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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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2
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Naguib M, Feldman N, Zarodkiewicz P, Shropshire H, Biamis C, El-Halfawy OM, McCain J, Dezanet C, Décout JL, Chen Y, Cosa G, Valvano MA. An evolutionary conserved detoxification system for membrane lipid-derived peroxyl radicals in Gram-negative bacteria. PLoS Biol 2022; 20:e3001610. [PMID: 35580139 PMCID: PMC9113575 DOI: 10.1371/journal.pbio.3001610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/18/2022] [Indexed: 11/30/2022] Open
Abstract
How double-membraned Gram-negative bacteria overcome lipid peroxidation is virtually unknown. Bactericidal antibiotics and superoxide ion stress stimulate the transcription of the Burkholderia cenocepacia bcnA gene that encodes a secreted lipocalin. bcnA gene orthologs are conserved in bacteria and generally linked to a conserved upstream gene encoding a cytochrome b561 membrane protein (herein named lcoA, lipocalin-associated cytochrome oxidase gene). Mutants in bcnA, lcoA, and in a gene encoding a conserved cytoplasmic aldehyde reductase (peroxidative stress-associated aldehyde reductase gene, psrA) display enhanced membrane lipid peroxidation. Compared to wild type, the levels of the peroxidation biomarker malondialdehyde (MDA) increase in the mutants upon exposure to sublethal concentrations of the bactericidal antibiotics polymyxin B and norfloxacin. Microscopy with lipid peroxidation-sensitive fluorescent probes shows that lipid peroxyl radicals accumulate at the bacterial cell poles and septum and peroxidation is associated with a redistribution of anionic phospholipids and reduced antimicrobial resistance in the mutants. We conclude that BcnA, LcoA, and PsrA are components of an evolutionary conserved, hitherto unrecognized peroxidation detoxification system that protects the bacterial cell envelope from lipid peroxyl radicals.
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Affiliation(s)
- Marwa Naguib
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Nicolás Feldman
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Paulina Zarodkiewicz
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Holly Shropshire
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Christina Biamis
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Omar M. El-Halfawy
- Department of Chemistry and Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Julia McCain
- Department of Chemistry and Quebec Center for Advanced Materials, McGill University, Montreal, Québec, Canada
| | - Clément Dezanet
- Department of Molecular Pharmacochemistry, Université Grenoble Alpes/CNRS, Grenoble, France
| | - Jean-Luc Décout
- Department of Molecular Pharmacochemistry, Université Grenoble Alpes/CNRS, Grenoble, France
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials, McGill University, Montreal, Québec, Canada
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
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3
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Wang KH, Zheng DH, Yuan GQ, Lin W, Li QQ. A yceI Gene Involves in the Adaptation of Ralstonia solanacearum to Methyl Gallate and Other Stresses. Microorganisms 2021; 9:microorganisms9091982. [PMID: 34576877 PMCID: PMC8472277 DOI: 10.3390/microorganisms9091982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Ralstonia solanacearum is a plant-pathogenic bacterium causing plant bacterial wilt, and can be strongly inhibited by methyl gallate (MG). Our previous transcriptome sequencing of MG-treated R. solanacearum showed that the yceI gene AVT05_RS03545 of Rs-T02 was up-regulated significantly under MG stress. In this study, a deletion mutant (named DM3545) and an over-expression strain (named OE3545) for yceI were constructed to confirm this hypothesis. No significant difference was observed among the growth of wild-type strain, DM3545 and OE3545 strains without MG treatment. Mutant DM3545 showed a lower growth ability than that of the wild type and OE3545 strains under MG treatment, non-optimal temperature, or 1% NaCl. The ability of DM3545 for rhizosphere colonization was lower than that of the wild-type and OE3545 strains. The DM3545 strain showed substantially reduced virulence toward tomato plants than its wild-type and OE3545 counterpart. Moreover, DM3545 was more sensitive to MG in plants than the wild-type and OE3545 strains. These results suggest that YceI is involved in the adaptability of R. solanacearum to the presence of MG and the effect of other tested abiotic stresses. This protein is also possibly engaged in the virulence potential of R. solanacearum.
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Affiliation(s)
| | | | | | | | - Qi-Qin Li
- Correspondence: (D.-H.Z.); (Q.-Q.L.)
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4
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Patel JS, Norambuena J, Al-Tameemi H, Ahn YM, Perryman AL, Wang X, Daher SS, Occi J, Russo R, Park S, Zimmerman M, Ho HP, Perlin DS, Dartois V, Ekins S, Kumar P, Connell N, Boyd JM, Freundlich JS. Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus. ACS Infect Dis 2021; 7:2508-2521. [PMID: 34342426 DOI: 10.1021/acsinfecdis.1c00265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the application of Bayesian modeling to identify chemical tools and/or drug discovery entities pertinent to drug-resistant Staphylococcus aureus infections. The quinoline JSF-3151 was predicted by modeling and then empirically demonstrated to be active against in vitro cultured clinical methicillin- and vancomycin-resistant strains while also exhibiting efficacy in a mouse peritonitis model of methicillin-resistant S. aureus infection. We highlight the utility of an intrabacterial drug metabolism (IBDM) approach to probe the mechanism by which JSF-3151 is transformed within the bacteria. We also identify and then validate two mechanisms of resistance in S. aureus: one mechanism involves increased expression of a lipocalin protein, and the other arises from the loss of function of an azoreductase. The computational and experimental approaches, discovery of an antibacterial agent, and elucidated resistance mechanisms collectively hold promise to advance our understanding of therapeutic regimens for drug-resistant S. aureus.
