1
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Yue XJ, Wang JR, Zhao JN, Pan Z, Li YZ. Determination of the chromosomal position effects for plug-and-play application in the Myxococcus xanthus chassis cells. Synth Syst Biotechnol 2024; 9:540-548. [PMID: 38680947 PMCID: PMC11046052 DOI: 10.1016/j.synbio.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024] Open
Abstract
The chromosomal position effect can significantly affect the transgene expression, which may provide an efficient strategy for the inauguration of alien genes in new hosts, but has been less explored rationally. The bacterium Myxococcus xanthus harbors a large circular high-GC genome, and the position effect in this chassis may result in a thousand-fold expression variation of alien natural products. In this study, we conducted transposon insertion at TA sites on the M. xanthus genome, and used enrichment and dilution indexes to respectively appraise high and low expression potentials of alien genes at insertion sites. The enrichment sites are characteristically distributed along the genome, and the dilution sites are overlapped well with the horizontal transfer genes. We experimentally demonstrated the enrichment sites as high expression integration sites (HEISs), and the dilution sites unsuitable for gene integration expression. This work highlights that HEISs are the plug-and-play sites for efficient expression of integrated genes.
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Affiliation(s)
- Xin-jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, PR China
| | - Jia-rui Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, PR China
| | - Jun-ning Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, PR China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, PR China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, PR China
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2
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Lefrançois LH, Nitschke J, Wu H, Panis G, Prados J, Butler RE, Mendum TA, Hanna N, Stewart GR, Soldati T. Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals the genetic requirement for virulence and survival in amoebae and microglial cells. mSystems 2024; 9:e0132623. [PMID: 38270456 PMCID: PMC10878075 DOI: 10.1128/msystems.01326-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Tuberculosis remains the most pervasive infectious disease and the recent emergence of drug-resistant strains emphasizes the need for more efficient drug treatments. A key feature of pathogenesis, conserved between the human pathogen Mycobacterium tuberculosis and the model pathogen Mycobacterium marinum, is the metabolic switch to lipid catabolism and altered expression of virulence genes at different stages of infection. This study aims to identify genes involved in sustaining viable intracellular infection. We applied transposon sequencing (Tn-Seq) to M. marinum, an unbiased genome-wide strategy combining saturation insertional mutagenesis and high-throughput sequencing. This approach allowed us to identify the localization and relative abundance of insertions in pools of transposon mutants. Gene essentiality and fitness cost of mutations were quantitatively compared between in vitro growth and different stages of infection in two evolutionary distinct phagocytes, the amoeba Dictyostelium discoideum and the murine BV2 microglial cells. In the M. marinum genome, 57% of TA sites were disrupted and 568 genes (10.2%) were essential, which is comparable to previous Tn-Seq studies on M. tuberculosis and M. bovis. Major pathways involved in the survival of M. marinum during infection of D. discoideum are related to DNA damage repair, lipid and vitamin metabolism, the type VII secretion system (T7SS) ESX-1, and the Mce1 lipid transport system. These pathways, except Mce1 and some glycolytic enzymes, were similarly affected in BV2 cells. These differences suggest subtly distinct nutrient availability or requirement in different host cells despite the known predominant use of lipids in both amoeba and microglial cells.IMPORTANCEThe emergence of biochemically and genetically tractable host model organisms for infection studies holds the promise to accelerate the pace of discoveries related to the evolution of innate immunity and the dissection of conserved mechanisms of cell-autonomous defenses. Here, we have used the genetically and biochemically tractable infection model system Dictyostelium discoideum/Mycobacterium marinum to apply a genome-wide transposon-sequencing experimental strategy to reveal comprehensively which mutations confer a fitness advantage or disadvantage during infection and compare these to a similar experiment performed using the murine microglial BV2 cells as host for M. marinum to identify conservation of virulence pathways between hosts.
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Affiliation(s)
- Louise H. Lefrançois
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Jahn Nitschke
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Huihai Wu
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
- Bioinformatics Support Platform for data analysis, Geneva University, Medicine Faculty, Geneva, Switzerland
| | - Rachel E. Butler
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Tom A. Mendum
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Nabil Hanna
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Graham R. Stewart
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
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3
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Qin X, Gong M, Li Y, Huo Y, Li D, Li P, Chang X, Li K, Yang H. Psychrophilic phage phiGM22-3 efficiently controls Pseudomonas fluorescens contamination in cold-stored milk. Int J Food Microbiol 2024; 411:110525. [PMID: 38128262 DOI: 10.1016/j.ijfoodmicro.2023.110525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
Pseudomonas fluorescens is a common spoilage causing microbe found in milk. Antibiotic preservatives may cause emergence of multidrug resistance, posing food safety related risks to public health. Phage treatment may be used as an alternative to antibiotics in controlling P. fluorescens contaminations. Here we reported that P. fluorescens phage phiGM22-3 reproduced rapidly over a broad temperature range of 4 through 30°C, and the optimum growth of phiGM22-3 occurred at 10°C, indicating that it was a psychrophilic virus. Genome analysis revealed that phiGM22-3 has a genome of 42,662 bp with an identical terminal direct repeat sequence of 328 bp and encodes 58 predicted proteins. Evidence revealed that phiGM22-3 recognized lipopolysaccharides (LPS) as receptor for infection. Additionally, two phage mutants phiMX2 and phiMX8 with different host ranges were identified in the phiGM22-3 population. Phage killing efficiency of P. fluorescens cells artificially inoculated in milk was evaluated. Phage phiGM22-3 and the cocktails containing phiMX2 and phiMX8 can lyse almost 100% bacterial cells at 4°C within 24 h. Taken together, our data indicated that the psychrophilic virus phiGM22-3 and its two mutants can efficiently inhibit bacteria growth at 4°C, showing a great potential to be used as alternatives to conventional antibiotics against P. fluorescens in refrigerated foods.
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Affiliation(s)
- Xuying Qin
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengxin Gong
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yutong Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yansheng Huo
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Peize Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinxin Chang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Kexin Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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4
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Bourgeois J, Camilli A. High-Throughput Mutant Screening via Transposon Sequencing. Cold Spring Harb Protoc 2023; 2023:707-9. [PMID: 36931734 PMCID: PMC10601705 DOI: 10.1101/pdb.top107867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Transposon mutagenesis has been the method of choice for genetic screens and selections in bacteria by virtue of the transposon being linked to the disrupted gene, simplifying its identification. Transposon sequencing (Tn-seq) is a high-throughput version of transposon mutant screening, in which massively parallel sequencing is used to simultaneously follow the fitness of all mutants in a complex library. In a single experiment, one can use Tn-seq to interrogate the contribution of all genes of a bacterium to fitness under a condition of interest. Here, we introduce a method to construct a saturating transposon insertion library in Gram-negative bacteria, to capture the transposon junctions en masse, and to identify essential genes and conditional genes using massively parallel sequencing. The accompanying protocol was developed as part of Cold Spring Harbor's Advanced Bacterial Genetics course.
