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Wang S, Huang CH, Lin TS, Yeh YQ, Fan YS, Wang SW, Tseng HC, Huang SJ, Chang YY, Jeng US, Chang CI, Tzeng SR. Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI. Nat Commun 2024; 15:5461. [PMID: 38937433 PMCID: PMC11211486 DOI: 10.1038/s41467-024-49552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.
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Affiliation(s)
- Shen Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Qi Yeh
- Soft Matter Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yun-Sheng Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Si-Wei Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsi-Ching Tseng
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Yu-Yang Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - U-Ser Jeng
- Soft Matter Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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Mavroidi A, Froukala E, Tsakris A. Comparative Genomics of an Emerging Multidrug-Resistant blaNDM-Carrying ST182 Lineage in Enterobacter cloacae Complex. Antibiotics (Basel) 2024; 13:535. [PMID: 38927201 PMCID: PMC11200890 DOI: 10.3390/antibiotics13060535] [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: 05/16/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Enterobacter cloacae, E. hormaechei and related subspecies remain the most clinically relevant among the Enterobacter cloacae complex (ECC). Carbapenemase-producing ECC strains are increasingly identified in hospital-acquired infections and usually belong to four main multilocus sequence types (MLST STs) named ST114, ST93, ST90 and ST78. Instead, ST182 has been sporadically reported among E. hormaechei strains, and recently, outbreaks of blaNDM-producing ST182 clonal strains have emerged. Herein, we aimed to investigate the presence of ST182 and explore its evolution and modes of blaNDM acquisition. METHODS A phylogenetic analysis of 646 MLST STs identified among 4685 E. hormaechei whole-genome sequencing (WGS) assemblies deposited in public repositories was performed, as well as an in silico comparative and phylogenomic analyses for 55 WGS assemblies of ST182. blaNDM-harboring contigs were also compared to published plasmid sequences. RESULTS ST182 E. hormaechei strains were recovered from patients on five continents during 2011-2021. They were divided into three major genomic clusters, comprising a separate clonal complex with six other STs. In 30 out of 55 ST182 WGS assemblies, blaNDM-harboring structures were identified that were similar to the plasmids predominant in Gram-negative bacteria, harboring resistance genes to multiple antibiotic classes and virulence genes. No associations between the genomic clusters and the country/continent of isolation or the presence and the plasmid types of the blaNDM-harboring contigs were observed. CONCLUSIONS Our findings show that ST182 E. hormaechei strains have been identified in the past decade worldwide; 54.5% of them carried diverse blaNDM genetic structures, suggesting recent acquisition of the blaNDM alleles. Thus, blaNDM-harboring ST182 is an emerging multidrug-resistant and virulent lineage in ECC strains that requires close monitoring.
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Affiliation(s)
- Angeliki Mavroidi
- Department of Microbiology, Faculty of Medicine, General University Hospital of Patras, 26504 Patras, Greece;
| | - Elisavet Froukala
- Department of Microbiology, Medical School, University of Athens, 11527 Athens, Greece;
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, University of Athens, 11527 Athens, Greece;
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Chen Q, Zhang F, Bai J, Che Q, Xiang L, Zhang Z, Wang Y, Sjöling Å, Martín-Rodríguez AJ, Zhu B, Fu L, Zhou Y. Bacteriophage-resistant carbapenem-resistant Klebsiella pneumoniae shows reduced antibiotic resistance and virulence. Int J Antimicrob Agents 2024; 64:107221. [PMID: 38810938 DOI: 10.1016/j.ijantimicag.2024.107221] [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: 07/23/2023] [Revised: 04/21/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Phage therapy has shown great promise in the treatment of bacterial infections. However, the effectiveness of phage therapy is compromised by the inevitable emergence of phage-resistant strains. In this study, a phage-resistant carbapenem-resistant Klebsiella pneumoniae strain SWKP1711R, derived from parental carbapenem-resistant K. pneumoniae strain SWKP1711 was identified. The mechanism of bacteriophage resistance in SWKP1711R was investigated and the molecular determinants causing altered growth characteristics, antibiotic resistance, and virulence of SWKP1711R were tested. Compared to SWKP1711, SWKP1711R showed slower growth, smaller colonies, filamentous cells visible under the microscope, reduced production of capsular polysaccharide (CPS) and lipopolysaccharide, and reduced resistance to various antibiotics accompanied by reduced virulence. Adsorption experiments showed that phage vB_kpnM_17-11 lost the ability to adsorb onto SWKP1711R, and the adsorption receptor was identified to be bacterial surface polysaccharides. Genetic variation analysis revealed that, compared to the parental strain, SWKP1711R had