1
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Do H, Li ZR, Tripathi PK, Mitra S, Guerra S, Dash A, Weerasekera D, Makthal N, Shams S, Aggarwal S, Singh BB, Gu D, Du Y, Olsen RJ, LaRock C, Zhang W, Kumaraswami M. Engineered probiotic overcomes pathogen defences using signal interference and antibiotic production to treat infection in mice. Nat Microbiol 2024; 9:502-513. [PMID: 38228859 PMCID: PMC10847043 DOI: 10.1038/s41564-023-01583-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Probiotic supplements are suggested to promote human health by preventing pathogen colonization. However, the mechanistic bases for their efficacy in vivo are largely uncharacterized. Here using metabolomics and bacterial genetics, we show that the human oral probiotic Streptococcus salivarius K12 (SAL) produces salivabactin, an antibiotic that effectively inhibits pathogenic Streptococcus pyogenes (GAS) in vitro and in mice. However, prophylactic dosing with SAL enhanced GAS colonization in mice and ex vivo in human saliva. We showed that, on co-colonization, GAS responds to a SAL intercellular peptide signal that controls SAL salivabactin production. GAS produces a secreted protease, SpeB, that targets SAL-derived salivaricins and enhances GAS survival. Using this knowledge, we re-engineered probiotic SAL to prevent signal eavesdropping by GAS and potentiate SAL antimicrobials. This engineered probiotic demonstrated superior efficacy in preventing GAS colonization in vivo. Our findings show that knowledge of interspecies interactions can identify antibiotic- and probiotic-based strategies to combat infection.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Research unit of cryogenic novel material, Korea Polar Research Institute, Incheon, South Korea
| | - Zhong-Rui Li
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Praveen Kumar Tripathi
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Sonali Mitra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Stephanie Guerra
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Ananya Dash
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Dulanthi Weerasekera
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Syed Shams
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Shifu Aggarwal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Bharat Bhushan Singh
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Christopher LaRock
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, GA, USA
- Emory Antibiotic Resistance Center, Emory School of Medicine, Atlanta, GA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
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2
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Aggarwal S, Huang E, Do H, Makthal N, Li Y, Bapteste E, Lopez P, Bernard C, Kumaraswami M. The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes. Nat Commun 2023; 14:5947. [PMID: 37741855 PMCID: PMC10518010 DOI: 10.1038/s41467-023-41719-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
The human pathogen Streptococcus pyogenes secretes a short peptide (leaderless communication peptide, LCP) that mediates intercellular communication and controls bacterial virulence through interaction with its receptor, RopB. Here, we show that LCP and RopB homologues are present in other Firmicutes. We experimentally validate that LCPs with distinct peptide communication codes act as bacterial intercellular signals and regulate gene expression in Streptococcus salivarius, Streptococcus porcinus, Enterococcus malodoratus and Limosilactobacillus reuteri. Our results indicate that LCPs are more widespread than previously thought, and their characterization may uncover new signaling mechanisms and roles in coordinating diverse bacterial traits.
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Affiliation(s)
- Shifu Aggarwal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Elaine Huang
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Yanyan Li
- Communication Molecules and Adaptation of Microorganisms (MCAM), CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Sorbonne Université, CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Sorbonne Université, CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Charles Bernard
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA.
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3
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Aggarwal S, Kumaraswami M. Managing Manganese: The Role of Manganese Homeostasis in Streptococcal Pathogenesis. Front Cell Dev Biol 2022; 10:921920. [PMID: 35800897 PMCID: PMC9253540 DOI: 10.3389/fcell.2022.921920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Pathogenic streptococci require manganese for survival in the host. In response to invading pathogens, the host recruits nutritional immune effectors at infection sites to withhold manganese from the pathogens and control bacterial growth. The manganese scarcity impairs several streptococcal processes including oxidative stress defenses, de novo DNA synthesis, bacterial survival, and virulence. Emerging evidence suggests that pathogens also encounter manganese toxicity during infection and manganese excess impacts streptococcal virulence by manganese mismetallation of non-cognate molecular targets involved in bacterial antioxidant defenses and cell division. To counter host-imposed manganese stress, the streptococcal species employ a sophisticated sensory system that tightly coordinates manganese stress-specific molecular strategies to negate host induced manganese stress and proliferate in the host. Here we review the molecular details of host-streptococcal interactions in the battle for manganese during infection and the significance of streptococcal effectors involved to bacterial pathophysiology.
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Affiliation(s)
- Shifu Aggarwal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, United States
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, United States
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, United States
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, United States
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4
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Tsai CR, Wang Y, Jacobson A, Sankoorikkal N, Chirinos JD, Burra S, Makthal N, Kumaraswami M, Galko MJ. Pvr and distinct downstream signaling factors are required for hemocyte spreading and epidermal wound closure at Drosophila larval wound sites. G3 (Bethesda) 2021; 12:6423993. [PMID: 34751396 PMCID: PMC8728012 DOI: 10.1093/g3journal/jkab388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/12/2021] [Indexed: 12/03/2022]
Abstract
Tissue injury is typically accompanied by inflammation. In Drosophila melanogaster larvae, wound-induced inflammation involves adhesive capture of hemocytes at the wound surface followed by hemocyte spreading to assume a flat, lamellar morphology. The factors that mediate this cell spreading at the wound site are not known. Here, we discover a role for the platelet-derived growth factor/vascular endothelial growth factor-related receptor (Pvr) and its ligand, Pvf1, in blood cell spreading at the wound site. Pvr and Pvf1 are required for spreading in vivo and in an in vitro spreading assay where spreading can be directly induced by Pvf1 application or by constitutive Pvr activation. In an effort to identify factors that act downstream of Pvr, we performed a genetic screen in which select candidates were tested to determine if they could suppress the lethality of Pvr overexpression in the larval epidermis. Some of the suppressors identified are required for epidermal wound closure (WC), another Pvr-mediated wound response, some are required for hemocyte spreading in vitro, and some are required for both. One of the downstream factors, Mask, is also required for efficient wound-induced hemocyte spreading in vivo. Our data reveal that Pvr signaling is required for wound responses in hemocytes (cell spreading) and defines distinct downstream signaling factors that are required for either epidermal WC or hemocyte spreading.