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Affiliation(s)
- Jimmy S. Patel
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Hassan Al-Tameemi
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Yong-Mo Ahn
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Xin Wang
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Samer S. Daher
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - James Occi
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Riccardo Russo
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Steven Park
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Matthew Zimmerman
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Hsin-Pin Ho
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - David S. Perlin
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Véronique Dartois
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
| | - Pradeep Kumar
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Nancy Connell
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
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5
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Eisenbart SK, Alzheimer M, Pernitzsch SR, Dietrich S, Stahl S, Sharma CM. A Repeat-Associated Small RNA Controls the Major Virulence Factors of Helicobacter pylori. Mol Cell 2020; 80:210-226.e7. [PMID: 33002424 DOI: 10.1016/j.molcel.2020.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/29/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
Abstract
Many bacterial pathogens regulate their virulence genes via phase variation, whereby length-variable simple sequence repeats control the transcription or coding potential of those genes. Here, we have exploited this relationship between DNA structure and physiological function to discover a globally acting small RNA (sRNA) regulator of virulence in the gastric pathogen Helicobacter pylori. Our study reports the first sRNA whose expression is affected by a variable thymine (T) stretch in its promoter. We show the sRNA post-transcriptionally represses multiple major pathogenicity factors of H. pylori, including CagA and VacA, by base pairing to their mRNAs. We further demonstrate transcription of the sRNA is regulated by the nickel-responsive transcriptional regulator NikR (thus named NikS for nickel-regulated sRNA), thereby linking virulence factor regulation to nickel concentrations. Using in-vitro infection experiments, we demonstrate NikS affects host cell internalization and epithelial barrier disruption. Together, our results show NikS is a phase-variable, post-transcriptional global regulator of virulence properties in H. pylori.
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Affiliation(s)
- Sara K Eisenbart
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Mona Alzheimer
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Sandy R Pernitzsch
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Sascha Dietrich
- Core Unit Systems Medicine, Interdisciplinary Center for Clinical Research (IZKF) of the University Hospital Würzburg, 97080 Würzburg, Germany
| | - Stephanie Stahl
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Cynthia M Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany.
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6
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Lee C, Kim MI, Park J, Kim J, Oh H, Cho Y, Son J, Jeon BY, Ka H, Hong M. Crystal structure of the Pseudomonas aeruginosa PA0423 protein and its functional implication in antibiotic sequestration. Biochem Biophys Res Commun 2020; 528:85-91. [PMID: 32451086 DOI: 10.1016/j.bbrc.2020.05.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 01/06/2023]
Abstract
Pseudomonas aeruginosa is a widely found opportunistic pathogen. The emergence of multidrug-resistant strains and persistent chronic infections have increased. The protein encoded by the pa0423 gene in P. aeruginosa is proposed to be critical for pathogenesis and could be a virulence-promoting protease or a bacterial lipocalin that binds a lipid-like antibiotic for drug resistance. Although two functions of proteolysis and antibiotic resistance are mutually related to bacterial survival in the host, it is very unusual for a single-domain protein to target unrelated ligand molecules such as protein substrates and lipid-like antibiotics. To clearly address the biological role of the PA0423 protein, we performed structural and biochemical studies. We found that PA0423 adopts a single-domain β-barrel structure and belongs to the lipocalin family. The PA0423 structure houses an internal tubular cavity, which accommodates a ubiquinone-8 molecule. Furthermore, we reveal that PA0423 can directly interact with the polymyxin B antibiotic using the internal cavity, suggesting that PA0423 has a physiological function in the antibiotic resistance of P. aeruginosa.
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Affiliation(s)
- Choongdeok Lee
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Meong Il Kim
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Jaewan Park
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Junghun Kim
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Hansol Oh
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Yoeseph Cho
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Junghyun Son
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Biological Chemistry, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Bo-Young Jeon
- Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea.
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7
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Toulouse C, Schmucker S, Metesch K, Pfannstiel J, Michel B, Starke I, Möller HM, Stefanski V, Steuber J. Mechanism and impact of catecholamine conversion by Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:478-487. [PMID: 30986392 DOI: 10.1016/j.bbabio.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens are influenced by signaling molecules including the catecholamines adrenaline and noradrenaline which are host-derived hormones and neurotransmitters. Adrenaline and noradrenaline modulate growth, motility and virulence of bacteria. We show that adrenaline is converted by the pathogen Vibrio cholerae to adrenochrome in the course of respiration, and demonstrate that superoxide produced by the respiratory, Na+ - translocating NADH:quinone oxidoreductase (NQR) acts as electron acceptor in the oxidative conversion of adrenaline to adrenochrome. Adrenochrome stimulates growth of V. cholerae, and triggers specific responses in V. cholerae and in immune cells. We performed a quantitative proteome analysis of V. cholerae grown in minimal medium with glucose as carbon source without catecholamines, or with adrenaline, noradrenaline or adrenochrome. Significant regulation of proteins participating in iron transport and iron homeostasis, in energy metabolism, and in signaling was observed upon exposure to adrenaline, noradrenaline or adrenochrome. On the host side, adrenochrome inhibited lipopolysaccharide-triggered formation of TNF-α by THP-1 monocytes, though to a lesser extent than adrenaline. It is proposed that adrenochrome produced from adrenaline by respiring V. cholerae functions as effector molecule in pathogen-host interaction.