only one thymine deletion at position 78 of the open reading frame of the lpcA gene, resulting in a frameshift mutation that caused alteration of the bacterial surface polysaccharide and inhibition of phage adsorption, ultimately leading to phage resistance. Transcriptome analysis and quantitative reverse transcriptase PCR revealed that genes encoding lipopolysaccharide synthesis, ompK35, blaTEM-1, and type II and Hha-TomB toxin-antitoxin systems, were all downregulated in SWKP1711R. Taken together, the evidence presented here indicates that the phenotypic alterations and phage resistance displayed by the mutant may be related to the frameshift mutation of lpcA and altered gene expression. While evolution of phage resistance remains an issue, our study suggests that the reduced antibiotic resistance and virulence of phage-resistant strain derivatives might be beneficial in alleviating the burden caused by multidrug-resistant bacteria.
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Affiliation(s)
- Qiao Chen
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Feiyang Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiawei Bai
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Qian Che
- Sichuan Center For Disease Control And Prevention, Chengdu, 610000, China
| | - Li Xiang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhikun Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Ying Wang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Alberto J Martín-Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Clinical Sciences, University of Las Palmas de Gran Canaria, 35016, Las Palmas de Gran Canaria, Spain
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Fu
- The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, China.
| | - Yingshun Zhou
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China; Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, China.
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4
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Jung M, Ahn YJ. Growth-enhancing effect of bacterial and plant heat shock proteins in Escherichia coli. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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The division protein FtsZ interacts with the small heat shock protein IbpA in Acholeplasma laidlawii. Biochim Biophys Acta Gen Subj 2022; 1866:130220. [DOI: 10.1016/j.bbagen.2022.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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Vasicek EM, O'Neal L, Parsek MR, Fitch J, White P, Gunn JS. L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation. Front Cell Infect Microbiol 2021; 11:698146. [PMID: 34368016 PMCID: PMC8341724 DOI: 10.3389/fcimb.2021.698146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022] Open
Abstract
L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.
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Affiliation(s)
- Erin M Vasicek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James Fitch
- The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - John S Gunn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Howitz N, Su T, Lazazzera BA. Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli. J Mol Biol 2020; 432:166716. [PMID: 33220263 DOI: 10.1016/j.jmb.2020.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.
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Affiliation(s)
- Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA 90095, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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8
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Obuchowski I, Piróg A, Stolarska M, Tomiczek B, Liberek K. Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates. PLoS Genet 2019; 15:e1008479. [PMID: 31652260 PMCID: PMC6834283 DOI: 10.1371/journal.pgen.1008479] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 11/06/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones that bind to aggregation-prone polypeptides at stress conditions. sHsps encage these polypeptides in assemblies, shielding them from further aggregation. To facilitate their subsequent solubilization and refolding by Hsp70 (DnaK) and Hsp100 (ClpB) chaperones, first, sHsps need to dissociate from the assemblies. In most γ-proteobacteria, these functions are fulfilled by a single sHsp (IbpA), but in a subset of Enterobacterales, a two-protein sHsp (IbpA and IbpB) system has evolved. To gain insight into the emergence of complexity within this chaperone system, we reconstructed the phylogeny of γ-proteobacteria and their sHsps. We selected proteins representative of systems comprising either one or two sHsps and analysed their ability to form sHsps-substrate assemblies. All the tested IbpA proteins, but not IbpBs, stably interact with an aggregating substrate. Moreover, in Escherichia coli cells, ibpA but not ibpB suppress the growth defect associated with low DnaK level, which points to the major protective role of IbpA during the breakdown of protein quality control. We also examined how sHsps affect the association of Hsp70 with the assemblies at the initial phase of disaggregation and how they affect protein recovery after stress. Our results suggest that a single gene duplication event has