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Affiliation(s)
- Chang-Ru Tsai
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Yan Wang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Alec Jacobson
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Niki Sankoorikkal
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Josue D Chirinos
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Sirisha Burra
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Nishanth Makthal
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Muthiah Kumaraswami
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Michael J Galko
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States.,Genetics & Epigenetics Graduate Program, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
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5
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - David W Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hoang A T Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - J Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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6
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. medRxiv 2020:2020.09.22.20199125. [PMID: 33024977 PMCID: PMC7536878 DOI: 10.1101/2020.09.22.20199125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.
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Affiliation(s)
- S. Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Paul A. Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - David W. Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hung-Che Kuo
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hoang A. T. Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - J. Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Jule Goike
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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Makthal N, Do H, Wendel BM, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Group A Streptococcus AdcR Regulon Participates in Bacterial Defense against Host-Mediated Zinc Sequestration and Contributes to Virulence. Infect Immun 2020; 88:e00097-20. [PMID: 32393509 PMCID: PMC7375770 DOI: 10.1128/iai.00097-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Colonization by pathogenic bacteria depends on their ability to overcome host nutritional defenses and acquire nutrients. The human pathogen group A streptococcus (GAS) encounters the host defense factor calprotectin (CP) during infection. CP inhibits GAS growth in vitro by imposing zinc (Zn) limitation. However, GAS counterstrategies to combat CP-mediated Zn limitation and the in vivo relevance of CP-GAS interactions to bacterial pathogenesis remain unknown. Here, we report that GAS upregulates the AdcR regulon in response to CP-mediated Zn limitation. The AdcR regulon includes genes encoding Zn import (adcABC), Zn sparing (rpsN.2), and Zn scavenging systems (adcAII, phtD, and phtY). Each gene in the AdcR regulon contributes to GAS Zn acquisition and CP resistance. The ΔadcC and ΔrpsN.2 mutant strains were the most susceptible to CP, whereas the ΔadcA, ΔadcAII, and ΔphtD mutant strains displayed less CP sensitivity during growth in vitro However, the ΔphtY mutant strain did not display an increased CP sensitivity. The varied sensitivity of the mutant strains to CP-mediated Zn limitation suggests distinct roles for individual AdcR regulon genes in GAS Zn acquisition. GAS upregulates the AdcR regulon during necrotizing fasciitis infection in WT mice but not in S100a9-/- mice lacking CP. This suggests that CP induces Zn deficiency in the host. Finally, consistent with the in vitro results, several of the AdcR regulon genes are critical for GAS virulence in WT mice, whereas they are dispensable for virulence in S100a9-/- mice, indicating the direct competition for Zn between CP and proteins encoded by the GAS AdcR regulon during infection.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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8
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Sathish Kumar P, Kumaraswami M, Ezhilarasan P, Durga Rao G, Sivasankar R, Ranga Rao V, Ramu K. Blooming of Gonyaulax polygramma along the southeastern Arabian Sea: Influence of upwelling dynamics and anthropogenic activities. Mar Pollut Bull 2020; 151:110817. [PMID: 32056611 DOI: 10.1016/j.marpolbul.2019.110817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/03/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The influence of upwelling on the phytoplankton community was examined during the upwelling-relaxation period in the southeastern Arabian Sea. Elevated upwelling intensity during the summer monsoon season of 2016 resulted in the re-suspension of harmful dinoflagellates into the surface water. Further, the surplus of phosphorus (P) inputs into the coastal waters from estuarine runoff during the upwelling-relaxation period induced blooming of Gonyaulax polygramma (4.9 × 106 cells L-1). Results from canonical correspondence analysis revealed that elevated upwelling intensity, P and salinity during the year 2016 likely triggered the bloom of G. polygramma in the study region. HABs like G. polygramma threaten fish stocks such as sardines which have a vital role in the ecosystem. Studies on phytoplankton communities and nutrient dynamics in upwelling systems would be useful in predicting the incidence/toxic effects of harmful algal blooms as these regions have a high potential for fisheries.
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Affiliation(s)
- P Sathish Kumar
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India; National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences, Chennai, India.
| | - M Kumaraswami
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
| | - P Ezhilarasan
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
| | - G Durga Rao
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
| | - R Sivasankar
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
| | - V Ranga Rao
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
| | - K Ramu
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences, NIOT Campus, Chennai, India
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9
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Do H, Makthal N, Chandrangsu P, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence. Nucleic Acids Res 2019; 47:7476-7493. [PMID: 31188450 PMCID: PMC6698748 DOI: 10.1093/nar/gkz524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023] Open
Abstract
Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and Fe acquisition systems (sia operon), and a metal-independent DNA synthesis enzyme (nrdFEI.2). To elucidate the mechanism of metal sensing and gene regulation by MtsR, we determined the crystal structure of MtsR. MtsR employs two Mn-sensing sites to monitor metal availability, and metal occupancy at each site influences MtsR regulatory activity. The site 1 acts as the primary Mn sensing site, and loss of metal at site 1 causes robust upregulation of mtsABC. The vacant site 2 causes partial induction of mtsABC, indicating that site 2 functions as secondary Mn sensing site. Furthermore, we show that the C-terminal FeoA domains of adjacent dimers participate in the oligomerization of MtsR on DNA, and multimerization is critical for MtsR regulatory activity. Finally, the mtsR mutant strains defective in metal sensing and oligomerization are attenuated for virulence in a mouse model of invasive infection, indicating that Mn sensing and gene regulation by MtsR are critical processes during S. pyogenes infection.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps College, Claremont, CA 91711, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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10
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Do H, Makthal N, Chandrangsu P, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence. Nucleic Acids Res 2019; 47:8333-8334. [PMID: 31329935 PMCID: PMC6736032 DOI: 10.1093/nar/gkz641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps College, Claremont, CA 91711, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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11
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Do H, Makthal N, VanderWal AR, Saavedra MO, Olsen RJ, Musser JM, Kumaraswami M. Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway. Nat Commun 2019; 10:2586. [PMID: 31197146 PMCID: PMC6565748 DOI: 10.1038/s41467-019-10556-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria control gene expression in concert with their population density by a process called quorum sensing, which is modulated by bacterial chemical signals and environmental factors. In the human pathogen Streptococcus pyogenes, production of secreted virulence factor SpeB is controlled by a quorum-sensing pathway and environmental pH. The quorum-sensing pathway consists of a secreted leaderless peptide signal (SIP), and its cognate receptor RopB. Here, we report that the SIP quorum-sensing pathway has a pH-sensing mechanism operative through a pH-sensitive histidine switch located at the base of the SIP-binding pocket of RopB. Environmental acidification induces protonation of His144 and reorganization of hydrogen bonding networks in RopB, which facilitates SIP recognition. The convergence of two disparate signals in the SIP signaling pathway results in induction of SpeB production and increased bacterial virulence. Our findings provide a model for investigating analogous crosstalk in other microorganisms.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA.
