Analysis of the BarA/UvrY Two-Component System in Shewanella oneidensis MR-1

Binnenkade, Lucas; Lassak, Jürgen; Thormann, Kai M.

doi:10.1371/journal.pone.0023440

Cited by 17 publications

(23 citation statements)

References 76 publications

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“…Gene expression experiments with SO_1860 and SO_3457 mutant strains suggest that CsrA is not a target of this two-component system in Shewanella (data not shown) demonstrating that this system may regulate different genes. There inferences were confirmed by a very recent report on barA and uvrY in MR-1 [37]. In a second example, we find that HK SO_2742 and RR SO_2648 have high cofitness (r = 0.85; Pearson correlation) and are required for optimal growth in minimal media with acetate, propionate, or butyrate as carbon sources (Figure 5A).…”

Section: Resultssupporting

confidence: 90%

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

et al. 2011

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Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes.

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Section: Resultssupporting

confidence: 90%

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

et al. 2011

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“…However, NarQ may serve as a sensory kinase for more than one response regulators as its E. coli counterpart. If so, SO1860 is likely another partner of NarQ, although it has been shown to be able to receive a phosphoryl group from an orphan sensor kinase SO3457 [36]. To test whether these proteins function together in regulation of nitrate/nitrite respiration, we performed the trans-phosphorylation assay.…”

Section: Resultsmentioning

confidence: 99%

A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

et al. 2012

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We have previously illustrated the nitrate/nitrite respiratory pathway of Shewanella oneidensis, which is renowned for its remarkable versatility in respiration. Here we investigated the systems regulating the pathway with a reliable approach which enables characterization of mutants impaired in nitrate/nitrite respiration by guaranteeing biomass. The S. oneidensis genome encodes an Escherichia coli NarQ/NarX homolog SO3981 and two E. coli NarP/NarL homologs SO1860 and SO3982. Results of physiological characterization and mutational analyses demonstrated that S. oneidensis possesses a single two-component system (TCS) for regulation of nitrate/nitrite respiration, consisting of the sensor kinase SO3981(NarQ) and the response regulator SO3982(NarP). The TCS directly controls the transcription of nap and nrfA (genes encoding nitrate and nitrite reductases, respectively) but regulates the former less tightly than the latter. Additionally, phosphorylation at residue 57 of SO3982 is essential for its DNA-binding capacity. At the global control level, Crp is found to regulate expression of narQP as well as nap and nrfA. In contrast to NarP-NarQ, Crp is more essential for nap rather than nrfA.

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“…Furthermore, a putative UvrY-binding box was identified upstream of the S. marcescens csrB and csrC genes (Fig. 1C) (Binnenkade et al, 2011;Kulkarni et al, 2006;Lenz et al, 2005). These observations suggest that the expression of the csrB and csrC genes is regulated by the BarA/UvrY two-component RNA was prepared from the exponential, transition from the exponential to stationary, and stationary growth phases in Kornberg media.…”

Section: Discussionmentioning

confidence: 78%

“…CsrA activity would be tightly regulated by two Csr sRNAs in the cell. Transcriptional regulation of Csr sRNAs by the two-component system has been reported in many other γ-proteobacterial species, including Pseudomonas and Shewanella (Binnenkade et al, 2011;Lapouge et al, 2008). Potential homologs to the E. coli BarA/UvrY system have been identified in the S. marcescens 2170 draft genome (accession no.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Csr system in Serratia marcescens 2170

Ito

Nomura

Sugimoto

et al. 2014

J. Gen. Appl. Microbiol.

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The carbon storage regulator (Csr) global regulatory system is conserved in many eubacteria and coordinates the expression of various genes that facilitate adaptation during the major physiological growth phase. The Csr system in Escherichia coli comprises an RNA-binding protein, CsrA; small non-coding RNAs, CsrB and CsrC; and a decay factor for small RNAs, CsrD. In this study, we identified the Csr system in Serratia marcescens 2170. S. marcescens CsrA was 97% identical to E. coli CsrA. CsrB and CsrC RNAs had typical stem-loop structures, including a GGA motif that is the CsrA binding site. CsrD was composed of N-terminal two times transmembrane region and HAMP-like, GGDEF, and EAL domains. Overexpression of S. marcescens csr genes complemented the phenotype of E. coli csr mutants. S. marcescens CsrD affected the decay of CsrB and CsrC RNAs in E. coli. These results suggest that the Csr system in S. marcescens is composed of an RNA-binding protein, two Csr small RNAs, and a decay factor for Csr small RNAs.Key words: Csr system; EAL domain; GGDEF domain; Serratia marcescens; small RNA IntroductionThe carbon storage regulator (Csr) and homologous repressor of secondary metabolite (Rsm) systems, which are the global regulatory systems found in many eubacteria, coordinate the expression of various genes that facilitate adaptation during the major physiological growth phase (Romeo, 1998). In Escherichia coli, the Csr system is composed of a 61-amino-acid RNA-binding protein, CsrA; 366 and 245 nucleotide (nt) small non-coding RNA (sRNA) molecules, CsrB and CsrC, respectively (Liu and Romeo, 1997;Weilbacher et al., 2003); and a predicted membranebound signaling protein, CsrD . CsrA functions as a dimer that binds to specific mRNAs, resulting in altered translation and/or message stability Mercante et al., 2006Mercante et al., , 2009Schubert et al., 2007). CsrA represses stationary-phase gene expression and processes, including gluconeogenesis, glycogen biosynthesis, glycogen catabolism, and biofilm formation, but activates glycolysis, acetate metabolism, and motility (Babitzke and Romeo, 2007;Romeo, 1998). The mechanism underlying CsrA-mediated repression of glycogen biosynthesis (glgCAP) has been elucidated in detail (Baker et al., 2002;Mercante et al., 2009). CsrA recognizes and specifically binds to the untranslated leader of glgCAP mRNA. One of the four binding sites overlaps the glgC Shine-Dalgarno (SD) sequence. The binding of CsrA to these sites regulates GlgC synthesis by preventing ribosome binding, leading to rapid degradation of the transcript (Baker et al., 2002;Mercante et al., 2009;Romeo, 1998).CsrA also activates gene expression, and an activation mechanism has been reported recently. The expression of flhDC, which encodes the master regulator of flagella synthesis and chemotaxis, was activated by CsrA (Wei et al., 2001). CsrA binds to two sites in the flhDC leader transcript and stabilizes it by inhibiting the 5 -end-dependent RNase E cleavage pathway (Yakhnin et al., 2013). A GGA motif is a highly con...

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Analysis of the BarA/UvrY Two-Component System in Shewanella oneidensis MR-1

Cited by 17 publications

References 76 publications

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

Identification of a Csr system in Serratia marcescens 2170

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