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Trottmann F, Fiedler J, Ishida K, Ishida-Ito M, Little RF, Hertweck C. Bacterial Pathogen Channels Medium-Sized Fatty Acids into Malleicyprol Biosynthesis. ACS Chem Biol 2023; 18:1557-1563. [PMID: 37319349 DOI: 10.1021/acschembio.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bacterial pathogens of the Burkholderia pseudomallei (BP) group cause life-threatening infections in both humans and animals. Critical for the virulence of these often antibiotic-resistant pathogens is the polyketide hybrid metabolite malleicyprol, which features two chains, a short cyclopropanol-substituted chain and a long hydrophobic alkyl chain. The biosynthetic origin of the latter has remained unknown. Here, we report the discovery of novel overlooked malleicyprol congeners with varied chain lengths and identify medium-sized fatty acids as polyketide synthase (PKS) starter units that constitute the hydrophobic carbon tails. Mutational and biochemical analyses show that a designated coenzyme A-independent fatty acyl-adenylate ligase (FAAL, BurM) is essential for recruiting and activating fatty acids in malleicyprol biosynthesis. In vitro reconstitution of the BurM-catalyzed PKS priming reaction and analysis of ACP-bound building blocks reveal a key role of BurM in the toxin assembly. Insights into the function and role of BurM hold promise for the development of enzyme inhibitors as novel antivirulence therapeutics to combat infections with BP pathogens.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jonas Fiedler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Rory F Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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Meethai C, Vanaporn M, Intarak N, Lerdsittikul V, Withatanung P, Janesomboon S, Vattanaviboon P, Chareonsudjai S, Wilkinson T, Stevens MP, Stevens JM, Korbsrisate S. Analysis of the role of the QseBC two-component sensory system in epinephrine-induced motility and intracellular replication of Burkholderia pseudomallei. PLoS One 2023; 18:e0282098. [PMID: 36821630 PMCID: PMC9949665 DOI: 10.1371/journal.pone.0282098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Burkholderia pseudomallei is a facultative intracellular bacterial pathogen that causes melioidosis, a severe invasive disease of humans. We previously reported that the stress-related catecholamine hormone epinephrine enhances motility of B. pseudomallei, transcription of flagellar genes and the production of flagellin. It has been reported that the QseBC two-component sensory system regulates motility and virulence-associated genes in other Gram-negative bacteria in response to stress-related catecholamines, albeit disparities between studies exist. We constructed and whole-genome sequenced a mutant of B. pseudomallei with a deletion spanning the predicted qseBC homologues (bpsl0806 and bpsl0807). The ΔqseBC mutant exhibited significantly reduced swimming and swarming motility and reduced transcription of fliC. It also exhibited a defect in biofilm formation and net intracellular survival in J774A.1 murine macrophage-like cells. While epinephrine enhanced bacterial motility and fliC transcription, no further reduction in these phenotypes was observed with the ΔqseBC mutant in the presence of epinephrine. Plasmid-mediated expression of qseBC suppressed bacterial growth, complicating attempts to trans-complement mutant phenotypes. Our data support a role for QseBC in motility, biofilm formation and net intracellular survival of B. pseudomallei, but indicate that it is not essential for epinephrine-induced motility per se.