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12
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Horstmann N, Tran CN, Brumlow C, DebRoy S, Yao H, Nogueras Gonzalez G, Makthal N, Kumaraswami M, Shelburne SA. Phosphatase activity of the control of virulence sensor kinase CovS is critical for the pathogenesis of group A streptococcus. PLoS Pathog 2018; 14:e1007354. [PMID: 30379939 PMCID: PMC6231683 DOI: 10.1371/journal.ppat.1007354] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/12/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The control of virulence regulator/sensor kinase (CovRS) two-component system is critical to the infectivity of group A streptococcus (GAS), and CovRS inactivating mutations are frequently observed in GAS strains causing severe human infections. CovS modulates the phosphorylation status and with it the regulatory effect of its cognate regulator CovR via its kinase and phosphatase activity. However, the contribution of each aspect of CovS function to GAS pathogenesis is unknown. We created isoallelic GAS strains that differ only by defined mutations which either abrogate CovR phosphorylation, CovS kinase or CovS phosphatase activity in order to test the contribution of CovR phosphorylation levels to GAS virulence, emergence of hypervirulent CovS-inactivated strains during infection, and GAS global gene expression. These sets of strains were created in both serotype M1 and M3 backgrounds, two prevalent GAS disease-causing serotypes, to ascertain whether our observations were serotype-specific. In both serotypes, GAS strains lacking CovS phosphatase activity (CovS-T284A) were profoundly impaired in their ability to cause skin infection or colonize the oropharynx in mice and to survive neutrophil killing in human blood. Further, response to the human cathelicidin LL-37 was abrogated. Hypervirulent GAS isolates harboring inactivating CovRS mutations were not recovered from mice infected with M1 strain M1-CovS-T284A and only sparsely recovered from mice infected with M3 strain M3-CovS-T284A late in the infection course. Consistent with our virulence data, transcriptome analyses revealed increased repression of a broad array of virulence genes in the CovS phosphatase deficient strains, including the genes encoding the key anti-phagocytic M protein and its positive regulator Mga, which are not typically part of the CovRS transcriptome. Taken together, these data establish a key role for CovS phosphatase activity in GAS pathogenesis and suggest that CovS phosphatase activity could be a promising therapeutic target in GAS without promoting emergence of hypervirulent CovS-inactivated strains. Group A streptococcus (GAS), also known as Streptococcus pyogenes, causes a broad array of human infections of varying severity. Tight control of production of virulence factors is critical to GAS pathogenesis, and the control of virulence two-component signaling system (CovRS) is central to this process. The activity of the bifunctional histidine kinase CovS determines the phosphorylation status and thereby the activity of its cognate response regulator CovR. Herein, we sought to determine how varying CovR phosphorylation level (CovR~P) impacts GAS pathophysiology. Using three infection models, we discovered that GAS strains lacking CovS phosphatase activity resulting in high CovR~P levels had markedly impaired infectivity. Transcriptome analysis revealed that the hypovirulent phenotype of CovS phosphatase deficient strains is due to down-regulation of numerous genes encoding GAS virulence factors. We identified repression of additional virulence genes that are typically not controlled by CovR, thus expanding the CovR regulon at high CovR~P concentrations. Our data indicate that phosphatase activity of CovS sensor kinase is crucial for spatiotemporal regulation of GAS virulence gene expression. Thus, we propose that targeting the phosphatase activity of CovS sensor kinase could be a promising novel therapeutic approach to combat GAS disease.
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Affiliation(s)
- Nicola Horstmann
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston TX, United States of America
| | - Chau Nguyen Tran
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston TX, United States of America
| | - Chelcy Brumlow
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston TX, United States of America
| | - Sruti DebRoy
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston TX, United States of America
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston TX, United States of America
| | - Graciela Nogueras Gonzalez
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston TX, United States of America
| | - Nishanth Makthal
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, United States of America
| | - Muthiah Kumaraswami
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, United States of America
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston TX, United States of America
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston TX, United States of America
- * E-mail:
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13
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Makthal N, Do H, VanderWal AR, Olsen RJ, Musser JM, Kumaraswami M. Signaling by a Conserved Quorum Sensing Pathway Contributes to Growth Ex Vivo and Oropharyngeal Colonization of Human Pathogen Group A Streptococcus. Infect Immun 2018; 86:e00169-18. [PMID: 29531135 PMCID: PMC5913841 DOI: 10.1128/iai.00169-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 02/06/2023] Open
Abstract
Bacterial virulence factor production is a highly coordinated process. The temporal pattern of bacterial gene expression varies in different host anatomic sites to overcome niche-specific challenges. The human pathogen group A streptococcus (GAS) produces a potent secreted protease, SpeB, that is crucial for pathogenesis. Recently, we discovered that a quorum sensing pathway comprised of a leaderless short peptide, SpeB-inducing peptide (SIP), and a cytosolic global regulator, RopB, controls speB expression in concert with bacterial population density. The SIP signaling pathway is active in vivo and contributes significantly to GAS invasive infections. In the current study, we investigated the role of the SIP signaling pathway in GAS-host interactions during oropharyngeal colonization. The SIP signaling pathway is functional during growth ex vivo in human saliva. SIP-mediated speB expression plays a crucial role in GAS colonization of the mouse oropharynx. GAS employs a distinct pattern of SpeB production during growth ex vivo in saliva that includes a transient burst of speB expression during early stages of growth coupled with sustained levels of secreted SpeB protein. SpeB production aids GAS survival by degrading LL37, an abundant human antimicrobial peptide. We found that SIP signaling occurs during growth in human blood ex vivo. Moreover, the SIP signaling pathway is critical for GAS survival in blood. SIP-dependent speB regulation is functional in strains of diverse emm types, indicating that SIP signaling is a conserved virulence regulatory mechanism. Our discoveries have implications for future translational studies.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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14
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Makthal N, Kumaraswami M. Zinc'ing it out: zinc homeostasis mechanisms and their impact on the pathogenesis of human pathogen group A streptococcus. Metallomics 2017; 9:1693-1702. [PMID: 29043347 DOI: 10.1039/c7mt00240h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Group A Streptococccus (GAS) is a major human pathogen that causes significant morbidity and mortality. Zinc is an essential trace element required for GAS growth, however, zinc can be toxic at excess concentrations. The bacterial strategies to maintain zinc sufficiency without incurring zinc toxicity play a crucial role in host-GAS interactions and have a significant impact on GAS pathogenesis. The host deploys nutritional immune mechanisms to retard GAS growth by causing either zinc deprivation or zinc poisoning. However, GAS overcomes the zinc-dependent host defenses and survives in the hostile environment by employing complex adaptive strategies. In this review, we describe the different host immune strategies that employ either zinc limitation or zinc toxicity in different host environments to control GAS infection. We also discuss the molecular mechanisms and machineries used by GAS to evade host nutritional defenses and establish successful infection. Emerging evidence suggests that the metal transporters are major GAS virulence factors as they compete against host nutritional immune mechanisms to acquire or expel metals and promote bacterial survival in the host. Thus, identification of GAS molecules and elucidation of the mechanisms by which GAS combats host-mediated alterations in zinc availability may lead to novel interference strategies targeting GAS metal acquisition systems.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
