Special Issue "Focus Update in Biomolecules"

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 December 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Jürg Bähler (Website)

Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
Fax: +44 2076 797096
Interests: gene regulation; genomics; transcriptomics; next-generation sequencing; non-coding RNAs; genome evolution; fission yeast; oxidative stress response; cellular quiescence and ageing

Special Issue Information

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 600 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Published Papers (6 papers)

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Research

Jump to: Review

Open AccessArticle Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA
Biomolecules 2014, 4(1), 140-159; doi:10.3390/biom4010140
Received: 25 December 2013 / Revised: 21 January 2014 / Accepted: 23 January 2014 / Published: 10 February 2014
Cited by 9 | PDF Full-text (746 KB) | HTML Full-text | XML Full-text
Abstract
Guanine is the most easily oxidized among the four DNA bases, and some guanine-rich sequences can form quadruplex structures. In a previous study using 6-mer DNA d(TGGGGT), which is the shortest oligomer capable of forming quadruplex structures, we demonstrated that guanine oxidation [...] Read more.
Guanine is the most easily oxidized among the four DNA bases, and some guanine-rich sequences can form quadruplex structures. In a previous study using 6-mer DNA d(TGGGGT), which is the shortest oligomer capable of forming quadruplex structures, we demonstrated that guanine oxidation products of quadruplex DNA differ from those of single-stranded DNA. Therefore, the hotooxidation products of double-stranded DNA (dsDNA) may also differ from that of quadruplex or single-stranded DNA, with the difference likely explaining the influence of DNA structures on guanine oxidation pathways. In this study, the guanine oxidation products of the dsDNA d(TGGGGT)/d(ACCCCA) were analyzed using HPLC and electrospray ionization-mass spectrometry (ESI-MS). As a result, the oxidation products in this dsDNA were identified as 2,5-diamino-4H-imidazol-4-one (Iz), 8-oxo-7,8-dihydroguanine (8oxoG), dehydroguanidinohydantoin (Ghox), and guanidinohydantoin (Gh). The major oxidation products in dsDNA were consistent with a combination of each major oxidation product observed in single-stranded and quadruplex DNA. We previously reported that the kinds of the oxidation products in single-stranded or quadruplex DNA depend on the ease of deprotonation of the guanine radical cation (G•+) at the N1 proton. Similarly, this mechanism was also involved in dsDNA. Deprotonation in dsDNA is easier than in quadruplex DNA and more difficult in single-stranded DNA, which can explain the formation of the four oxidation products in dsDNA. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
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Open AccessArticle Structural Evidence for the Tetrameric Assembly of Chemokine CCL11 and the Glycosaminoglycan Arixtra™
Biomolecules 2013, 3(4), 905-922; doi:10.3390/biom3040905
Received: 22 August 2013 / Revised: 23 October 2013 / Accepted: 29 October 2013 / Published: 6 November 2013
PDF Full-text (778 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Understanding chemokine interactions with glycosaminoglycans (GAG) is critical as these interactions have been linked to a number of inflammatory medical conditions, such as arthritis and asthma. To better characterize in vivo protein function, comprehensive knowledge of multimeric species, formed by chemokines under [...] Read more.
Understanding chemokine interactions with glycosaminoglycans (GAG) is critical as these interactions have been linked to a number of inflammatory medical conditions, such as arthritis and asthma. To better characterize in vivo protein function, comprehensive knowledge of multimeric species, formed by chemokines under native conditions, is necessary. Herein is the first report of a tetrameric assembly of the human chemokine CCL11, which was shown bound to the GAG Arixtra™. Isothermal titration calorimetry data indicated that CCL11 interacts with Arixtra, and ion mobility mass spectrometry (IM-MS) was used to identify ions corresponding to the CCL11 tetrameric species bound to Arixtra. Collisional cross sections (CCS) of the CCL11 tetramer-Arixtra noncovalent complex were compared to theoretical CCS values calculated using a preliminary structure of the complex deduced using X-ray crystallography. Experimental CCS values were in agreement with theoretical values, strengthening the IM-MS evidence for the formation of the noncovalent complex. Tandem mass spectrometry data of the complex indicated that the tetramer-GAG complex dissociates into a monomer and a trimer-GAG species, suggesting that two CC-like dimers are bridged by Arixtra. As development of chemokine inhibitors is of utmost importance to treatment of medical inflammatory conditions, these results provide vital insights into chemokine-GAG interactions. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
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Review

