Isolated Mitochondria

by Marina Makrecka-Kuka, Gerhard Krumschnabel and Erich Gnaiger

Biomolecules 2015, 5(3), 1319-1338; doi:10.3390/biom5031319

Received: 7 April 2015 / Revised: 8 June 2015 / Accepted: 8 June 2015 / Published: 29 June 2015

Cited by 10 | PDF Full-text (6362 KB) | HTML Full-text | XML Full-text

Abstract

Whereas mitochondria are well established as the source of ATP in oxidative phosphorylation (OXPHOS), it is debated if they are also the major cellular sources of reactive oxygen species (ROS). Here we describe the novel approach of combining high-resolution respirometry and fluorometric measurement

[...] Read more.

Whereas mitochondria are well established as the source of ATP in oxidative phosphorylation (OXPHOS), it is debated if they are also the major cellular sources of reactive oxygen species (ROS). Here we describe the novel approach of combining high-resolution respirometry and fluorometric measurement of hydrogen peroxide (H₂O₂) production, applied to mitochondrial preparations (permeabilized cells, tissue homogenate, isolated mitochondria). The widely used H₂O₂ probe Amplex Red inhibited respiration in intact and permeabilized cells and should not be applied at concentrations above 10 µM. H₂O₂ fluxes were generally less than 1% of oxygen fluxes in physiological substrate and coupling states, specifically in permeabilized cells. H₂O₂ flux was consistently highest in the Complex II-linked LEAK state, reduced with CI&II-linked convergent electron flow and in mitochondria respiring at OXPHOS capacity, and were further diminished in uncoupled mitochondria respiring at electron transfer system capacity. Simultaneous measurement of mitochondrial respiration and H₂O₂ flux requires careful optimization of assay conditions and reveals information on mitochondrial function beyond separate analysis of ROS production. Full article

(This article belongs to the Special Issue Oxidative Stress and Oxygen Radicals) Printed Edition available

Open AccessArticle Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

by Rebecca Bish, Nerea Cuevas-Polo, Zhe Cheng, Dolores Hambardzumyan, Mathias Munschauer, Markus Landthaler and Christine Vogel

Biomolecules 2015, 5(3), 1441-1466; doi:10.3390/biom5031441

Received: 10 May 2015 / Accepted: 15 June 2015 / Published: 15 July 2015

Cited by 5 | PDF Full-text (2421 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and

[...] Read more.

DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6’s multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6’s interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions—many of which are likely conserved across eukaryotes. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

► Figures

Open AccessArticle Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform

by Yiyan Fei, Yung-Shin Sun, Yanhong Li, Hai Yu, Kam Lau, James P. Landry, Zeng Luo, Nicole Baumgarth, Xi Chen and Xiangdong Zhu

Biomolecules 2015, 5(3), 1480-1498; doi:10.3390/biom5031480

Received: 26 May 2015 / Revised: 9 June 2015 / Accepted: 6 July 2015 / Published: 16 July 2015

Cited by 8 | PDF Full-text (1277 KB) | HTML Full-text | XML Full-text

Abstract

A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA), with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and

[...] Read more.

A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA), with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and track the pandemic potential of an influenza virus strain. We demonstrate a label-free glycan microarray assay platform for acquiring influenza virus binding profiles against a wide variety of glycan receptors. By immobilizing biotinylated receptors on a streptavidin-functionalized solid surface, we measured binding curves of five influenza A virus strains with 24 glycans of diverse structures and used the apparent equilibrium dissociation constants (avidity constants, 10–100 pM) as characterizing parameters of viral receptor profiles. Furthermore by measuring binding kinetic constants of solution-phase glycans to immobilized viruses, we confirmed that the glycan-HA affinity constant is in the range of 10 mM and the reaction is enthalpy-driven. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessArticle Co-Expression of NEU2 and GBA3 Causes a Drastic Reduction in Cytosolic Sialyl Free N-glycans in Human MKN45 Stomach Cancer Cells—Evidence for the Physical Interaction of NEU2 and GBA3

by Li Wang, Junichi Seino, Haruna Tomotake, Yoko Funakoshi, Hiroto Hirayama and Tadashi Suzuki

Biomolecules 2015, 5(3), 1499-1514; doi:10.3390/biom5031499

Received: 10 June 2015 / Revised: 6 July 2015 / Accepted: 7 July 2015 / Published: 16 July 2015

Cited by 3 | PDF Full-text (869 KB) | HTML Full-text | XML Full-text

Abstract

It is well known that the “free” form of glycans that are structurally related to asparagine (N)-linked glycans (“free N-glycans”) are found in a wide variety of organisms. The mechanisms responsible for the formation/degradation of high mannose-type free N-glycans have been

[...] Read more.

It is well known that the “free” form of glycans that are structurally related to asparagine (N)-linked glycans (“free N-glycans”) are found in a wide variety of organisms. The mechanisms responsible for the formation/degradation of high mannose-type free N-glycans have been extensively studied in mammalian cells. Recent evidence, however, also suggests that sialylated, complex-type free N-glycans are also present in the cytosol of various mammalian-derived cultured cells/tissues. We report herein on an investigation of the mechanism responsible for the degradation of such sialyl free N-glycans. The findings show that the amount of glycans is dramatically reduced upon the co-expression of cytosolic sialidase NEU2 with cytosolic β-glycosidase GBA3 in human stomach cancer-derived MKN45 cells. The physical interaction between NEU2 and GBA3 was confirmed by co-precipitation analyses as well as gel filtration assays. The NEU2 protein was found to be stabilized in the presence of GBA3 both in cellulo and in vitro. Our results thus indicate that cytosolic GBA3 is likely involved in the catabolism of cytosolic sialyl free N-glycans, possibly by stabilizing the activity of the NEU2 protein. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessArticle Mammalian Cell Surface Display as a Novel Method for Developing Engineered Lectins with Novel Characteristics

by Keisuke Soga, Hirohito Abo, Sheng-Ying Qin, Takuya Kyoutou, Keiko Hiemori, Hiroaki Tateno, Naoki Matsumoto, Jun Hirabayashi and Kazuo Yamamoto

Biomolecules 2015, 5(3), 1540-1562; doi:10.3390/biom5031540

Received: 17 May 2015 / Revised: 16 June 2015 / Accepted: 18 June 2015 / Published: 20 July 2015

Cited by 3 | PDF Full-text (3770 KB) | HTML Full-text | XML Full-text

Abstract

Leguminous lectins have a conserved carbohydrate recognition site comprising four loops (A–D). Here, we randomly mutated the sequence and length of loops C and D of peanut agglutinin (PNA) and expressed the proteins on the surface of mouse green fluorescent protein (GFP)-reporter cells.

[...] Read more.

Leguminous lectins have a conserved carbohydrate recognition site comprising four loops (A–D). Here, we randomly mutated the sequence and length of loops C and D of peanut agglutinin (PNA) and expressed the proteins on the surface of mouse green fluorescent protein (GFP)-reporter cells. Flow cytometry, limiting dilution, and cDNA cloning were used to screen for several mutated PNAs with distinct properties. The mutated PNA clones obtained using NeuAcα2-6(Galβ1-3)GalNAc as a ligand showed preference for NeuAcα2-6(Galβ1-3)GalNAc rather than non-sialylated Galβ1-3GlcNAc, whereas wild-type PNA binds to Galβ1-3GlcNAc but not sialylated Galβ1-3GalNAc. Sequence analyses revealed that for all of the glycan-reactive mutated PNA clones, (i) loop C was eight amino acids in length, (ii) loop D was identical to that of wild-type PNA, (iii) residue 127 was asparagine, (iv) residue 125 was tryptophan, and (v) residue 130 was hydrophobic tyrosine, phenylalanine, or histidine. The sugar-binding ability of wild-type PNA was increased nine-fold when Tyr125 was mutated to tryptophan, and that of mutated clone C was increased more than 30-fold after His130 was changed to tyrosine. These results provide an insight into the relationship between the amino acid sequences of the carbohydrate recognition site and sugar-binding abilities of leguminous lectins. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

► Figures

Open AccessArticle Toxic Oligomeric Alpha-Synuclein Variants Present in Human Parkinson’s Disease Brains Are Differentially Generated in Mammalian Cell Models

by Wei Xin, Sharareh Emadi, Stephanie Williams, Qiang Liu, Philip Schulz, Ping He, Now Bahar Alam, Jie Wu and Michael R. Sierks

Biomolecules 2015, 5(3), 1634-1651; doi:10.3390/biom5031634

Received: 15 January 2015 / Revised: 17 June 2015 / Accepted: 26 June 2015 / Published: 22 July 2015

Cited by 13 | PDF Full-text (4075 KB) | HTML Full-text | XML Full-text

Abstract

Misfolding and aggregation of α-synuclein into toxic soluble oligomeric α-synuclein aggregates has been strongly correlated with the pathogenesis of Parkinson’s disease (PD). Here, we show that two different morphologically distinct oligomeric α-synuclein aggregates are present in human post-mortem PD brain tissue and are

[...] Read more.