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15
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Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M. Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen. Proc Natl Acad Sci U S A 2017; 114:E8498-E8507. [PMID: 28923955 PMCID: PMC5635878 DOI: 10.1073/pnas.1705972114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Successful pathogens use complex signaling mechanisms to monitor their environment and reprogram global gene expression during specific stages of infection. Group A Streptococcus (GAS) is a major human pathogen that causes significant disease burden worldwide. A secreted cysteine protease known as streptococcal pyrogenic exotoxin B (SpeB) is a key virulence factor that is produced abundantly during infection and is critical for GAS pathogenesis. Although identified nearly a century ago, the molecular basis for growth phase control of speB gene expression remains unknown. We have discovered that GAS uses a previously unknown peptide-mediated intercellular signaling system to control SpeB production, alter global gene expression, and enhance virulence. GAS produces an eight-amino acid leaderless peptide [SpeB-inducing peptide (SIP)] during high cell density and uses the secreted peptide for cell-to-cell signaling to induce population-wide speB expression. The SIP signaling pathway includes peptide secretion, reimportation into the cytosol, and interaction with the intracellular global gene regulator Regulator of Protease B (RopB), resulting in SIP-dependent modulation of DNA binding and regulatory activity of RopB. Notably, SIP signaling causes differential expression of ∼14% of GAS core genes. Several genes that encode toxins and other virulence genes that enhance pathogen dissemination and infection are significantly up-regulated. Using three mouse infection models, we show that the SIP signaling pathway is active during infection and contributes significantly to GAS pathogenesis at multiple host anatomic sites. Together, our results delineate the molecular mechanisms involved in a previously undescribed virulence regulatory pathway of an important human pathogen and suggest new therapeutic strategies.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Mandy Rettel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nikolai Peschek
- Munich Center for Integrated Protein Science, Department of Microbiology, Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
| | - Kai Papenfort
- Munich Center for Integrated Protein Science, Department of Microbiology, Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030;
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
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Makthal N, Nguyen K, Do H, Gavagan M, Chandrangsu P, Helmann JD, Olsen RJ, Kumaraswami M. A Critical Role of Zinc Importer AdcABC in Group A Streptococcus-Host Interactions During Infection and Its Implications for Vaccine Development. EBioMedicine 2017; 21:131-141. [PMID: 28596134 PMCID: PMC5514391 DOI: 10.1016/j.ebiom.2017.05.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
Bacterial pathogens must overcome host immune mechanisms to acquire micronutrients for successful replication and infection. Streptococcus pyogenes, also known as group A streptococcus (GAS), is a human pathogen that causes a variety of clinical manifestations, and disease prevention is hampered by lack of a human GAS vaccine. Herein, we report that the mammalian host recruits calprotectin (CP) to GAS infection sites and retards bacterial growth by zinc limitation. However, a GAS-encoded zinc importer and a nuanced zinc sensor aid bacterial defense against CP-mediated growth inhibition and contribute to GAS virulence. Immunization of mice with the extracellular component of the zinc importer confers protection against systemic GAS challenge. Together, we identified a key early stage host-GAS interaction and translated that knowledge into a novel vaccine strategy against GAS infection. Furthermore, we provided evidence that a similar struggle for zinc may occur during other streptococcal infections, which raises the possibility of a broad-spectrum prophylactic strategy against multiple streptococcal pathogens. Host employs calprotectin to impose zinc (Zn) limitation on the human pathogen group A streptococcus (GAS) during infection. As a defense, GAS uses a sensor, AdcR, to monitor Zn availability, and a high-affinity transporter, AdcABC, to acquire Zn. Finally, we characterized the extracellular subunit of AdcA as a vaccine candidate to protect mice from GAS infections.
There is an urgent need for a human vaccine to protect against diseases caused by human pathogen, group A streptococcus (GAS). Herein, we identified the key molecular players involved in the battle between the host and invading bacteria for the critical nutrient zinc. The host recruits calprotectin at GAS infection sites to limit zinc availability to the pathogen. The pathogen senses the alterations in zinc availability using a sensor, AdcR, and outcompetes calprotectin by employing a high-affinity zinc uptake system, AdcABC. Using this knowledge, we developed a successful vaccination strategy by immunization with AdcA and demonstrated protection against GAS infections.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Kimberly Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Maire Gavagan
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, United States
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States.
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Do H, Kumaraswami M. Structural Mechanisms of Peptide Recognition and Allosteric Modulation of Gene Regulation by the RRNPP Family of Quorum-Sensing Regulators. J Mol Biol 2016; 428:2793-804. [PMID: 27283781 DOI: 10.1016/j.jmb.2016.05.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/19/2016] [Accepted: 05/29/2016] [Indexed: 11/19/2022]
Abstract
The members of RRNPP family of bacterial regulators sense population density-specific secreted oligopeptides and modulate the expression of genes involved in cellular processes, such as sporulation, competence, virulence, biofilm formation, conjugative plasmid transfer and antibiotic resistance. Signaling by RRNPP regulators include several steps: generation and secretion of the signaling oligopeptides, re-internalization of the signaling molecules into the cytoplasm, signal sensing by the cytosolic RRNPP regulators, signal-specific allosteric structural changes in the regulators, and interaction of the regulators with their respective regulatory target and gene regulation. The recently determined structures of the RRNPP regulators provide insight into the mechanistic aspects for several steps in this signaling circuit. In this review, we discuss the structural principles underlying peptide specificity, regulatory target recognition, and ligand-induced allostery in RRNPP regulators and its impact on gene regulation. Despite the conserved tertiary structure of these regulators, structural analyses revealed unexpected diversity in the mechanism of activation and molecular strategies that couple the peptide-induced allostery to gene regulation. Although these structural studies provide a sophisticated understanding of gene regulation by RRNPP regulators, much needs to be learned regarding the target DNA binding by yet-to-be characterized RNPP regulators and the several aspects of signaling by Rgg regulators.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital System, Houston, TX, 77030, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital System, Houston, TX, 77030, USA.