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Affiliation(s)
| | - Sonja Schmucker
- Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Kristina Metesch
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Bernd Michel
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Ines Starke
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Heiko M Möller
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Volker Stefanski
- Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany.
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8
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Rolig AS, Sweeney EG, Kaye LE, DeSantis MD, Perkins A, Banse AV, Hamilton MK, Guillemin K. A bacterial immunomodulatory protein with lipocalin-like domains facilitates host-bacteria mutualism in larval zebrafish. eLife 2018; 7:37172. [PMID: 30398151 PMCID: PMC6219842 DOI: 10.7554/elife.37172] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Stable mutualism between a host and its resident bacteria requires a moderated immune response to control bacterial population size without eliciting excessive inflammation that could harm both partners. Little is known about the specific molecular mechanisms utilized by bacterial mutualists to temper their hosts' responses and protect themselves from aggressive immune attack. Using a gnotobiotic larval zebrafish model, we identified an Aeromonas secreted immunomodulatory protein, AimA. AimA is required during colonization to prevent intestinal inflammation that simultaneously compromises both bacterial and host survival. Administration of exogenous AimA prevents excessive intestinal neutrophil accumulation and protects against septic shock in models of both bacterially and chemically induced intestinal inflammation. We determined the molecular structure of AimA, which revealed two related calycin-like domains with structural similarity to the mammalian immune modulatory protein, lipocalin-2. As a secreted bacterial protein required by both partners for optimal fitness, AimA is an exemplar bacterial mutualism factor.
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Affiliation(s)
- Annah S Rolig
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Lila E Kaye
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Michael D DeSantis
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Allison V Banse
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, United States.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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9
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Mukherjee K, Gupta R, Kumar G, Kumari S, Biswas S, Padmanabhan P. Synthesis of silver nanoparticles by Bacillus clausii and computational profiling of nitrate reductase enzyme involved in production. J Genet Eng Biotechnol 2018; 16:527-536. [PMID: 30733770 PMCID: PMC6353735 DOI: 10.1016/j.jgeb.2018.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 12/18/2022]
Abstract
Biogenic synthesis of silver nanoparticles using microorganisms has found interest recently since last decade because of their prospect to synthesize nanoparticles of various size, shape and morphology which are eco-friendly. Here, an eco-friendly method for production of silver nanoparticles from Bacillus clausii cultured from Enterogermina is explored. Along with the biosynthesis and conformity test, in silico studies was done on NADPH dependent nitrate reductase enzymes from the view point of designing a rational enzymatic strategy for the synthesis. The detailed characterization of the nanoparticles was carried out using UV-Vis spectroscopy, Dynamic Light Scattering (DLS) particle size analysis, Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) analysis. Computational profiling and in silico characterization of NADH dependent enzymes was carried out based on literature and work done so far. Nitrate reductase sequence was retrieved from NCBI for characterization. Secondary structure was evaluated and verified by JPred as well as SOPMA Tool. Tertiary structure was also modeled by MODELLER and ITASSER parallel and the best structure was selected based on energy values. Structure validation was done by GROMACS and RMSD, RMSF, temperature variation plot were also plotted. Interactions graphs between nitrate reductase and ligand silver nitrate was done through molecular docking using Hex.
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Affiliation(s)
- Koel Mukherjee
- Bioinformatics Laboratory, Bio-Engineering Department, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
| | - Rashmi Gupta
- Bioprocess Engineering Laboratory, Bio-Engineering Department, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
| | - Gourav Kumar
- Bioprocess Engineering Laboratory, Bio-Engineering Department, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
| | - Sarita Kumari
- Bioprocess Engineering Laboratory, Bio-Engineering Department, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
| | - Saptaswa Biswas
- Centre for Energy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Padmini Padmanabhan
- Bioprocess Engineering Laboratory, Bio-Engineering Department, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
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10
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13-Docosenamide release by bacteria in response to glucose during growth-fluorescein quenching and clinical application. Appl Microbiol Biotechnol 2018; 102:6673-6685. [PMID: 29860593 DOI: 10.1007/s00253-018-9127-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/10/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
Our investigations on extracellular biochemical events to find readily and sensitively detectable/measurable molecular targets for developing easier, simpler, and quicker diagnostic methods and tools for bacterial pathogens led to the observation that bacteria grown in the presence of glucose produced a compound capable of quenching fluorescein. Under the experimental conditions, among various sugars, glucose was found to induce maximum amount of the quencher when Escherichia coli was grown in presence of 50 mM glucose in rarified LB. The release of quencher closely following bacterial growth significantly from fourth hour after moderate inoculation. This fluorescein-quencher was purified using TLC and HPLC and identified using GC-MS as 13-docosenamide or erucamide, originally known as plant lipid, is a neuroactive compound in human and animals. Fluorescence and UV-absorption spectral analysis showed that the compound formed stable adduct with fluorescein in the ground state. Commercial 13-docosonamide enabled quantitation of the compound produced in micromolar quantities during glucose utilization from the medium. Twenty-seven different commonly encountered bacteria, pathogens or otherwise, could produce the quencher. A simple microplate-based growth monitoring method was developed exploiting quenching as an easily and readily measurable signal, either using a reader or an imager. While 13-docosenamide release by bacteria may be relevant in host-bacteria interactions, especially when growing under conditions that provide glucose, the new approach with inexpensive reagents can provide a new antibiogram technique.