Misfolding and aggregation of α-synuclein into toxic soluble oligomeric α-synuclein aggregates has been strongly correlated with the pathogenesis of Parkinson’s disease (PD). Here, we show that two different morphologically distinct oligomeric α-synuclein aggregates are present in human post-mortem PD brain tissue and are responsible for the bulk of α-synuclein induced toxicity in brain homogenates from PD samples. Two antibody fragments that selectively bind the different oligomeric α-synuclein variants block this α-synuclein induced toxicity and are useful tools to probe how various cell models replicate the α-synuclein aggregation pattern of human PD brain. Using these reagents, we show that mammalian cell type strongly influences α-synuclein aggregation, where neuronal cells best replicate the PD brain α-synuclein aggregation profile. Overexpression of α-synuclein in the different cell lines increased protein aggregation but did not alter the morphology of the oligomeric aggregates generated. Differentiation of the neuronal cells into a cholinergic-like or dopaminergic-like phenotype increased the levels of oligomeric α-synuclein where the aggregates were localized in cell neurites and cell bodies. Full article

(This article belongs to the Special Issue Exploring the Mechanisms by which α-Synuclein Kills Cells in Parkinson Disease)

Open AccessArticle Galectin Binding to Neo-Glycoproteins: LacDiNAc Conjugated BSA as Ligand for Human Galectin-3

by Sophia Böcker, Dominic Laaf and Lothar Elling

Biomolecules 2015, 5(3), 1671-1696; doi:10.3390/biom5031671

Received: 28 May 2015 / Revised: 26 June 2015 / Accepted: 10 July 2015 / Published: 24 July 2015

Cited by 7 | PDF Full-text (2638 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Carbohydrate-lectin interactions are relatively weak. As they play an important role in biological recognition processes, multivalent glycan ligands are designed to enhance binding affinity and inhibitory potency. We here report on novel neo-glycoproteins based on bovine serum albumin as scaffold for multivalent presentation

[...] Read more.

Carbohydrate-lectin interactions are relatively weak. As they play an important role in biological recognition processes, multivalent glycan ligands are designed to enhance binding affinity and inhibitory potency. We here report on novel neo-glycoproteins based on bovine serum albumin as scaffold for multivalent presentation of ligands for galectins. We prepared two kinds of tetrasaccharides (N-acetyllactosamine and N,N-diacetyllactosamine terminated) by multi-step chemo-enzymatic synthesis utilizing recombinant glycosyltransferases. Subsequent conjugation of these glycans to lysine groups of bovine serum albumin via squaric acid diethyl ester yielded a set of 22 different neo-glycoproteins with tuned ligand density. The neo-glycoproteins were analyzed by biochemical and chromatographic methods proving various modification degrees. The neo-glycoproteins were used for binding and inhibition studies with human galectin-3 showing high affinity. Binding strength and inhibition potency are closely related to modification density and show binding enhancement by multivalent ligand presentation. At galectin-3 concentrations comparable to serum levels of cancer patients, we detect the highest avidities. Selectivity of N,N-diacetyllactosamine terminated structures towards galectin-3 in comparison to galectin-1 is demonstrated. Moreover, we also see strong inhibitory potency of our scaffolds towards galectin-3 binding. These novel neo-glycoproteins may therefore serve as selective and strong galectin-3 ligands in cancer related biomedical research. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

► Figures

Open AccessArticle Extracellular Vesicles from Ovarian Carcinoma Cells Display Specific Glycosignatures

by Joana Gomes, Patrícia Gomes-Alves, Sofia B. Carvalho, Cristina Peixoto, Paula M. Alves, Peter Altevogt and Julia Costa

Biomolecules 2015, 5(3), 1741-1761; doi:10.3390/biom5031741

Received: 21 June 2015 / Revised: 22 June 2015 / Accepted: 28 July 2015 / Published: 4 August 2015

Cited by 8 | PDF Full-text (2635 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Cells release vesicles to the extracellular environment with characteristic nucleic acid, protein, lipid, and glycan composition. Here we have isolated and characterized extracellular vesicles (EVs) and total cell membranes (MBs) from ovarian carcinoma OVMz cells. EVs were enriched in specific markers, including Tsg101,

[...] Read more.

Cells release vesicles to the extracellular environment with characteristic nucleic acid, protein, lipid, and glycan composition. Here we have isolated and characterized extracellular vesicles (EVs) and total cell membranes (MBs) from ovarian carcinoma OVMz cells. EVs were enriched in specific markers, including Tsg101, CD63, CD9, annexin-I, and MBs contained markers of cellular membrane compartments, including calnexin, GRASP65, GS28, LAMP-1, and L1CAM. The glycoprotein galectin-3 binding protein (LGALS3BP) was strongly enriched in EVs and it contained sialylated complex N-glycans. Lectin blotting with a panel of lectins showed that EVs had specific glycosignatures relative to MBs. Furthermore, the presence of glycoproteins bearing complex N-glycans with α2,3-linked sialic acid, fucose, bisecting-GlcNAc and LacdiNAc structures, and O-glycans with the T-antigen were detected. The inhibition of N-glycosylation processing from high mannose to complex glycans using kifunensine caused changes in the composition of EVs and induced a decrease of several glycoproteins. In conclusion, the results showed that glycosignatures of EVs were specific and altered glycosylation within the cell affected the composition and/or dynamics of EVs release. Furthermore, the identified glycosignatures of EVs could provide novel biomarkers for ovarian cancer. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessArticle A Panel of Recombinant Mucins Carrying a Repertoire of Sialylated O-Glycans Based on Different Core Chains for Studies of Glycan Binding Proteins

by Reeja Maria Cherian, Chunsheng Jin, Jining Liu, Niclas G. Karlsson and Jan Holgersson

Biomolecules 2015, 5(3), 1810-1831; doi:10.3390/biom5031810

Received: 23 June 2015 / Revised: 3 August 2015 / Accepted: 4 August 2015 / Published: 12 August 2015

Cited by 2 | PDF Full-text (3506 KB) | HTML Full-text | XML Full-text

Abstract

Sialylated glycans serve as key elements of receptors for many viruses, bacteria, and bacterial toxins. The microbial recognition and their binding specificity can be affected by the linkage of the terminal sugar residue, types of underlying sugar chains, and the nature of the

[...] Read more.

Sialylated glycans serve as key elements of receptors for many viruses, bacteria, and bacterial toxins. The microbial recognition and their binding specificity can be affected by the linkage of the terminal sugar residue, types of underlying sugar chains, and the nature of the entire glycoconjugate. Owing to the pathobiological significance of sialylated glycans, we have engineered Chinese hamster ovary (CHO) cells to secrete mucin-type immunoglobulin-fused proteins carrying terminal α2,3- or α2,6-linked sialic acid on defined O-glycan core saccharide chains. Besides stably expressing P-selectin glycoprotein ligand-1/mouse immunoglobulin G2b cDNA (PSGL-1/mIgG2b), CHO cells were stably transfected with plasmids encoding glycosyltransferases to synthesize core 2 (GCNT1), core 3 (B3GNT6), core 4 (GCNT1 and B3GNT6), or extended core 1 (B3GNT3) chains with or without the type 1 chain-encoding enzyme B3GALT5 and ST6GAL1. Western blot and liquid chromatography-mass spectrometry analysis confirmed the presence of core 1, 2, 3, 4, and extended core 1 chains carrying either type 1 (Galb3GlcNAc) or type 2 (Galb4GlcNAc) outer chains with or without α2,6-linked sialic acids. This panel of recombinant mucins carrying a repertoire of sialylated O-glycans will be important tools in studies aiming at determining the fine O-glycan binding specificity of sialic acid-specific microbial adhesins and mammalian lectins. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessArticle Complementary LC-MS/MS-Based N-Glycan, N-Glycopeptide, and Intact N-Glycoprotein Profiling Reveals Unconventional Asn71-Glycosylation of Human Neutrophil Cathepsin G

by Ian Loke, Nicolle H. Packer and Morten Thaysen-Andersen

Biomolecules 2015, 5(3), 1832-1854; doi:10.3390/biom5031832

Received: 9 June 2015 / Revised: 20 July 2015 / Accepted: 6 August 2015 / Published: 12 August 2015

Cited by 10 | PDF Full-text (2604 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Neutrophil cathepsin G (nCG) is a central serine protease in the human innate immune system, but the importance of its N-glycosylation remains largely undescribed. To facilitate such investigations, we here use complementary LC-MS/MS-based N-glycan, N-glycopeptide, and intact glycoprotein profiling to

[...] Read more.