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Makthal N, Gavagan M, Do H, Olsen RJ, Musser JM, Kumaraswami M. Structural and functional analysis of RopB: a major virulence regulator in Streptococcus pyogenes. Mol Microbiol 2016; 99:1119-33. [PMID: 26714274 PMCID: PMC4794775 DOI: 10.1111/mmi.13294] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/02/2015] [Indexed: 01/12/2023]
Abstract
Group A Streptococcus (GAS) is an exclusive human pathogen that causes significant disease burden. Global regulator RopB of GAS controls the expression of several major virulence factors including secreted protease SpeB during high cell density. However, the molecular mechanism for RopB-dependent speB expression remains unclear. To understand the mechanism of transcription activation by RopB, we determined the crystal structure of the C-terminal domain of RopB. RopB-CTD has the TPR motif, a signature motif involved in protein-peptide interactions and shares significant structural homology with the quorum sensing RRNPP family regulators. Characterization of the high cell density-specific cell-free growth medium demonstrated the presence of a low molecular weight proteinaceous secreted factor that upregulates RopB-dependent speB expression. Together, these results suggest that RopB and its cognate peptide signals constitute an intercellular signalling machinery that controls the virulence gene expression in concert with population density. Structure-guided mutational analyses of RopB dimer interface demonstrated that single alanine substitutions at this critical interface significantly altered RopB-dependent speB expression and attenuated GAS virulence. Results presented here suggested that a properly aligned RopB dimer interface is important for GAS pathogenesis and highlighted the dimerization interactions as a plausible therapeutic target for the development of novel antimicrobials.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Maire Gavagan
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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Sanson M, Makthal N, Flores AR, Olsen RJ, Musser JM, Kumaraswami M. Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence. Nucleic Acids Res 2014; 43:418-32. [PMID: 25510500 PMCID: PMC4288194 DOI: 10.1093/nar/gku1304] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Altering zinc bioavailability to bacterial pathogens is a key component of host innate immunity. Thus, the ability to sense and adapt to the alterations in zinc concentrations is critical for bacterial survival and pathogenesis. To understand the adaptive responses of group A Streptococcus (GAS) to zinc limitation and its regulation by AdcR, we characterized gene regulation by AdcR. AdcR regulates the expression of 70 genes involved in zinc acquisition and virulence. Zinc-bound AdcR interacts with operator sequences in the negatively regulated promoters and mediates differential regulation of target genes in response to zinc deficiency. Genes involved in zinc mobilization and conservation are derepressed during mild zinc deficiency, whereas the energy-dependent zinc importers are upregulated during severe zinc deficiency. Further, we demonstrated that transcription activation by AdcR occurs by direct binding to the promoter. However, the repression and activation by AdcR is mediated by its interactions with two distinct operator sequences. Finally, mutational analysis of the metal ligands of AdcR caused impaired DNA binding and attenuated virulence, indicating that zinc sensing by AdcR is critical for GAS pathogenesis. Together, we demonstrate that AdcR regulates GAS adaptive responses to zinc limitation and identify molecular components required for GAS survival during zinc deficiency.
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Affiliation(s)
- Misu Sanson
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA Escuela de Biotecnología y Alimentos, Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Monterrey, NL, Mexico
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - Anthony R Flores
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA Section of Infectious Diseases, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
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Sanson M, O'Neill BE, Kachroo P, Anderson JR, Flores AR, Valson C, Cantu CC, Makthal N, Karmonik C, Fittipaldi N, Kumaraswami M, Musser JM, Olsen RJ. A naturally occurring single amino acid replacement in multiple gene regulator of group A Streptococcus significantly increases virulence. Am J Pathol 2014; 185:462-71. [PMID: 25476528 DOI: 10.1016/j.ajpath.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 12/27/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common source of genetic variation within a species; however, few investigations demonstrate how naturally occurring SNPs may increase strain virulence. We recently used group A Streptococcus as a model pathogen to study bacteria strain genotype-patient disease phenotype relationships. Whole-genome sequencing of approximately 800 serotype M59 group A Streptococcus strains, recovered during an outbreak of severe invasive infections across North America, identified a disproportionate number of SNPs in the gene encoding multiple gene regulator of group A Streptococcus (mga). Herein, we report results of studies designed to test the hypothesis that the most commonly occurring SNP, encoding a replacement of arginine for histidine at codon 201 of Mga (H201R), significantly increases virulence. Whole transcriptome analysis revealed that the H201R replacement significantly increased expression of mga and 54 other genes, including many proven virulence factors. Compared to the wild-type strain, a H201R isogenic mutant strain caused significantly larger skin lesions in mice. Serial quantitative bacterial culture and noninvasive magnetic resonance imaging also demonstrated that the isogenic H201R strain was significantly more virulent in a nonhuman primate model of joint infection. These findings show that the H201R replacement in Mga increases the virulence of M59 group A Streptococcus and provide new insight to how a naturally occurring SNP in bacteria contributes to human disease phenotypes.
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Affiliation(s)
- Misu Sanson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas; School of Biotechnology, School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Brian E O'Neill
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Priyanka Kachroo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Jeff R Anderson
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Anthony R Flores
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas; Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Chandni Valson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Concepcion C Cantu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Nishanth Makthal
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Christof Karmonik
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Nahuel Fittipaldi
- Department of Laboratory Medicine and Pathobiology, Public Health Ontario, University of Toronto, Toronto, Ontario, Canada
| | - Muthiah Kumaraswami
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas.
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21
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Makthal N, Rastegari S, Sanson M, Ma Z, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Crystal structure of peroxide stress regulator from Streptococcus pyogenes provides functional insights into the mechanism of oxidative stress sensing. J Biol Chem 2013; 288:18311-24. [PMID: 23645680 DOI: 10.1074/jbc.m113.456590] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulation of oxidative stress responses by the peroxide stress regulator (PerR) is critical for the in vivo fitness and virulence of group A Streptococcus. To elucidate the molecular mechanism of DNA binding, peroxide sensing, and gene regulation by PerR, we performed biochemical and structural characterization of PerR. Sequence-specific DNA binding by PerR does not require regulatory metal occupancy. However, metal binding promotes higher affinity PerR-DNA interactions. PerR metallated with iron directly senses peroxide stress and dissociates from operator sequences. The crystal structure revealed that PerR exists as a homodimer with two metal-binding sites per subunit as follows: a structural zinc site and a regulatory metal site that is occupied in the crystals by nickel. The regulatory metal-binding site in PerR involves a previously unobserved HXH motif located in its unique N-terminal extension. Mutational analysis of the regulatory site showed that the PerR metal ligands are involved in regulatory metal binding, and integrity of this site is critical for group A Streptococcus virulence. Interestingly, the metal-binding HXH motif is not present in the structurally characterized members of ferric uptake regulator (Fur) family but is fully conserved among PerR from the genus Streptococcus. Thus, it is likely that the PerR orthologs from streptococci share a common mechanism of metal binding, peroxide sensing, and gene regulation that is different from that of well characterized PerR from Bacillus subtilis. Together, our findings provide key insights into the peroxide sensing and regulation of the oxidative stress-adaptive responses by the streptococcal subfamily of PerR.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, Texas 77030, USA
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Olsen RJ, Laucirica DR, Watkins ME, Feske ML, Garcia-Bustillos JR, Vu C, Cantu C, Shelburne SA, Fittipaldi N, Kumaraswami M, Shea P, Flores AR, Beres SB, Lovgren M, Tyrrell GJ, Efstratiou A, Low DE, Van Beneden CA, Musser JM. Polymorphisms in regulator of protease B (RopB) alter disease phenotype and strain virulence of serotype M3 Group A
Streptococcus. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.1034.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Randall J Olsen
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Daniel R Laucirica
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Melanie E Watkins
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Marsha L Feske
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | | | - Chau Vu
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Concepcion Cantu
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | | | - Nahuel Fittipaldi
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Muthiah Kumaraswami
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | - Patrick Shea
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | | | - Stephen B Beres
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
| | | | | | | | | | | | - James M Musser
- Pathology and Genomic MedicineThe Methodist Hospital Research InstituteHoustonTX
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Olsen RJ, Laucirica DR, Watkins ME, Feske ML, Garcia-Bustillos JR, Vu C, Cantu C, Shelburne SA, Fittipaldi N, Kumaraswami M, Shea PR, Flores AR, Beres SB, Lovgren M, Tyrrell GJ, Efstratiou A, Low DE, Van Beneden CA, Musser JM. Polymorphisms in regulator of protease B (RopB) alter disease phenotype and strain virulence of serotype M3 group A Streptococcus. J Infect Dis 2012; 205:1719-29. [PMID: 22262791 DOI: 10.1093/infdis/jir825] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Whole-genome sequencing of serotype M3 group A streptococci (GAS) from oropharyngeal and invasive infections in Ontario recently showed that the gene encoding regulator of protease B (RopB) is highly polymorphic in this population. To test the hypothesis that ropB is under diversifying selective pressure among all serotype M3 GAS strains, we sequenced this gene in 1178 strains collected from different infection types, geographic regions, and time periods. The results confirmed our hypothesis and discovered a significant association between mutant ropB alleles, decreased activity of its major regulatory target SpeB, and pharyngitis. Additionally, isoallelic strains with ropB polymorphisms were significantly less virulent in a mouse model of necrotizing fasciitis. These studies provide a model strategy for applying whole-genome sequencing followed by deep single-gene sequencing to generate new insight to the rapid evolution and virulence regulation of human pathogens.
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Affiliation(s)
- Randall J Olsen
- Department of Pathology and Laboratory Medicine, The Methodist Hospital Research Institute, Houston, TX, USA.
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Shelburne SA, Olsen RJ, Makthal N, Brown NG, Sahasrabhojane P, Watkins EM, Palzkill T, Musser JM, Kumaraswami M. An amino-terminal signal peptide of Vfr protein negatively influences RopB-dependent SpeB expression and attenuates virulence in Streptococcus pyogenes. Mol Microbiol 2011; 82:1481-95. [PMID: 22040048 DOI: 10.1111/j.1365-2958.2011.07902.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Streptococcal pyrogenic exotoxin B (SpeB) is an extracellular cysteine protease that is a critical virulence factor made by the major human pathogen group A Streptococcus (GAS). speB expression is dependent on the regulator of proteinase B (RopB) and is upregulated with increasing cell density and during infection. Because computer modelling suggested significant structural similarity between RopB and peptide-sensing regulatory proteins made by other Gram-positive bacteria, we hypothesized that speB expression is influenced by RopB-peptide interactions. Inactivation of the gene (vfr) encoding the virulence factor related (Vfr) protein resulted in increased speB transcript level during the exponential growth phase, whereas provision of only the amino-terminal region of Vfr comprising the secretion signal sequence in trans restored a wild-type speB expression profile. Addition of the culture supernatant from a Vfr signal peptide-expressing GAS strain restored wild-type speB transcript level to a vfr-inactivated isogenic mutant strain. A distinct peptide in the Vfr secretion signal sequence specifically bound to recombinant RopB. Finally, overexpression of the Vfr secretion signal sequence significantly decreased speB transcript level and attenuated GAS virulence in two mouse models of invasive infection. Taken together, these data delineate a previously unknown small peptide-mediated regulatory system that controls GAS virulence factor production.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX, USA
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Horstmann N, Sahasrabhojane P, Suber B, Kumaraswami M, Olsen RJ, Flores A, Musser JM, Brennan RG, Shelburne SA. Distinct single amino acid replacements in the control of virulence regulator protein differentially impact streptococcal pathogenesis. PLoS Pathog 2011; 7:e1002311. [PMID: 22028655 PMCID: PMC3197619 DOI: 10.1371/journal.ppat.1002311] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 08/26/2011] [Indexed: 01/08/2023] Open
Abstract
Sequencing of invasive strains of group A streptococci (GAS) has revealed a diverse array of single nucleotide polymorphisms in the gene encoding the control of virulence regulator (CovR) protein. However, there is limited information regarding the molecular mechanisms by which CovR single amino acid replacements impact GAS pathogenesis. The crystal structure of the CovR C-terminal DNA-binding domain was determined to 1.50 Å resolution and revealed a three-stranded β-sheet followed by a winged helix-turn-helix DNA binding motif. Modeling of the CovR protein-DNA complex indicated that CovR single amino acid replacements observed in clinical GAS isolates could directly alter protein-DNA interaction and impact protein structure. Isoallelic GAS strains that varied by a single amino acid replacement in the CovR DNA binding domain had significantly different transcriptomes compared to wild-type and to each other. Similarly, distinct recombinant CovR variants had differential binding affinity for DNA from the promoter regions of several virulence factor-encoding genes. Finally, mice that were challenged with GAS CovR isoallelic strains had significantly different survival times, which correlated with the transcriptome and protein-DNA binding studies. Taken together, these data provide structural and functional insights into the critical and distinct effects of variation in the CovR protein on GAS pathogenesis. Group A Streptococcus (GAS) causes a variety of human infections including invasive disease that can often be deadly. GAS strains that cause serious infections may have alterations in the amino acid sequence of the control of virulence regulator (CovR) protein, but mechanisms by which changes in the CovR protein influence GAS disease are not understood. We determined the crystal structure of the CovR DNA binding region and found that alterations in the CovR protein observed in clinical, invasive GAS isolates are likely to disrupt CovR-DNA interaction and overall CovR structure. In accord with the structural data, CovR proteins with a single amino acid change had distinctly different binding affinities for various GAS virulence-factor encoding genes. Similarly, GAS strains that differed by only the presence of a single CovR amino acid change had distinct gene expression profiles. Finally, mice that were challenged with GAS strains that differed by only a single CovR amino acid replacement had significantly different survival times consistent with the idea that alterations in the CovR protein are a key determinant of clinical outcomes in GAS human infections. These findings provide mechanistic insights into how subtle genetic differences can profoundly impact the severity of bacterial infections.
