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Cross-regulation of amino acid synthesis and anaerobic electron transfer by MetR-mediated methionine signaling

ABSTRACT: Microorganisms living in nutrient- and energy-limited environments must finely coordinate anabolic and catabolic pathways. However, the molecular mechanisms underlying this balance remain poorly understood. Here, we report a mechanism cross-regulating amino acid biosynthesis and anaerobic respiration in bacterial cells. Using the model bacterium Shewanella oneidensis MR-1, we demonstrated that methionine activates extracellular electron transfer activity at submillimolar concentrations. This regulation is mediated by the transcription factor MetR, a canonical regulator of methionine biosynthesis. Under methionine-limited conditions, MR-1 upregulates methionine biosynthesis genes while repressing genes involved in extracellular electron transfer (metal reduction) and other anaerobic respiratory processes. Conversely, methionine availability relieves this repression, enhancing extracellular electron transfer. Furthermore, the MetR-mediated regulation of extracellular electron transfer was observed in Aeromonas hydrophila. These findings reveal a novel physiological role for MetR, suggesting its involvement in the coordinated energy distribution between anabolic and catabolic pathways.

ORGANISM(S): Shewanella oneidensis MR-1

PROVIDER: GSE282263 | GEO | 2026/06/01

REPOSITORIES: GEO

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Cross-regulation of amino acid synthesis and anaerobic electron transfer by MetR-mediated methionine signaling

Project description:Microorganisms living in nutrient- and energy-limited environments must finely coordinate anabolic and catabolic pathways. However, the molecular mechanisms underlying this balance remain poorly understood. Here, we report a mechanism cross-regulating amino acid biosynthesis and anaerobic respiration in bacterial cells. Using the model bacterium Shewanella oneidensis MR-1, we demonstrated that methionine activates extracellular electron transfer activity at submillimolar concentrations. This regulation is mediated by the transcription factor MetR, a canonical regulator of methionine biosynthesis. Under methionine-limited conditions, MR-1 upregulates methionine biosynthesis genes while repressing genes involved in extracellular electron transfer (metal reduction) and other anaerobic respiratory processes. Conversely, methionine availability relieves this repression, enhancing extracellular electron transfer. Furthermore, the MetR-mediated regulation of extracellular electron transfer was observed in Aeromonas hydrophila. These findings reveal a novel physiological role for MetR, suggesting its involvement in the coordinated energy distribution between anabolic and catabolic pathways.

2026-06-01 | GSE282264 | GEO

Overexpression of the adenylate cyclase gene cyaC facilitates current generation by Shewanella oneidensis in bioelectrochemical systems

Project description:Electrochemically active bacteria (EAB) are capable of electrochemical interactions with electrodes via extracellular electron transfer (EET) pathways and serve as essential components in bioelectrochemical systems. Previous studies have suggested that EAB, such as Shewanella oneidensis MR-1, use cyclic AMP (cAMP) receptor proteins for coordinately regulating the expression of catabolic and EET-related genes, allowing us to hypothesize that the intracellular cAMP concentration is an important factor determining electrochemical activities of EAB. The present study constructed an MR-1 mutant, cyaC-OE that overexpressed cyaC, a gene encoding a membrane-bound class III adenylate cyclase, and examined its electrochemical and transcriptomic characteristics. We show that intracellular cAMP concentration in cyaC-OE is more than double that in wild-type MR-1, and cya-OE generates approximately two-fold higher current in BES than the wild type. In addition, the expression of genes involved in EET and anaerobic carbon catabolism is up-regulated in cya-OE as compared to that in the wild type. These results suggest that enhancement of the intracellular cAMP level is a promising approach for constructing an EAB with high catabolic and electrochemical activities.