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Affiliation(s)
- Jacob Bourgeois
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02067, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02067, USA
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5
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Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2. mSystems 2023; 8:e0117422. [PMID: 36786610 PMCID: PMC10134887 DOI: 10.1128/msystems.01174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Strain inoculation (bioaugmentation) is a potentially useful technology to provide microbiomes with new functionalities. However, there is limited understanding of the genetic factors contributing to successful establishment of inoculants. This work aimed to characterize the genes implicated in proliferation of the monoaromatic compound-degrading Pseudomonas veronii 1YdBTEX2 in nonsterile polluted soils. We generated two independent mutant libraries by random minitransposon-delivered marker insertion followed by deep sequencing (Tn-seq) with a total of 5.0 × 105 unique insertions. Libraries were grown in multiple successive cycles for up to 50 generations either in batch liquid medium or in two types of soil microcosms with different resident microbial content (sand or silt) in the presence of toluene. Analysis of gene insertion abundances at different time points (passed generations of metapopulation growth), in comparison to proportions at start and to in silico generated randomized insertion distributions, allowed to define ~800 essential genes common to both libraries and ~2,700 genes with conditional fitness effects in either liquid or soil (195 of which resulted in fitness gain). Conditional fitness genes largely overlapped among all growth conditions but affected approximately twice as many functions in liquid than in soil. This indicates soil to be a more promiscuous environment for mutant growth, probably because of additional nutrient availability. Commonly depleted genes covered a wide range of biological functions and metabolic pathways, such as inorganic ion transport, fatty acid metabolism, amino acid biosynthesis, or nucleotide and cofactor metabolism. Only sparse gene sets were uncovered whose insertion caused fitness decrease exclusive for soils, which were different between silt and sand. Despite detectable higher resident bacteria and potential protist predatory counts in silt, we were, therefore, unable to detect any immediately obvious candidate genes affecting P. veronii biological competitiveness. In contrast to liquid growth conditions, mutants inactivating flagella biosynthesis and motility consistently gained strong fitness advantage in soils and displayed higher growth rates than wild type. In conclusion, although many gene functions were found to be important for growth in soils, most of these are not specific as they affect growth in liquid minimal medium more in general. This indicates that P. veronii does not need major metabolic reprogramming for proliferation in soil with accessible carbon and generally favorable growth conditions. IMPORTANCE Restoring damaged microbiomes is still a formidable challenge. Classical widely adopted approaches consist of augmenting communities with pure or mixed cultures in the hope that these display their intended selected properties under in situ conditions. Ecological theory, however, dictates that introduction of a nonresident microbe is unlikely to lead to its successful proliferation in a foreign system such as a soil microbiome. In an effort to study this systematically, we used random transposon insertion scanning to identify genes and possibly, metabolic subsystems, that are crucial for growth and survival of a bacterial inoculant (Pseudomonas veronii) for targeted degradation of monoaromatic compounds in contaminated nonsterile soils. Our results indicate that although many gene functions are important for proliferation in soil, they are general factors for growth and not exclusive for soil. In other words, P. veronii is a generalist that is not a priori hindered by the soil for its proliferation and would make a good bioaugmentation candidate.
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6
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Leshchiner D, Rosconi F, Sundaresh B, Rudmann E, Ramirez LMN, Nishimoto AT, Wood SJ, Jana B, Buján N, Li K, Gao J, Frank M, Reeve SM, Lee RE, Rock CO, Rosch JW, van Opijnen T. A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance. Nat Commun 2022; 13:3165. [PMID: 35672367 PMCID: PMC9174251 DOI: 10.1038/s41467-022-30967-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Detailed knowledge on how bacteria evade antibiotics and eventually develop resistance could open avenues for novel therapeutics and diagnostics. It is thereby key to develop a comprehensive genome-wide understanding of how bacteria process antibiotic stress, and how modulation of the involved processes affects their ability to overcome said stress. Here we undertake a comprehensive genetic analysis of how the human pathogen Streptococcus pneumoniae responds to 20 antibiotics. We build a genome-wide atlas of drug susceptibility determinants and generated a genetic interaction network that connects cellular processes and genes of unknown function, which we show can be used as therapeutic targets. Pathway analysis reveals a genome-wide atlas of cellular processes that can make a bacterium less susceptible, and often tolerant, in an antibiotic specific manner. Importantly, modulation of these processes confers fitness benefits during active infections under antibiotic selection. Moreover, screening of sequenced clinical isolates demonstrates that mutations in genes that decrease antibiotic sensitivity and increase tolerance readily evolve and are frequently associated with resistant strains, indicating such mutations could be harbingers for the emergence of antibiotic resistance.
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Affiliation(s)
| | - Federico Rosconi
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Andrew T Nishimoto
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen J Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Bimal Jana
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Noemí Buján
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Kaicheng Li
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Matthew Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephanie M Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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7
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Dammann AN, Chamby AB, Catomeris AJ, Davidson KM, Tettelin H, van Pijkeren JP, Gopalakrishna KP, Keith MF, Elder JL, Ratner AJ, Hooven TA. Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits. PLoS Pathog 2021; 17:e1009116. [PMID: 33684178 PMCID: PMC7971860 DOI: 10.1371/journal.ppat.1009116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/18/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Streptococcus agalactiae (group B Streptococcus; GBS) remains a dominant cause of serious neonatal infections. One aspect of GBS that renders it particularly virulent during the perinatal period is its ability to invade the chorioamniotic membranes and persist in amniotic fluid, which is nutritionally deplete and rich in fetal immunologic factors such as antimicrobial peptides. We used next-generation sequencing of transposon-genome junctions (Tn-seq) to identify five GBS genes that promote survival in the presence of human amniotic fluid. We confirmed our Tn-seq findings using a novel CRISPR inhibition (CRISPRi) gene expression knockdown system. This analysis showed that one gene, which encodes a GntR-class transcription factor that we named MrvR, conferred a significant fitness benefit to GBS in amniotic fluid. We generated an isogenic targeted deletion of the mrvR gene, which had a growth defect in amniotic fluid relative to the wild type parent strain. The mrvR deletion strain also showed a significant biofilm defect in vitro. Subsequent in vivo studies showed that while the mutant was able to cause persistent murine vaginal colonization, pregnant mice colonized with the mrvR deletion strain did not develop preterm labor despite consistent GBS invasion of the uterus and the fetoplacental units. In contrast, pregnant mice colonized with wild type GBS consistently deliver prematurely. In a sepsis model the mrvR deletion strain showed significantly decreased lethality. In order to better understand the mechanism by which this newly identified transcription factor controls GBS virulence, we performed RNA-seq on wild type and mrvR deletion GBS strains, which revealed that the transcription factor affects expression of a wide range of genes across the GBS chromosome. Nucleotide biosynthesis and salvage pathways were highly represented among the set of differentially expressed genes, suggesting that MrvR may be involved in regulating nucleotide availability. Group B Streptococcus (GBS) is a species of Gram-positive bacteria that often colonizes the healthy adult intestinal and reproductive tracts without causing serious symptoms. During pregnancy, however, GBS can invade the pregnant uterus, where it can cause infection of the placenta, fetal membranes, and fetus—a condition known as chorioamnionitis. Chorioamnionitis is associated with serious adverse pregnancy outcomes, including stillbirth, preterm labor, and severe infection of the newborn. GBS can survive in human amniotic fluid, which is low in bacterial nutrients and contains immune molecules that limit microbial persistence, and this ability likely contributes to GBS chorioamnionitis. This study is focused on a single GBS gene that encodes a genetic regulator we called MrvR, which we show is important for GBS resistance to human amniotic fluid. Using a series of genetic techniques combined with animal models of GBS colonization and infection, we show that MrvR also plays a key role in allowing GBS to invade the bloodstream and trigger the inflammatory responses that lead to preterm labor and stillbirth. The study concludes with a survey of other GBS genes whose activity is regulated by MrvR, which seems to be an important contributor to GBS virulence.