Neutrophil cathepsin G (nCG) is a central serine protease in the human innate immune system, but the importance of its N-glycosylation remains largely undescribed. To facilitate such investigations, we here use complementary LC-MS/MS-based N-glycan, N-glycopeptide, and intact glycoprotein profiling to accurately establish the micro- and macro-heterogeneity of nCG from healthy individuals. The fully occupied Asn71 carried unconventional N-glycosylation consisting of truncated chitobiose core (GlcNAcβ: 55.2%; Fucα1,6GlcNAcβ: 22.7%), paucimannosidic N-glycans (Manβ1,4GlcNAcβ1,4GlcNAcβ: 10.6%; Manβ1,4GlcNAcβ1,4(Fucα1,6)GlcNAcβ: 7.9%; Manα1,6Manβ1,4GlcNAcβ1,4GlcNAcβ: 3.7%, trace level of Manα1,6Manβ1,4GlcNAcβ1,4(Fucα1,6)GlcNAcβ), and trace levels of monoantennary α2,6- and α2,3-sialylated complex N-glycans. High-resolution/mass accuracy LC-MS profiling of intact nCG confirmed the Asn71-glycoprofile and identified two C-terminal truncation variants at Arg243 (57.8%) and Ser244 (42.2%), both displaying oxidation of solvent-accessible Met152. Asn71 appeared proximal (~19 Å) to the active site of nCG, but due to the truncated nature of Asn71-glycans (~5–17 Å) we questioned their direct modulation of the proteolytic activity of the protein. This work highlights the continued requirement of using complementary technologies to accurately profile even relatively simple glycoproteins and illustrates important challenges associated with the analysis of unconventional protein N-glycosylation. Importantly, this study now facilitates investigation of the functional role of nCG Asn71-glycosylation. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

► Figures

Open AccessArticle Optimized Production of Xylitol from Xylose Using a Hyper-Acidophilic Candida tropicalis

by Elena Tamburini, Stefania Costa, Maria Gabriella Marchetti and Paola Pedrini

Biomolecules 2015, 5(3), 1979-1989; doi:10.3390/biom5031979

Received: 6 May 2015 / Revised: 31 July 2015 / Accepted: 3 August 2015 / Published: 19 August 2015

Cited by 2 | PDF Full-text (644 KB) | HTML Full-text | XML Full-text

Abstract

The yeast Candida tropicalis DSM 7524 produces xylitol, a natural, low-calorie sweetener, by fermentation of xylose. In order to increase xylitol production rate during the submerged fermentation process, some parameters-substrate (xylose) concentration, pH, aeration rate, temperature and fermentation strategy-have been optimized. The maximum

[...] Read more.

The yeast Candida tropicalis DSM 7524 produces xylitol, a natural, low-calorie sweetener, by fermentation of xylose. In order to increase xylitol production rate during the submerged fermentation process, some parameters-substrate (xylose) concentration, pH, aeration rate, temperature and fermentation strategy-have been optimized. The maximum xylitol yield reached at 60–80 g/L initial xylose concentration, pH 5.5 at 37 °C was 83.66% (w/w) on consumed xylose in microaerophilic conditions (k_La = 2·h⁻¹). Scaling up on 3 L fermenter, with a fed-batch strategy, the best xylitol yield was 86.84% (w/w), against a 90% of theoretical yield. The hyper-acidophilic behaviour of C. tropicalis makes this strain particularly promising for industrial application, due to the possibility to work in non-sterile conditions. Full article

Open AccessArticle Histone Deacetylase Inhibitors Activate Tristetraprolin Expression through Induction of Early Growth Response Protein 1 (EGR1) in Colorectal Cancer Cells

by Cyril Sobolewski, Sandhya Sanduja, Fernando F. Blanco, Liangyan Hu and Dan A. Dixon

Biomolecules 2015, 5(3), 2035-2055; doi:10.3390/biom5032035

Received: 21 May 2015 / Revised: 30 July 2015 / Accepted: 10 August 2015 / Published: 28 August 2015

Cited by 10 | PDF Full-text (2288 KB) | HTML Full-text | XML Full-text

Abstract

The RNA-binding protein tristetraprolin (TTP) promotes rapid decay of mRNAs bearing 3' UTR AU-rich elements (ARE). In many cancer types, loss of TTP expression is observed allowing for stabilization of ARE-mRNAs and their pathologic overexpression. Here we demonstrate that histone deacetylase (HDAC) inhibitors

[...] Read more.

The RNA-binding protein tristetraprolin (TTP) promotes rapid decay of mRNAs bearing 3' UTR AU-rich elements (ARE). In many cancer types, loss of TTP expression is observed allowing for stabilization of ARE-mRNAs and their pathologic overexpression. Here we demonstrate that histone deacetylase (HDAC) inhibitors (Trichostatin A, SAHA and sodium butyrate) promote TTP expression in colorectal cancer cells (HCA-7, HCT-116, Moser and SW480 cells) and cervix carcinoma cells (HeLa). We found that HDAC inhibitors-induced TTP expression, promote the decay of COX-2 mRNA, and inhibit cancer cell proliferation. HDAC inhibitors were found to promote TTP transcription through activation of the transcription factor Early Growth Response protein 1 (EGR1). Altogether, our findings indicate that loss of TTP in tumors occurs through silencing of EGR1 and suggests a therapeutic approach to rescue TTP expression in colorectal cancer. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

Review

Jump to: Research

Open AccessReview New Insights into the Functions of Transcription Factors that Bind the RNA Polymerase Secondary Channel

by Nikolay Zenkin and Yulia Yuzenkova

Biomolecules 2015, 5(3), 1195-1209; doi:10.3390/biom5031195

Received: 17 March 2015 / Revised: 6 May 2015 / Accepted: 9 June 2015 / Published: 25 June 2015

Cited by 5 | PDF Full-text (1461 KB) | HTML Full-text | XML Full-text

Abstract

Transcription elongation is regulated at several different levels, including control by various accessory transcription elongation factors. A distinct group of these factors interacts with the RNA polymerase secondary channel, an opening at the enzyme surface that leads to its active center. Despite investigation

[...] Read more.

Transcription elongation is regulated at several different levels, including control by various accessory transcription elongation factors. A distinct group of these factors interacts with the RNA polymerase secondary channel, an opening at the enzyme surface that leads to its active center. Despite investigation for several years, the activities and in vivo roles of some of these factors remain obscure. Here, we review the recent progress in understanding the functions of the secondary channel binding factors in bacteria. In particular, we highlight the surprising role of global regulator DksA in fidelity of RNA synthesis and the resolution of RNA polymerase traffic jams by the Gre factor. These findings indicate a potential link between transcription fidelity and collisions of the transcription and replication machineries. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

Open AccessReview Synthetic Proteins and Peptides for the Direct Interrogation of α-Synuclein Posttranslational Modifications

by Matthew R. Pratt, Tharindumala Abeywardana and Nicholas P. Marotta

Biomolecules 2015, 5(3), 1210-1227; doi:10.3390/biom5031210

Received: 17 March 2015 / Revised: 17 May 2015 / Accepted: 9 June 2015 / Published: 25 June 2015

Cited by 2 | PDF Full-text (3205 KB) | HTML Full-text | XML Full-text

Abstract

α-Synuclein is the aggregation-prone protein associated with Parkinson’s disease (PD) and related neurodegenerative diseases. Complicating both its biological functions and toxic aggregation are a variety of posttranslational modifications. These modifications have the potential to either positively or negatively affect α-synuclein aggregation, raising the

[...] Read more.

α-Synuclein is the aggregation-prone protein associated with Parkinson’s disease (PD) and related neurodegenerative diseases. Complicating both its biological functions and toxic aggregation are a variety of posttranslational modifications. These modifications have the potential to either positively or negatively affect α-synuclein aggregation, raising the possibility that the enzymes that add or remove these modifications could be therapeutic targets in PD. Synthetic protein chemistry is uniquely positioned to generate site-specifically and homogeneously modified proteins for biochemical study. Here, we review the application of synthetic peptides and proteins towards understanding the effects of α-synuclein posttranslational modifications. Full article

(This article belongs to the Special Issue Exploring the Mechanisms by which α-Synuclein Kills Cells in Parkinson Disease)

Open AccessReview Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

by Mark S. Paget

Biomolecules 2015, 5(3), 1245-1265; doi:10.3390/biom5031245

Received: 20 March 2015 / Revised: 20 May 2015 / Accepted: 1 June 2015 / Published: 26 June 2015

Cited by 22 | PDF Full-text (2547 KB) | HTML Full-text | XML Full-text

Abstract

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the

[...] Read more.

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2–4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor. Full article

(This article belongs to the Special Issue Bacterial RNA Polymerase)

Open AccessReview NF-kappaB Signaling in Chronic Inflammatory Airway Disease

by Michael Schuliga

Biomolecules 2015, 5(3), 1266-1283; doi:10.3390/biom5031266

Received: 28 April 2015 / Revised: 31 May 2015 / Accepted: 4 June 2015 / Published: 26 June 2015

Cited by 31 | PDF Full-text (274 KB) | HTML Full-text | XML Full-text

Abstract

Asthma and chronic obstructive pulmonary disease (COPD) are obstructive airway disorders which differ in their underlying causes and phenotypes but overlap in patterns of pharmacological treatments. In both asthma and COPD, oxidative stress contributes to airway inflammation by inducing inflammatory gene expression. The

[...] Read more.