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11
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Tang Y, Cawthraw S, Bagnall MC, Gielbert AJ, Woodward MJ, Petrovska L. Identification of temperature regulated factors of Campylobacter jejuni and their potential roles in virulence. AIMS Microbiol 2017; 3:885-898. [PMID: 31294195 PMCID: PMC6604965 DOI: 10.3934/microbiol.2017.4.885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/24/2017] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni is the major cause of bacterial gastroenteritis in man, while it is generally regarded as a commensal of the avian gut. Consumption and handling of contaminated poultry meat products are major risk factors for human infection. The body temperature in man (37 °C) and chickens (42 °C) differ markedly, and differential gene regulation and protein expression at different temperatures may in part explain the behaviour in the two hosts. We performed proteomics analyses with C. jejuni cells grown at 37 °C and 42 °C. Time-of-flight mass spectrometry (Q-Tof) analysis was carried out after samples were digested with the Filter-Aided Sample Preparation (FASP) method and peptides were fractionated by strong anion exchanges. Differentially regulated proteins were identified by Mascot and Scaffold analyses. Triple quadrupole (QQQ) mass spectrometer analysis confirmed that a total of 33 proteins were differentially regulated between 37 °C and 42 °C. Several upregulated proteins were selected for their corresponding gene knock-out mutants to be tested for their virulence in the Galleria mellonella model. To correlate with other tissue/animal models, the GADH mutant was selected for its reduced ability to colonize chickens. At 37 °C, the mutants of outer membrane protein Omp50 and Chaperone GroEL significantly increased virulence; while at 42 °C, the mutants of YceI, Omp50, and GADH reduced virulence against Galleria mellonella compared with the wild type strains. The results of current and previous studies indicate that GADH is a virulent factor in G. mellonella and a colonization factor in chickens. The workflow of this study may prove a new way to identify stress related virulent factors. The implications of these findings are discussed for pathogenesis in the model and other hosts.
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Affiliation(s)
- Yue Tang
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Mary C Bagnall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Adriana J Gielbert
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Martin J Woodward
- Food and Nutritional Sciences, University of Reading, Whiteknights, Reading RG6 6AP, UK
| | - Liljana Petrovska
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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12
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Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance. mBio 2017; 8:mBio.00225-17. [PMID: 28292982 PMCID: PMC5350466 DOI: 10.1128/mbio.00225-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential for microbes to overcome antibiotics of different classes before they reach bacterial cells is largely unexplored. Here we show that a soluble bacterial lipocalin produced by Burkholderia cenocepacia upon exposure to sublethal antibiotic concentrations increases resistance to diverse antibiotics in vitro and in vivo These phenotypes were recapitulated by heterologous expression in B. cenocepacia of lipocalin genes from Pseudomonas aeruginosa, Mycobacterium tuberculosis, and methicillin-resistant Staphylococcus aureus Purified lipocalin bound different classes of bactericidal antibiotics and contributed to bacterial survival in vivo Experimental and X-ray crystal structure-guided computational studies revealed that lipocalins counteract antibiotic action by capturing antibiotics in the extracellular space. We also demonstrated that fat-soluble vitamins prevent antibiotic capture by binding bacterial lipocalin with higher affinity than antibiotics. Therefore, bacterial lipocalins contribute to antimicrobial resistance by capturing diverse antibiotics in the extracellular space at the site of infection, which can be counteracted by known vitamins.IMPORTANCE Current research on antibiotic action and resistance focuses on targeting essential functions within bacterial cells. We discovered a previously unrecognized mode of general bacterial antibiotic resistance operating in the extracellular space, which depends on bacterial protein molecules called lipocalins. These molecules are highly conserved in most bacteria and have the ability to capture different classes of antibiotics outside bacterial cells. We also discovered that liposoluble vitamins, such as vitamin E, overcome in vitro and in vivo antibiotic resistance mediated by bacterial lipocalins, providing an unexpected new alternative to combat resistance by using this vitamin or its derivatives as antibiotic adjuvants.