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Affiliation(s)
- Nicola Horstmann
- Department of Biochemistry and Molecular Biology, MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Bryce Suber
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, United States of America
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, United States of America
| | - Anthony Flores
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas, United States of America
| | - Richard G. Brennan
- Department of Biochemistry and Molecular Biology, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Samuel A. Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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Kumaraswami M, Avanigadda L, Rai R, Park HW, Howe MM. Genetic analysis of phage Mu Mor protein amino acids involved in DNA minor groove binding and conformational changes. J Biol Chem 2011; 286:35852-35862. [PMID: 21859715 DOI: 10.1074/jbc.m111.269860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene expression during lytic development of bacteriophage Mu occurs in three phases: early, middle, and late. Transcription from the middle promoter, P(m), requires the phage-encoded activator protein Mor and the bacterial RNA polymerase. The middle promoter has a -10 hexamer, but no -35 hexamer. Instead P(m) has a hyphenated inverted repeat that serves as the Mor binding site overlapping the position of the missing -35 element. Mor binds to this site as a dimer and activates transcription by recruiting RNA polymerase. The crystal structure of the His-Mor dimer revealed three structural elements: an N-terminal dimerization domain, a C-terminal helix-turn-helix DNA-binding domain, and a β-strand linker between the two domains. We predicted that the highly conserved residues in and flanking the β-strand would be essential for the conformational flexibility and DNA minor groove binding by Mor. To test this hypothesis, we carried out single codon-specific mutagenesis with degenerate oligonucleotides. The amino acid substitutions were identified by DNA sequencing. The mutant proteins were characterized for their overexpression, solubility, DNA binding, and transcription activation. This analysis revealed that the Gly-Gly motif formed by Gly-65 and Gly-66 and the β-strand side chain of Tyr-70 are crucial for DNA binding by His-tagged Mor. Mutant proteins with substitutions at Gly-74 retained partial activity. Treatment with the minor groove- and GC-specific chemical chromomycin A(3) demonstrated that chromomycin prevented His-Mor binding but could not disrupt a pre-formed His-Mor·DNA complex, consistent with the prediction that Mor interacts with the minor groove of the GC-rich spacer in the Mor binding site.
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Affiliation(s)
- Muthiah Kumaraswami
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Lakshmi Avanigadda
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Rajendra Rai
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Hee-Won Park
- Department of Pharmacology, Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G1L7 Canada
| | - Martha M Howe
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
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Shelburne SA, Sahasrobhajane P, Suber B, Keith DB, Davenport MT, Horstmann N, Kumaraswami M, Olsen RJ, Brennan RG, Musser JM. Niche-specific contribution to streptococcal virulence of a MalR-regulated carbohydrate binding protein. Mol Microbiol 2011; 81:500-14. [PMID: 21645132 DOI: 10.1111/j.1365-2958.2011.07708.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Low G+C Gram-positive bacteria typically contain multiple LacI/GalR regulator family members, which often have highly similar amino-terminal DNA binding domains, suggesting significant overlap in target DNA sequences. The LacI/GalR family regulator catabolite control protein A (CcpA) is a global regulator of the Group A Streptococcus (GAS) transcriptome and contributes to GAS virulence in diverse infection sites. Herein, we studied the role of the maltose repressor (MalR), another LacI/GalR family member, in GAS global gene expression and virulence. MalR inactivation reduced GAS colonization of the mouse oropharynx but did not detrimentally affect invasive infection. The MalR transcriptome was limited to only 25 genes, and a highly conserved MalR DNA-binding sequence was identified. Variation of the MalR binding sequence significantly reduced MalR binding in vitro. In contrast, CcpA bound to the same DNA sequences as MalR but tolerated variation in the promoter sequences with minimal change in binding affinity. Inactivation of pulA, a MalR regulated gene which encodes a cell surface carbohydrate binding protein, significantly reduced GAS human epithelial cell adhesion and mouse oropharyngeal colonization but did not affect GAS invasive disease. These data delineate a molecular mechanism by which hierarchical regulation of carbon source utilization influences bacterial pathogenesis in a site-specific fashion.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA.
