Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
4.1
Journals
Microorganisms
Special Issues
The Structure and Properties of Microbial Enzymes
share announcement

The Structure and Properties of Microbial Enzymes

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (15 August 2023) | Viewed by 13827

Special Issue Editor

Prof. Dr. Stephane Rety

E-Mail Website
Guest Editor
Laboratory of Biology and Modeling of the Cell, Ecole Normale Superieure de Lyon, Lyon, France
Interests: helicases; telomerase; G-quadruplexes; aquaporins; X-ray crystallography; SAXS; cryo-EM

Special Issue Information

Dear Colleagues,

Microbes are probably the most ancient form of life, appeared on Earth 3.5 billion years ago. These unicellular organisms as archaea, bacteria, fungi or yeast have colonized almost all environments, even the more hostile, and exhibit an extraordinary ecologic diversity. They have been intensively studied because they are used since a long time in food transformation. Microbial proteins are of high interest because they are usually easy to produce in high yield, and have valuable properties. Because of their stability, activity in various extreme conditions and particular catalytic activity, microbial enzymes have many industrial applications and are an alternative to polluting chemical processes. However microbes are also sometimes pathogenic for human and cattle. Because they are involved in functions not found in mammals, microbial proteins can be specifically targeted by antibiotics. Microbial protein could thus be considered as secret weapons but also as Achilles heel.

Search for new enzymes with specific catalytic activity may lead to technological revolutions as PCR or CRISPR/Cas9. Specificity and efficiency can also be improved by protein engineering. The increase of complete genome sequenced and the development of successful algorithms for predicting protein structures provide a large reservoir of microbial proteins with original structures and functions not yet discovered. Genomes and structure databases are therefore useful for fundamental and applied science in order to understand how protein structure and functions have evolved.

The scope of this special issue is to collect articles and reviews on structure-function relationships in microbial proteins. The contributions can be on evolution of protein families, specific features of new structures, engineering of protein stability or catalytic properties. Works focused on proteins involved in virulence are also welcomed.

Prof. Dr. Stephane Rety
Guest Editor

Manuscript Submission Information

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. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short 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 thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly 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 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • 3D structure
  • protein engineering
  • fold
  • extremophile
  • protein evolution
  • enzymes
  • virulence
  • archea
  • bacteria
  • yeast
  • fungi
  • crystallography
  • cryoEM
  • NMR
  • SAX

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Editorial

Jump to: Research

2 pages, 147 KiB  
Editorial
The Structure and Properties of Microbial Enzymes
by Stéphane Réty
Microorganisms 2024, 12(1), 45; https://doi.org/10.3390/microorganisms12010045 - 27 Dec 2023
Viewed by 1112
Abstract
Many microbes are pathogens not only to humans but also to cattle and crops [...] Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)

Research

Jump to: Editorial

21 pages, 3840 KiB  
Article
Cross-Linked Enzyme Aggregate (CLEA) Preparation from Waste Activated Sludge
by Ziyi Liu and Stephen R. Smith
Microorganisms 2023, 11(8), 1902; https://doi.org/10.3390/microorganisms11081902 - 27 Jul 2023
Cited by 1 | Viewed by 1717
Abstract
Enzymes are used extensively as industrial bio-catalysts in various manufacturing and processing sectors. However, commercial enzymes are expensive in part due to the high cost of the nutrient medium for the biomass culture. Activated sludge (AS) is a waste product of biological wastewater [...] Read more.
Enzymes are used extensively as industrial bio-catalysts in various manufacturing and processing sectors. However, commercial enzymes are expensive in part due to the high cost of the nutrient medium for the biomass culture. Activated sludge (AS) is a waste product of biological wastewater treatment and consists of microbial biomass that degrades organic matter by producing substantial quantities of hydrolytic enzymes. Recovering enzymes from AS therefore offers a potential alternative to conventional production techniques. A carrier-free, cross-linked enzyme aggregate (CLEA) was produced from crude AS enzyme extract for the first time. A major advantage of the CLEA is the combined immobilization, purification, and stabilization of the crude enzymes into a single step, thereby avoiding large amounts of inert carriers in the final enzyme product. The AS CLEA contained a variety of hydrolytic enzymes and demonstrated high potential for the bio-conversion of complex organic substrates. Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)
►▼ Show Figures