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13
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Tavares R, Pathak SK. Helicobacter pylori Secreted Protein HP1286 Triggers Apoptosis in Macrophages via TNF-Independent and ERK MAPK-Dependent Pathways. Front Cell Infect Microbiol 2017; 7:58. [PMID: 28293545 PMCID: PMC5329642 DOI: 10.3389/fcimb.2017.00058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/13/2017] [Indexed: 01/10/2023] Open
Abstract
Macrophages constitute a powerful line of defense against H. pylori. The final disease outcome is highly dependent on the bacterial ability to modulate the effector functions of activated macrophages. Here, we report that H. pylori secreted protein HP1286 is a novel regulator of macrophage responses. Differential expression and release of HP1286 homologues were observed among H. pylori strains. Recombinant purified HP1286 (rHP1286) had the ability to bind to primary human monocyte-derived macrophages (MDM) and macrophage cell lines. Exposure to rHP1286 induced apoptosis in macrophages in a dose- and time-dependent manner. Although interaction of rHP1286 was observed for several other cell types, such as human monocytes, differentiated neutrophil-like HL60 cells, and the T lymphocyte Jurkat cell line, rHP1286 failed to induce apoptosis under similar conditions, indicating a macrophage-specific effect of the protein. A mutant strain of H. pylori lacking HP1286 protein expression was significantly impaired in its ability to induce apoptosis in macrophages. Significantly higher caspase 3 activity was detected in rHP1286-challenged macrophages. Furthermore, rHP1286-induced macrophages apoptosis was not inhibited in the presence of neutralizing antibodies against TNF. These observations indicate that rHP1286 induced a caspase-dependent and TNF-independent macrophage apoptosis. Pre-treatment of macrophages with U0126, an inhibitor of the ERK MAPK signaling pathway significantly reduced rHP1286-induced apoptosis. Furthermore, nuclear translocation of ERK and phosphorylation of c-Fos was detected in rHP1286-treated macrophages. These results provide functional insight into the potential role of HP1286 during H. pylori infection. Considering the ability of HP1286 to induce macrophage apoptosis, the protein could possibly help in the bacterial escape from the activated macrophages and persistence in the stomach.
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Affiliation(s)
- Raquel Tavares
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Sushil Kumar Pathak
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
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14
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Sidibé A, Simao-Beaunoir AM, Lerat S, Giroux L, Toussaint V, Beaulieu C. Proteome Analyses of Soil Bacteria Grown in the Presence of Potato Suberin, a Recalcitrant Biopolymer. Microbes Environ 2016; 31:418-426. [PMID: 27795492 PMCID: PMC5158114 DOI: 10.1264/jsme2.me15195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Suberin is a complex lipidic plant polymer found in various tissues including the potato periderm. The biological degradation of suberin is attributed to fungi. Soil samples from a potato field were used to inoculate a culture medium containing suberin as the carbon source, and a metaproteomic approach was used to identify bacteria that developed in the presence of suberin over a 60-d incubation period. The normalized spectral counts of predicted extracellular proteins produced by the soil bacterial community markedly decreased from day 5 to day 20 and then slowly increased, revealing a succession of bacteria. The population of fast-growing pseudomonads declined and was replaced by species with the ability to develop in the presence of suberin. The recalcitrance of suberin was demonstrated by the emergence of auxotrophic bacteria such as Oscillatoria on the last days of the assay. Nevertheless, two putative lipases from Rhodanobacter thiooxydans (I4WGM2) and Myxococcus xanthus (Q1CWS1) were detected in the culture supernatants, suggesting that at least some bacterial species degrade suberin. When grown in suberin-containing medium, R. thiooxydans strain LCS2 and M. xanthus strain DK 1622 both produced three lipases, including I4WGM2 and Q1CWS1. These strains also produced other proteins linked to lipid metabolism, including fatty acid and lipid transporters and β-oxidation enzymes, suggesting that they participate in the degradation of suberin. However, only the R. thiooxydans strain appeared to retrieve sufficient carbon and energy from this recalcitrant polymer in order to maintain its population over an extended period of time.
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Affiliation(s)
- Amadou Sidibé
- Centre SÈVE, Département de Biologie, Université de Sherbrooke
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15
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Parker ML, Houston S, Pětrošová H, Lithgow KV, Hof R, Wetherell C, Kao WC, Lin YP, Moriarty TJ, Ebady R, Cameron CE, Boulanger MJ. The Structure of Treponema pallidum Tp0751 (Pallilysin) Reveals a Non-canonical Lipocalin Fold That Mediates Adhesion to Extracellular Matrix Components and Interactions with Host Cells. PLoS Pathog 2016; 12:e1005919. [PMID: 27683203 PMCID: PMC5040251 DOI: 10.1371/journal.ppat.1005919] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/08/2016] [Indexed: 12/02/2022] Open
Abstract