Asthma and chronic obstructive pulmonary disease (COPD) are obstructive airway disorders which differ in their underlying causes and phenotypes but overlap in patterns of pharmacological treatments. In both asthma and COPD, oxidative stress contributes to airway inflammation by inducing inflammatory gene expression. The redox-sensitive transcription factor, nuclear factor (NF)-kappaB (NF-κB), is an important participant in a broad spectrum of inflammatory networks that regulate cytokine activity in airway pathology. The anti-inflammatory actions of glucocorticoids (GCs), a mainstay treatment for asthma, involve inhibition of NF-κB induced gene transcription. Ligand bound GC receptors (GRs) bind NF-κB to suppress the transcription of NF-κB responsive genes (i.e., transrepression). However, in severe asthma and COPD, the transrepression of NF-κB by GCs is negated as a consequence of post-translational changes to GR and histones involved in chromatin remodeling. Therapeutics which target NF-κB activation, including inhibitors of IκB kinases (IKKs) are potential treatments for asthma and COPD. Furthermore, reversing GR/histone acetylation shows promise as a strategy to treat steroid refractory airway disease by augmenting NF-κB transrepression. This review examines NF-κB signaling in airway inflammation and its potential as target for treatment of asthma and COPD. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Molecular Interactions between NR4A Orphan Nuclear Receptors and NF-κB Are Required for Appropriate Inflammatory Responses and Immune Cell Homeostasis

by Evelyn P. Murphy and Daniel Crean

Biomolecules 2015, 5(3), 1302-1318; doi:10.3390/biom5031302

Received: 30 April 2015 / Revised: 16 June 2015 / Accepted: 16 June 2015 / Published: 29 June 2015

Cited by 11 | PDF Full-text (271 KB) | HTML Full-text | XML Full-text

Abstract

Appropriate innate and adaptive immune responses are essential for protection and resolution against chemical, physical or biological insults. Immune cell polarization is fundamental in orchestrating distinct phases of inflammation, specifically acute phase responses followed by resolution and tissue repair. Dysregulation of immune cell

[...] Read more.

Appropriate innate and adaptive immune responses are essential for protection and resolution against chemical, physical or biological insults. Immune cell polarization is fundamental in orchestrating distinct phases of inflammation, specifically acute phase responses followed by resolution and tissue repair. Dysregulation of immune cell and inflammatory responses is a hallmark of multiple diseases encompassing atherosclerosis, rheumatoid arthritis, psoriasis and metabolic syndromes. A master transcriptional mediator of diverse inflammatory signaling and immune cell function is NF-κB, and altered control of this key regulator can lead to an effective switch from acute to chronic inflammatory responses. Members of the nuclear receptor (NR) superfamily of ligand-dependent transcription factors crosstalk with NF-κB to regulate immune cell function(s). Within the NR superfamily the NR4A1-3 orphan receptors have emerged as important regulators of immune cell polarization and NF-κB signaling. NR4A receptors modulate NF-κB activity in a dynamic fashion, either repressing or enhancing target gene expression leading to altered inflammatory outcome. Here we will discuss the pivotal role NR4A’s receptors play in orchestrating immune cell homeostasis through molecular crosstalk with NF-κB. Specifically, we will examine such NR4A/NF-κB interactions within the context of distinct cell phenotypes, including monocyte, macrophage, T cells, endothelial, and mesenchymal cells, which play a role in inflammation-associated disease. Finally, we review the therapeutic potential of altering NR4A/NF-κB interactions to limit hyper-inflammatory responses in vivo. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

► Figures

Open AccessReview Biomolecules and Biomarkers Used in Diagnosis of Alcohol Drinking and in Monitoring Therapeutic Interventions

by Radu M. Nanau and Manuela G. Neuman

Biomolecules 2015, 5(3), 1339-1385; doi:10.3390/biom5031339

Received: 9 April 2015 / Revised: 15 May 2015 / Accepted: 29 May 2015 / Published: 29 June 2015

Cited by 17 | PDF Full-text (228 KB) | HTML Full-text | XML Full-text

Abstract

Background: The quantitative, measurable detection of drinking is important for the successful treatment of alcohol misuse in transplantation of patients with alcohol disorders, people living with human immunodeficiency virus that need to adhere to medication, and special occupational hazard offenders, many of whom

[...] Read more.

Background: The quantitative, measurable detection of drinking is important for the successful treatment of alcohol misuse in transplantation of patients with alcohol disorders, people living with human immunodeficiency virus that need to adhere to medication, and special occupational hazard offenders, many of whom continually deny drinking. Their initial misconduct usually leads to medical problems associated with drinking, impulsive social behavior, and drunk driving. The accurate identification of alcohol consumption via biochemical tests contributes significantly to the monitoring of drinking behavior. Methods: A systematic review of the current methods used to measure biomarkers of alcohol consumption was conducted using PubMed and Google Scholar databases (2010–2015). The names of the tests have been identified. The methods and publications that correlate between the social instruments and the biochemical tests were further investigated. There is a clear need for assays standardization to ensure the use of these biochemical tests as routine biomarkers. Findings: Alcohol ingestion can be measured using a breath test. Because alcohol is rapidly eliminated from the circulation, the time for detection by this analysis is in the range of hours. Alcohol consumption can alternatively be detected by direct measurement of ethanol concentration in blood or urine. Several markers have been proposed to extend the interval and sensitivities of detection, including ethyl glucuronide and ethyl sulfate in urine, phosphatidylethanol in blood, and ethyl glucuronide and fatty acid ethyl esters in hair, among others. Moreover, there is a need to correlate the indirect biomarker carbohydrate deficient transferrin, which reflects longer lasting consumption of higher amounts of alcohol, with serum γ-glutamyl transpeptidase, another long term indirect biomarker that is routinely used and standardized in laboratory medicine. Full article

(This article belongs to the collection Multi-Organ Alcohol-Related Damage: Mechanisms and Treatment)

Open AccessReview Transcription of Interleukin-8: How Altered Regulation Can Affect Cystic Fibrosis Lung Disease

by Karim Jundi and Catherine M. Greene

Biomolecules 2015, 5(3), 1386-1398; doi:10.3390/biom5031386

Received: 1 May 2015 / Revised: 19 June 2015 / Accepted: 20 June 2015 / Published: 1 July 2015

Cited by 14 | PDF Full-text (176 KB) | HTML Full-text | XML Full-text

Abstract

Interleukin-8 (IL-8) is a neutrophil chemokine that is encoded on the CXCL8 gene. Normally CXCL8 expression is repressed due to histone deacetylation, octamer-1 binding to the promoter and the inhibitory effect of nuclear factor-κB repressing factor (NRF). However, in response to a suitable

[...] Read more.

Interleukin-8 (IL-8) is a neutrophil chemokine that is encoded on the CXCL8 gene. Normally CXCL8 expression is repressed due to histone deacetylation, octamer-1 binding to the promoter and the inhibitory effect of nuclear factor-κB repressing factor (NRF). However, in response to a suitable stimulus, the human CXCL8 gene undergoes transcription due to its inducible promoter that is regulated by the transcription factors nuclear factor-κB (NF-κB), activating protein (AP-1), CAAT/enhancer-binding protein β (C/EBPβ, also known as NF-IL-6), C/EBP homologous protein (CHOP) and cAMP response element binding protein (CREB). CXCL8 mRNA is then stabilised by the activity of p38 mitogen-activated protein kinase (p38 MAPK). Cystic fibrosis (CF) lung disease is characterised by a neutrophil-dominated airway inflammatory response. A major factor contributing to the large number of neutrophils is the higher than normal levels of IL-8 that are present within the CF lung. Infection and inflammation, together with intrinsic alterations in CF airway cells are responsible for the abnormally high intrapulmonary levels of IL-8. Strategies to inhibit aberrantly high CXCL8 expression hold therapeutic potential for CF lung disease. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Activation of Proinflammatory Responses in Cells of the Airway Mucosa by Particulate Matter: Oxidant- and Non-Oxidant-Mediated Triggering Mechanisms

by Johan Øvrevik, Magne Refsnes, Marit Låg, Jørn A. Holme and Per E. Schwarze

Biomolecules 2015, 5(3), 1399-1440; doi:10.3390/biom5031399

Received: 18 May 2015 / Revised: 16 June 2015 / Accepted: 16 June 2015 / Published: 2 July 2015

Cited by 22 | PDF Full-text (3314 KB) | HTML Full-text | XML Full-text

Abstract

Inflammation is considered to play a central role in a diverse range of disease outcomes associated with exposure to various types of inhalable particulates. The initial mechanisms through which particles trigger cellular responses leading to activation of inflammatory responses are crucial to clarify

[...] Read more.