Graphical abstract

17 pages, 2684 KiB  
Article
Laccase Production from Agrocybe pediades: Purification and Functional Characterization of a Consistent Laccase Isoenzyme in Liquid Culture
by Paulina González-González, Saúl Gómez-Manzo, Araceli Tomasini, José Luis Martínez y Pérez, Edelmira García Nieto, Arely Anaya-Hernández, Elvia Ortiz Ortiz, Rosa Angélica Castillo Rodríguez, Jaime Marcial-Quino and Alba Mónica Montiel-González
Microorganisms 2023, 11(3), 568; https://doi.org/10.3390/microorganisms11030568 - 24 Feb 2023
Cited by 8 | Viewed by 2738
Abstract
Laccases are valuable enzymes as an excellent ecological alternative for bioremediation issues because they can oxidize persistent xenobiotic compounds. The production and characterization of extracellular laccases from saprotrophic fungi from disturbed environments have been scarcely explored, even though this could diversify their functional [...] Read more.
Laccases are valuable enzymes as an excellent ecological alternative for bioremediation issues because they can oxidize persistent xenobiotic compounds. The production and characterization of extracellular laccases from saprotrophic fungi from disturbed environments have been scarcely explored, even though this could diversify their functional characteristics and expand the conditions in which they carry out their catalysis. Agrocybe pediades, isolated from a disturbed forest, produces an extracellular laccase in liquid culture. The enzyme was purified, identified and characterized. Copper and hexachlorobenzene do not function as inducers for the laccase produced. Partial amino acid sequences were obtained by LC-MS/MS that share similarity with laccases from other fungi. Purified laccase is a monomer with a molecular mass between 55–60 kDa and had an optimum activity at pH 5.0 and the optimum temperature at 45 °C using 2,6-dimethoxyphenol (2,6-DMP) as substrate. The Km and Vmax also determined with 2,6-DMP were 100 μM and 285 μmol∙min−1∙mg−1, respectively, showing that the laccase of A. pediades has a higher affinity for this substrate than that of other Agaricales. These features could provide a potential catalyst for different toxic substrates and in the future laccase could be used in environmental recovery processes. Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)
►▼ Show Figures

Figure 1

14 pages, 4917 KiB  
Article
Structural Studies of Pif1 Helicases from Thermophilic Bacteria
by Stéphane Réty, Yingzi Zhang, Wentong Fu, Shan Wang, Wei-Fei Chen and Xu-Guang Xi
Microorganisms 2023, 11(2), 479; https://doi.org/10.3390/microorganisms11020479 - 14 Feb 2023
Cited by 1 | Viewed by 2181
Abstract
Pif1 proteins are DNA helicases belonging to Superfamily 1, with 5′ to 3′ directionality. They are conserved from bacteria to human and have been shown to be particularly important in eukaryotes for replication and nuclear and mitochondrial genome stability. However, Pif1 functions in [...] Read more.
Pif1 proteins are DNA helicases belonging to Superfamily 1, with 5′ to 3′ directionality. They are conserved from bacteria to human and have been shown to be particularly important in eukaryotes for replication and nuclear and mitochondrial genome stability. However, Pif1 functions in bacteria are less known. While most Pif1 from mesophilic bacteria consist of the helicase core with limited N-terminal and C-terminal extensions, some Pif1 from thermophilic bacteria exhibit a C-terminal WYL domain. We solved the crystal structures of Pif1 helicase cores from thermophilic bacteria Deferribacter desulfuricans and Sulfurihydrogenibium sp. in apo and nucleotide bound form. We show that the N-terminal part is important for ligand binding. The full-length Pif1 helicase was predicted based on the Alphafold algorithm and the nucleic acid binding on the Pif1 helicase core and the WYL domain was modelled based on known crystallographic structures. The model predicts that amino acids in the domains 1A, WYL, and linker between the Helicase core and WYL are important for nucleic acid binding. Therefore, the N-terminal and C-terminal extensions may be necessary to strengthen the binding of nucleic acid on these Pif1 helicases. This may be an adaptation to thermophilic conditions. Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)
►▼ Show Figures