Jump to: Research

Open AccessReview Re-Configuration of Sphingolipid Metabolism by Oncogenic Transformation
Biomolecules 2014, 4(1), 315-353; doi:10.3390/biom4010315
Received: 24 December 2013 / Revised: 11 February 2014 / Accepted: 27 February 2014 / Published: 14 March 2014
Cited by 6 | PDF Full-text (863 KB) | HTML Full-text | XML Full-text
Abstract
The sphingolipids are one of the major lipid families in eukaryotes, incorporating a diverse array of structural variants that exert a powerful influence over cell fate and physiology. Increased expression of sphingosine kinase 1 (SPHK1), which catalyses the synthesis of the pro-survival, [...] Read more.
The sphingolipids are one of the major lipid families in eukaryotes, incorporating a diverse array of structural variants that exert a powerful influence over cell fate and physiology. Increased expression of sphingosine kinase 1 (SPHK1), which catalyses the synthesis of the pro-survival, pro-angiogenic metabolite sphingosine 1-phosphate (S1P), is well established as a hallmark of multiple cancers. Metabolic alterations that reduce levels of the pro-apoptotic lipid ceramide, particularly its glucosylation by glucosylceramide synthase (GCS), have frequently been associated with cancer drug resistance. However, the simple notion that the balance between ceramide and S1P, often referred to as the sphingolipid rheostat, dictates cell survival contrasts with recent studies showing that highly potent and selective SPHK1 inhibitors do not affect cancer cell proliferation or survival, and studies demonstrating higher ceramide levels in some metastatic cancers. Recent reports have implicated other sphingolipid metabolic enzymes such as acid sphingomyelinase (ASM) more strongly in cancer pathogenesis, and highlight lysosomal sphingolipid metabolism as a possible weak point for therapeutic targeting in cancer. This review describes the evidence implicating different sphingolipid metabolic enzymes and their products in cancer pathogenesis, and suggests how newer systems-level approaches may improve our overall understanding of how oncogenic transformation reconfigures sphingolipid metabolism. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
Open AccessReview Structure and Function of the Bi-Directional Bacterial Flagellar Motor
Biomolecules 2014, 4(1), 217-234; doi:10.3390/biom4010217
Received: 30 December 2013 / Revised: 24 January 2014 / Accepted: 4 February 2014 / Published: 18 February 2014
Cited by 10 | PDF Full-text (1017 KB) | HTML Full-text | XML Full-text
Abstract
The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and [...] Read more.
The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
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Open AccessReview Long Noncoding RNAs in Imprinting and X Chromosome Inactivation
Biomolecules 2014, 4(1), 76-100; doi:10.3390/biom4010076
Received: 25 November 2013 / Revised: 18 December 2013 / Accepted: 27 December 2013 / Published: 7 January 2014
Cited by 12 | PDF Full-text (569 KB) | HTML Full-text | XML Full-text
Abstract
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Technological advancements and deep-sequencing of the transcriptome have facilitated the identification of numerous new lncRNAs, many with unusual properties, however, the function of most of these molecules [...] Read more.
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Technological advancements and deep-sequencing of the transcriptome have facilitated the identification of numerous new lncRNAs, many with unusual properties, however, the function of most of these molecules is still largely unknown. Some evidence suggests that several of these lncRNAs may regulate their own transcription in cis, and that of nearby genes, by recruiting remodeling factors to local chromatin. Notably, lncRNAs are known to exist at many imprinted gene clusters. Genomic imprinting is a complex and highly regulated process resulting in the monoallelic silencing of certain genes, based on the parent-of-origin of the allele. It is thought that lncRNAs may regulate many imprinted loci, however, the mechanism by which they exert such influence is poorly understood. This review will discuss what is known about the lncRNAs of major imprinted loci, and the roles they play in the regulation of imprinting. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
Open AccessReview Control of Cell Differentiation by Mitochondria, Typically Evidenced in Dictyostelium Development
Biomolecules 2013, 3(4), 943-966; doi:10.3390/biom3040943
Received: 28 September 2013 / Revised: 1 November 2013 / Accepted: 2 November 2013 / Published: 11 November 2013
Cited by 7 | PDF Full-text (1075 KB) | HTML Full-text | XML Full-text
Abstract
In eukaryotic cells, mitochondria are self-reproducing organelles with their own DNA and they play a central role in adenosine triphosphate (ATP) synthesis by respiration. Increasing evidence indicates that mitochondria also have critical and multiple functions in the initiation of cell differentiation, cell-type [...] Read more.
In eukaryotic cells, mitochondria are self-reproducing organelles with their own DNA and they play a central role in adenosine triphosphate (ATP) synthesis by respiration. Increasing evidence indicates that mitochondria also have critical and multiple functions in the initiation of cell differentiation, cell-type determination, cell movement, and pattern formation. This has been most strikingly realized in development of the cellular slime mold Dictyostelium. For example, the expression of the mitochondrial ribosomal protein S4 (mt-rps4) gene is required for the initial differentiation. The Dictyostelium homologue (Dd-TRAP1) of TRAP-1 (tumor necrosis receptor-associated protein 1), a mitochondrial molecular chaperone belonging to the Hsp90 family, allows the prompt transition of cells from growth to differentiation through a novel prestarvation factor (PSF-3) in growth medium. Moreover, a cell-type-specific organelle named a prespore-specific vacuole (PSV) is constructed by mitochondrial transformation with the help of the Golgi complex. Mitochondria are also closely involved in a variety of cellular activities including CN-resistant respiration and apoptosis. These mitochondrial functions are reviewed in this article, with special emphasis on the regulation of Dictyostelium development. Full article
(This article belongs to the Special Issue Focus Update in Biomolecules)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Title:
Complex Formation between Holliday Junction (HJ) Recombinatorial Intermediate Structures and the Yeast Orthologs of Bloom’s Syndrome Helicase/Topoisomerase
Author
: Ferez S. Nallaseth
Affiliation
: Center for Advanced Biotechnology and Medicine/Rutgers University, Piscataway, NJ, USA; E-Mail: ferez.nallaseth@gmail.com
Abstract:
Mutant BLM the human ortholog of the prototypical  E.coli RecQ helicase family forms heterocomplexes with a number of tumor suppressor and DNA repair proteins associated with elevated recombination frequencies, genomic instability and cancer. The yeast (S. cerevisiae) ortholog of this human heteromer is Sgs1 helicase (BLM), Top3 topoisomerase (TOPO IIIα) and Rmi1 (hRMI1) trimer. Using EMSAs and a ‘Pull Down Assay’ we have shown that among 10 DNA  structures tested, the Rmi1 monomer preferentially binds to HJ and pseudo-replication forks (pRF). The contributions of each subunit of the yeast Sgs1 / Top3 / Rmi1 trimer to complex formation with non-branch migratable HJs was assayed with a gentle biotinylated DNA / Streptavidin-Sepharose bead ‘Pull Down Assay’. In the presence of Rmi1 the binding of Top3 to HJs is not only significantly elevated it also acquires a preference for HJs. Once bound to HJs, Top3 displaces Rmi1 from these complexes. Both interactions are identical to those of TOPO IIIα with hRMI1 on dHJs. Finally, low level binding to HJs by Sgs1 Helicase N-terminus domains (that interact with Top3) is stimulated by the Rmi1 / Top3 dimer but inhibited by either monomer alone. However, as DNA unwinding by helicases is a pre-requisite for replication the subsequent requirement for Top3 / Rmi1 in retaining preloaded Sgs1 on HJ by-products of replication seems redundant. One explanation is a distinction between DNA helicase and dHJ dissolution / resolution functions of Sgs1 that is imposed by DNA structure. This requires unloading and reloading of Sgs1 from dHJ at stalled forks. Consistent with this interpretation, the affinity for HJ of the Rmi1 moiety of the heteromer is ~6x higher than it’s affinity for pRF as measured by EMSAs. These results may identify pre-requisites for fork progression through double dHJs.