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Affiliation(s)
- Allison N. Dammann
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
| | - Anna B. Chamby
- University of Vermont Larner College of Medicine, Burlington, Vermont, United States of America
| | - Andrew J. Catomeris
- Georgetown University School of Medicine, Washington, District of Columbia, United States of America
| | - Kyle M. Davidson
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hervé Tettelin
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kathyayini P. Gopalakrishna
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Mary F. Keith
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jordan L. Elder
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Adam J. Ratner
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University, New York, New York, United States of America
| | - Thomas A. Hooven
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Richard King Mellon Institute for Pediatric Research, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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8
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Zhu Z, Surujon D, Ortiz-Marquez JC, Huo W, Isberg RR, Bento J, van Opijnen T. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nat Commun 2020; 11:4365. [PMID: 32868761 PMCID: PMC7458919 DOI: 10.1038/s41467-020-18134-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.
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Affiliation(s)
- Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - José Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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9
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Transposon Mutagenesis Screen of Klebsiella pneumoniae Identifies Multiple Genes Important for Resisting Antimicrobial Activities of Neutrophils in Mice. Infect Immun 2020; 88:IAI.00034-20. [PMID: 31988174 DOI: 10.1128/iai.00034-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/25/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterial pathogen that causes a range of infections, including pneumonias, urinary tract infections, and septicemia, in otherwise healthy and immunocompromised patients. K. pneumoniae has become an increasing concern due to the rise and spread of antibiotic-resistant and hypervirulent strains. However, its virulence determinants remain understudied. To identify novel K. pneumoniae virulence factors needed to cause pneumonia, a high-throughput screen was performed with an arrayed library of over 13,000 K. pneumoniae transposon insertion mutants in the lungs of wild-type (WT) and neutropenic mice using transposon sequencing (Tn-seq). Insertions in 166 genes resulted in K. pneumoniae mutants that were significantly less fit in the lungs of WT mice than in those of neutropenic mice. Of these, mutants with insertions in 51 genes still had significant defects in neutropenic mice, while mutants with insertions in 52 genes recovered significantly. In vitro screens using a minilibrary of K. pneumoniae transposon mutants identified putative functions for a subset of these genes, including in capsule content and resistance to reactive oxygen and nitrogen species. Lung infections in mice confirmed roles in K. pneumoniae virulence for the ΔdedA, ΔdsbC, ΔgntR, Δwzm-wzt, ΔyaaA, and ΔycgE mutants, all of which were defective in either capsule content or growth in reactive oxygen or nitrogen species. The fitness of the ΔdedA, ΔdsbC, ΔgntR, ΔyaaA, and ΔycgE mutants was higher in neutropenic mouse lungs, indicating that these genes encode proteins that protect K. pneumoniae against neutrophil-related effector functions.
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10
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Adaptation to Adversity: the Intermingling of Stress Tolerance and Pathogenesis in Enterococci. Microbiol Mol Biol Rev 2019; 83:83/3/e00008-19. [PMID: 31315902 DOI: 10.1128/mmbr.00008-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enterococcus is a diverse and rugged genus colonizing the gastrointestinal tract of humans and numerous hosts across the animal kingdom. Enterococci are also a leading cause of multidrug-resistant hospital-acquired infections. In each of these settings, enterococci must contend with changing biophysical landscapes and innate immune responses in order to successfully colonize and transit between hosts. Therefore, it appears that the intrinsic durability that evolved to make enterococci optimally competitive in the host gastrointestinal tract also ideally positioned them to persist in hospitals, despite disinfection protocols, and acquire new antibiotic resistances from other microbes. Here, we discuss the molecular mechanisms and regulation employed by enterococci to tolerate diverse stressors and highlight the role of stress tolerance in the biology of this medically relevant genus.
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11
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Rowe HM, Karlsson E, Echlin H, Chang TC, Wang L, van Opijnen T, Pounds SB, Schultz-Cherry S, Rosch JW. Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts. Cell Host Microbe 2019; 25:884-891.e6. [PMID: 31126758 DOI: 10.1016/j.chom.2019.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/18/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023]
Abstract
The capacity of Streptococcus pneumoniae to successfully transmit and colonize new human hosts is a critical aspect of pneumococcal population biology and a prerequisite for invasive disease. However, the bacterial mechanisms underlying this process remain largely unknown. To identify bacterial factors required for transmission, we conducted a high-throughput genetic screen with a transposon sequencing (Tn-seq) library of a pneumococcal strain in a ferret transmission model. Key players in both metabolism and transcriptional regulation were identified as required for efficient bacterial transmission. Targeted deletion of the putative C3-degrading protease CppA, iron transporter PiaA, or competence regulatory histidine kinase ComD significantly decreased transmissibility in a mouse model, further validating the screen. Maternal vaccination with recombinant surface-exposed PiaA and CppA alone or in combination blocked transmission in offspring and were more effective than capsule-based vaccines. These data underscore the possibility of targeting pneumococcal transmission as a means of eliminating invasive disease in the population.
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Affiliation(s)
- Hannah M Rowe
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Wang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA.
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12
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Bennett BD, Redford KE, Gralnick JA. Survival of Anaerobic Fe 2+ Stress Requires the ClpXP Protease. J Bacteriol 2018; 200:e00671-17. [PMID: 29378887 PMCID: PMC5869471 DOI: 10.1128/jb.00671-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis strain MR-1 is a versatile bacterium capable of respiring extracellular, insoluble ferric oxide minerals under anaerobic conditions. The respiration of iron minerals results in the production of soluble ferrous ions, which at high concentrations are toxic to living organisms. It is not fully understood how Fe2+ is toxic to cells anaerobically, nor is it fully understood how S. oneidensis is able to resist high levels of Fe2+ Here we describe the results of a transposon mutant screen and subsequent deletion of the genes clpX and clpP in S. oneidensis, which demonstrate that the protease ClpXP is required for anaerobic Fe2+ resistance. Many cellular processes are known to be regulated by ClpXP, including entry into stationary phase, envelope stress response, and turnover of stalled ribosomes. However, none of these processes appears to be responsible for mediating anaerobic Fe2+ resistance in S. oneidensis Protein trapping studies were performed to identify ClpXP targets in S. oneidensis under Fe2+ stress, implicating a wide variety of protein targets. Escherichia coli strains lacking clpX or clpP also display increased sensitivity to Fe2+ anaerobically, indicating Fe2+ resistance may be a conserved role for the ClpXP protease system. Hypotheses regarding the potential role(s) of ClpXP during periods of high Fe2+ are discussed. We speculate that metal-containing proteins are misfolded under conditions of high Fe2+ and that the ClpXP protease system is necessary for their turnover.IMPORTANCE Prior to the evolution of cyanobacteria and oxygenic photosynthesis, life arose and flourished in iron-rich oceans. Today, aqueous iron-rich environments are less common, constrained to low-pH conditions and anaerobic systems such as stratified lakes and seas, digestive tracts, subsurface environments, and sediments. The latter two ecosystems often favor dissimilatory metal reduction, a process that produces soluble Fe2+ from iron oxide minerals. Dissimilatory metal-reducing bacteria must therefore have mechanisms to tolerate anaerobic Fe2+ stress, and studying resistance in these organisms may help elucidate the basis of toxicity. Shewanella oneidensis is a model dissimilatory metal-reducing bacterium isolated from metal-rich sediments. Here we demonstrate a role for ClpXP, a protease system widely conserved in bacteria, in anaerobic Fe2+ resistance in both S. oneidensis and Escherichia coli.