Figure 1

17 pages, 4085 KiB  
Article
Structure Prediction and Characterization of Thermostable Aldehyde Dehydrogenase from Newly Isolated Anoxybacillus geothermalis Strain D9
by Nur Ezzati Rosli, Mohd Shukuri Mohamad Ali, Nor Hafizah Ahmad Kamarudin, Malihe Masomian, Wahhida Latip, Shazleen Saadon and Raja Noor Zaliha Raja Abd Rahman
Microorganisms 2022, 10(7), 1444; https://doi.org/10.3390/microorganisms10071444 - 18 Jul 2022
Cited by 9 | Viewed by 2352
Abstract
In nature, aldehyde dehydrogenase (ALDH) is widely distributed and mainly involved in the oxidation of aldehydes. Thermostability is one of the key features for industrial enzymes. The ability of enzymes to withstand a high operating temperature offers many advantages, including enhancing productivity in [...] Read more.
In nature, aldehyde dehydrogenase (ALDH) is widely distributed and mainly involved in the oxidation of aldehydes. Thermostability is one of the key features for industrial enzymes. The ability of enzymes to withstand a high operating temperature offers many advantages, including enhancing productivity in industries. This study was conducted to understand the structural and biochemical features of ALDH from thermophilic bacterium, Anoxybacillus geothermalis strain D9. The 3D structure of A. geothermalis ALDH was predicted by YASARA software and composed of 24.3% β-sheet located at the center core region. The gene, which encodes 504 amino acids with a molecular weight of ~56 kDa, was cloned into pET51b(+) and expressed in E.coli Transetta (DE3). The purified A. geothermalis ALDH showed remarkable thermostability with optimum temperature at 60 °C and stable at 70 °C for 1 h. The melting point of the A. geothermalis ALDH is at 65.9 °C. Metal ions such as Fe3+ ions inhibited the enzyme activity, while Li+ and Mg2+ enhanced by 38.83% and 105.83%, respectively. Additionally, this enzyme showed tolerance to most non-polar organic solvents tested (xylene, n-dedocane, n-tetradecane, n-hexadecane) in a concentration of 25% v/v. These findings have generally improved the understanding of thermostable A. geothermalis ALDH so it can be widely used in the industry. Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)
►▼ Show Figures

Figure 1

18 pages, 3280 KiB  
Article
Biochemical and Kinetic Characterization of the Glucose-6-Phosphate Dehydrogenase from Helicobacter pylori Strain 29CaP
by Paulina Ortiz-Ramírez, Beatriz Hernández-Ochoa, Daniel Ortega-Cuellar, Abigail González-Valdez, Víctor Martínez-Rosas, Laura Morales-Luna, Roberto Arreguin-Espinosa, Rosa Angélica Castillo-Rodríguez, Luis Miguel Canseco-Ávila, Noemi Cárdenas-Rodríguez, Verónica Pérez de la Cruz, Alba Mónica Montiel-González, Fernando Gómez-Chávez and Saúl Gómez-Manzo
Microorganisms 2022, 10(7), 1359; https://doi.org/10.3390/microorganisms10071359 - 6 Jul 2022
Cited by 4 | Viewed by 2305
Abstract
Helicobacter pylori (H. pylori) has been proposed as the foremost risk factor for the development of gastric cancer. We found that H. pylori express the enzyme glucose-6-phosphate dehydrogenase (HpG6PD), which participates in glucose metabolism via the pentose phosphate pathway. Thus, we [...] Read more.
Helicobacter pylori (H. pylori) has been proposed as the foremost risk factor for the development of gastric cancer. We found that H. pylori express the enzyme glucose-6-phosphate dehydrogenase (HpG6PD), which participates in glucose metabolism via the pentose phosphate pathway. Thus, we hypothesized that if the biochemical and physicochemical characteristics of HpG6PD contrast with the host G6PD (human G6PD, HsG6PD), HpG6PD becomes a potential target for novel drugs against H. pylori. In this work, we characterized the biochemical properties of the HpG6PD from the H.pylori strain 29CaP and expressed the active recombinant protein, to analyze its steady-state kinetics, thermostability, and biophysical aspects. In addition, we analyzed the HpG6PD in silico structural properties to compare them with those of the HsG6PD. The optimal pH for enzyme activity was 7.5, with a T1/2 of 46.6 °C, at an optimum stability temperature of 37 °C. The apparent Km values calculated for G6P and NADP+ were 75.0 and 12.8 µM, respectively. G6P does not protect HpG6PD from trypsin digestion, but NADP+ does protect the enzyme from trypsin and guanidine hydrochloride (Gdn-HCl). The biochemical characterization of HpG6PD contributes to knowledge regarding H. pylori metabolism and opens up the possibility of using this enzyme as a potential target for specific and efficient treatment against this pathogen; structural alignment indicates that the three-dimensional (3D) homodimer model of the G6PD protein from H. pylori is different from the 3D G6PD of Homo sapiens. Full article
(This article belongs to the Special Issue The Structure and Properties of Microbial Enzymes)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop