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Molecular Advances in Microbial Metabolism

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 (27 December 2022) | Viewed by 20738

Special Issue Editors


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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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Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, 03690 San Vicente del Raspeig, Spain
Interests: archaeal; denitrification; nitrogen cycle
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

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
Dr. Carmen Lucía Pire-Galiana
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

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

Published Papers (9 papers)

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Editorial

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3 pages, 212 KiB  
Editorial
Molecular Advances in Microbial Metabolism
by Rosa María Martínez-Espinosa and Carmen Pire
Int. J. Mol. Sci. 2023, 24(9), 8015; https://doi.org/10.3390/ijms24098015 - 28 Apr 2023
Viewed by 1013
Abstract
Climate change, global pollution due to plastics, greenhouse gasses, or heavy metals among other pollutants, as well as limited natural sources due to unsustainable lifestyles and consumption patterns, are revealing the need for more research to understand ecosystems, biodiversity, and global concerns from [...] Read more.
Climate change, global pollution due to plastics, greenhouse gasses, or heavy metals among other pollutants, as well as limited natural sources due to unsustainable lifestyles and consumption patterns, are revealing the need for more research to understand ecosystems, biodiversity, and global concerns from the microscale to the macroscale [...] Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)

Research

Jump to: Editorial

15 pages, 2079 KiB  
Article
The Presence of Plasmids in Lactococcus lactis IL594 Determines Changes in the Host Phenotype and Expression of Chromosomal Genes
by Katarzyna Kosiorek, Anna Koryszewska-Bagińska, Marek Skoneczny, Lidia Stasiak-Różańska and Tamara Aleksandrzak-Piekarczyk
Int. J. Mol. Sci. 2023, 24(1), 793; https://doi.org/10.3390/ijms24010793 - 2 Jan 2023
Cited by 2 | Viewed by 1980
Abstract
The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently [...] Read more.
The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently described, however the knowledge of global changes in host phenotype and transcriptome remains poor. In the present study, global phenotypic analyses were combined with transcriptomic studies to evaluate a potential influence of plasmidic genes on overall gene expression in industrially important L. lactis strains. High-throughput screening of phenotypes differences revealed pronounced phenotypic differences in favor of IL594 during the metabolism of some C-sources, including lactose and β-glucosides. A plasmids-bearing strain presented increased resistance to unfavorable growth conditions, including the presence of heavy metal ions and antimicrobial compounds. Global comparative transcriptomic study of L. lactis strains revealed variation in the expression of over 370 of chromosomal genes caused by plasmids presence. The general trend presented upregulated energy metabolism and biosynthetic genes, differentially expressed regulators, prophages and cell resistance proteins. Our findings suggest that plasmids maintenance leads to significant perturbation in global gene regulation that provides change in central metabolic pathways and adaptive properties of the IL594 cells. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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15 pages, 1519 KiB  
Article
Revealing the Phenotypic and Genomic Background for PHA Production from Rapeseed-Biodiesel Crude Glycerol Using Photobacterium ganghwense C2.2
by Irina Lascu, Ana Maria Tănase, Piotr Jablonski, Iulia Chiciudean, Maria Irina Preda, Sorin Avramescu, Knut Irgum and Ileana Stoica
Int. J. Mol. Sci. 2022, 23(22), 13754; https://doi.org/10.3390/ijms232213754 - 9 Nov 2022
Cited by 2 | Viewed by 1872
Abstract
Polyhydroxyalkanoates (PHA) are promising biodegradable and biocompatible bioplastics, and extensive knowledge of the employed bacterial strain’s metabolic capabilities is necessary in choosing economically feasible production conditions. This study aimed to create an in-depth view of the utilization of Photobacterium ganghwense C2.2 for PHA [...] Read more.