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Affiliation(s)
- Chatruthai Meethai
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narin Intarak
- Department of Physiology, Faculty of Dentistry, Genomics and Precision, Chulalongkorn University, Bangkok, Thailand
| | - Varintip Lerdsittikul
- Microbiology Laboratory, Faculty of Veterinary Science, Veterinary Diagnostic Center, Mahidol University, Nakhon Pathom, Thailand
| | - Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sujintana Janesomboon
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Toby Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Mark P. Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Joanne M. Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (JMS); (SK)
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail: (JMS); (SK)
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Kinch LN, Cong Q, Jaishankar J, Orth K. Co-component signal transduction systems: Fast-evolving virulence regulation cassettes discovered in enteric bacteria. Proc Natl Acad Sci U S A 2022; 119:e2203176119. [PMID: 35648808 PMCID: PMC9214523 DOI: 10.1073/pnas.2203176119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/08/2022] [Indexed: 01/31/2023] Open
Abstract
Bacterial signal transduction systems sense changes in the environment and transmit these signals to control cellular responses. The simplest one-component signal transduction systems include an input sensor domain and an output response domain encoded in a single protein chain. Alternatively, two-component signal transduction systems transmit signals by phosphorelay between input and output domains from separate proteins. The membrane-tethered periplasmic bile acid sensor that activates the Vibrio parahaemolyticus type III secretion system adopts an obligate heterodimer of two proteins encoded by partially overlapping VtrA and VtrC genes. This co-component signal transduction system binds bile acid using a lipocalin-like domain in VtrC and transmits the signal through the membrane to a cytoplasmic DNA-binding transcription factor in VtrA. Using the domain and operon organization of VtrA/VtrC, we identify a fast-evolving superfamily of co-component systems in enteric bacteria. Accurate machine learning–based fold predictions for the candidate co-components support their homology in the twilight zone of rapidly evolving sequences and provide mechanistic hypotheses about previously unrecognized lipid-sensing functions.
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Affiliation(s)
- Lisa N. Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jananee Jaishankar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Krishnakumar R, Ruffing AM. OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PLoS Comput Biol 2022; 18:e1009731. [PMID: 34986143 PMCID: PMC8765615 DOI: 10.1371/journal.pcbi.1009731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/18/2022] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability. Bacteria and archaea, single-cell organisms collectively known as prokaryotes, live in all imaginable environments and comprise the majority of living organisms on this planet. Prokaryotes play a critical role in the homeostasis of multicellular organisms (such as animals and plants) and ecosystems. In addition, bacteria can be pathogenic and cause a variety of diseases in these same hosts and ecosystems. In short, understanding the biology and molecular functions of bacteria and archaea and devising mechanisms to engineer and optimize their properties are critical scientific endeavors with significant implications in healthcare, agriculture, manufacturing, and climate science among others. One major molecular difference between unicellular and multicellular organisms is the way they express genes–multicellular organisms make individual RNA molecules for each gene while, prokaryotes express operons (i.e., a group of genes coding functionally related proteins) in contiguous polycistronic RNA molecules. Understanding which genes exist within operons is critical for elucidating basic biology and for engineering organisms. In this work, we use a combination of statistical and machine learning-based methods to use next-generation sequencing data to predict operon structure across a range of prokaryotes. Our method provides an easily implemented, robust, accurate, and flexible way to determine operon structure in an organism-agnostic manner using readily available data.
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Affiliation(s)
- Raga Krishnakumar
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| | - Anne M. Ruffing
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, New Mexico, United States of America
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Schnetterle M, Gorgé O, Nolent F, Boughammoura A, Sarilar V, Vigier C, Guillier S, Koch L, Degand N, Ramisse V, Tichadou X, Girleanu M, Favier AL, Valade E, Biot F, Neulat-Ripoll F. Genomic and RT-qPCR analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates. PLoS Negl Trop Dis 2021; 15:e0008913. [PMID: 33592059 PMCID: PMC7909661 DOI: 10.1371/journal.pntd.0008913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/26/2021] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Melioidosis is an endemic disease in southeast Asia and northern Australia caused by the saprophytic bacteria Burkholderia pseudomallei, with a high mortality rate. The clinical presentation is multifaceted, with symptoms ranging from acute septicemia to multiple chronic abscesses. Here, we report a chronic case of melioidosis in a patient who lived in Malaysia in the 70s and was suspected of contracting tuberculosis. Approximately 40 years later, in 2014, he was diagnosed with pauci-symptomatic melioidosis during a routine examination. Four strains were isolated from a single sample. They showed divergent morphotypes and divergent antibiotic susceptibility, with some strains showing resistance to trimethoprim-sulfamethoxazole and fluoroquinolones. In 2016, clinical samples were still positive for B. pseudomallei, and only one type of strain, showing atypical resistance to meropenem, was isolated. PRINCIPAL FINDINGS We performed whole genome sequencing and RT-qPCR analysis on the strains isolated during this study to gain further insights into their differences. We thus identified two types of resistance mechanisms in these clinical strains. The first one was an adaptive and transient mechanism that disappeared during the course of laboratory sub-cultures; the second was a mutation in the efflux pump regulator amrR, associated with the overexpression of the related transporter. CONCLUSION The development of such mechanisms may have a clinical impact on antibiotic treatment. Indeed, their transient nature could lead to an undiagnosed resistance. Efflux overexpression due to mutation leads to an important multiple resistance, reducing the effectiveness of antibiotics during treatment.
