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Pei N, Sun W, He J, Li Y, Chen X, Liang T, Kristiansen K, Liu W, Li J. Genome-wide association study of Klebsiella pneumoniae identifies variations linked to carbapenems resistance. Front Microbiol 2022; 13:997769. [PMID: 36386631 PMCID: PMC9664935 DOI: 10.3389/fmicb.2022.997769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023] Open
Abstract
Klebsiella pneumoniae (KP) is one of the microorganisms that can acquire carbapenem-resistance (CR), and few antimicrobial therapy options exist for infections caused by Carbapenem-Resistant KP (CRKP). In recent years, with the increase of carbapenem resistance rates, treating CRKP has become a serious public health threat in clinical practice. We have collected 2,035 clinical KP isolates from a tertiary hospital in China. Whole genome sequencing data coupled with their binary antimicrobial susceptibility testing data were obtained to conduct the genome-wide association study using a bayesian-based method, including single nucleotide polymorphisms (SNPs) and genes. We identified 28 and 37 potential maker genes associated with imipenem and meropenem resistance, respectively. Among which 19 of them were selected in both drugs by genome-wide association study (GWAS), 11 genes among them were simultaneously validated in independent datasets. These genes were likely related to biofilm formation, efflux pump, and DNA repairing. Moreover, we identified 13 significant CR related SNPs in imipenem or meropenem, with one SNP located in the non-coding region and validated in the independent datasets. Our study indicates complex mechanisms of carbapenems resistance and further investigation of CRKP-related factors are warranted to better understand their contributions to carbapenems resistance. These identified biomarkers may provide targets for future drug interventions or treatments.
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Affiliation(s)
- Na Pei
- BGI-Shenzhen, Shenzhen, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jingxuan He
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Yanming Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Xia Chen
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Tianzhu Liang
- BGI-Shenzhen, Shenzhen, China,Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Junhua Li, ; Wenen Liu,
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China,Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China,*Correspondence: Junhua Li, ; Wenen Liu,
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Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone. Proc Natl Acad Sci U S A 2022; 119:e2207856119. [PMID: 36191235 PMCID: PMC9565160 DOI: 10.1073/pnas.2207856119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AAA+ ATPases are ubiquitous proteins associated with most cellular processes, including DNA unwinding and protein unfolding. Their functional and structural properties are typically determined by domains and motifs added to the conserved ATPases domain. Currently, the molecular function and structure of many ATPases remain elusive. Here, we report the crystal structure and biochemical analyses of YjoB, a Bacillus subtilis AAA+ protein. The crystal structure revealed that the YjoB hexamer forms a bucket hat-shaped structure with a porous chamber. Biochemical analyses showed that YjoB prevents the aggregation of vegetative catalase KatA and gluconeogenesis-specific glyceraldehyde-3 phosphate dehydrogenase GapB but not citrate synthase, a conventional substrate. Structural and biochemical analyses further showed that the internal chamber of YjoB is necessary for inhibition of substrate aggregation. Our results suggest that YjoB, conserved in the class Bacilli, is a potential molecular chaperone acting in the starvation/stationary phases of B. subtilis growth.