Polyhydroxyalkanoates (PHA) are promising biodegradable and biocompatible bioplastics, and extensive knowledge of the employed bacterial strain’s metabolic capabilities is necessary in choosing economically feasible production conditions. This study aimed to create an in-depth view of the utilization of Photobacterium ganghwense C2.2 for PHA production by linking a wide array of characterization methods: metabolic pathway annotation from the strain’s complete genome, high-throughput phenotypic tests, and biomass analyses through plate-based assays and flask and bioreactor cultivations. We confirmed, in PHA production conditions, urea catabolization, fatty acid degradation and synthesis, and high pH variation and osmotic stress tolerance. With urea as a nitrogen source, pure and rapeseed-biodiesel crude glycerol were analyzed comparatively as carbon sources for fermentation at 20 °C. Flask cultivations yielded 2.2 g/L and 2 g/L PHA at 120 h, respectively, with molecular weights of 428,629 g/mol and 81,515 g/mol. Bioreactor batch cultivation doubled biomass accumulation (10 g/L and 13.2 g/L) in 48 h, with a PHA productivity of 0.133 g/(L·h) and 0.05 g/(L·h). Thus, phenotypic and genomic analyses determined the successful use of Photobacterium ganghwense C2.2 for PHA production using urea and crude glycerol and 20 g/L NaCl, without pH adjustment, providing the basis for a viable fermentation process. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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19 pages, 4470 KiB  
Article
Transcriptomic Response of the Diazotrophic Bacteria Gluconacetobacter diazotrophicus Strain PAL5 to Iron Limitation and Characterization of the fur Regulatory Network
by Cleiton de Paula Soares, Michelle Zibetti Trada-Sfeir, Leonardo Araújo Terra, Jéssica de Paula Ferreira, Carlos Magno Dos-Santos, Izamara Gesiele Bezerra de Oliveira, Jean Luiz Simões Araújo, Carlos Henrique Salvino Gadelha Meneses, Emanuel Maltempi de Souza, José Ivo Baldani and Marcia Soares Vidal
Int. J. Mol. Sci. 2022, 23(15), 8533; https://doi.org/10.3390/ijms23158533 - 1 Aug 2022
Cited by 3 | Viewed by 1977
Abstract
Gluconacetobacter diazotrophicus has been the focus of several studies aiming to understand the mechanisms behind this endophytic diazotrophic bacterium. The present study is the first global analysis of the early transcriptional response of exponentially growing G. diazotrophicus to iron, an essential cofactor for [...] Read more.
Gluconacetobacter diazotrophicus has been the focus of several studies aiming to understand the mechanisms behind this endophytic diazotrophic bacterium. The present study is the first global analysis of the early transcriptional response of exponentially growing G. diazotrophicus to iron, an essential cofactor for many enzymes involved in various metabolic pathways. RNA-seq, targeted gene mutagenesis and computational motif discovery tools were used to define the G. diazotrophicusfur regulon. The data analysis showed that genes encoding functions related to iron homeostasis were significantly upregulated in response to iron limitations. Certain genes involved in secondary metabolism were overexpressed under iron-limited conditions. In contrast, it was observed that the expression of genes involved in Fe-S cluster biosynthesis, flagellar biosynthesis and type IV secretion systems were downregulated in an iron-depleted culture medium. Our results support a model that controls transcription in G. diazotrophicus by fur function. The G. diazotrophicusfur protein was able to complement an E. colifur mutant. These results provide new insights into the effects of iron on the metabolism of G. diazotrophicus, as well as demonstrate the essentiality of this micronutrient for the main characteristics of plant growth promotion by G. diazotrophicus. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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25 pages, 2814 KiB  
Article
Fine-Tuning Modulation of Oxidation-Mediated Posttranslational Control of Bradyrhizobium diazoefficiens FixK2 Transcription Factor
by Sergio Parejo, Juan J. Cabrera, Andrea Jiménez-Leiva, Laura Tomás-Gallardo, Eulogio J. Bedmar, Andrew J. Gates and Socorro Mesa
Int. J. Mol. Sci. 2022, 23(9), 5117; https://doi.org/10.3390/ijms23095117 - 4 May 2022
Cited by 4 | Viewed by 2137
Abstract
FixK2 is a CRP/FNR-type transcription factor that plays a central role in a sophisticated regulatory network for the anoxic, microoxic and symbiotic lifestyles of the soybean endosymbiont Bradyrhizobium diazoefficiens. Aside from the balanced expression of the fixK2 gene under microoxic [...] Read more.