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Affiliation(s)
- Brittany D Bennett
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Kaitlyn E Redford
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
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13
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Shields RC, Zeng L, Culp DJ, Burne RA. Genomewide Identification of Essential Genes and Fitness Determinants of Streptococcus mutans UA159. mSphere 2018; 3:e00031-18. [PMID: 29435491 PMCID: PMC5806208 DOI: 10.1128/msphere.00031-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 11/20/2022] Open
Abstract
Transposon mutagenesis coupled with next-generation DNA sequencing (Tn-seq) is a powerful tool for discovering regions of the genome that are required for the survival of bacteria in different environments. We adapted this technique to the dental caries pathogen Streptococcus mutans UA159 and identified 11% of the genome as essential, with many genes encoding products required for replication, translation, lipid metabolism, and cell wall biogenesis. Comparison of the essential genome of S. mutans UA159 with those of selected other streptococci for which such information is available revealed several metabolic pathways and genes that are required in S. mutans, but not in some Streptococcus spp. We further identified genes that are essential for sustained growth in rich or defined medium, as well as for persistence in vivo in a rodent model of oral infection. Collectively, our results provide a novel and comprehensive view of the genes required for essential processes of S. mutans, many of which could represent potential targets for therapeutics. IMPORTANCE Tooth decay (dental caries) is a common cause of pain, impaired quality of life, and tooth loss in children and adults. It begins because of a compositional change in the microorganisms that colonize the tooth surface driven by repeated and sustained carbohydrate intake. Although several bacterial species are associated with tooth decay, Streptococcus mutans is the most common cause. Therefore, it is important to identify biological processes that contribute to the survival of S. mutans in the human mouth, with the aim of disrupting the processes with antimicrobial agents. We successfully applied Tn-seq to S. mutans, discovering genes that are required for survival, growth, and persistence, both in laboratory environments and in a mouse model of tooth decay. This work highlights new avenues for the control of an important human pathogen.
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Affiliation(s)
- Robert C. Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Lin Zeng
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - David J. Culp
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
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14
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Genome-Wide Screens Reveal New Gene Products That Influence Genetic Competence in Streptococcus mutans. J Bacteriol 2017; 200:JB.00508-17. [PMID: 29109185 DOI: 10.1128/jb.00508-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/26/2017] [Indexed: 12/11/2022] Open
Abstract
A network of genes and at least two peptide signaling molecules tightly control when Streptococcus mutans becomes competent to take up DNA from its environment. Widespread changes in the expression of genes occur when S. mutans is presented with competence signal peptides in vitro, including the increased production of the alternative sigma factor, ComX, which activates late competence genes. Still, the way that gene products that are regulated by competence peptides influence DNA uptake and cellular physiology are not well understood. Here, we developed and employed comprehensive transposon mutagenesis of the S. mutans genome, with a screen to identify mutants that aberrantly expressed comX, coupled with transposon sequencing (Tn-seq) to gain a more thorough understanding of the factors modulating comX expression and progression to the competent state. The screens effectively identified genes known to affect competence, e.g., comR, comS, comD, comE, cipB, clpX, rcrR, and ciaH, but disclosed an additional 20 genes that were not previously competence associated. The competence phenotypes of mutants were characterized, including by fluorescence microscopy to determine at which stage the mutants were impaired for comX activation. Among the novel genes studied were those implicated in cell division, the sensing of cell envelope stress, cell envelope biogenesis, and RNA stability. Our results provide a platform for determining the specific chemical and physical cues that are required for genetic competence in S. mutans, while highlighting the effectiveness of using Tn-seq in S. mutans to discover and study novel biological processes.IMPORTANCE Streptococcus mutans acquires DNA from its environment by becoming genetically competent, a physiologic state triggered by cell-cell communication using secreted peptides. Competence is important for acquiring novel genetic traits and has a strong influence on the expression of virulence-associated traits of S. mutans Here, we used transposon mutagenesis and genomic technologies to identify novel genes involved in competence development. In addition to identifying genes previously known to be required for comX expression, 20 additional genes were identified and characterized. The findings create opportunities to diminish the pathogenic potential of S. mutans, while validating technologies that can rapidly advance our understanding of the physiology, biology, and genetics of S. mutans and related pathogens.
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15
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The Streptococcus agalactiae Stringent Response Enhances Virulence and Persistence in Human Blood. Infect Immun 2017; 86:IAI.00612-17. [PMID: 29109175 PMCID: PMC5736797 DOI: 10.1128/iai.00612-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) causes serious infections in neonates. We previously reported a transposon sequencing (Tn-seq) system for performing genomewide assessment of gene fitness in GBS. In order to identify molecular mechanisms required for GBS to transition from a mucosal commensal lifestyle to bloodstream invasion, we performed Tn-seq on GBS strain A909 with human whole blood. Our analysis identified 16 genes conditionally essential for GBS survival in blood, of which 75% were members of the capsular polysaccharide (cps) operon. Among the non-cps genes identified as conditionally essential was relA, which encodes an enzyme whose activity is central to the bacterial stringent response—a conserved adaptation to environmental stress. We used blood coincubation studies of targeted knockout strains to confirm the expected growth defects of GBS deficient in capsule or stringent response activation. Unexpectedly, we found that the relA knockout strains demonstrated decreased expression of β-hemolysin/cytolysin, an important cytotoxin implicated in facilitating GBS invasion. Furthermore, chemical activation of the stringent response with serine hydroxamate increased β-hemolysin/cytolysin expression. To establish a mechanism by which the stringent response leads to increased cytotoxicity, we performed transcriptome sequencing (RNA-seq) on two GBS strains grown under stringent response or control conditions. This revealed a conserved decrease in the expression of genes in the arginine deiminase pathway during stringent response activation. Through coincubation with supplemental arginine and the arginine antagonist canavanine, we show that arginine availability is a determinant of GBS cytotoxicity and that the pathway between stringent response activation and increased virulence is arginine dependent.
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16
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Genome Scale Mutational Analysis of Geobacter sulfurreducens Reveals Distinct Molecular Mechanisms for Respiration and Sensing of Poised Electrodes versus Fe(III) Oxides. J Bacteriol 2017; 199:JB.00340-17. [PMID: 28674067 PMCID: PMC5585712 DOI: 10.1128/jb.00340-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/23/2017] [Indexed: 12/11/2022] Open
Abstract
Geobacter sulfurreducens generates electrical current by coupling intracellular oxidation of organic acids to the reduction of proteins on the cell surface that are able to interface with electrodes. This ability is attributed to the bacterium's capacity to respire other extracellular electron acceptors that require contact, such as insoluble metal oxides. To directly investigate the genetic basis of electrode-based respiration, we constructed Geobacter sulfurreducens transposon-insertion sequencing (Tn-Seq) libraries for growth, with soluble fumarate or an electrode as the electron acceptor. Libraries with >33,000 unique insertions and an average of 9 insertions/kb allowed an assessment of each gene's fitness in a single experiment. Mutations in 1,214 different genomic features impaired growth with fumarate, and the significance of 270 genes unresolved by annotation due to the presence of one or more functional homologs was determined. Tn-Seq analysis of −0.1 V versus standard hydrogen electrode (SHE) electrode-grown cells identified mutations in a subset of genes encoding cytochromes, processing systems for proline-rich proteins, sensory networks, extracellular structures, polysaccharides, and metabolic enzymes that caused at least a 50% reduction in apparent growth rate. Scarless deletion mutants of select genes identified via Tn-Seq revealed a new putative porin-cytochrome conduit complex (extABCD) crucial for growth with electrodes, which was not required for Fe(III) oxide reduction. In addition, four mutants lacking components of a putative methyl-accepting chemotaxis–cyclic dinucleotide sensing network (esnABCD) were defective in electrode colonization but grew normally with Fe(III) oxides. These results suggest that G. sulfurreducens possesses distinct mechanisms for recognition, colonization, and reduction of electrodes compared to Fe(III) oxides. IMPORTANCE Since metal oxide electron acceptors are insoluble, one hypothesis is that cells sense and reduce metals using the same molecular mechanisms used to form biofilms on electrodes and produce electricity. However, by simultaneously comparing thousands of Geobacter sulfurreducens transposon mutants undergoing electrode-dependent respiration, we discovered new cytochromes and chemosensory proteins supporting growth with electrodes that are not required for metal respiration. This supports an emerging model where G. sulfurreducens recognizes surfaces and forms conductive biofilms using mechanisms distinct from those used for growth with metal oxides. These findings provide a possible explanation for studies that correlate electricity generation with syntrophic interspecies electron transfer by Geobacter and reveal many previously unrecognized targets for engineering this useful capability in other organisms.
