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Molecular Advances in Microbial Metabolism 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 9883

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Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, E-03080 Alicante, Spain
Interests: extremophiles; omics-based technologies; gene regulation; microbial metabolism; carotenoids; polyhydroxyalkanoates; biogeochemical cycles; system biology
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, "Molecular Advances in Microbial Metabolism". Microbial metabolism is one of the main driving forces behind the development and maintenance of the biosphere. Due to the relevance of these metabolic pathways, this Special Issue focuses on molecular mechanisms underlying microbial metabolism, not only to improve the knowledge around processes carried out by microbes to obtain energy and nutrients to live and reproduce, but also to shed light on microbial evolution and potential applications of metabolic pathways carried out by microbes in biotechnology and industrial processes. This multidisciplinary topic comprises several disciplines, such as microbiology, molecular biology, genetics, chemistry, microbial ecology, biochemistry, biophysics, and all omics-based sciences which offer insight into the impact that modern technologies have on microbiological research today. Original investigations, as well as concise review manuscripts, from experts in the relevant research fields will be considered for publication.

Prof. Dr. Rosa María Martínez-Espinosa
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.

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Keywords

  • central metabolism
  • secondary metabolism
  • ancient molecules
  • evolution
  • systems biology
  • aerobic metabolism
  • anaerobic metabolism
  • fermentation

Published Papers (6 papers)

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Editorial

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3 pages, 186 KiB  
Editorial
Molecular Advances in Microbial Metabolism 2.0
by Rosa María Martínez-Espinosa
Int. J. Mol. Sci. 2024, 25(2), 1361; https://doi.org/10.3390/ijms25021361 - 22 Jan 2024
Viewed by 995
Abstract
The advances in molecular biology techniques and omics approaches have made it possible to take giant steps in applied research in life sciences [...] Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)

