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Miles J, Lozano GL, Rajendhran J, Stabb EV, Handelsman J, Broderick NA. Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster. mSystems 2024; 9:e0131723. [PMID: 38380971 PMCID: PMC10949475 DOI: 10.1128/msystems.01317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing [Tn-Seq, also known as insertion sequencing (INSeq)] to identify genes in P. aeruginosa that contribute to fitness during the colonization of Drosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies on P. aeruginosa identified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen in Drosophila, demonstrate the power of Tn-Seq in the fly model system and advance the existing knowledge of intestinal pathogenesis by D. melanogaster, revealing bacterial colonization determinants that contribute to a comprehensive portrait of P. aeruginosa lifestyles across habitats.IMPORTANCEDrosophila melanogaster is a powerful model for understanding host-pathogen interactions. Research with this system has yielded notable insights into mechanisms of host immunity and defense, many of which emerged from the analysis of bacterial mutants defective for well-characterized virulence factors. These foundational studies-and advances in high-throughput sequencing of transposon mutants-support unbiased screens of bacterial mutants in the fly. To investigate mechanisms of host-pathogen interplay and exploit the tractability of this model host, we used a high-throughput, genome-wide mutant analysis to find genes that enable the pathogen P. aeruginosa to colonize the fly. Our analysis reveals critical mediators of P. aeruginosa establishment in its host, some of which are required across fly and mouse systems. These findings demonstrate the utility of massively parallel mutant analysis and provide a platform for aligning the fly toolkit with comprehensive bacterial genomics.
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Affiliation(s)
- Jessica Miles
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Graduate Program in Microbiology, Yale University, New Haven, Connecticut, USA
| | - Gabriel L. Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jeyaprakash Rajendhran
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
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Miles J, Lozano GL, Rajendhran J, Stabb EV, Handelsman J, Broderick NA. Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster. bioRxiv 2023:2023.11.20.567573. [PMID: 38045230 PMCID: PMC10690197 DOI: 10.1101/2023.11.20.567573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing (Tn-Seq, also known as INSeq) to identify genes in P. aeruginosa that contribute to fitness during colonization of Drosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies of P. aeruginosa identified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen in Drosophila, demonstrate the power of Tn-Seq in the fly model system and advance existing knowledge of intestinal pathogenesis by D. melanogaster, revealing bacterial colonization determinants that contribute to a comprehensive portrait of P. aeruginosa lifestyles across habitats.
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Affiliation(s)
- Jessica Miles
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Graduate Program in Microbiology, Yale University, New Haven, CT, USA
| | - Gabriel L. Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Current address: Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeyaprakash Rajendhran
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Current address: Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, TN, India
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Current address: Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
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Li C, Hurley A, Hu W, Warrick JW, Lozano GL, Ayuso JM, Pan W, Handelsman J, Beebe DJ. Social motility of biofilm-like microcolonies in a gliding bacterium. Nat Commun 2021; 12:5700. [PMID: 34588437 PMCID: PMC8481357 DOI: 10.1038/s41467-021-25408-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/09/2021] [Indexed: 11/27/2022] Open
Abstract
Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix, and are typically stationary. Studies of bacterial collective movement have largely focused on swarming motility mediated by flagella or pili, in the absence of a biofilm. Here, we describe a unique mode of collective movement by a self-propelled, surface-associated biofilm-like multicellular structure. Flavobacterium johnsoniae cells, which move by gliding motility, self-assemble into spherical microcolonies with EPS cores when observed by an under-oil open microfluidic system. Small microcolonies merge, creating larger ones. Microscopic analysis and computer simulation indicate that microcolonies move by cells at the base of the structure, attached to the surface by one pole of the cell. Biochemical and mutant analyses show that an active process drives microcolony self-assembly and motility, which depend on the bacterial gliding apparatus. We hypothesize that this mode of collective bacterial movement on solid surfaces may play potential roles in biofilm dynamics, bacterial cargo transport, or microbial adaptation. However, whether this collective motility occurs on plant roots or soil particles, the native environment for F. johnsoniae, is unknown. Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix. Here, the authors describe a unique mode of collective movement by self-propelled, surface-associated spherical microcolonies with EPS cores in the gliding bacterium Flavobacterium johnsoniae.