Inflammation is considered to play a central role in a diverse range of disease outcomes associated with exposure to various types of inhalable particulates. The initial mechanisms through which particles trigger cellular responses leading to activation of inflammatory responses are crucial to clarify in order to understand what physico-chemical characteristics govern the inflammogenic activity of particulate matter and why some particles are more harmful than others. Recent research suggests that molecular triggering mechanisms involved in activation of proinflammatory genes and onset of inflammatory reactions by particles or soluble particle components can be categorized into direct formation of reactive oxygen species (ROS) with subsequent oxidative stress, interaction with the lipid layer of cellular membranes, activation of cell surface receptors, and direct interactions with intracellular molecular targets. The present review focuses on the immediate effects and responses in cells exposed to particles and central down-stream signaling mechanisms involved in regulation of proinflammatory genes, with special emphasis on the role of oxidant and non-oxidant triggering mechanisms. Importantly, ROS act as a central second-messenger in a variety of signaling pathways. Even non-oxidant mediated triggering mechanisms are therefore also likely to activate downstream redox-regulated events. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Is Cell Death Primary or Secondary in the Pathophysiology of Idiopathic Parkinson’s Disease?

by Walter J. Schulz-Schaeffer

Biomolecules 2015, 5(3), 1467-1479; doi:10.3390/biom5031467

Received: 24 March 2015 / Revised: 21 May 2015 / Accepted: 1 July 2015 / Published: 16 July 2015

Cited by 8 | PDF Full-text (261 KB) | HTML Full-text | XML Full-text

Abstract

Currently, the pathophysiology of idiopathic Parkinson’s disease is explained by a loss of mainly dopaminergic nerve cells that causes a neurotransmitter deficiency. In the final stage of the disease, there is a marked loss of neurons in the substantia nigra. In addition, Lewy

[...] Read more.

Currently, the pathophysiology of idiopathic Parkinson’s disease is explained by a loss of mainly dopaminergic nerve cells that causes a neurotransmitter deficiency. In the final stage of the disease, there is a marked loss of neurons in the substantia nigra. In addition, Lewy bodies can be found in some of the remaining neurons, which serve as the pathological hallmark of the disease. These Lewy bodies are composed mainly of aggregated α-synuclein, a physiological presynaptic protein. Lewy bodies were thought to be the pathophysiologically relevant form of α-synuclein because their appearance coincided with neuron loss in the substantia nigra. In consequence, neuron loss was thought to be the primary step in the neurodegeneration in Parkinson’s disease. On the other hand, the clinical syndrome suggests a synaptic disorder. If α-synuclein aggregation was causally linked to the pathophysiology of disease, α-synuclein pathology should be found at the synapse. As recently demonstrated, one to two orders of magnitude more α-synuclein aggregates are present in presynaptic terminals than in Lewy bodies or Lewy neurites. Degeneration of dendritic spines associated with synaptic α-synuclein aggregates has been shown to occur in human disease. In experiments, using transgenic mice or cell cultures, mild (two- to three-fold) overexpression of α-synuclein caused an altered vesicle turnover and led to a reduction in neurotransmitter release. Different approaches linked these alterations to presynaptic aggregation of α-synuclein. These findings may fundamentally change the pathophysiological concept of Parkinson’s disease: not nerve cell loss, but the synaptic dysfunction of still existing nerve cells should become the focus of attention. From recent findings, it is quite evident that the death of dopaminergic neurons is a secondary event in the pathophysiology of Parkinson’s disease. Full article

(This article belongs to the Special Issue Exploring the Mechanisms by which α-Synuclein Kills Cells in Parkinson Disease)

Open AccessReview The 3' to 5' Exoribonuclease DIS3: From Structure and Mechanisms to Biological Functions and Role in Human Disease

by Sophie R. Robinson, Antony W. Oliver, Timothy J. Chevassut and Sarah F. Newbury

Biomolecules 2015, 5(3), 1515-1539; doi:10.3390/biom5031515

Received: 18 May 2015 / Revised: 1 July 2015 / Accepted: 6 July 2015 / Published: 17 July 2015

Cited by 6 | PDF Full-text (3761 KB) | HTML Full-text | XML Full-text

Abstract

DIS3 is a conserved exoribonuclease and catalytic subunit of the exosome, a protein complex involved in the 3' to 5' degradation and processing of both nuclear and cytoplasmic RNA species. Recently, aberrant expression of DIS3 has been found to be implicated in a

[...] Read more.

DIS3 is a conserved exoribonuclease and catalytic subunit of the exosome, a protein complex involved in the 3' to 5' degradation and processing of both nuclear and cytoplasmic RNA species. Recently, aberrant expression of DIS3 has been found to be implicated in a range of different cancers. Perhaps most striking is the finding that DIS3 is recurrently mutated in 11% of multiple myeloma patients. Much work has been done to elucidate the structural and biochemical characteristics of DIS3, including the mechanistic details of its role as an effector of RNA decay pathways. Nevertheless, we do not understand how DIS3 mutations can lead to cancer. There are a number of studies that pertain to the function of DIS3 at the organismal level. Mutant phenotypes in S. pombe, S. cerevisiae and Drosophila suggest DIS3 homologues have a common role in cell-cycle progression and microtubule assembly. DIS3 has also recently been implicated in antibody diversification of mouse B-cells. This article aims to review current knowledge of the structure, mechanisms and functions of DIS3 as well as highlighting the genetic patterns observed within myeloma patients, in order to yield insight into the putative role of DIS3 mutations in oncogenesis. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

► Figures

Open AccessReview Roles of Chemokines and Chemokine Receptors in Obesity-Associated Insulin Resistance and Nonalcoholic Fatty Liver Disease

by Liang Xu, Hironori Kitade, Yinhua Ni and Tsuguhito Ota

Biomolecules 2015, 5(3), 1563-1579; doi:10.3390/biom5031563

Received: 31 May 2015 / Revised: 6 July 2015 / Accepted: 7 July 2015 / Published: 21 July 2015

Cited by 28 | PDF Full-text (1394 KB) | HTML Full-text | XML Full-text

Abstract

Abundant evidence has demonstrated that obesity is a state of low-grade chronic inflammation that triggers the release of lipids, aberrant adipokines, pro-inflammatory cytokines, and several chemokines from adipose tissue. This low-grade inflammation underlies the development of insulin resistance and associated metabolic comorbidities such

[...] Read more.

Abundant evidence has demonstrated that obesity is a state of low-grade chronic inflammation that triggers the release of lipids, aberrant adipokines, pro-inflammatory cytokines, and several chemokines from adipose tissue. This low-grade inflammation underlies the development of insulin resistance and associated metabolic comorbidities such as type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD). During this development, adipose tissue macrophages accumulate through chemokine (C-C motif) receptor 2 and the ligand for this receptor, monocyte chemoattractant protein-1 (MCP-1), is considered to be pivotal for the development of insulin resistance. To date, the chemokine system is known to be comprised of approximately 40 chemokines and 20 chemokine receptors that belong to the seven-transmembrane G protein-coupled receptor family and, as a result, chemokines appear to exhibit a high degree of functional redundancy. Over the past two decades, the physiological and pathological properties of many of these chemokines and their receptors have been elucidated. The present review highlights chemokines and chemokine receptors as key contributing factors that link obesity to insulin resistance, T2DM, and NAFLD. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Functional Integration of mRNA Translational Control Programs

by Melanie C. MacNicol, Chad E. Cragle, Karthik Arumugam, Bruno Fosso, Graziano Pesole and Angus M. MacNicol

Biomolecules 2015, 5(3), 1580-1599; doi:10.3390/biom5031580

Received: 22 April 2015 / Revised: 20 June 2015 / Accepted: 14 July 2015 / Published: 21 July 2015

PDF Full-text (879 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Regulated mRNA translation plays a key role in control of cell cycle progression in a variety of physiological and pathological processes, including in the self-renewal and survival of stem cells and cancer stem cells. While targeting mRNA translation presents an attractive strategy for

[...] Read more.

Regulated mRNA translation plays a key role in control of cell cycle progression in a variety of physiological and pathological processes, including in the self-renewal and survival of stem cells and cancer stem cells. While targeting mRNA translation presents an attractive strategy for control of aberrant cell cycle progression, mRNA translation is an underdeveloped therapeutic target. Regulated mRNAs are typically controlled through interaction with multiple RNA binding proteins (RBPs) but the mechanisms by which the functions of distinct RBPs bound to a common target mRNA are coordinated are poorly understood. The challenge now is to gain insight into these mechanisms of coordination and to identify the molecular mediators that integrate multiple, often conflicting, inputs. A first step includes the identification of altered mRNA ribonucleoprotein complex components that assemble on mRNAs bound by multiple, distinct RBPs compared to those recruited by individual RBPs. This review builds upon our knowledge of combinatorial control of mRNA translation during the maturation of oocytes from Xenopus laevis, to address molecular strategies that may mediate RBP diplomacy and conflict resolution for coordinated control of mRNA translational output. Continued study of regulated ribonucleoprotein complex dynamics promises valuable new insights into mRNA translational control and may suggest novel therapeutic strategies for the treatment of disease. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

► Figures

Open AccessReview Transcription Blockage Leads to New Beginnings

by Leonardo C. Andrade-Lima, Artur Veloso and Mats Ljungman

Biomolecules 2015, 5(3), 1600-1617; doi:10.3390/biom5031600

Received: 23 June 2015 / Revised: 9 July 2015 / Accepted: 16 July 2015 / Published: 21 July 2015

Cited by 2 | PDF Full-text (2071 KB) | HTML Full-text | XML Full-text

Abstract

Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of

[...] Read more.

Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes. Full article

(This article belongs to the Special Issue DNA Damage Response)

Open AccessReview Chromatin Remodeling and Transcriptional Control in Innate Immunity: Emergence of Akirin2 as a Novel Player

by Sarang Tartey and Osamu Takeuchi

Biomolecules 2015, 5(3), 1618-1633; doi:10.3390/biom5031618

Received: 12 May 2015 / Revised: 15 June 2015 / Accepted: 24 June 2015 / Published: 22 July 2015

Cited by 5 | PDF Full-text (4132 KB) | HTML Full-text | XML Full-text

Abstract

Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate

[...] Read more.

Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional regulation. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Inhibition of Topoisomerase (DNA) I (TOP1): DNA Damage Repair and Anticancer Therapy

by Yang Xu and Chengtao Her

Biomolecules 2015, 5(3), 1652-1670; doi:10.3390/biom5031652

Received: 22 May 2015 / Accepted: 14 July 2015 / Published: 22 July 2015

Cited by 25 | PDF Full-text (636 KB) | HTML Full-text | XML Full-text

Abstract

Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained

[...] Read more.

Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained proliferation is a common feature of cancer [1,2]. Rapid DNA replication is essential for highly proliferative cells, thus blocking of DNA replication will create numerous mutations and/or chromosome rearrangements—ultimately triggering cell death [3]. Along these lines, DNA topoisomerase inhibitors are of great interest because they help to maintain strand breaks generated by topoisomerases during replication. In this article, we discuss the characteristics of topoisomerase (DNA) I (TOP1) and its inhibitors, as well as the underlying DNA repair pathways and the use of TOP1 inhibitors in cancer therapy. Full article

(This article belongs to the Special Issue DNA Damage Response)

Open AccessReview Direct and/or Indirect Roles for SUMO in Modulating Alpha-Synuclein Toxicity

by Shamini Vijayakumaran, Mathew B. Wong, Helma Antony and Dean L. Pountney

Biomolecules 2015, 5(3), 1697-1716; doi:10.3390/biom5031697

Received: 28 May 2015 / Revised: 3 July 2015 / Accepted: 9 July 2015 / Published: 24 July 2015

Cited by 3 | PDF Full-text (2675 KB) | HTML Full-text | XML Full-text

Abstract

α-Synuclein inclusion bodies are a pathological hallmark of several neurodegenerative diseases, including Parkinson’s disease, and contain aggregated α-synuclein and a variety of recruited factors, including protein chaperones, proteasome components, ubiquitin and the small ubiquitin-like modifier, SUMO-1. Cell culture and animal model studies suggest

[...] Read more.

α-Synuclein inclusion bodies are a pathological hallmark of several neurodegenerative diseases, including Parkinson’s disease, and contain aggregated α-synuclein and a variety of recruited factors, including protein chaperones, proteasome components, ubiquitin and the small ubiquitin-like modifier, SUMO-1. Cell culture and animal model studies suggest that misfolded, aggregated α-synuclein is actively translocated via the cytoskeletal system to a region of the cell where other factors that help to lessen the toxic effects can also be recruited. SUMO-1 covalently conjugates to various intracellular target proteins in a way analogous to ubiquitination to alter cellular distribution, function and metabolism and also plays an important role in a growing list of cellular pathways, including exosome secretion and apoptosis. Furthermore, SUMO-1 modified proteins have recently been linked to cell stress responses, such as oxidative stress response and heat shock response, with increased SUMOylation being neuroprotective in some cases. Several recent studies have linked SUMOylation to the ubiquitin-proteasome system, while other evidence implicates the lysosomal pathway. Other reports depict a direct mechanism whereby sumoylation reduced the aggregation tendency of α-synuclein, and reduced the toxicity. However, the precise role of SUMO-1 in neurodegeneration remains unclear. In this review, we explore the potential direct or indirect role(s) of SUMO-1 in the cellular response to misfolded α-synuclein in neurodegenerative disorders. Full article

(This article belongs to the Special Issue Exploring the Mechanisms by which α-Synuclein Kills Cells in Parkinson Disease)

Open AccessReview Pre-mRNA Splicing in Plants: In Vivo Functions of RNA-Binding Proteins Implicated in the Splicing Process

by Katja Meyer, Tino Koester and Dorothee Staiger

Biomolecules 2015, 5(3), 1717-1740; doi:10.3390/biom5031717

Received: 29 May 2015 / Revised: 16 July 2015 / Accepted: 20 July 2015 / Published: 24 July 2015

Cited by 10 | PDF Full-text (402 KB) | HTML Full-text | XML Full-text

Abstract

Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects,

[...] Read more.

Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance. Full article

(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)

Open AccessReview Bacterial Genotoxins: Merging the DNA Damage Response into Infection Biology

by Francesca Grasso and Teresa Frisan

Biomolecules 2015, 5(3), 1762-1782; doi:10.3390/biom5031762

Received: 14 July 2015 / Revised: 5 August 2015 / Accepted: 6 August 2015 / Published: 11 August 2015

Cited by 11 | PDF Full-text (1826 KB) | HTML Full-text | XML Full-text

Abstract

Bacterial genotoxins are unique among bacterial toxins as their molecular target is DNA. The consequence of intoxication or infection is induction of DNA breaks that, if not properly repaired, results in irreversible cell cycle arrest (senescence) or death of the target cells. At

[...] Read more.

Bacterial genotoxins are unique among bacterial toxins as their molecular target is DNA. The consequence of intoxication or infection is induction of DNA breaks that, if not properly repaired, results in irreversible cell cycle arrest (senescence) or death of the target cells. At present, only three bacterial genotoxins have been identified. Two are protein toxins: the cytolethal distending toxin (CDT) family produced by a number of Gram-negative bacteria and the typhoid toxin produced by Salmonella enterica serovar Typhi. The third member, colibactin, is a peptide-polyketide genotoxin, produced by strains belonging to the phylogenetic group B2 of Escherichia coli. This review will present the cellular effects of acute and chronic intoxication or infection with the genotoxins-producing bacteria. The carcinogenic properties and the role of these effectors in the context of the host-microbe interaction will be discussed. We will further highlight the open questions that remain to be solved regarding the biology of this unusual family of bacterial toxins. Full article

(This article belongs to the Special Issue DNA Damage Response)

Open AccessReview Challenges in Antibody Development against Tn and Sialyl-Tn Antigens

by Liliana R. Loureiro, Mylène A. Carrascal, Ana Barbas, José S. Ramalho, Carlos Novo, Philippe Delannoy and Paula A. Videira

Biomolecules 2015, 5(3), 1783-1809; doi:10.3390/biom5031783

Received: 9 June 2015 / Revised: 19 July 2015 / Accepted: 31 July 2015 / Published: 11 August 2015

Cited by 9 | PDF Full-text (2280 KB) | HTML Full-text | XML Full-text

Abstract

The carbohydrate antigens Tn and sialyl-Tn (STn) are expressed in most carcinomas and usually absent in healthy tissues. These antigens have been correlated with cancer progression and poor prognosis, and associated with immunosuppressive microenvironment. Presently they are used in clinical trials as therapeutic

[...] Read more.

The carbohydrate antigens Tn and sialyl-Tn (STn) are expressed in most carcinomas and usually absent in healthy tissues. These antigens have been correlated with cancer progression and poor prognosis, and associated with immunosuppressive microenvironment. Presently they are used in clinical trials as therapeutic vaccination, but with limited success due to their low immunogenicity. Alternatively, anti-Tn and/or STn antibodies may be used to harness the immune system against tumor cells. Whilst the development of antibodies against these antigens had a boost two decades ago for diagnostic use, so far no such antibody entered into clinical trials. Possible limitations are the low specificity and efficiency of existing antibodies and that novel antibodies are still necessary. The vast array of methodologies available today will allow rapid antibody development and novel formats. Following the advent of hybridoma technology, the immortalization of human B cells became a methodology to obtain human monoclonal antibodies with better specificity. Advances in molecular biology including phage display technology for high throughput screening, transgenic mice and more recently molecularly engineered antibodies enhanced the field of antibody production. The development of novel antibodies against Tn and STn taking advantage of innovative technologies and engineering techniques may result in innovative therapeutic antibodies for cancer treatment. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

► Figures

Open AccessReview Genome Instability in Development and Aging: Insights from Nucleotide Excision Repair in Humans, Mice, and Worms

by Diletta Edifizi and Björn Schumacher

Biomolecules 2015, 5(3), 1855-1869; doi:10.3390/biom5031855

Received: 16 July 2015 / Revised: 6 August 2015 / Accepted: 7 August 2015 / Published: 13 August 2015

Cited by 7 | PDF Full-text (12295 KB) | HTML Full-text | XML Full-text

Abstract

DNA damage causally contributes to aging and cancer. Congenital defects in nucleotide excision repair (NER) lead to distinct cancer-prone and premature aging syndromes. The genetics of NER mutations have provided important insights into the distinct consequences of genome instability. Recent work in mice

[...] Read more.

DNA damage causally contributes to aging and cancer. Congenital defects in nucleotide excision repair (NER) lead to distinct cancer-prone and premature aging syndromes. The genetics of NER mutations have provided important insights into the distinct consequences of genome instability. Recent work in mice and C. elegans has shed new light on the mechanisms through which developing and aging animals respond to persistent DNA damage. The various NER mouse mutants have served as important disease models for Xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD), while the traceable genetics of C. elegans have allowed the mechanistic delineation of the distinct outcomes of genome instability in metazoan development and aging. Intriguingly, highly conserved longevity assurance mechanisms respond to transcription-blocking DNA lesions in mammals as well as in worms and counteract the detrimental consequences of persistent DNA damage. The insulin-like growth factor signaling (IIS) effector transcription factor DAF-16 could indeed overcome DNA damage-driven developmental growth delay and functional deterioration even when DNA damage persists. Longevity assurance mechanisms might thus delay DNA damage-driven aging by raising the threshold when accumulating DNA damage becomes detrimental for physiological tissue functioning. Full article

(This article belongs to the Special Issue DNA Damage Response)

Open AccessReview Oxidative Stress and Maxi Calcium-Activated Potassium (BK) Channels

by Anton Hermann, Guzel F. Sitdikova and Thomas M. Weiger

Biomolecules 2015, 5(3), 1870-1911; doi:10.3390/biom5031870

Received: 8 May 2015 / Revised: 17 July 2015 / Accepted: 20 July 2015 / Published: 17 August 2015

Cited by 7 | PDF Full-text (939 KB) | HTML Full-text | XML Full-text

Abstract

All cells contain ion channels in their outer (plasma) and inner (organelle) membranes. Ion channels, similar to other proteins, are targets of oxidative impact, which modulates ion fluxes across membranes. Subsequently, these ion currents affect electrical excitability, such as action potential discharge (in

[...] Read more.

All cells contain ion channels in their outer (plasma) and inner (organelle) membranes. Ion channels, similar to other proteins, are targets of oxidative impact, which modulates ion fluxes across membranes. Subsequently, these ion currents affect electrical excitability, such as action potential discharge (in neurons, muscle, and receptor cells), alteration of the membrane resting potential, synaptic transmission, hormone secretion, muscle contraction or coordination of the cell cycle. In this chapter we summarize effects of oxidative stress and redox mechanisms on some ion channels, in particular on maxi calcium-activated potassium (BK) channels which play an outstanding role in a plethora of physiological and pathophysiological functions in almost all cells and tissues. We first elaborate on some general features of ion channel structure and function and then summarize effects of oxidative alterations of ion channels and their functional consequences. Full article

(This article belongs to the Special Issue Oxidative Stress and Oxygen Radicals) Printed Edition available

Open AccessReview Targeting the Checkpoint to Kill Cancer Cells

by Jan Benada and Libor Macurek

Biomolecules 2015, 5(3), 1912-1937; doi:10.3390/biom5031912

Received: 2 July 2015 / Revised: 7 August 2015 / Accepted: 11 August 2015 / Published: 18 August 2015

Cited by 28 | PDF Full-text (1370 KB) | HTML Full-text | XML Full-text

Abstract

Cancer treatments such as radiotherapy and most of the chemotherapies act by damaging DNA of cancer cells. Upon DNA damage, cells stop proliferation at cell cycle checkpoints, which provides them time for DNA repair. Inhibiting the checkpoint allows entry to mitosis despite the

[...] Read more.

Cancer treatments such as radiotherapy and most of the chemotherapies act by damaging DNA of cancer cells. Upon DNA damage, cells stop proliferation at cell cycle checkpoints, which provides them time for DNA repair. Inhibiting the checkpoint allows entry to mitosis despite the presence of DNA damage and can lead to cell death. Importantly, as cancer cells exhibit increased levels of endogenous DNA damage due to an excessive replication stress, inhibiting the checkpoint kinases alone could act as a directed anti-cancer therapy. Here, we review the current status of inhibitors targeted towards the checkpoint effectors and discuss mechanisms of their actions in killing of cancer cells. Full article

(This article belongs to the Special Issue DNA Damage Response)

► Figures

Open AccessReview Macrophage Expression of Inflammatory Genes in Response to EMCV Infection

by Zachary R. Shaheen and John A. Corbett

Biomolecules 2015, 5(3), 1938-1954; doi:10.3390/biom5031938

Received: 16 June 2015 / Revised: 6 August 2015 / Accepted: 8 August 2015 / Published: 18 August 2015

PDF Full-text (679 KB) | HTML Full-text | XML Full-text

Abstract

The expression and production of type 1 interferon is the classic cellular response to virus infection. In addition to this antiviral response, virus infection also stimulates the production of proinflammatory mediators. In this review, the pathways controlling the induction of inflammatory genes and

[...] Read more.

The expression and production of type 1 interferon is the classic cellular response to virus infection. In addition to this antiviral response, virus infection also stimulates the production of proinflammatory mediators. In this review, the pathways controlling the induction of inflammatory genes and the roles that these inflammatory mediators contribute to host defense against viral pathogens will be discussed. Specific focus will be on the role of the chemokine receptor CCR5, as a signaling receptor controlling the activation of pathways leading to virus-induced inflammatory gene expression. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

by Norio Matsushima, Hiroki Miyashita, Purevjav Enkhbayar and Robert H. Kretsinger

Biomolecules 2015, 5(3), 1955-1978; doi:10.3390/biom5031955

Received: 21 July 2015 / Revised: 10 August 2015 / Accepted: 11 August 2015 / Published: 18 August 2015

Cited by 2 | PDF Full-text (4869 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

The NOD-like receptors (NLRs) and Toll-like receptors (TLRs) are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs) that are responsible for ligand interactions. In LRRs short β-strands stack parallel

[...] Read more.

The NOD-like receptors (NLRs) and Toll-like receptors (TLRs) are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs) that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids). The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side. Full article

Open AccessReview Functional Role of NBS1 in Radiation Damage Response and Translesion DNA Synthesis

by Yuichiro Saito and Kenshi Komatsu

Biomolecules 2015, 5(3), 1990-2002; doi:10.3390/biom5031990

Received: 30 June 2015 / Revised: 11 August 2015 / Accepted: 13 August 2015 / Published: 20 August 2015

Cited by 3 | PDF Full-text (630 KB) | HTML Full-text | XML Full-text

Abstract

Nijmegen breakage syndrome (NBS) is a recessive genetic disorder characterized by increased sensitivity to ionizing radiation (IR) and a high frequency of malignancies. NBS1, a product of the mutated gene in NBS, contains several protein interaction domains in the N-terminus and C-terminus. The

[...] Read more.

Nijmegen breakage syndrome (NBS) is a recessive genetic disorder characterized by increased sensitivity to ionizing radiation (IR) and a high frequency of malignancies. NBS1, a product of the mutated gene in NBS, contains several protein interaction domains in the N-terminus and C-terminus. The C-terminus of NBS1 is essential for interactions with MRE11, a homologous recombination repair nuclease, and ATM, a key player in signal transduction after the generation of DNA double-strand breaks (DSBs), which is induced by IR. Moreover, NBS1 regulates chromatin remodeling during DSB repair by histone H2B ubiquitination through binding to RNF20 at the C-terminus. Thus, NBS1 is considered as the first protein to be recruited to DSB sites, wherein it acts as a sensor or mediator of DSB damage responses. In addition to DSB response, we showed that NBS1 initiates Polη-dependent translesion DNA synthesis by recruiting RAD18 through its binding at the NBS1 C-terminus after UV exposure, and it also functions after the generation of interstrand crosslink DNA damage. Thus, NBS1 has multifunctional roles in response to DNA damage from a variety of genotoxic agents, including IR. Full article

(This article belongs to the Special Issue DNA Damage Response)

Open AccessReview Determinants of Glycosaminoglycan (GAG) Structure

by Kristian Prydz

Biomolecules 2015, 5(3), 2003-2022; doi:10.3390/biom5032003

Received: 29 May 2015 / Revised: 17 August 2015 / Accepted: 18 August 2015 / Published: 21 August 2015

Cited by 11 | PDF Full-text (156 KB) | HTML Full-text | XML Full-text

Abstract

Proteoglycans (PGs) are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG) chains in the secretory pathway of animal cells. The most common GAG attachment site is a

[...] Read more.

