Editorial

3 pages, 212 KiB

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Molecular Advances in Microbial Metabolism

by Rosa María Martínez-Espinosa and Carmen Pire

Int. J. Mol. Sci. 2023, 24(9), 8015; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24098015 - 28 Apr 2023

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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)

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15 pages, 2079 KiB

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms24010793 - 02 Jan 2023

Cited by 2 | Viewed by 1850

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms232213754 - 09 Nov 2022

Cited by 2 | Viewed by 1737

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158533 - 01 Aug 2022

Cited by 3 | Viewed by 1794

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms23095117 - 04 May 2022

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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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031486 - 27 Jan 2022

Cited by 6 | Viewed by 2650

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111925 - 03 Nov 2021

Cited by 4 | Viewed by 2134

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910202 - 22 Sep 2021

Cited by 2 | Viewed by 1662

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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147596 - 15 Jul 2021

Cited by 19 | Viewed by 3274

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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