Research

Jump to: Editorial

19 pages, 3747 KiB  
Article
The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS
by Panning Wang, Yaqian Xiao, Donghao Gao, Yan Long and Zhixiong Xie
Int. J. Mol. Sci. 2023, 24(16), 12632; https://doi.org/10.3390/ijms241612632 - 10 Aug 2023
Cited by 1 | Viewed by 1309
Abstract
The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT’s biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid [...] Read more.
The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT’s biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17–21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
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27 pages, 4540 KiB  
Article
Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules of Haemophilus influenzae Rd KW20
by Miguel Fernández-García, Manuel Ares-Arroyo, Emilia Wedel, Natalia Montero, Coral Barbas, Mª Fernanda Rey-Stolle, Bruno González-Zorn and Antonia García
Int. J. Mol. Sci. 2023, 24(13), 11150; https://doi.org/10.3390/ijms241311150 - 6 Jul 2023
Cited by 1 | Viewed by 1853
Abstract
Haemophilus influenzae is a gram-negative bacterium of relevant clinical interest. H. influenzae Rd KW20 was the first organism to be sequenced and for which a genome-scale metabolic model (GEM) was developed. However, current H. influenzae GEMs are unable to capture several aspects of [...] Read more.
Haemophilus influenzae is a gram-negative bacterium of relevant clinical interest. H. influenzae Rd KW20 was the first organism to be sequenced and for which a genome-scale metabolic model (GEM) was developed. However, current H. influenzae GEMs are unable to capture several aspects of metabolome nature related to metabolite pools. To directly and comprehensively characterize the endometabolome of H. influenzae Rd KW20, we performed a multiplatform MS-based metabolomics approach combining LC-MS, GC-MS and CE-MS. We obtained direct evidence of 15–20% of the endometabolome present in current H. influenzae GEMs and showed that polar metabolite pools are interconnected through correlating metabolite islands. Notably, we obtained high-quality evidence of 18 metabolites not previously included in H. influenzae GEMs, including the antimicrobial metabolite cyclo(Leu-Pro). Additionally, we comprehensively characterized and evaluated the quantitative composition of the phospholipidome of H. influenzae, revealing that the fatty acyl chain composition is largely independent of the lipid class, as well as that the probability distribution of phospholipids is mostly related to the conditional probability distribution of individual acyl chains. This finding enabled us to provide a rationale for the observed phospholipid profiles and estimate the abundance of low-level species, permitting the expansion of the phospholipidome characterization through predictive probabilistic modelling. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
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13 pages, 2422 KiB  
Article
Control of Bacterial Phenotype and Chromosomal Gene Expression by Single Plasmids of Lactococcus lactis IL594
by Katarzyna Kosiorek, Anna Koryszewska-Bagińska, Marek Skoneczny and Tamara Aleksandrzak-Piekarczyk
Int. J. Mol. Sci. 2023, 24(12), 9877; https://doi.org/10.3390/ijms24129877 - 8 Jun 2023
Cited by 1 | Viewed by 1168
Abstract
Plasmid-free Lactococcus lactis IL1403 is one of the best-characterized representatives of lactic acid bacteria (LAB), intensively used in broad microbiology worldwide. Its parent strain, L. lactis IL594, contains seven plasmids (pIL1–pIL7) with resolved DNA sequences and an indicated role for overall plasmid load [...] Read more.
Plasmid-free Lactococcus lactis IL1403 is one of the best-characterized representatives of lactic acid bacteria (LAB), intensively used in broad microbiology worldwide. Its parent strain, L. lactis IL594, contains seven plasmids (pIL1–pIL7) with resolved DNA sequences and an indicated role for overall plasmid load in enhancing host-adaptive potential. To determine how individual plasmids manipulate the expression of phenotypes and chromosomal genes, we conducted global comparative phenotypic analyses combined with transcriptomic studies in plasmid-free L. lactis IL1403, multiplasmid L. lactis IL594, and its single-plasmid derivatives. The presence of pIL2, pIL4, and pIL5 led to the most pronounced phenotypic differences in the metabolism of several carbon sources, including some β-glycosides and organic acids. The pIL5 plasmid also contributed to increased tolerance to some antimicrobial compounds and heavy metal ions, especially those in the toxic cation group. Comparative transcriptomics showed significant variation in the expression levels of up to 189 chromosomal genes due to the presence of single plasmids and 435 unique chromosomal genes that were resultant of the activity of all plasmids, which may suggest that the observed phenotypic changes are not only the result of a direct action of their own genes but also originate from indirect actions through crosstalk between plasmids and the chromosome. The data obtained here indicate that plasmid maintenance leads to the development of important mechanisms of global gene regulation that provide changes in the central metabolic pathways and adaptive properties of L. lactis and suggest the possibility of a similar phenomenon among other groups of bacteria. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
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18 pages, 3409 KiB  
Article
Proteomic Analysis of Arsenic Resistance during Cyanide Assimilation by Pseudomonas pseudoalcaligenes CECT 5344
by Karolina A. Biełło, Purificación Cabello, Gema Rodríguez-Caballero, Lara P. Sáez, Víctor M. Luque-Almagro, María Dolores Roldán, Alfonso Olaya-Abril and Conrado Moreno-Vivián
Int. J. Mol. Sci. 2023, 24(8), 7232; https://doi.org/10.3390/ijms24087232 - 13 Apr 2023
Cited by 2 | Viewed by 1724
Abstract
Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR [...] Read more.
Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR analysis and determination of analytes in the cyanide-assimilating bacterium Pseudomonas pseudoalcaligenes CECT 5344. Several proteins encoded by two ars gene clusters and other Ars-related proteins were up-regulated by arsenite, even during cyanide assimilation. Although some proteins encoded by the cio gene cluster responsible for cyanide-insensitive respiration decreased in the presence of arsenite, the nitrilase NitC required for cyanide assimilation was unaffected, thus allowing bacterial growth with cyanide and arsenic. Two complementary As-resistance mechanisms were developed in this bacterium, the extrusion of As(III) and its extracellular sequestration in biofilm, whose synthesis increased in the presence of arsenite, and the formation of organoarsenicals such as arseno-phosphoglycerate and methyl-As. Tetrahydrofolate metabolism was also stimulated by arsenite. In addition, the ArsH2 protein increased in the presence of arsenite or cyanide, suggesting its role in the protection from oxidative stress caused by both toxics. These results could be useful for the development of bioremediation strategies for industrial wastes co-contaminated with cyanide and arsenic. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
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15 pages, 3657 KiB  
Article
New Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling
by Blas Blázquez, David San León, Antonia Rojas, Marta Tortajada and Juan Nogales
Int. J. Mol. Sci. 2023, 24(8), 7091; https://doi.org/10.3390/ijms24087091 - 11 Apr 2023
Cited by 6 | Viewed by 2237
Abstract
Bacillus subtilis is an effective workhorse for the production of many industrial products. The high interest aroused by B. subtilis has guided a large metabolic modeling effort of this species. Genome-scale metabolic models (GEMs) are powerful tools for predicting the metabolic capabilities of [...] Read more.
Bacillus subtilis is an effective workhorse for the production of many industrial products. The high interest aroused by B. subtilis has guided a large metabolic modeling effort of this species. Genome-scale metabolic models (GEMs) are powerful tools for predicting the metabolic capabilities of a given organism. However, high-quality GEMs are required in order to provide accurate predictions. In this work, we construct a high-quality, mostly manually curated genome-scale model for B. subtilis (iBB1018). The model was validated by means of growth performance and carbon flux distribution and provided significantly more accurate predictions than previous models. iBB1018 was able to predict carbon source utilization with great accuracy while identifying up to 28 metabolites as potential novel carbon sources. The constructed model was further used as a tool for the construction of the panphenome of B. subtilis as a species, by means of multistrain genome-scale reconstruction. The panphenome space was defined in the context of 183 GEMs representative of 183 B. subtilis strains and the array of carbon sources sustaining growth. Our analysis highlights the large metabolic versatility of the species and the important role of the accessory metabolism as a driver of the panphenome, at a species level. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
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