2019-11-01 | GSE129679 | GEO

Regulation of Gene Expression During Electron Acceptor Limitation and Bacterial Nanowire Formation in Shewanella oneidensis MR-1

Project description:In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA-Seq analysis was employed to determine differential gene expression over time from cultures maintained in a chemostat and limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including transcription of genes encoding MtrA, MtrC and OmcA, and properly positions these decaheme cytochromes in or near the outer membrane during nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remain unaffected or decrease during nanowire formation. The ompW gene, encoding a small outer membrane porin, has 50-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator CRP and the extracytoplasmic function sigma factor RpoE are among transcription factor genes with increased expression. RpoE could function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA. The transcriptome and mutant analysis of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires.

2016-07-13 | GSE79964 | GEO

Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with different concentrations of methionine

Project description:metR (SPD_0588) mutant (TH9197) cannot grow in chemically defined medium (CDM) and had significant growth defect in CDM with 1 µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39. We compared the transcriptome of WT and metR mutant in CDM with 50 µg/ml methionine by RNA-seq to see if the regulation of MetR is methionine concentration-dependdent.We also want to identify the regulon of SPD_0588 in the two RNA-seq.

2021-05-18 | GSE166818 | GEO

Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with 1 µg/ml methionine

Project description:metR (SPD_0588) mutant (TH9197) cannot grow in chemically defined medium (CDM) without methionine and had significant growth defect in CDM with 1 µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39. We also want to identify the regulon of SPD_0588.

2021-06-01 | GSE142362 | GEO

MR-1 nitrate sample to fumarate sample

Project description:One of the most striking observations in the S. oneidensis genome regarding nitrate respiration is that napC is missing and nrfBCD is degenerated. To gain insights into candidate genes encoding the protein(s) in place of NapC and NrfBCD function, i.e., delivering electrons to NapA and NrfA, transcriptional profiling was carried out using the S. oneidensis whole-genome cDNA microarray. Cells of MR-1 grown on nitrate or fumarate under anaerobic conditions were sampled at the exponential phase for the analysis. The quality of the array data was statistically assessed using the method reported previously. Keywords: Compararive microarray study Compare transcriptional profiles of MR-1 grown on nitrate and Fumarate aiming at finding the electron transfer proteins to NapA and NrfA.

2010-05-19 | E-GEOD-11198 | biostudies-arrayexpress

ChIP-seq of Streptococcus pneumoniae D39 metR over-expression strain with 3×flag tag in CDM without methionine

Project description:In our study, we found that MetR as a transcriptional regulator may regulate the expression of genes not involved in methionine synthesis. To verify our hypothesis, we firstly construct a strain with metR over-expression in D39 and with 3×flag tag and culture this strain in chemically defined medium (CDM) without methionine. Then collect bacteria for ChIP-seq to identify the genes that can be directly transcriptionally regulated by MetR.

2021-05-18 | GSE167148 | GEO

Transcript map of Shewanella oneidensis MR-1

Project description:High-resolution tiling analysis of the MR-1 transcriptome under diverse growth conditions The conditions include aerobic growth in Luria-Bertani broth (LB), aerobic growth in defined lactate minimal medium, anaerobic growth in defined lactate minimal medium with 20mM dimethyl sulfoxide as the electron acceptor, anaerobic growth in defined lactate minimal medium with 10mM iron (III) citrate as the electron acceptor, 10 minutes post heat shock at 42oC see GSE39468 for tiling data on lactate minimal media

2013-03-18 | GSE45217 | GEO

Transcript map of Shewanella oneidensis MR-1

2013-03-18 | E-GEOD-45217 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisiae

Project description:In this study we focus on two Saccharomyces cerevisiae strains with varying production of heterologous α-amylase and we compare the metabolic fluxes and transcriptional regulation at aerobic and anaerobic conditions, in particular with the objective to identify the final electron acceptor for protein folding. We found that anaerobic conditions showed high amount of amylase productions when comparing to aerobic conditions and the genome-scale transcriptional analysis suggested that genes related to the endoplasmic reticulum (ER), lipid synthesis and stress responses were generally up-regulated at anaerobic conditions. Moreover, we proposed a model for the electron transfer from ER to the final electron acceptor, fumarate under anaerobic conditions.

2013-01-17 | GSE38848 | GEO

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