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Affiliation(s)
- Chao Li
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Hurley
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Wei Hu
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Jay W Warrick
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriel L Lozano
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.,Divisions of Infectious Diseases and Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jose M Ayuso
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Morgridge Institute for Research, Madison, WI, USA
| | - Wenxiao Pan
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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Mongui A, Lozano GL, Handelsman J, Restrepo S, Junca H. Design and validation of a transposon that promotes expression of genes in episomal DNA. J Biotechnol 2020; 310:1-5. [PMID: 31954761 DOI: 10.1016/j.jbiotec.2020.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/15/2020] [Indexed: 01/20/2023]
Abstract
Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.
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Affiliation(s)
- Alvaro Mongui
- Molecular Biotechnology, Corporación CorpoGen, Bogotá, Colombia; Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
| | - Gabriel L Lozano
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Diseases, Universidad de los Andes, Bogotá, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Microbiomas Foundation, Chía, Colombia
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Sivakumar R, Ranjani J, Vishnu US, Jayashree S, Lozano GL, Miles J, Broderick NA, Guan C, Gunasekaran P, Handelsman J, Rajendhran J. Evaluation of INSeq To Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization. G3 (Bethesda) 2019; 9:651-661. [PMID: 30705119 PMCID: PMC6404608 DOI: 10.1534/g3.118.200928] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/19/2019] [Indexed: 01/19/2023]
Abstract
The reciprocal interaction between rhizosphere bacteria and their plant hosts results in a complex battery of genetic and physiological responses. In this study, we used insertion sequencing (INSeq) to reveal the genetic determinants responsible for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. We generated a random transposon mutant library of Pseudomonas aeruginosa PGPR2 comprising 39,500 unique insertions and identified genes required for growth in culture and on corn roots. A total of 108 genes were identified as contributing to the fitness of strain PGPR2 on roots. The importance in root colonization of four genes identified in the INSeq screen was verified by constructing deletion mutants in the genes and testing them for the ability to colonize corn roots singly or in competition with the wild type. All four mutants were affected in corn root colonization, displaying 5- to 100-fold reductions in populations in single inoculations, and all were outcompeted by the wild type by almost 100-fold after seven days on corn roots in mixed inoculations of the wild type and mutant. The genes identified in the screen had homology to genes involved in amino acid catabolism, stress adaptation, detoxification, signal transduction, and transport. INSeq technology proved a successful tool to identify fitness factors in Paeruginosa PGPR2 for root colonization.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jothi Ranjani
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Gabriel L Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
| | - Jessica Miles
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
| | - Nichole A Broderick
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT
| | | | | | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI 53715
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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Stulberg ER, Lozano GL, Morin JB, Park H, Baraban EG, Mlot C, Heffelfinger C, Phillips GM, Rush JS, Phillips AJ, Broderick NA, Thomas MG, Stabb EV, Handelsman J. Genomic and Secondary Metabolite Analyses of Streptomyces sp. 2AW Provide Insight into the Evolution of the Cycloheximide Pathway. Front Microbiol 2016; 7:573. [PMID: 27199910 PMCID: PMC4853412 DOI: 10.3389/fmicb.2016.00573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The dearth of new antibiotics in the face of widespread antimicrobial resistance makes developing innovative strategies for discovering new antibiotics critical for the future management of infectious disease. Understanding the genetics and evolution of antibiotic producers will help guide the discovery and bioengineering of novel antibiotics. We discovered an isolate in Alaskan boreal forest soil that had broad antimicrobial activity. We elucidated the corresponding antimicrobial natural products and sequenced the genome of this isolate, designated Streptomyces sp. 2AW. This strain illustrates the chemical virtuosity typical of the Streptomyces genus, producing cycloheximide as well as two other biosynthetically unrelated antibiotics, neutramycin, and hygromycin A. Combining bioinformatic and chemical analyses, we identified the gene clusters responsible for antibiotic production. Interestingly, 2AW appears dissimilar from other cycloheximide producers in that the gene encoding the polyketide synthase resides on a separate part of the chromosome from the genes responsible for tailoring cycloheximide-specific modifications. This gene arrangement and our phylogenetic analyses of the gene products suggest that 2AW holds an evolutionarily ancestral lineage of the cycloheximide pathway. Our analyses support the hypothesis that the 2AW glutaramide gene cluster is basal to the lineage wherein cycloheximide production diverged from other glutarimide antibiotics. This study illustrates the power of combining modern biochemical and genomic analyses to gain insight into the evolution of antibiotic-producing microorganisms.
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Affiliation(s)
- Elizabeth R Stulberg
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Gabriel L Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Jesse B Morin
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Hyunjun Park
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Ezra G Baraban
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Christine Mlot
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | | | | | - Jason S Rush
- Department of Chemistry, Yale University New Haven, CT, USA
| | | | - Nichole A Broderick
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia Athens, GA, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
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