FixK2 is a CRP/FNR-type transcription factor that plays a central role in a sophisticated regulatory network for the anoxic, microoxic and symbiotic lifestyles of the soybean endosymbiont Bradyrhizobium diazoefficiens. Aside from the balanced expression of the fixK2 gene under microoxic conditions (induced by the two-component regulatory system FixLJ and negatively auto-repressed), FixK2 activity is posttranslationally controlled by proteolysis, and by the oxidation of a singular cysteine residue (C183) near its DNA-binding domain. To simulate the permanent oxidation of FixK2, we replaced C183 for aspartic acid. Purified C183D FixK2 protein showed both low DNA binding and in vitro transcriptional activation from the promoter of the fixNOQP operon, required for respiration under symbiosis. However, in a B. diazoefficiens strain coding for C183D FixK2, expression of a fixNOQP’-‘lacZ fusion was similar to that in the wild type, when both strains were grown microoxically. The C183D FixK2 encoding strain also showed a wild-type phenotype in symbiosis with soybeans, and increased fixK2 gene expression levels and FixK2 protein abundance in cells. These two latter observations, together with the global transcriptional profile of the microoxically cultured C183D FixK2 encoding strain, suggest the existence of a finely tuned regulatory strategy to counterbalance the oxidation-mediated inactivation of FixK2 in vivo. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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15 pages, 2585 KiB  
Article
Regulation of the Emissions of the Greenhouse Gas Nitrous Oxide by the Soybean Endosymbiont Bradyrhizobium diazoefficiens
by Emilio Bueno, Daniel Mania, Socorro Mesa, Eulogio J. Bedmar, Åsa Frostegård, Lars R. Bakken and María J. Delgado
Int. J. Mol. Sci. 2022, 23(3), 1486; https://doi.org/10.3390/ijms23031486 - 27 Jan 2022
Cited by 6 | Viewed by 2825
Abstract
The greenhouse gas nitrous oxide (N2O) has strong potential to drive climate change. Soils are a major source of N2O, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont Bradyrhizobium diazoefficiens is [...] Read more.
The greenhouse gas nitrous oxide (N2O) has strong potential to drive climate change. Soils are a major source of N2O, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model microorganism to study denitrification, a process that depends on a set of reductases, encoded by the napEDABC, nirK, norCBQD, and nosRZDYFLX genes, which sequentially reduce nitrate (NO3) to nitrite (NO2), nitric oxide (NO), N2O, and dinitrogen (N2). In this bacterium, the regulatory network and environmental cues governing the expression of denitrification genes rely on the FixK2 and NnrR transcriptional regulators. To understand the role of FixK2 and NnrR proteins in N2O turnover, we monitored real-time kinetics of NO3, NO2, NO, N2O, N2, and oxygen (O2) in a fixK2 and nnrR mutant using a robotized incubation system. We confirmed that FixK2 and NnrR are regulatory determinants essential for NO3 respiration and N2O reduction. Furthermore, we demonstrated that N2O reduction by B. diazoefficiens is independent of canonical inducers of denitrification, such as the nitrogen oxide NO3, and it is negatively affected by acidic and alkaline conditions. These findings advance the understanding of how specific environmental conditions and two single regulators modulate N2O turnover in B. diazoefficiens. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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18 pages, 3438 KiB  
Article
Central Carbon Metabolism, Sodium-Motive Electron Transfer, and Ammonium Formation by the Vaginal Pathogen Prevotella bivia
by Lena Schleicher, Sebastian Herdan, Günter Fritz, Andrej Trautmann, Jana Seifert and Julia Steuber
Int. J. Mol. Sci. 2021, 22(21), 11925; https://doi.org/10.3390/ijms222111925 - 3 Nov 2021
Cited by 4 | Viewed by 2288
Abstract
Replacement of the Lactobacillus dominated vaginal microbiome by a mixed bacterial population including Prevotella bivia is associated with bacterial vaginosis (BV). To understand the impact of P. bivia on this microbiome, its growth requirements and mode of energy production were studied. Anoxic growth [...] Read more.
Replacement of the Lactobacillus dominated vaginal microbiome by a mixed bacterial population including Prevotella bivia is associated with bacterial vaginosis (BV). To understand the impact of P. bivia on this microbiome, its growth requirements and mode of energy production were studied. Anoxic growth with glucose depended on CO2 and resulted in succinate formation, indicating phosphoenolpyruvate carboxylation and fumarate reduction as critical steps. The reductive branch of fermentation relied on two highly active, membrane-bound enzymes, namely the quinol:fumarate reductase (QFR) and Na+-translocating NADH:quinone oxidoreductase (NQR). Both enzymes were characterized by activity measurements, in-gel fluorography, and VIS difference spectroscopy, and the Na+-dependent build-up of a transmembrane voltage was demonstrated. NQR is a potential drug target for BV treatment since it is neither found in humans nor in Lactobacillus. In P. bivia, the highly active enzymes L-asparaginase and aspartate ammonia lyase catalyze the conversion of asparagine to the electron acceptor fumarate. However, the by-product ammonium is highly toxic. It has been proposed that P. bivia depends on ammonium-utilizing Gardnerella vaginalis, another typical pathogen associated with BV, and provides key nutrients to it. The product pattern of P. bivia growing on glucose in the presence of mixed amino acids substantiates this notion. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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16 pages, 2596 KiB  