Proteoglycans (PGs) are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG) chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-), from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis. Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessReview Alcoholic Liver Disease: Role of Cytokines

by Manuela G. Neuman, Yaakov Maor, Radu M. Nanau, Ehud Melzer, Haim Mell, Mihai Opris, Lawrence Cohen and Stephen Malnick

Biomolecules 2015, 5(3), 2023-2034; doi:10.3390/biom5032023

Received: 3 July 2015 / Revised: 21 August 2015 / Accepted: 24 August 2015 / Published: 28 August 2015

Cited by 7 | PDF Full-text (91 KB) | HTML Full-text | XML Full-text

Abstract

The present review spans a broad spectrum of topics dealing with alcoholic liver disease (ALD), including clinical and translational research. It focuses on the role of the immune system and the signaling pathways of cytokines in the pathogenesis of ALD. An additional factor

[...] Read more.

The present review spans a broad spectrum of topics dealing with alcoholic liver disease (ALD), including clinical and translational research. It focuses on the role of the immune system and the signaling pathways of cytokines in the pathogenesis of ALD. An additional factor that contributes to the pathogenesis of ALD is lipopolysaccharide (LPS), which plays a central role in the induction of steatosis, inflammation, and fibrosis in the liver. LPS derived from the intestinal microbiota enters the portal circulation, and is recognized by macrophages (Kupffer cells) and hepatocytes. In individuals with ALD, excessive levels of LPS in the liver affect immune, parenchymal, and non-immune cells, which in turn release various inflammatory cytokines and recruit neutrophils and other inflammatory cells. In this review, we elucidate the mechanisms by which alcohol contributes to the activation of Kupffer cells and the inflammatory cascade. The role of the stellate cells in fibrogenesis is also discussed. Full article

(This article belongs to the collection Multi-Organ Alcohol-Related Damage: Mechanisms and Treatment)

Open AccessReview Notable Aspects of Glycan-Protein Interactions

by Miriam Cohen

Biomolecules 2015, 5(3), 2056-2072; doi:10.3390/biom5032056

Received: 5 August 2015 / Revised: 27 August 2015 / Accepted: 27 August 2015 / Published: 1 September 2015

Cited by 6 | PDF Full-text (3056 KB) | HTML Full-text | XML Full-text

Abstract

This mini review highlights several interesting aspects of glycan-mediated interactions that are common between cells, bacteria, and viruses. Glycans are ubiquitously found on all living cells, and in the extracellular milieu of multicellular organisms. They are known to mediate initial binding and recognition

[...] Read more.

This mini review highlights several interesting aspects of glycan-mediated interactions that are common between cells, bacteria, and viruses. Glycans are ubiquitously found on all living cells, and in the extracellular milieu of multicellular organisms. They are known to mediate initial binding and recognition events of both immune cells and pathogens with their target cells or tissues. The host target tissues are hidden under a layer of secreted glycosylated decoy targets. In addition, pathogens can utilize and display host glycans to prevent identification as foreign by the host’s immune system (molecular mimicry). Both the host and pathogens continually evolve. The host evolves to prevent infection and the pathogens evolve to evade host defenses. Many pathogens express both glycan-binding proteins and glycosidases. Interestingly, these proteins are often located at the tip of elongated protrusions in bacteria, or in the leading edge of the cell. Glycan-protein interactions have low affinity and, as a result, multivalent interactions are often required to achieve biologically relevant binding. These enable dynamic forms of adhesion mechanisms, reviewed here, and include rolling (cells), stick and roll (bacteria) or surfacing (viruses). Full article

(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)

Open AccessReview Splicing Regulation of Pro-Inflammatory Cytokines and Chemokines: At the Interface of the Neuroendocrine and Immune Systems

by Felitsiya Shakola, Parul Suri and Matteo Ruggiu

Biomolecules 2015, 5(3), 2073-2100; doi:10.3390/biom5032073

Received: 22 April 2015 / Accepted: 28 August 2015 / Published: 7 September 2015

Cited by 1 | PDF Full-text (2299 KB) | HTML Full-text | XML Full-text

Abstract

Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates protein diversity, and alters protein function. More than 90%

[...] Read more.

Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates protein diversity, and alters protein function. More than 90% of human genes undergo alternative splicing, and alternative splicing is especially prevalent in the nervous and immune systems, tissues where cells need to react swiftly and adapt to changes in the environment through carefully regulated mechanisms of cell differentiation, migration, targeting, and activation. Given its prevalence and complexity, this highly regulated mode of gene expression is prone to be affected by disease. In the following review, we look at how alternative splicing of signaling molecules—cytokines and their receptors—changes in different pathological conditions, from chronic inflammation to neurologic disorders, providing means of functional interaction between the immune and neuroendocrine systems. Switches in alternative splicing patterns can be very dynamic and can produce signaling molecules with distinct or antagonistic functions and localization to different subcellular compartments. This newly discovered link expands our understanding of the biology of immune and neuroendocrine cells, and has the potential to open new windows of opportunity for treatment of neurodegenerative disorders. Full article

(This article belongs to the Special Issue Transcriptional Regulation of Pro-Inflammatory Genes)

Open AccessReview The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions

by Gabriel Piedrafita, Markus A Keller and Markus Ralser

Biomolecules 2015, 5(3), 2101-2122; doi:10.3390/biom5032101

Received: 6 May 2015 / Revised: 3 August 2015 / Accepted: 31 August 2015 / Published: 10 September 2015

Cited by 9 | PDF Full-text (1507 KB) | HTML Full-text | XML Full-text

Abstract

Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme

[...] Read more.

Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease—age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network. Full article

(This article belongs to the Special Issue Oxidative Stress and Oxygen Radicals) Printed Edition available

► Figures

Open AccessReview Managing Single-Stranded DNA during Replication Stress in Fission Yeast

by Sarah A. Sabatinos and Susan L. Forsburg

Biomolecules 2015, 5(3), 2123-2139; doi:10.3390/biom5032123

Received: 31 July 2015 / Revised: 28 August 2015 / Accepted: 1 September 2015 / Published: 18 September 2015

Cited by 4 | PDF Full-text (4438 KB) | HTML Full-text | XML Full-text

Abstract

Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation

[...] Read more.

Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation and recombination. Therefore, managing ssDNA levels is crucial to chromosome integrity. Limited ssDNA accumulation occurs in wild-type cells under stress. In contrast, cells lacking the replication checkpoint cannot arrest forks properly and accumulate large amounts of ssDNA. This likely occurs when the replication fork polymerase and helicase units are uncoupled. Some cells with mutations in the replication helicase (mcm-ts) mimic checkpoint-deficient cells, and accumulate extensive areas of ssDNA to trigger the G2-checkpoint. Another category of helicase mutant (mcm4-degron) causes fork stalling in early S-phase due to immediate loss of helicase function. Intriguingly, cells realize that ssDNA is present, but fail to detect that they accumulate ssDNA, and continue to divide. Thus, the cellular response to replication stalling depends on checkpoint activity and the time that replication stress occurs in S-phase. In this review we describe the signs, signals, and symptoms of replication arrest from an ssDNA perspective. We explore the possible mechanisms for these effects. We also advise the need for caution when detecting and interpreting data related to the accumulation of ssDNA. Full article

(This article belongs to the Special Issue DNA Damage Response)

► Figures

Open AccessReview The Altered Hepatic Tubulin Code in Alcoholic Liver Disease

by Jennifer L. Groebner and Pamela L. Tuma

Biomolecules 2015, 5(3), 2140-2159; doi:10.3390/biom5032140

Received: 22 July 2015 / Revised: 21 August 2015 / Accepted: 24 August 2015 / Published: 18 September 2015

Cited by 2 | PDF Full-text (514 KB) | HTML Full-text | XML Full-text

Abstract

The molecular mechanisms that lead to the progression of alcoholic liver disease have been actively examined for decades. Because the hepatic microtubule cytoskeleton supports innumerable cellular processes, it has been the focus of many such mechanistic studies. It has long been appreciated that

[...] Read more.

The molecular mechanisms that lead to the progression of alcoholic liver disease have been actively examined for decades. Because the hepatic microtubule cytoskeleton supports innumerable cellular processes, it has been the focus of many such mechanistic studies. It has long been appreciated that α-tubulin is a major target for modification by highly reactive ethanol metabolites and reactive oxygen species. It is also now apparent that alcohol exposure induces post-translational modifications that are part of the natural repertoire, mainly acetylation. In this review, the modifications of the “tubulin code” are described as well as those adducts by ethanol metabolites. The potential cellular consequences of microtubule modification are described with a focus on alcohol-induced defects in protein trafficking and enhanced steatosis. Possible mechanisms that can explain hepatic dysfunction are described and how this relates to the onset of liver injury is discussed. Finally, we propose that agents that alter the cellular acetylation state may represent a novel therapeutic strategy for treating liver disease. Full article

(This article belongs to the collection Multi-Organ Alcohol-Related Damage: Mechanisms and Treatment)

Journal Menu

E-Mail Alert

Journal Browser

Table of Contents

Biomolecules, Volume 5, Issue 3 (September 2015), Pages 1195-2159

Research

Jump to: Review

Review

Jump to: Research

Journal Contact