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17
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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18
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Peng X, Zhang Y, Bai G, Zhou X, Wu H. Cyclic di-AMP mediates biofilm formation. Mol Microbiol 2016; 99:945-59. [PMID: 26564551 PMCID: PMC5003771 DOI: 10.1111/mmi.13277] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 12/27/2022]
Abstract
Cyclic di-AMP (c-di-AMP) is an emerging second messenger in bacteria. It has been shown to play important roles in bacterial fitness and virulence. However, transduction of c-di-AMP signaling in bacteria and the role of c-di-AMP in biofilm formation are not well understood. The level of c-di-AMP is modulated by activity of di-adenylyl cyclase that produces c-di-AMP and phosphodiesterase (PDE) that degrades c-di-AMP. In this study, we determined that increased c-di-AMP levels by deletion of the pdeA gene coding for a PDE promoted biofilm formation in Streptococcus mutans. Deletion of pdeA upregulated expression of gtfB, the gene coding for a major glucan producing enzyme. Inactivation of gtfB blocked the increased biofilm by the pdeA mutant. Two c-di-AMP binding proteins including CabPA (SMU_1562) and CabPB (SMU_1708) were identified. Interestingly, only CabPA deficiency inhibited both the increased biofilm formation and the upregulated expression of GtfB observed in the pdeA mutant. In addition, CabPA but not CabPB interacted with VicR, a known transcriptional factor that regulates expression of gtfB, suggesting that a signaling link between CabPA and GtfB through VicR. Increased biofilm by the pdeA deficiency also enhanced bacterial colonization of Drosophila in vivo. Taken together, our studies reveal a new role of c-di-AMP in mediating biofilm formation through a CabPA/VicR/GtfB signaling network in S. mutans.
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Affiliation(s)
- Xian Peng
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, AL, USA
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
| | - Yang Zhang
- Center for Immunology and Microbial Disease, MC-151, Albany Medical College, 47 New Scotland Avenue, Albany, NY, USA
| | - Guangchun Bai
- Center for Immunology and Microbial Disease, MC-151, Albany Medical College, 47 New Scotland Avenue, Albany, NY, USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, AL, USA
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19
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van der Beek SL, Le Breton Y, Ferenbach AT, Chapman RN, van Aalten DMF, Navratilova I, Boons GJ, McIver KS, van Sorge NM, Dorfmueller HC. GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD). Mol Microbiol 2015; 98:946-62. [PMID: 26278404 PMCID: PMC4832382 DOI: 10.1111/mmi.13169] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 12/29/2022]
Abstract
The sugar nucleotide dTDP‐L‐rhamnose is critical for the biosynthesis of the Group A Carbohydrate, the molecular signature and virulence determinant of the human pathogen Group A Streptococcus (GAS). The final step of the four‐step dTDP‐L‐rhamnose biosynthesis pathway is catalyzed by dTDP‐4‐dehydrorhamnose reductases (RmlD). RmlD from the Gram‐negative bacterium Salmonella is the only structurally characterized family member and requires metal‐dependent homo‐dimerization for enzymatic activity. Using a biochemical and structural biology approach, we demonstrate that the only RmlD homologue from GAS, previously renamed GacA, functions in a novel monomeric manner. Sequence analysis of 213 Gram‐negative and Gram‐positive RmlD homologues predicts that enzymes from all Gram‐positive species lack a dimerization motif and function as monomers. The enzymatic function of GacA was confirmed through heterologous expression of gacA in a S. mutans rmlD knockout, which restored attenuated growth and aberrant cell division. Finally, analysis of a saturated mutant GAS library using Tn‐sequencing and generation of a conditional‐expression mutant identified gacA as an essential gene for GAS. In conclusion, GacA is an essential monomeric enzyme in GAS and representative of monomeric RmlD enzymes in Gram‐positive bacteria and a subset of Gram‐negative bacteria. These results will help future screens for novel inhibitors of dTDP‐L‐rhamnose biosynthesis.
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Affiliation(s)
- Samantha L van der Beek
- University Medical Center Utrecht, Medical Microbiology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, 3124 Biosciences Research Building, College Park, MD 20742, USA
| | - Andrew T Ferenbach
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Robert N Chapman
- Complex Carbohydrate Research Center, Department of Chemistry, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Daan M F van Aalten
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Iva Navratilova
- Division of Biological Chemistry and Drug Discovery, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, Department of Chemistry, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, 3124 Biosciences Research Building, College Park, MD 20742, USA
| | - Nina M van Sorge
- University Medical Center Utrecht, Medical Microbiology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK.,Rutherford Appleton Laboratory, Research Complex at Harwell, OX11 0FA, Didcot, UK
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20
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Gray AN, Koo BM, Shiver AL, Peters JM, Osadnik H, Gross CA. High-throughput bacterial functional genomics in the sequencing era. Curr Opin Microbiol 2015; 27:86-95. [PMID: 26336012 DOI: 10.1016/j.mib.2015.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/17/2023]
Abstract
High-throughput functional genomic technologies are accelerating progress in understanding the diversity of bacterial life and in developing a systems-level understanding of model bacterial organisms. Here we highlight progress in deep-sequencing-based functional genomics, show how whole genome sequencing is enabling phenotyping in organisms recalcitrant to genetic approaches, recount the rapid proliferation of functional genomic approaches to non-growth phenotypes, and discuss how advances are enabling genome-scale resource libraries for many different bacteria.
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Affiliation(s)
- Andrew N Gray
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Anthony L Shiver
- Graduate Group in Biophysics, University of California, San Francisco, CA 94158, USA
| | - Jason M Peters
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158, USA.
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21
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Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries. PLoS One 2015; 10:e0126070. [PMID: 25938432 PMCID: PMC4418687 DOI: 10.1371/journal.pone.0126070] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/28/2015] [Indexed: 11/28/2022] Open
Abstract
Tn-seq is a high throughput technique for analysis of transposon mutant libraries. Tn-seq Explorer was developed as a convenient and easy-to-use package of tools for exploration of the Tn-seq data. In a typical application, the user will have obtained a collection of sequence reads adjacent to transposon insertions in a reference genome. The reads are first aligned to the reference genome using one of the tools available for this task. Tn-seq Explorer reads the alignment and the gene annotation, and provides the user with a set of tools to investigate the data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. Emphasis is placed on providing flexibility in selecting parameters and methodology most appropriate for each particular dataset. Tn-seq Explorer is written in Java as a menu-driven, stand-alone application. It was tested on Windows, Mac OS, and Linux operating systems. The source code is distributed under the terms of GNU General Public License. The program and the source code are available for download at http://www.cmbl.uga.edu/downloads/programs/Tn_seq_Explorer/ and https://github.com/sina-cb/Tn-seqExplorer.