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Carroll RK, Shelburne SA, Olsen RJ, Suber B, Sahasrabhojane P, Kumaraswami M, Beres SB, Shea PR, Flores AR, Musser JM. Naturally occurring single amino acid replacements in a regulatory protein alter streptococcal gene expression and virulence in mice. J Clin Invest 2011; 121:1956-68. [PMID: 21490401 DOI: 10.1172/jci45169] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/02/2011] [Indexed: 11/17/2022] Open
Abstract
Infection with different strains of the same species of bacteria often results in vastly different clinical outcomes. Despite extensive investigation, the genetic basis of microbial strain-specific virulence remains poorly understood. Recent whole-genome sequencing has revealed that SNPs are the most prevalent form of genetic diversity among different strains of the same species of bacteria. For invasive serotype M3 group A streptococci (GAS) strains, the gene encoding regulator of proteinase B (RopB) has the highest frequency of SNPs. Here, we have determined that ropB polymorphisms alter RopB function and modulate GAS host-pathogen interactions. Sequencing of ropB in 171 invasive serotype M3 GAS strains identified 19 distinct ropB alleles. Inactivation of the ropB gene in strains producing distinct RopB variants had dramatically divergent effects on GAS global gene expression. Additionally, generation of isoallelic GAS strains differing only by a single amino acid in RopB confirmed that variant proteins affected transcript levels of the gene encoding streptococcal proteinase B, a major RopB-regulated virulence factor. Comparison of parental, RopB-inactivated, and RopB isoallelic strains in mouse infection models demonstrated that ropB polymorphisms influence GAS virulence and disease manifestations. These data detail a paradigm in which unbiased, whole-genome sequence analysis of populations of clinical bacterial isolates creates new avenues of productive investigation into the pathogenesis of common human infections.
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Affiliation(s)
- Ronan K Carroll
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Laboratory Medicine, The Methodist Hospital, Houston, Texas, USA
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Kumaraswami M, Newberry KJ, Brennan RG. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. J Mol Biol 2010; 398:264-75. [PMID: 20230832 DOI: 10.1016/j.jmb.2010.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 03/03/2010] [Accepted: 03/06/2010] [Indexed: 11/19/2022]
Abstract
The multidrug-binding transcription regulator BmrR from Bacillus subtilis is a MerR family member that binds to a wide array of cationic lipophilic toxins to activate the transcription of the multidrug efflux pump gene bmr. Transcription activation from the sigma(A)-dependent bmr operator requires BmrR to remodel the nonoptimal 19-bp spacer between the -10 promoter element and the -35 promoter element in order to facilitate productive RNA polymerase binding. Despite the availability of several structures of BmrR bound to DNA and drugs, the lack of a BmrR structure in its unliganded or apo (DNA free and drug free) state hinders our full understanding of the structural transitions required for DNA binding and transcription activation. Here, we report the crystal structure of the constitutively active, unliganded BmrR mutant BmrR(E253Q/R275E). Superposition of the ligand-free (apo BmrR(E253Q/R275E)) and DNA-bound BmrR structures reveals that apo BmrR must undergo significant rearrangement in order to assume the DNA-bound conformation, including an outward rotation of minor groove binding wings, an inward movement of helix-turn-helix motifs, and a downward relocation of pliable coiled-coil helices. Computational analysis of the DNA-free and DNA-bound structures reveals a flexible joint that is located at the center of the coiled-coil helices. This region, which is composed of residues 94 through 98, overlaps the helical bulge that is observed only in the apo BmrR structure. This conformational hinge is likely common to other MerR family members with large effector-binding domains, but appears to be missing from the smaller metal-binding MerR family members. Interestingly, the center-to-center distance of the recognition helices of apo BmrR is 34 A and suggests that the conformational change from the apo BmrR structure to the bmr operator-bound BmrR structure is initiated by the binding of this transcription activator to a more B-DNA-like conformation.
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Affiliation(s)
- Muthiah Kumaraswami
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Structure and Function, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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Kumaraswami M, Schuman JT, Seo SM, Kaatz GW, Brennan RG. Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA. Nucleic Acids Res 2009; 37:1211-24. [PMID: 19129225 PMCID: PMC2651776 DOI: 10.1093/nar/gkn1046] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
MepR is a multidrug binding transcription regulator that represses expression of the Staphylococcus aureus multidrug efflux pump gene, mepA, as well as its own gene. MepR is induced by multiple cationic toxins, which are also substrates of MepA. In order to understand the gene regulatory and drug-binding mechanisms of MepR, we carried out biochemical, in vivo and structural studies. The 2.40 A resolution structure of drug-free MepR reveals the most open MarR family protein conformation to date, which will require a huge conformational change to bind cognate DNA. DNA-binding data show that MepR uses a dual regulatory binding mode as the repressor binds the mepA operator as a dimer of dimers, but binds the mepR operator as a single dimer. Alignment of the six half sites reveals the consensus MepR binding site, 5'-GTTAGAT-3'. 'Drug' binding studies show that MepR binds to ethidium and DAPI with comparable affinities (K(d) = 2.6 and 4.5 microM, respectively), but with significantly lower affinity to the larger rhodamine 6G (K(d) = 62.6 microM). Mapping clinically relevant or in vitro selected MepR mutants onto the MepR structure suggests that their defective repressor phenotypes are due to structural and allosteric defects.
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Affiliation(s)
- Muthiah Kumaraswami
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Kumaraswami M, Howe MM, Park HW. Crystal Structure of the Mor Protein of Bacteriophage Mu, a Member of the Mor/C Family of Transcription Activators. J Biol Chem 2004; 279:16581-90. [PMID: 14729670 DOI: 10.1074/jbc.m313555200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription from the middle promoter, Pm, of bacteriophage Mu requires the phage-encoded activator protein Mor and bacterial RNA polymerase. Mor is a sequence-specific DNA-binding protein that mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. Here we present the first structure for a member of the Mor/C family of transcription activators, the crystal structure of Mor to 2.2-A resolution. Each monomer of the Mor dimer is composed of two domains, the N-terminal dimerization domain and C-terminal DNA-binding domain, which are connected by a linker containing a beta strand. The N-terminal dimerization domain has an unusual mode of dimerization; helices alpha1 and alpha2 of both monomers are intertwined to form a four-helix bundle, generating a hydrophobic core that is further stabilized by antiparallel interactions between the two beta strands. Mutational analysis of key leucine residues in helix alpha1 demonstrated a role for this hydrophobic core in protein solubility and function. The C-terminal domain has a classical helix-turn-helix DNA-binding motif that is located at opposite ends of the elongated dimer. Since the distance between the two helix-turn-helix motifs is too great to allow binding to two adjacent major grooves of the 16-bp Mor-binding site, we propose that conformational changes in the protein and DNA will be required for Mor to interact with the DNA. The highly conserved glycines flanking the beta strand may act as pivot points, facilitating the conformational changes of Mor, and the DNA may be bent.
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Affiliation(s)
- Muthiah Kumaraswami
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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