Type of Paper: Review
Title: Structure and Function of the Bi-Directional Bacterial Flagellar Motor
Authors: Yusuke Morimoto and Tohru Minamino *
Affiliation: Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; * E-Mail: tohru@fbs.osaka-u.ac.jp (T.M.)
Abstract: The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical screw. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of four proteins, FliF, FliG, FliM, and FliN, and a dozen stators consisting of two integral membrane proteins, MotA and MotB. FliG, FliM, and FliN act as a switch complex, enabling the motor to spin in both counterclockwise and clockwise directions. The stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel to torque generation. Highly conserved charged residues at the stator-rotor interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will focus on the structure and function of the proton-driven bacterial flagellar motor.

Type of Paper: Review
Title:
Control of cell differentiation by mitochondria, typically evidenced in Dictyostelium development
Authors:
Yasuo Maeda1,* and Junji Chida 2
Affiliations:
1Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan; E-mail: kjygy352@ybb.ne.jp (Y.M.); 2Division of Molecular Neurobiology, Institute for Enzyme Research, The University of Tokushima, Kuramoto-cho, Tokushima 770-8503, Japan; E-Mail: jchida@tokushima-u.ac.jp (J.C.)
Abstract:
In eukaryotic cells, mitochondria are self-reproducing organelles with their own DNA and they play a central role in adenosine triphosphate (ATP) synthesis by respiration. Increasing evidence indicates that mitochondria also have critical and multiple functions in the initiation of cell differentiation, cell-type determination, cell movement, and pattern formation. This has been most strikingly realized in development of the cellular slime mold Dictyostelium. For example, the expression of the mitochondrial ribosomal protein S4 (mt-rps4) gene is required for the initial differentiation. The Dictyostelium homologue (Dd-TRAP1) of TRAP-1 (tumor necrosis receptor-associated protein 1), a mitochondrial molecular chaperone belonging to the Hsp90 family, allows the prompt transition of cells from growth to differentiation through a novel prestarvation factor (PSF-3) in growth medium. Moreover, a cell-type-specific organelle named a prespore-specific vacuole (PSV) is constructed by mitochondrial transformation with the help of the Golgi complex. Mitochondria are also closely involved in a variety of cellular activities including CN-resistant respiration and apoptosis. These mitochondrial functions are reviewed in this article, with special emphasis on the regulation of Dictyostelium development.
Key
words: Differentiation, Mitochondria, Mitochondrial ribosomal protein S4 (mt-RPS4), tumor necrosis receptor-associated protein 1 (TRAP-1), CN-resistant respiration, Prespore-specific vacuole (PSV), Dictyostelium

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