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22
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Carter R, Wolf J, van Opijnen T, Muller M, Obert C, Burnham C, Mann B, Li Y, Hayden RT, Pestina T, Persons D, Camilli A, Flynn PM, Tuomanen EI, Rosch JW. Genomic analyses of pneumococci from children with sickle cell disease expose host-specific bacterial adaptations and deficits in current interventions. Cell Host Microbe 2015; 15:587-599. [PMID: 24832453 DOI: 10.1016/j.chom.2014.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/10/2014] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Sickle cell disease (SCD) patients are at high risk of contracting pneumococcal infection. To address this risk, they receive pneumococcal vaccines, and antibiotic prophylaxis and treatment. To assess the impact of SCD and these interventions on pneumococcal genetic architecture, we examined the genomes of more than 300 pneumococcal isolates from SCD patients over 20 years. Modern SCD strains retained invasive capacity but shifted away from the serotypes used in vaccines. These strains had specific genetic changes related to antibiotic resistance, capsule biosynthesis, metabolism, and metal transport. A murine SCD model coupled with Tn-seq mutagenesis identified 60 noncapsular pneumococcal genes under differential selective pressure in SCD, which correlated with aspects of SCD pathophysiology. Further, virulence determinants in the SCD context were distinct from the general population, and protective capacity of potential antigens was lost over time in SCD. This highlights the importance of understanding bacterial pathogenesis in the context of high-risk individuals.
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Affiliation(s)
- Robert Carter
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tim van Opijnen
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Martha Muller
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Caroline Obert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Corinna Burnham
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Yimei Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tamara Pestina
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Derek Persons
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Andrew Camilli
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA.,Howard Hughes Medical Institute, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Patricia M Flynn
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
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Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 2015; 1279:79-95. [PMID: 25636614 DOI: 10.1007/978-1-4939-2398-4_6] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transposon sequencing (TnSeq) is a next-generation deep sequencing-based method to quantitatively assess the composition of complex mutant transposon libraries after pressure from selection. Although this method can be used for any organism in which transposon mutagenesis is possible, this chapter describes its use in Mycobacterium tuberculosis. More specifically, the methods for generating complex libraries through transposon mutagenesis, design of selective pressure, extraction of genomic DNA, amplification and quantification of transposon insertions through next-generation deep sequencing are covered. Determining gene essentiality and statistical analysis on data collected are also discussed.
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Affiliation(s)
- Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
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24
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Johnson CM, Grossman AD. Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis. Mol Microbiol 2014; 93:1284-301. [PMID: 25069588 DOI: 10.1111/mmi.12736] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2014] [Indexed: 01/28/2023]
Abstract
Conjugation, a major type of horizontal gene transfer in bacteria, involves transfer of DNA from a donor to a recipient using donor-encoded conjugation machinery. Using a high-throughput screen (Tn-seq), we identified genes in recipients that contribute to acquisition of the integrative and conjugative element ICEBs1 by Bacillus subtilis. We found that null mutations in some genes caused an increase, and others a decrease in conjugation efficiency. Some mutations affected conjugation only when present in recipients. Other mutations affected conjugation when present in donors or recipients. Most of the genes identified are known or predicted to affect the cell envelope. Several encode enzymes involved in phospholipid biosynthesis and one encodes a homologue of penicillin-binding proteins. Two of the genes identified also affected conjugation of Tn916, indicating that their roles in conjugation may be general. We did not identify any genes in recipients that were essential for ICEBs1 conjugation, indicating that if there are such genes, then these are either essential for cell growth or redundant. Our results indicate that acquisition of ICEBs1, and perhaps other conjugative elements, is robust and not easily avoided by mutation and that several membrane-related functions affect the efficiency of conjugation.
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Affiliation(s)
- Christopher M Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Gao B, Lara-Tejero M, Lefebre M, Goodman AL, Galán JE. Novel components of the flagellar system in epsilonproteobacteria. mBio 2014; 5:e01349-14. [PMID: 24961693 PMCID: PMC4073491 DOI: 10.1128/mbio.01349-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Motility is essential for the pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a cell wall-anchored motor using chemical energy. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant differences in the flagellar structures of different bacterial species. The molecular bases for these differences, however, are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. Using next-generation sequencing combined with transposon mutagenesis, we have conducted a comprehensive high-throughput genetic screen in Campylobacter jejuni, which identified several novel components of its flagellar system. Biochemical analyses detected interactions between the identified proteins and known components of the flagellar machinery, and in vivo imaging located them to the bacterial poles, where flagella assemble. Most of the identified new components are conserved within but restricted to epsilonproteobacteria. These studies provide insight into the divergent flagella of this group of bacteria and highlight the complexity of this remarkable structure, which has adapted to carry out its conserved functions in the context of widely diverse bacterial species. IMPORTANCE Motility is essential for the normal physiology and pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a motor that uses chemical energy as fuel. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant divergence in the flagellar structures across bacterial species. However, the molecular bases for these differences are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. We conducted a comprehensive genetic screen in Campylobacter jejuni and identified several novel components of the flagellar system. These studies provide important information to understand how flagella have adapted to function in the context of widely diverse sets of bacterial species and bring unique insight into the evolution and function of this remarkable bacterial organelle.
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Affiliation(s)
- Beile Gao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Maria Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Matthew Lefebre
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, Luan HH, Nguyen N, Nelson SF, Li X, Wu TT, Sun R. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep 2014; 4:4942. [PMID: 24820965 PMCID: PMC4018626 DOI: 10.1038/srep04942] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/16/2014] [Indexed: 01/12/2023] Open
Abstract
Genetic research on influenza virus biology has been informed in large part by nucleotide variants present in seasonal or pandemic samples, or individual mutants generated in the laboratory, leaving a substantial part of the genome uncharacterized. Here, we have developed a single-nucleotide resolution genetic approach to interrogate the fitness effect of point mutations in 98% of the amino acid positions in the influenza A virus hemagglutinin (HA) gene. Our HA fitness map provides a reference to identify indispensable regions to aid in drug and vaccine design as targeting these regions will increase the genetic barrier for the emergence of escape mutations. This study offers a new platform for studying genome dynamics, structure-function relationships, virus-host interactions, and can further rational drug and vaccine design. Our approach can also be applied to any virus that can be genetically manipulated.
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Affiliation(s)
- Nicholas C Wu
- 1] Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA [2] Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA [3]
| | - Arthur P Young
- 1] Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA [2]
| | - Laith Q Al-Mawsawi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - C Anders Olson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jun Feng
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Hangfei Qi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - I-Hsuan Lu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Robert G Chin
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Harding H Luan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Nguyen Nguyen
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- 1] Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA [2] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ren Sun
- 1] Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA [2] Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA [3] AIDS Institute, University of California, Los Angeles, CA 90095, USA
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Yuen GJ, Ausubel FM. Enterococcus infection biology: lessons from invertebrate host models. J Microbiol 2014; 52:200-10. [PMID: 24585051 PMCID: PMC4556283 DOI: 10.1007/s12275-014-4011-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 01/21/2014] [Indexed: 12/29/2022]
Abstract
The enterococci are commensals of the gastrointestinal tract of many metazoans, from insects to humans. While they normally do not cause disease in the intestine, they can become pathogenic when they infect sites outside of the gut. Recently, the enterococci have become important nosocomial pathogens, with the majority of human enterococcal infections caused by two species, Enterococcus faecalis and Enterococcus faecium. Studies using invertebrate infection models have revealed insights into the biology of enterococcal infections, as well as general principles underlying host innate immune defense. This review highlights recent findings on Enterococcus infection biology from two invertebrate infection models, the greater wax moth Galleria mellonella and the free-living bacteriovorous nematode Caenorhabditis elegans.