given rise to the sHsp system consisting of a strong canonical binder, IbpA, and its non-canonical paralog IbpB that enhances sHsps dissociation from the assemblies. The cooperation between the sHsps reduces the demand for Hsp70 needed to outcompete them from the assemblies by promoting sHsps dissociation without compromising assembly formation at heat shock. This potentially increases the robustness and elasticity of sHsps protection against irreversible aggregation. Small heat shock proteins (sHsps) are a class of molecular chaperones playing an important role in maintaining cell proteostasis. Their most widespread and evolutionarily conserved function is binding to denaturing polypeptides. Small Hsps shield their substrates from further aggregation until conditions are favourable for their refolding by chaperones from the Hsp70 and Hsp100 families. To exert this function, at stress conditions, oligomeric sHsps dissociate into dimers and scavenge partially unfolded substrates, forming assemblies containing both substrate proteins and sHsps. Substrate proteins in such assemblies are refolding-competent. Later, when a cell recovers from stress, sHsps need to dissociate from the assemblies to make the substrates available for the disaggregating and refolding chaperones. Most bacteria possess one sHsp-encoding gene. However, their single sHsp is burdened with a trade-off: on one hand, it has to rapidly associate with the misfolding proteins, on the other, it needs to dissociate from them to allow effective disaggregation. With phylogenetic and biochemical approaches, we analysed a two-sHsp system distinctive of the Enterobacterales order, unravelling a potential evolutionary advantage granted by functional cooperation between the two sHsps. Our results indicate that after a gene duplication event, one sHsp specialized in tight substrate binding, whereas another sHsp became important for efficient dissociation of both sHsps to enable recovery of proteins trapped in the assemblies.
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Affiliation(s)
- Igor Obuchowski
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Artur Piróg
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Milena Stolarska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Bartłomiej Tomiczek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
| | - Krzysztof Liberek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland
- * E-mail:
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9
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Cardoso MH, de Almeida KC, Cândido ES, Fernandes GDR, Dias SC, de Alencar SA, Franco OL. Comparative transcriptome analyses of magainin I-susceptible and -resistant Escherichia coli strains. Microbiology (Reading) 2018; 164:1383-1393. [DOI: 10.1099/mic.0.000725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marlon H. Cardoso
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
| | - Keyla C. de Almeida
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
| | - Elizabete S. Cândido
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
| | - Gabriel da R. Fernandes
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 4Oswaldo Cruz Foundation, René Rachou Research Center, Belo Horizonte, MG, Brazil
| | - Simoni C. Dias
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 5Programa de Pós Graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil
| | - Sérgio A. de Alencar
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
| | - Octávio L. Franco
- 3S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS, Brazil
- 1Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília- DF, Brazil
- 2Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
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10
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Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng 2018; 48:233-242. [DOI: 10.1016/j.ymben.2018.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 11/20/2022]
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11
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Selber-Hnatiw S, Rukundo B, Ahmadi M, Akoubi H, Al-Bizri H, Aliu AF, Ambeaghen TU, Avetisyan L, Bahar I, Baird A, Begum F, Ben Soussan H, Blondeau-Éthier V, Bordaries R, Bramwell H, Briggs A, Bui R, Carnevale M, Chancharoen M, Chevassus T, Choi JH, Coulombe K, Couvrette F, D'Abreau S, Davies M, Desbiens MP, Di Maulo T, Di Paolo SA, Do Ponte S, Dos Santos Ribeiro P, Dubuc-Kanary LA, Duncan PK, Dupuis F, El-Nounou S, Eyangos CN, Ferguson NK, Flores-Chinchilla NR, Fotakis T, Gado Oumarou H D M, Georgiev M, Ghiassy S, Glibetic N, Grégoire Bouchard J, Hassan T, Huseen I, Ibuna Quilatan MF, Iozzo T, Islam S, Jaunky DB, Jeyasegaram A, Johnston MA, Kahler MR, Kaler K, Kamani C, Karimian Rad H, Konidis E, Konieczny F, Kurianowicz S, Lamothe P, Legros K, Leroux S, Li J, Lozano Rodriguez ME, Luponio-Yoffe S, Maalouf Y, Mantha J, McCormick M, Mondragon P, Narayana T, Neretin E, Nguyen TTT, Niu I, Nkemazem RB, O'Donovan M, Oueis M, Paquette S, Patel N, Pecsi E, Peters J, Pettorelli A, Poirier C, Pompa VR, Rajen H, Ralph RO, Rosales-Vasquez J, Rubinshtein D, Sakr S, Sebai MS, Serravalle L, Sidibe F, Sinnathurai A, Soho D, Sundarakrishnan A, Svistkova V, Ugbeye TE, Vasconcelos MS, Vincelli M, Voitovich O, Vrabel P, Wang L, Wasfi M, Zha CY, Gamberi C. Human Gut Microbiota: Toward an Ecology of Disease. Front Microbiol 2017; 8:1265. [PMID: 28769880 PMCID: PMC5511848 DOI: 10.3389/fmicb.2017.01265] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics.