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Durand S, Gilet L, Bessières P, Nicolas P, Condon C. Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet 2012; 8:e1002520. [PMID: 22412379 PMCID: PMC3297567 DOI: 10.1371/journal.pgen.1002520] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/20/2011] [Indexed: 12/02/2022] Open
Abstract
Bacillus subtilis possesses three essential enzymes thought to be involved in mRNA decay to varying degrees, namely RNase Y, RNase J1, and RNase III. Using recently developed high-resolution tiling arrays, we examined the effect of depletion of each of these enzymes on RNA abundance over the whole genome. The data are consistent with a model in which the degradation of a significant number of transcripts is dependent on endonucleolytic cleavage by RNase Y, followed by degradation of the downstream fragment by the 5′–3′ exoribonuclease RNase J1. However, many full-size transcripts also accumulate under conditions of RNase J1 insufficiency, compatible with a model whereby RNase J1 degrades transcripts either directly from the 5′ end or very close to it. Although the abundance of a large number of transcripts was altered by depletion of RNase III, this appears to result primarily from indirect transcriptional effects. Lastly, RNase depletion led to the stabilization of many low-abundance potential regulatory RNAs, both in intergenic regions and in the antisense orientation to known transcripts. RNA turnover is an important way of controlling gene expression. While the characterization of the pathways and enzymes for RNA degradation are well-advanced in Escherichia coli and yeast, studies in Gram-positive bacteria have lagged behind. This tiling array study shows that two essential enzymes, the single-strand specific endonuclease RNase Y and the 5′–3′ exoribonuclease RNase J1, play central roles in the degradation of mRNAs in Bacillus subtilis. The double-strand specific enzyme RNase III plays a more minor role in RNA turnover, but has significant indirect effects on transcription. Depleting cells of these key enzymes led to the stabilization of many potentially regulatory RNAs, which were otherwise revealed only through testing a wide variety of experimental conditions. It is now possible to tell at a glance which of these three RNases is involved in the turnover of your favorite mRNA.
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Affiliation(s)
- Sylvain Durand
- CNRS UPR 9073, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Laetitia Gilet
- CNRS UPR 9073, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | | | - Pierre Nicolas
- INRA UR1077, Mathématique Informatique et Génome, Jouy en Josas, France
| | - Ciarán Condon
- CNRS UPR 9073, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- * E-mail:
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Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis. Appl Environ Microbiol 2009; 75:7356-64. [PMID: 19820159 DOI: 10.1128/aem.01560-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Essential membrane proteins are generally recognized as relevant potential drug targets due to their exposed localization in the cell envelope. Unfortunately, high-level production of membrane proteins for functional and structural analyses is often problematic. This is mainly due to their high overall hydrophobicity. To develop new concepts for membrane protein overproduction, we investigated whether the biogenesis of overproduced membrane proteins is affected by stress response-related proteolytic systems in the membrane. For this purpose, the well-established expression host Bacillus subtilis was used to overproduce eight essential membrane proteins from B. subtilis and Staphylococcus aureus. The results show that the sigma(W) regulon (responding to cell envelope perturbations) and the CssRS two-component regulatory system (responding to unfolded exported proteins) set critical limits to membrane protein production in large quantities. The identified sigW or cssRS mutant B. subtilis strains with significantly improved capacity for membrane protein production are interesting candidate expression hosts for fundamental research and biotechnological applications. Importantly, our results pinpoint the interdependent expression and function of membrane-associated proteases as key parameters in bacterial membrane protein production.
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Butcher BG, Helmann JD. Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Mol Microbiol 2006; 60:765-82. [PMID: 16629676 DOI: 10.1111/j.1365-2958.2006.05131.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis produces many antibiotics of varying structures and specificity. Here we identify a prominent role for sigma(W), an extracytoplasmic function (ECF) sigma factor, in providing intrinsic resistance to antimicrobial compounds produced by other Bacilli. By using a panel of B. subtilis mutants disrupted for each of the 30 known sigma(W)-dependent operons we identified resistance genes for at least three different antimicrobial compounds. The ydbST and fosB genes contribute to resistance to antimicrobial compound(s) produced by B. amyloliquefaciens FZB42, the yqeZyqfAB operon provides resistance to the SPbeta prophage-encoded bacteriocin sublancin, and the yknWXYZ operon and yfhL provide resistance to the antimicrobial peptide SdpC. YfhL encodes a paralogue of SdpI, a membrane protein that provides immunity to SdpC. In competition experiments, we identify sigma(W) as a key factor in allowing B. subtilis to resist antibiotic killing and encroachment by competing strains. Together with the previous observation that sigma(W) provides inducible resistance against the Streptomyces antibiotic fosfomycin, these studies support the notion that sigma(W) controls an antibiosis regulon important in the microbial ecology of soil bacteria.
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Affiliation(s)
- Bronwyn G Butcher
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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