The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism

Han, Ah Reum; Kang, Hye Ri; Son, Jonghyeon; Kwon, Do Hoon; Kim, Sulhee; Lee, Woo Cheol; Song, Hyun Kyu; Song, Mee Hyun; Hwang, Kwang Yeon

doi:10.1093/nar/gkw775

Cited by 21 publications

(16 citation statements)

References 44 publications

(66 reference statements)

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“…Five out of the twelve mutants contained mutations in codY ; one had a point mutation resulting in a premature stop codon, two had a 60-bp deletion, and two had independent point mutations resulting in nonsynonymous mutations ( Table 1 ) and ( Fig 3A ). We then mapped the mutations to identify their position within the CodY protein structure (PDB ID:5EY0) [ 59 ]. All mutations occurred in the linker region between the metabolite sensing domain and the DNA-binding domain ( Fig 3B ).…”

Section: Resultsmentioning

confidence: 99%

Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

et al. 2018

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Staphylococcus aureus requires branched-chain amino acids (BCAAs; isoleucine, leucine, valine) for protein synthesis, branched-chain fatty acid synthesis, and environmental adaptation by responding to their availability via the global transcriptional regulator CodY. The importance of BCAAs for S. aureus physiology necessitates that it either synthesize them or scavenge them from the environment. Indeed S. aureus uses specialized transporters to scavenge BCAAs, however, its ability to synthesize them has remained conflicted by reports that it is auxotrophic for leucine and valine despite carrying an intact BCAA biosynthetic operon. In revisiting these findings, we have observed that S. aureus can engage in leucine and valine synthesis, but the level of BCAA synthesis is dependent on the BCAA it is deprived of, leading us to hypothesize that each BCAA differentially regulates the biosynthetic operon. Here we show that two mechanisms of transcriptional repression regulate the level of endogenous BCAA biosynthesis in response to specific BCAA availability. We identify a trans-acting mechanism involving isoleucine-dependent repression by the global transcriptional regulator CodY and a cis-acting leucine-responsive attenuator, uncovering how S. aureus regulates endogenous biosynthesis in response to exogenous BCAA availability. Moreover, given that isoleucine can dominate CodY-dependent regulation of BCAA biosynthesis, and that CodY is a global regulator of metabolism and virulence in S. aureus, we extend the importance of isoleucine availability for CodY-dependent regulation of other metabolic and virulence genes. These data resolve the previous conflicting observations regarding BCAA biosynthesis, and reveal the environmental signals that not only induce BCAA biosynthesis, but that could also have broader consequences on S. aureus environmental adaptation and virulence via CodY.

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Section: Resultsmentioning

confidence: 99%

Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

et al. 2018

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“…(Brinsmade, ; Colomer‐Winter, Flores‐Mireles, Kundra, Hultgren, & Lemos, ; Daou et al, ; Geiger & Wolz, ; Li, Freedman, Evans, & McClane, ; Mlynek et al, ; Richardson, Somerville, & Sonenshein, ). The DNA‐binding affinity of CodY from B. subtilis and most other species is increased by interaction with two types of ligands, the branched‐chain amino acids (isoleucine, leucine and valine) and GTP (Han et al, ; Richardson et al, ; Sonenshein, ). The response of CodY to these effectors ties its activity to the ability of the cell to make RNA, protein and branched‐chain fatty acids, the primary membrane fatty acids in CodY‐encoding species.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide identification of Listeria monocytogenes CodY‐binding sites

Biswas

Sonenshein

Belitsky

2020

Molecular Microbiology

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CodY is a global transcriptional regulator that controls, directly or indirectly, the expression of dozens of genes and operons in Listeria monocytogenes. We used in vitro DNA affinity purification combined with massively parallel sequencing (IDAP‐Seq) to identify genome‐wide L. monocytogenes chromosomal DNA regions that CodY binds in vitro. The total number of CodY‐binding regions exceeded 2,000, but they varied significantly in their strengths of binding at different CodY concentrations. The 388 strongest CodY‐binding regions were chosen for further analysis. A strand‐specific analysis of the data allowed pinpointing CodY‐binding sites at close to single‐nucleotide resolution. Gel shift and DNase I footprinting assays confirmed the presence and locations of several CodY‐binding sites. Surprisingly, most of the sites were located within genes’ coding regions. The binding site within the beginning of the coding sequence of the prfA gene, which encodes the master regulator of virulence genes, has been previously implicated in regulation of prfA, but this site was weaker in vitro than hundreds of other sites. The L. monocytogenes CodY protein was functionally similar to Bacillus subtilis CodY when expressed in B. subtilis cells. Based on the sequences of the CodY‐binding sites, a model of CodY interaction with DNA is proposed.

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“…A recent crystal structure study of full-length CodY demonstrates that GTP binds to a site located in the hinge region connecting the N- and C-terminal domains. In comparison to the CodY proteins that are activated by GTP, the CodY proteins of L. lactis and S. pneumoniae exhibit the substitution of three amino acids in the proposed GTP binding site, which may explain the specificity of the cofactors [ 13 ]. The CodY binding consensus sequence, 5’-AATTTTCWGAAAATT, has been defined in B. subtilis and L. lactis [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius

et al. 2018

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BackgroundStreptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5.5, with limited and excessive glucose supply were determined.ResultsThe transcriptomic analysis revealed that CodY was most active at pH 7 under conditions of glucose limitation. Based on whether a CodY binding consensus could be located in the 5′ flanking region of the identified target, the transcriptomic analysis also found that CodY shaped the transcriptome via both direct and indirect regulation. Inactivation of codY reduced the glycolytic capacity and the viability of S. salivarius at pH 5.5 or in the presence of H2O2. Studies using the Galleria mellonella larva model showed that CodY was essential for the toxicity generated from S. salivarius infection, suggesting that CodY regulation was critical for immune evasion and systemic infections. Furthermore, the CodY-null mutant strain exhibited a clumping phenotype and reduced attachment in biofilm assays, suggesting that CodY also modulates cell wall metabolism. Finally, the expression of genes belonging to the CovR regulon was affected by codY inactivation, but CodY and CovR regulated these genes in opposite directions.ConclusionsMetabolic adaptation in response to nutrient availability and growth pH is tightly linked to stress responses and virulence expression in S. salivarius. The regulation of metabolism by CodY allows for the maximal utilization of available nutrients and ATP production. The counteractive regulation of the CovR regulon could fine tune the transcriptomes in response to environmental changes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4781-z) contains supplementary material, which is available to authorized users.

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The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism

Cited by 21 publications

References 44 publications

Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

Genome‐wide identification of Listeria monocytogenes CodY‐binding sites

Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius

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