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Affiliation(s)
| | - Belise Rukundo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hayfa Akoubi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hend Al-Bizri
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Adelekan F Aliu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lilit Avetisyan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Irmak Bahar
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alexandra Baird
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fatema Begum
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Helene Bramwell
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alicia Briggs
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Richard Bui
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Talia Chevassus
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jin H Choi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Karyne Coulombe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Meghan Davies
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tamara Di Maulo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Paola K Duncan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Sara El-Nounou
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tanya Fotakis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Metodi Georgiev
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tazkia Hassan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Iman Huseen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tania Iozzo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Safina Islam
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Dilan B Jaunky
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Cedric Kamani
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Filip Konieczny
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Karina Legros
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Jun Li
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Yara Maalouf
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jessica Mantha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Thi T T Nguyen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Ian Niu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Matthew Oueis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Nehal Patel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Emily Pecsi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jackie Peters
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | | | | | - Surya Sakr
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lisa Serravalle
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fily Sidibe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Dominique Soho
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | - Olga Voitovich
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Pamela Vrabel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Lu Wang
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Maryse Wasfi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Cong Y Zha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Chiara Gamberi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
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Acetylation of Lysine 201 Inhibits the DNA-Binding Ability of PhoP to Regulate Salmonella Virulence. PLoS Pathog 2016; 12:e1005458. [PMID: 26943369 PMCID: PMC4778762 DOI: 10.1371/journal.ppat.1005458] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/25/2016] [Indexed: 12/21/2022] Open
Abstract
The two-component system PhoP-PhoQ is highly conserved in bacteria and regulates virulence in response to various signals for bacteria within the mammalian host. Here, we demonstrate that PhoP could be acetylated by Pat and deacetylated by deacetylase CobB enzymatically in vitro and in vivo in Salmonella Typhimurium. Specifically, the conserved lysine residue 201(K201) in winged helix-turn-helix motif at C-terminal DNA-binding domain of PhoP could be acetylated, and its acetylation level decreases dramatically when bacteria encounter low magnesium, acid stress or phagocytosis of macrophages. PhoP has a decreased acetylation and increased DNA-binding ability in the deletion mutant of pat. However, acetylation of K201 does not counteract PhoP phosphorylation, which is essential for PhoP activity. In addition, acetylation of K201 (mimicked by glutamine substitute) in S. Typhimurium causes significantly attenuated intestinal inflammation as well as systemic infection in mouse model, suggesting that deacetylation of PhoP K201 is essential for Salmonella pathogenesis. Therefore, we propose that the reversible acetylation of PhoP K201 may ensure Salmonella promptly respond to different stresses in host cells. These findings suggest that reversible lysine acetylation in the DNA-binding domain, as a novel regulatory mechanism of gene expression, is involved in bacterial virulence across microorganisms.
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