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Affiliation(s)
- Grace J. Yuen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. mBio 2014; 5:e00926-13. [PMID: 24520057 PMCID: PMC3950516 DOI: 10.1128/mbio.00926-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, an often fatal infectious disease for which there is no vaccine. B. pseudomallei is listed as a tier 1 select agent, and as current therapeutic options are limited due to its natural resistance to most antibiotics, the development of new antimicrobial therapies is imperative. To identify drug targets and better understand the complex B. pseudomallei genome, we sought a genome-wide approach to identify lethal gene targets. As B. pseudomallei has an unusually large genome spread over two chromosomes, an extensive screen was required to achieve a comprehensive analysis. Here we describe transposon-directed insertion site sequencing (TraDIS) of a library of over 106 transposon insertion mutants, which provides the level of genome saturation required to identify essential genes. Using this technique, we have identified a set of 505 genes that are predicted to be essential in B. pseudomallei K96243. To validate our screen, three genes predicted to be essential, pyrH, accA, and sodB, and a gene predicted to be nonessential, bpss0370, were independently investigated through the generation of conditional mutants. The conditional mutants confirmed the TraDIS predictions, showing that we have generated a list of genes predicted to be essential and demonstrating that this technique can be used to analyze complex genomes and thus be more widely applied. Burkholderia pseudomallei is a lethal human pathogen that is considered a potential bioterrorism threat and has limited treatment options due to an unusually high natural resistance to most antibiotics. We have identified a set of genes that are required for bacterial growth and thus are excellent candidates against which to develop potential novel antibiotics. To validate our approach, we constructed four mutants in which gene expression can be turned on and off conditionally to confirm that these genes are required for the bacteria to survive.
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Kamp HD, Patimalla-Dipali B, Lazinski DW, Wallace-Gadsden F, Camilli A. Gene fitness landscapes of Vibrio cholerae at important stages of its life cycle. PLoS Pathog 2013; 9:e1003800. [PMID: 24385900 PMCID: PMC3873450 DOI: 10.1371/journal.ppat.1003800] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022] Open
Abstract
Vibrio cholerae has evolved to adeptly transition between the human small intestine and aquatic environments, leading to water-borne spread and transmission of the lethal diarrheal disease cholera. Using a host model that mimics the pathology of human cholera, we applied high density transposon mutagenesis combined with massively parallel sequencing (Tn-seq) to determine the fitness contribution of >90% of all non-essential genes of V. cholerae both during host infection and dissemination. Targeted mutagenesis and validation of 35 genes confirmed our results for the selective conditions with a total false positive rate of 4%. We identified 165 genes never before implicated for roles in dissemination that reside within pathways controlling many metabolic, catabolic and protective processes, from which a central role for glycogen metabolism was revealed. We additionally identified 76 new pathogenicity factors and 414 putatively essential genes for V. cholerae growth. Our results provide a comprehensive framework for understanding the biology of V. cholerae as it colonizes the small intestine, elicits profuse secretory diarrhea, and disseminates into the aquatic environment.
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Affiliation(s)
- Heather D. Kamp
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Bharathi Patimalla-Dipali
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - David W. Lazinski
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Faith Wallace-Gadsden
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Andrew Camilli
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
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van Opijnen T, Camilli A. Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat Rev Microbiol 2013; 11:435-42. [PMID: 23712350 PMCID: PMC3842022 DOI: 10.1038/nrmicro3033] [Citation(s) in RCA: 333] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Our knowledge of gene function has increasingly lagged behind gene discovery, hindering our understanding of the genetic basis of microbial phenotypes. Recently, however, massively parallel sequencing has been combined with traditional transposon mutagenesis in techniques referred to as transposon sequencing (Tn-seq), high-throughput insertion tracking by deep sequencing (HITS), insertion sequencing (INSeq) and transposon-directed insertion site sequencing (TraDIS), making it possible to identify putative gene functions in a high-throughput manner. Here, we describe the similarities and differences of these related techniques and discuss their application to the probing of gene function and higher-order genome organization.
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Affiliation(s)
- Tim van Opijnen
- Biology Department, Boston College, 140 Commonwealth Avenue, 420 Higgins Hall, Chestnut Hill, Massachusetts 02467, USA.
| | - Andrew Camilli
- Howard Hughes Medical Institute and the Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, USA.
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31
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Nontypeable Haemophilus influenzae carbonic anhydrase is important for environmental and intracellular survival. J Bacteriol 2013; 195:2737-46. [PMID: 23564172 DOI: 10.1128/jb.01870-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is one of the leading causes of noninvasive mucosal infections, such as otitis media, sinusitis, and conjunctivitis. During its life cycle, NTHi is exposed to different CO2 levels, which vary from ∼0.04% in ambient air during transmission to a new host to over 5% in the respiratory tract and tissues of the human host during colonization and disease. We used the next-generation sequencing Tn-seq technology to identify genes essential for NTHi adaptation to changes in environmental CO2 levels. It appeared that H. influenzae carbonic anhydrase (HICA), which catalyzes the reversible hydration of CO2 to bicarbonate, is a molecular factor that is conditionally essential for NTHi survival in ambient air. Growth of NTHi Δcan strains was restored under 5% CO2-enriched conditions, by supplementation of the growth medium with sodium bicarbonate, or by genetic complementation with the can gene. Finally, we showed that HICA not only is essential for environmental survival but also appeared to be important for intracellular survival in host cells. Hence, HICA is important for NTHi niche adaptation.
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Klein BA, Tenorio EL, Lazinski DW, Camilli A, Duncan MJ, Hu LT. Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis. BMC Genomics 2012; 13:578. [PMID: 23114059 PMCID: PMC3547785 DOI: 10.1186/1471-2164-13-578] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/24/2012] [Indexed: 01/09/2023] Open
Abstract
Background Porphyromonas gingivalis is a Gram-negative anaerobic bacterium associated with periodontal disease onset and progression. Genetic tools for the manipulation of bacterial genomes allow for in-depth mechanistic studies of metabolism, physiology, interspecies and host-pathogen interactions. Analysis of the essential genes, protein-coding sequences necessary for survival of P. gingivalis by transposon mutagenesis has not previously been attempted due to the limitations of available transposon systems for the organism. We adapted a Mariner transposon system for mutagenesis of P. gingivalis and created an insertion mutant library. By analyzing the location of insertions using massively-parallel sequencing technology we used this mutant library to define genes essential for P. gingivalis survival under in vitro conditions. Results In mutagenesis experiments we identified 463 genes in P. gingivalis strain ATCC 33277 that are putatively essential for viability in vitro. Comparing the 463 P. gingivalis essential genes with previous essential gene studies, 364 of the 463 are homologues to essential genes in other species; 339 are shared with more than one other species. Twenty-five genes are known to be essential in P. gingivalis and B. thetaiotaomicron only. Significant enrichment of essential genes within Cluster of Orthologous Groups ‘D’ (cell division), ‘I’ (lipid transport and metabolism) and ‘J’ (translation/ribosome) were identified. Previously, the P. gingivalis core genome was shown to encode 1,476 proteins out of a possible 1,909; 434 of 463 essential genes are contained within the core genome. Thus, for the species P. gingivalis twenty-two, seventy-seven and twenty-three percent of the genome respectively are devoted to essential, core and accessory functions. Conclusions A Mariner transposon system can be adapted to create mutant libraries in P. gingivalis amenable to analysis by next-generation sequencing technologies. In silico analysis of genes essential for in vitro growth demonstrates that although the majority are homologous across bacterial species as a whole, species and strain-specific subsets are apparent. Understanding the putative essential genes of P. gingivalis will provide insights into metabolic pathways and niche adaptations as well as clinical therapeutic strategies.