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Affiliation(s)
- Marine Schnetterle
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Olivier Gorgé
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Flora Nolent
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Aïda Boughammoura
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Véronique Sarilar
- Molecular Biology Unit, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Cécile Vigier
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Sophie Guillier
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Lionel Koch
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Nicolas Degand
- Laboratoire de bactériologie, Hôpital de l’Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Vincent Ramisse
- DGA MNRBC- Le Bouchet, Division Biologie, ABIO, Vert-le-Petit, France
| | - Xavier Tichadou
- DGA MNRBC- Le Bouchet, Division Biologie, ABIO, Vert-le-Petit, France
| | - Maria Girleanu
- Imagery Unit, Departement of plateforms and technology research, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Imagery Unit, Departement of plateforms and technology research, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Eric Valade
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
- Ecole du Val de Grace, Paris, France
| | - Fabrice Biot
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
| | - Fabienne Neulat-Ripoll
- Bacteriology Unit, UMR-MD1 INSERM 1261, French Armed Biomedical Research Institut, Brétigny-sur-Orge, France
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Abstract
The regulation and timely expression of bacterial genes during infection is critical for a pathogen to cause an infection. Bacteria have multiple mechanisms to regulate gene expression in response to their environment, one of which is two-component systems (TCS). TCS have two components. One component is a sensory histidine kinase (HK) that autophosphorylates when activated by a signal. The activated sensory histidine kinase then transfers the phosphoryl group to the second component, the response regulator, which activates transcription of target genes. The genus Burkholderia contains members that cause human disease and are often extensively resistant to many antibiotics. The Burkholderia cepacia complex (BCC) can cause severe lung infections in patients with cystic fibrosis (CF) or chronic granulomatous disease (CGD). BCC members have also recently been associated with several outbreaks of bacteremia from contaminated pharmaceutical products. Separate from the BCC is Burkholderia pseudomallei, which is the causative agent of melioidosis, a serious disease that occurs in the tropics, and a potential bioterrorism weapon. Bioinformatic analysis of sequenced Burkholderia isolates predicts that most strains have at least 40 TCS. The vast majority of these TCS are uncharacterized both in terms of the signals that activate them and the genes that are regulated by them. This review will highlight TCS that have been described to play a role in virulence in either the BCC or B. pseudomallei Since many of these TCS are involved in virulence, TCS are potential novel therapeutic targets, and elucidating their function is critical for understanding Burkholderia pathogenesis.
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Alwis PA, Treerat P, Gong L, Deveson Lucas D, Allwood EM, Prescott M, Devenish RJ, Adler B, Boyce JD. Disruption of the Burkholderia pseudomallei two-component signal transduction system BbeR-BbeS leads to increased extracellular DNA secretion and altered biofilm formation. Vet Microbiol 2020; 242:108603. [PMID: 32122607 DOI: 10.1016/j.vetmic.2020.108603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
Two-component signal transduction systems (TCSTS) are abundant among prokaryotes and regulate important functions, including drug resistance and virulence. The Gram-negative bacterium Burkholderia pseudomallei, which causes the severe infectious disease melioidosis, encodes 136 putative TCSTS components. In silico analyses of these TCSTS indicated that the predicted BbeR-BbeS system (BPSL1036-BPSL1037) displayed significant amino acid sequence similarity to the Shigella flexneri virulence-associated OmpR-EnvZ osmoregulator. To assess the function of the B. pseudomallei BbeR-BbeS system, we constructed by allelic exchange a ΔbbeRS double mutant strain lacking both genes, and single ΔbbeR and ΔbbeS mutants. All three mutant strains caused disease in the BALB/c acute melioidosis model at the same rate as the wild-type strain, displayed unchanged swarming motility on semi-solid medium, and were unaffected for viability on high-osmolarity media. However, when cultured at 37 °C for at least 14 days, ΔbbeS and ΔbbeR colonies developed a distinct, hypermucoid morphology absent in similarly-cultured wild-type colonies. At both 30 °C and 37 °C, these hypermucoid strains produced wild-type levels of type I capsule but released increased quantities of extracellular DNA (eDNA). Upon static growth in liquid medium, all B. pseudomallei strains produced pellicle biofilms that contained DNA in close association with bacterial cells; however, the ΔbbeS and ΔbbeR strains produced increased biofilms with altered microscopic architecture compared to the wild-type. Unusually, while the ΔbbeS and ΔbbeR single-deletion mutants displayed clear phenotypes, the ΔbbeRS double-deletion mutant was indistinguishable from the wild-type strain. We propose that BbeR-BbeS indirectly affects eDNA secretion and biofilm formation through cross-talk with one or more other TCSTS.