Syphilis is a chronic disease caused by the bacterium Treponema pallidum subsp. pallidum. Treponema pallidum disseminates widely throughout the host and extravasates from the vasculature, a process that is at least partially dependent upon the ability of T. pallidum to interact with host extracellular matrix (ECM) components. Defining the molecular basis for the interaction between T. pallidum and the host is complicated by the intractability of T. pallidum to in vitro culturing and genetic manipulation. Correspondingly, few T. pallidum proteins have been identified that interact directly with host components. Of these, Tp0751 (also known as pallilysin) displays a propensity to interact with the ECM, although the underlying mechanism of these interactions remains unknown. Towards establishing the molecular mechanism of Tp0751-host ECM attachment, we first determined the crystal structure of Tp0751 to a resolution of 2.15 Å using selenomethionine phasing. Structural analysis revealed an eight-stranded beta-barrel with a profile of short conserved regions consistent with a non-canonical lipocalin fold. Using a library of native and scrambled peptides representing the full Tp0751 sequence, we next identified a subset of peptides that showed statistically significant and dose-dependent interactions with the ECM components fibrinogen, fibronectin, collagen I, and collagen IV. Intriguingly, each ECM-interacting peptide mapped to the lipocalin domain. To assess the potential of these ECM-coordinating peptides to inhibit adhesion of bacteria to host cells, we engineered an adherence-deficient strain of the spirochete Borrelia burgdorferi to heterologously express Tp0751. This engineered strain displayed Tp0751 on its surface and exhibited a Tp0751-dependent gain-of-function in adhering to human umbilical vein endothelial cells that was inhibited in the presence of one of the ECM-interacting peptides (p10). Overall, these data provide the first structural insight into the mechanisms of Tp0751-host interactions, which are dependent on the protein’s lipocalin fold. The Treponema pallidum protein, Tp0751, possesses adhesive properties and has been previously reported to mediate attachment to the host extracellular matrix components laminin, fibronectin, and fibrinogen. Herein we demonstrate that Tp0751 adopts an eight-stranded beta barrel-containing lipocalin structure, and using a peptide library approach we show that the extracellular matrix component adhesive functionality of Tp0751 is localized to the lipocalin domain. Further, using a heterologous expression system we demonstrate that Tp0751 mediates attachment to endothelial cells, and that this interaction is specifically inhibited by a peptide derived from the Tp0751 lipocalin domain. Through these studies we have delineated the regions of the Tp0751 protein that mediate interaction with host extracellular matrix components and endothelial cells. These findings enhance our understanding of the role of this protein in treponemal dissemination via the bloodstream and provide defined regions of the Tp0751 protein that can be targeted to disrupt the treponemal-host interaction.
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Affiliation(s)
- Michelle L. Parker
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Helena Pětrošová
- Matrix Dynamics Group, Faculty of Dentistry, Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karen V. Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Rebecca Hof
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Charmaine Wetherell
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Wei-Chien Kao
- Matrix Dynamics Group, Faculty of Dentistry, Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yi-Pin Lin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Tara J. Moriarty
- Matrix Dynamics Group, Faculty of Dentistry, Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rhodaba Ebady
- Matrix Dynamics Group, Faculty of Dentistry, Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (CEC); (MJB)
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (CEC); (MJB)
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Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:165. [PMID: 26448785 PMCID: PMC4596283 DOI: 10.1186/s13068-015-0347-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Recent metabolic engineering efforts have generated microorganisms that can produce biofuels, including bio-jet fuels, however these fuels are often toxic to cells, limiting production yields. There are natural examples of microorganisms that have evolved mechanisms for tolerating hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. RESULTS Using genomic DNA from the hydrocarbon-degrading microbe Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy with a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. CONCLUSIONS The genomes of hydrocarbon-tolerant microbes represent a rich resource for tolerance engineering. Using a transgenic library, we were able to identify a single gene that improves E. coli's tolerance to the bio-jet fuel precursor pinene.
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Affiliation(s)
- Timothy A. Tomko
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
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17
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Donnarumma D, Golfieri G, Brier S, Castagnini M, Veggi D, Bottomley MJ, Delany I, Norais N. Neisseria meningitis GNA1030 is a ubiquinone-8 binding protein. FASEB J 2015; 29:2260-7. [PMID: 25713028 DOI: 10.1096/fj.14-263954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/20/2015] [Indexed: 11/11/2022]
Abstract
Bexsero, a new vaccine against Neisseria meningitidis serogroup B (MenB), is composed of 3 main recombinant proteins and an outer membrane vesicle component. One of the main bactericidal antigens, neisseria heparin binding antigen (NHBA), is present as a fusion protein with the accessory protein genome-derived neisserial antigen (GNA) 1030 to further increase its immunogenicity. The gene encoding for GNA1030 is present and highly conserved in all Neisseria strains, and although orthologs are present in numerous species, its biologic function is unknown. Native mass spectrometry was used to demonstrate that GNA1030 forms a homodimer associated with 2 molecules of ubiquinone-8 (Ub8), a cofactor mainly involved in the electron transport chain and with antioxidant properties. Disc diffusion assays on the wild-type and knockout mutant of GNA1030, in the presence of various compounds, suggested that GNA1030 is not involved in oxidative stress or electron chain transport per se, although it contributes to constitutive refilling of the inner membrane with Ub8. These studies shed light on an accessory protein present in Bexsero and reveal functional insights into the family of related proteins. On the basis of our findings, we propose to name the protein neisseria ubiquinone binding protein (NUbp).