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Affiliation(s)
- Brian A Klein
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111, USA
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Genome walking by next generation sequencing approaches. BIOLOGY 2012; 1:495-507. [PMID: 24832505 PMCID: PMC4009806 DOI: 10.3390/biology1030495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/31/2012] [Accepted: 09/25/2012] [Indexed: 01/07/2023]
Abstract
Genome Walking (GW) comprises a number of PCR-based methods for the identification of nucleotide sequences flanking known regions. The different methods have been used for several purposes: from de novo sequencing, useful for the identification of unknown regions, to the characterization of insertion sites for viruses and transposons. In the latter cases Genome Walking methods have been recently boosted by coupling to Next Generation Sequencing technologies. This review will focus on the development of several protocols for the application of Next Generation Sequencing (NGS) technologies to GW, which have been developed in the course of analysis of insertional libraries. These analyses find broad application in protocols for functional genomics and gene therapy. Thanks to the application of NGS technologies, the original vision of GW as a procedure for walking along an unknown genome is now changing into the possibility of observing the parallel marching of hundreds of thousands of primers across the borders of inserted DNA molecules in host genomes.
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Brutinel ED, Gralnick JA. Anomalies of the anaerobic tricarboxylic acid cycle inShewanella oneidensisrevealed by Tn-seq. Mol Microbiol 2012; 86:273-83. [DOI: 10.1111/j.1365-2958.2012.08196.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Evan D. Brutinel
- BioTechnology Institute and Department of Microbiology; University of Minnesota-Twin Cities; St Paul; MN; 55108; USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Microbiology; University of Minnesota-Twin Cities; St Paul; MN; 55108; USA
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Identification of MrtAB, an ABC transporter specifically required for Yersinia pseudotuberculosis to colonize the mesenteric lymph nodes. PLoS Pathog 2012; 8:e1002828. [PMID: 22876175 PMCID: PMC3410872 DOI: 10.1371/journal.ppat.1002828] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 06/15/2012] [Indexed: 12/26/2022] Open
Abstract
A highly conserved virulence plasmid encoding a type III secretion system is shared by the three Yersinia species most pathogenic for mammals. Although factors encoded on this plasmid enhance the ability of Yersinia to thrive in their mammalian hosts, the loss of this virulence plasmid does not eliminate growth or survival in host organs. Most notably, yields of viable plasmid-deficient Yersinia pseudotuberculosis (Yptb) are indistinguishable from wild-type Yptb within mesenteric lymph nodes. To identify chromosomal virulence factors that allow for plasmid-independent survival during systemic infection of mice, we generated transposon insertions in plasmid-deficient Yptb, and screened a library having over 20,000 sequence-identified insertions. Among the previously uncharacterized loci, insertions in mrtAB, an operon encoding an ABC family transporter, had the most profound phenotype in a plasmid-deficient background. The absence of MrtAB, however, had no effect on growth in the liver and spleen of a wild type strain having an intact virulence plasmid, but caused a severe defect in colonization of the mesenteric lymph nodes. Although this result is consistent with lack of expression of the type III secretion system by Wt Yptb in the mesenteric lymph nodes, a reporter for YopE indicated that expression of the system was robust. We demonstrate that the ATPase activity of MrtB is required for growth in mice, indicating that transport activity is required for virulence. Indeed, MrtAB appears to function as an efflux pump, as the ATPase activity enhances resistance to ethidium bromide while increasing sensitivity to pyocyanin, consistent with export across the inner membrane.
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Abstract
A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We describe a high-throughput strategy based on the method Tn-seq that can be applied to any genetically manipulatable microorganism. By screening 17 in vitro and two in vivo (carriage and infection) conditions for the pathogen Streptococcus pneumoniae, we create a resource consisting of >1800 interactions that is rich in new genotype–phenotype relationships. We describe genes that are involved in differential carbon source utilization in the host, as well as genes that are involved both in virulence and in resistance against specific in vitro stresses, thereby revealing selection pressures that the pathogen experiences in vivo. We reveal the secondary response to an antibiotic, including a dual role efflux pump also involved in resistance to pH stress. Through genetic-interaction mapping and gene-expression analysis we define the mechanism of attenuation and the regulatory relationship between a two-component system and a core biosynthetic pathway specific to microorganisms. Thus, we have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae and provided a road map for similar discovery in other microorganisms.
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Affiliation(s)
- Tim van Opijnen
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI, Rosch JW. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 2012; 8:e1002788. [PMID: 22807675 PMCID: PMC3395615 DOI: 10.1371/journal.ppat.1002788] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/22/2012] [Indexed: 01/10/2023] Open
Abstract
Small noncoding RNAs (sRNAs) play important roles in gene regulation in both prokaryotes and eukaryotes. Thus far, no sRNA has been assigned a definitive role in virulence in the major human pathogen Streptococcus pneumoniae. Based on the potential coding capacity of intergenic regions, we hypothesized that the pneumococcus produces many sRNAs and that they would play an important role in pathogenesis. We describe the application of whole-genome transcriptional sequencing to systematically identify the sRNAs of Streptococcus pneumoniae. Using this approach, we have identified 89 putative sRNAs, 56 of which are newly identified. Furthermore, using targeted genetic approaches and Tn-seq transposon screening, we demonstrate that many of the identified sRNAs have important global and niche-specific roles in virulence. These data constitute the most comprehensive analysis of pneumococcal sRNAs and provide the first evidence of the extensive roles of sRNAs in pneumococcal pathogenesis.
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Affiliation(s)
- Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Tim van Opijnen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jianmin Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Caroline Obert
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Yong-Dong Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Robert Carter
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Daniel J. McGoldrick
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Granger Ridout
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Andrew Camilli
- Howard Hughes Medical Institute and Tufts University School of Medicine, Department of Molecular Biology and Microbiology, Boston, Massachusetts, United States of America
| | - Elaine I. Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
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Goodman AL, Wu M, Gordon JI. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat Protoc 2011; 6:1969-80. [PMID: 22094732 DOI: 10.1038/nprot.2011.417] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq is based on a modified mariner transposon containing MmeI sites at its ends, allowing cleavage at chromosomal sites 16-17 bp from the inserted transposon. Genomic regions adjacent to the transposons are amplified by linear PCR with a biotinylated primer. Products are bound to magnetic beads, digested with MmeI and barcoded with sample-specific linkers appended to each restriction fragment. After limited PCR amplification, fragments are sequenced using a high-throughput instrument. The sequence of each read can be used to map the location of a transposon in the genome. Read count measures the relative abundance of that mutant in the population. Solid-phase library preparation makes this protocol rapid (18 h), easy to scale up, amenable to automation and useful for a variety of samples. A protocol for characterizing libraries of transposon mutant strains clonally arrayed in a multiwell format is provided.
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Affiliation(s)
- Andrew L Goodman
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.
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Ahmer BMM, Gunn JS. Interaction of Salmonella spp. with the Intestinal Microbiota. Front Microbiol 2011; 2:101. [PMID: 21772831 PMCID: PMC3131049 DOI: 10.3389/fmicb.2011.00101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/25/2011] [Indexed: 12/20/2022] Open
Abstract
Salmonella spp. are major cause of human morbidity and mortality worldwide. Upon entry into the human host, Salmonella spp. must overcome the resistance to colonization mediated by the gut microbiota and the innate immune system. They successfully accomplish this by inducing inflammation and mechanisms of innate immune defense. Many models have been developed to study Salmonella spp. interaction with the microbiota that have helped to identify factors necessary to overcome colonization resistance and to mediate disease. Here we review the current state of studies into this important pathogen/microbiota/host interaction in the mammalian gastrointestinal tract.
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Affiliation(s)
- Brian M M Ahmer
- The Department of Microbiology, The Ohio State University Columbus, OH, USA
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