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Affiliation(s)
- Priyangi A Alwis
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Puthayalai Treerat
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Lan Gong
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Elizabeth M Allwood
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Mark Prescott
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Rodney J Devenish
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Ben Adler
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - John D Boyce
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Melbourne, Victoria, Australia.
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate. Appl Environ Microbiol 2019; 85:AEM.01741-18. [PMID: 30478234 PMCID: PMC6344628 DOI: 10.1128/aem.01741-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/17/2018] [Indexed: 01/08/2023] Open
Abstract
Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens. The rhizobacterium Pseudomonas pseudoalcaligenes AVO110, isolated by the enrichment of competitive avocado root tip colonizers, controls avocado white root rot disease caused by Rosellinia necatrix. Here, we applied signature-tagged mutagenesis (STM) during the growth and survival of AVO110 in fungal exudate-containing medium with the goal of identifying the molecular mechanisms linked to the interaction of this bacterium with R. necatrix. A total of 26 STM mutants outcompeted by the parental strain in fungal exudate, but not in rich medium, were selected and named growth-attenuated mutants (GAMs). Twenty-one genes were identified as being required for this bacterial-fungal interaction, including membrane transporters, transcriptional regulators, and genes related to the metabolism of hydrocarbons, amino acids, fatty acids, and aromatic compounds. The bacterial traits identified here that are involved in the colonization of fungal hyphae include proteins involved in membrane maintenance (a dynamin-like protein and ColS) or cyclic-di-GMP signaling and chemotaxis. In addition, genes encoding a DNA helicase (recB) and a regulator of alginate production (algQ) were identified as being required for efficient colonization of the avocado rhizosphere. IMPORTANCE Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens.
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10
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Bochkareva OO, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics 2018; 19:965. [PMID: 30587126 PMCID: PMC6307245 DOI: 10.1186/s12864-018-5245-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/14/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. RESULTS We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. CONCLUSIONS This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
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Affiliation(s)
- Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena V. Moroz
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Iakov I. Davydov
- Department of Ecology and Evolution & Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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Relationships Between Resistance and Virulence in Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0119-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yang P, Zhang M, van Elsas JD. Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil. Sci Rep 2017; 7:2997. [PMID: 28592860 PMCID: PMC5462819 DOI: 10.1038/s41598-017-02959-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/21/2017] [Indexed: 12/25/2022] Open
Abstract
Burkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella. Electron microcopy and motility testing revealed that strain BS001 produces polar flagella and can swim on semi-solid R2A agar. Flagellum- and T4P-negative mutants were then constructed to examine the ecological roles of the respective systems. Both in liquid media and on swimming agar, the mutant strains showed similar fitness to the wild-type strain in mixed culture. The flagellar mutant had completely lost its flagella, as well as its swimming capacity. It also lost its co-migration ability with two soil-exploring fungi, Lyophyllum sp. strain Karsten and Trichoderma asperellum 302, in soil microcosms. In contrast, the T4P mutant showed reduced surface twitching motility, whereas its co-migration ability in competition with the wild-type strain was slightly reduced. We conclude that the co-migration of strain BS001 with fungal hyphae through soil is dependent on the presence of functional flagella conferring swimming motility, with the T4P system having a minor effect.
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Affiliation(s)
- Pu Yang
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Miaozhi Zhang
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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