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18
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Svensson SL, Huynh S, Hyunh S, Parker CT, Gaynor EC. The Campylobacter jejuni CprRS two-component regulatory system regulates aspects of the cell envelope. Mol Microbiol 2015; 96:189-209. [PMID: 25582441 DOI: 10.1111/mmi.12927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Campylobacter jejuni is a leading cause of food-borne gastroenteritis in humans. It lives commensally in the gastrointestinal tract of animals, and tolerates variable conditions during transit/colonization of susceptible hosts. The C. jejuni CprRS two-component system contains an essential response regulator (CprR), and deletion of the cprS sensor kinase enhances biofilms. We sought to identify CprRS-regulated genes and better understand how the system affects survival. Expression from the cprR promoter was highest during logarithmic growth and dependent on CprS. CprR(D52A) did not support viability, indicating that CprR phosphorylation is essential despite the dispensability of CprS. We identified a GTAAAC consensus bound by the CprR C-terminus; the Asp52 residue of full-length CprR was required for binding, suggesting phosphorylation is required. Transcripts differing in expression in ΔcprS compared with wildtype (WT) contained a putative CprR binding site upstream of their promoter region and encoded htrA (periplasmic protease upstream of cprRS) and peb4 (SurA-like chaperone). Consistent with direct regulation, the CprR consensus in the htrA promoter was bound by CprR(CTD). Finally, ΔhtrA formed enhanced biofilms, and ΔcprS biofilms were suppressed by Mg(2+). CprRS is the first C. jejuni regulatory system shown to control genes related to the cell envelope, the first line of interaction between pathogen and changing environments.
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Affiliation(s)
- Sarah L Svensson
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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19
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Martí-Arbona R, Mu F, Nowak-Lovato KL, Wren MS, Unkefer CJ, Unkefer PJ. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. BMC Genomics 2014; 15:1142. [PMID: 25523622 PMCID: PMC4349456 DOI: 10.1186/1471-2164-15-1142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity. RESULTS A software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018. CONCLUSION These studies provide the proof of concept and validation of a systematic approach to the discovery of the biological activity for proteins of unknown function, in this case a TR. Bxe_B3018 is a methylglyoxal responsive TR that controls the expression of an operon composed of a putative efflux system.
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Affiliation(s)
- Ricardo Martí-Arbona
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA.
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20
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Lu Y, Zhou Y, Nakai S, Hosomi M, Zhang H, Kronzucker HJ, Shi W. Stimulation of nitrogen removal in the rhizosphere of aquatic duckweed by root exudate components. PLANTA 2014; 239:591-603. [PMID: 24271005 PMCID: PMC3928532 DOI: 10.1007/s00425-013-1998-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 11/06/2013] [Indexed: 05/21/2023]
Abstract
Plants can stimulate bacterial nitrogen (N) removal by secretion of root exudates that may serve as carbon sources as well as non-nutrient signals for denitrification. However, there is a lack of knowledge about the specific non-nutrient compounds involved in this stimulation. Here, we use a continuous root exudate-trapping system in two common aquatic duckweed species, Spirodela polyrrhiza (HZ1) and Lemna minor (WX3), under natural and aseptic conditions. An activity-guided bioassay using denitrifying bacterium Pseudomonas fluorescens showed that crude root exudates of the two species strongly enhanced the nitrogen-removal efficiency (NRE) of P. fluorescens (P < 0.05) under both conditions. Water-insoluble fractions (F) obtained under natural conditions stimulated NRE to a significant extent, promoting rates by about 30%. Among acidic, neutral and basic fractions, a pronounced stimulatory effect was also observed for the neutral fractions from HZ1 and WX3 under both conditions, whereas the acidic fractions from WX3 displayed an inhibitory effect. Analysis of the active fractions using gas chromatography/mass spectrometry (GC/MS) revealed that duckweed released fatty acid methyl esters and fatty acid amides, specifically: methyl hexadecanoate, methyl (Z)-7-hexadecenoate, methyl dodecanoate, methyl-12-hydroxystearate, oleamide, and erucamide. Methyl (Z)-7-hexadecenoate and erucamide emerged as the effective N-removal stimulants (maximum stimulation of 25.9 and 33.4%, respectively), while none of the other tested compounds showed stimulatory effects. These findings provide the first evidence for a function of fatty acid methyl esters and fatty acid amides in stimulating N removal of denitrifying bacteria, affording insight into the "crosstalk" between aquatic plants and bacteria in the rhizosphere.
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Affiliation(s)
- Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yingru Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Satoshi Nakai
- Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527 Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588 Japan
| | - Hailin Zhang
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078-6028 USA
| | - Herbert J. Kronzucker
- Department of Biological Sciences, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
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Zanotti G, Cendron L. Structural and functional aspects of the Helicobacter pylori secretome. World J Gastroenterol 2014; 20:1402-1423. [PMID: 24587618 PMCID: PMC3925851 DOI: 10.3748/wjg.v20.i6.1402] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/06/2014] [Indexed: 02/06/2023] Open
Abstract
Proteins secreted by Helicobacter pylori (H. pylori), an important human pathogen responsible for severe gastric diseases, are reviewed from the point of view of their biochemical characterization, both functional and structural. Despite the vast amount of experimental data available on the proteins secreted by this bacterium, the precise size of the secretome remains unknown. In this review, we consider as secreted both proteins that contain a secretion signal for the periplasm and proteins that have been detected in the external medium in in vitro experiments. In this way, H. pylori’s secretome appears to be composed of slightly more than 160 proteins, but this number must be considered very cautiously, not only because the definition of secretome itself is ambiguous but also because the included proteins were observed as secreted in in vitro experiments that were not representative of the environmental situation in vivo. The proteins that appear to be secreted can be grouped into different classes: enzymes (48 proteins), outer membrane proteins (43), components of flagella (11), members of the cytotoxic-associated genes pathogenicity island or other toxins (8 and 5, respectively), binding and transport proteins (9), and others (11). A final group, which includes 28 members, is represented by hypothetical uncharacterized proteins. Despite the large amount of data accumulated on the H. pylori secretome, a considerable amount of work remains to reach a full comprehension of the system at the molecular level.