Article
Na+-Coupled Respiration and Reshaping of Extracellular Polysaccharide Layer Counteract Monensin-Induced Cation Permeability in Prevotella bryantii B14
by Andrej Trautmann, Lena Schleicher, Jana Pfirrmann, Christin Boldt, Julia Steuber and Jana Seifert
Int. J. Mol. Sci. 2021, 22(19), 10202; https://doi.org/10.3390/ijms221910202 - 22 Sep 2021
Cited by 2 | Viewed by 1808
Abstract
Monensin is an ionophore for monovalent cations, which is frequently used to prevent ketosis and to enhance performance in dairy cows. Studies have shown the rumen bacteria Prevotella bryantii B14 being less affected by monensin. The present study aimed to reveal [...] Read more.
Monensin is an ionophore for monovalent cations, which is frequently used to prevent ketosis and to enhance performance in dairy cows. Studies have shown the rumen bacteria Prevotella bryantii B14 being less affected by monensin. The present study aimed to reveal more information about the respective molecular mechanisms in P.bryantii, as there is still a lack of knowledge about defense mechanisms against monensin. Cell growth experiments applying increasing concentrations of monensin and incubations up to 72 h were done. Harvested cells were used for label-free quantitative proteomics, enzyme activity measurements, quantification of intracellular sodium and extracellular glucose concentrations and fluorescence microscopy. Our findings confirmed an active cell growth and fermentation activity of P.bryantii B14 despite monensin concentrations up to 60 µM. An elevated abundance and activity of the Na+-translocating NADH:quinone oxidoreductase counteracted sodium influx caused by monensin. Cell membranes and extracellular polysaccharides were highly influenced by monensin indicated by a reduced number of outer membrane proteins, an increased number of certain glucoside hydrolases and an elevated concentration of extracellular glucose. Thus, a reconstruction of extracellular polysaccharides in P.bryantii in response to monensin is proposed, which is expected to have a negative impact on the substrate binding capacities of this rumen bacterium. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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16 pages, 4505 KiB  
Article
Integration of Transcriptome and Metabolome Reveals the Genes and Metabolites Involved in Bifidobacterium bifidum Biofilm Formation
by Zongmin Liu, Lingzhi Li, Zhifeng Fang, Yuankun Lee, Jianxin Zhao, Hao Zhang, Wei Chen, Haitao Li and Wenwei Lu
Int. J. Mol. Sci. 2021, 22(14), 7596; https://doi.org/10.3390/ijms22147596 - 15 Jul 2021
Cited by 21 | Viewed by 3457
Abstract
Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both [...] Read more.
Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both B. bifidum biofilm and planktonic cells was performed to identify key genes and metabolites involved in biofilm formation. Two hundred thirty-five nonredundant differentially expressed genes (DEGs) (including vanY, pstS, degP, groS, infC, groL, yajC, tadB and sigA) and 219 nonredundant differentially expressed metabolites (including L-threonine, L-cystine, L-tyrosine, ascorbic acid, niacinamide, butyric acid and sphinganine) were identified. Thirteen pathways were identified during the integration of both transcriptomics and metabolomics data, including ABC transporters; quorum sensing; two-component system; oxidative phosphorylation; cysteine and methionine metabolism; glutathione metabolism; glycine, serine and threonine metabolism; and valine, leucine and isoleucine biosynthesis. The DEGs that relate to the integration pathways included asd, atpB, degP, folC, ilvE, metC, pheA, pstS, pyrE, serB, ulaE, yajC and zwf. The differentially accumulated metabolites included L-cystine, L-serine, L-threonine, L-tyrosine, methylmalonate, monodehydroascorbate, nicotinamide, orthophosphate, spermine and tocopherol. These results indicate that quorum sensing, two-component system and amino acid metabolism are essential during B. bifidum biofilm formation. Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism)
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