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Chemical communication of antibiotic resistance by a highly resistant subpopulation of bacterial cells. PLoS One 2013; 8:e68874. [PMID: 23844246 PMCID: PMC3700957 DOI: 10.1371/journal.pone.0068874] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/03/2013] [Indexed: 01/05/2023] Open
Abstract
The overall antibiotic resistance of a bacterial population results from the combination of a wide range of susceptibilities displayed by subsets of bacterial cells. Bacterial heteroresistance to antibiotics has been documented for several opportunistic Gram-negative bacteria, but the mechanism of heteroresistance is unclear. We use Burkholderia cenocepacia as a model opportunistic bacterium to investigate the implications of heterogeneity in the response to the antimicrobial peptide polymyxin B (PmB) and also other bactericidal antibiotics. Here, we report that B. cenocepacia is heteroresistant to PmB. Population analysis profiling also identified B. cenocepacia subpopulations arising from a seemingly homogenous culture that are resistant to higher levels of polymyxin B than the rest of the cells in the culture, and can protect the more sensitive cells from killing, as well as sensitive bacteria from other species, such as Pseudomonas aeruginosa and Escherichia coli. Communication of resistance depended on upregulation of putrescine synthesis and YceI, a widely conserved low-molecular weight secreted protein. Deletion of genes for the synthesis of putrescine and YceI abrogate protection, while pharmacologic inhibition of putrescine synthesis reduced resistance to polymyxin B. Polyamines and YceI were also required for heteroresistance of B. cenocepacia to various bactericidal antibiotics. We propose that putrescine and YceI resemble "danger" infochemicals whose increased production by a bacterial subpopulation, becoming more resistant to bactericidal antibiotics, communicates higher level of resistance to more sensitive members of the population of the same or different species.
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23
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de Menezes A, Clipson N, Doyle E. Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ Microbiol 2012; 14:2577-88. [PMID: 22625871 DOI: 10.1111/j.1462-2920.2012.02781.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8-fold to 33-fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P-type ATPases and thioredoxin transcripts were more abundant in the phenanthrene-amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.
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Affiliation(s)
- Alexandre de Menezes
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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O'Grady EP, Sokol PA. Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment. Front Cell Infect Microbiol 2011; 1:15. [PMID: 22919581 PMCID: PMC3417382 DOI: 10.3389/fcimb.2011.00015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/20/2011] [Indexed: 01/08/2023] Open
Abstract
Members of the Burkholderia cepacia complex (Bcc) are important in medical, biotechnological, and agricultural disciplines. These bacteria naturally occur in soil and water environments and have adapted to survive in association with plants and animals including humans. All Bcc species are opportunistic pathogens including Burkholderia cenocepacia that causes infections in cystic fibrosis and chronic granulomatous disease patients. The adaptation of B. cenocepacia to the host environment was assessed in a rat chronic respiratory infection model and compared to that of high cell-density in vitro grown cultures using transcriptomics. The distribution of genes differentially expressed on chromosomes 1, 2, and 3 was relatively proportional to the size of each genomic element, whereas the proportion of plasmid-encoded genes differentially expressed was much higher relative to its size and most genes were induced in vivo. The majority of genes encoding known virulence factors, components of types II and III secretion systems and chromosome 2-encoded type IV secretion system were similarly expressed between in vitro and in vivo environments. Lower expression in vivo was detected for genes encoding N-acyl-homoserine lactone synthase CepI, orphan LuxR homolog CepR2, zinc metalloproteases ZmpA and ZmpB, LysR-type transcriptional regulator ShvR, nematocidal protein AidA, and genes associated with flagellar motility, Flp type pilus formation, and type VI secretion. Plasmid-encoded type IV secretion genes were markedly induced in vivo. Additional genes induced in vivo included genes predicted to be involved in osmotic stress adaptation or intracellular survival, metal ion, and nutrient transport, as well as those encoding outer membrane proteins. Genes identified in this study are potentially important for virulence during host–pathogen interactions and may be associated with survival and adaptation to the host environment during chronic lung infections.
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Affiliation(s)
- Eoin P O'Grady
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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Zanotti G, Cendron L. Functional and structural aspects of Helicobacter pylori acidic stress response factors. IUBMB Life 2011; 62:715-23. [PMID: 20960531 DOI: 10.1002/iub.382] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori is a striking example of adaptation of a bacterium to a very peculiar niche, the human stomach. Despite being a neutralophile, a sophisticated control of gene expression allows it to live and to proliferate in an environment that cycles from nearly neutral to very acidic. Despite the numerous studies performed on the mechanisms of acid adaptation, the physiological function of a large part of the genes products that are up-regulated or down-regulated is often not clear, in particular in the context of the response of the bacterium to an acidic stress. In this review, we discuss the molecular and functional aspects of some of the proteins that are commonly found overexpressed during the acid stress.
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Affiliation(s)
- Giuseppe Zanotti
- Department of Biological Chemistry, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy.
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