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Jouan R, Lextrait G, Lachat J, Yokota A, Cossard R, Naquin D, Timchenko T, Kikuchi Y, Ohbayashi T, Mergaert P. Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola. ISME COMMUNICATIONS 2024; 4:ycad001. [PMID: 38282642 PMCID: PMC10809759 DOI: 10.1093/ismeco/ycad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/30/2024]
Abstract
Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.
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Grants
- JSPS Research Fellowship for Young Scientists, Japan
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan
- Ministry of Higher Education, Research, and Innovation, France
- CNRS International Research Project, France
- JSPS-CNRS Bilateral Open Partnership Joint Research Project, France-Japan
- Agence Nationale de la Recherche, France
- Saclay Plant Sciences-SPS
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Affiliation(s)
- Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, Sapporo 062-8517, Japan
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
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Riccardi C, Koper P, Innocenti G, diCenzo GC, Fondi M, Mengoni A, Perrin E. Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria. Microb Genom 2023; 9. [PMID: 37185344 DOI: 10.1099/mgen.0.001025] [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: 05/17/2023] Open
Abstract
Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.
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Affiliation(s)
- Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Piotr Koper
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Gabriel Innocenti
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - George C diCenzo
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario, K7L 3N6, Canada
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
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O'Connor A, Jurado‐Martín I, Mysior MM, Manzira AL, Drabinska J, Simpson JC, Lucey M, Schaffer K, Berisio R, McClean S. A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis. Microbiologyopen 2023; 12:e1311. [PMID: 36825886 PMCID: PMC9733578 DOI: 10.1002/mbo3.1311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
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Affiliation(s)
- Andrew O'Connor
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
| | - Irene Jurado‐Martín
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Margaritha M. Mysior
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Anotidaishe L. Manzira
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Jeremy C. Simpson
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Mary Lucey
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Kirsten Schaffer
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
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Saroha T, Patil PP, Rana R, Kumar R, Kumar S, Singhal L, Gautam V, Patil PB. Genomic features, antimicrobial susceptibility, and epidemiological insights into Burkholderia cenocepacia clonal complex 31 isolates from bloodstream infections in India. Front Cell Infect Microbiol 2023; 13:1151594. [PMID: 37153161 PMCID: PMC10155701 DOI: 10.3389/fcimb.2023.1151594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Burkholderia cepacia complex (Bcc) clonal complex (CC) 31, the predominant lineage causing devastating outbreaks globally, has been a growing concern of infections in non-cystic fibrosis (NCF) patients in India. B. cenocepacia is very challenging to treat owing to its virulence determinants and antibiotic resistance. Improving the management of these infections requires a better knowledge of their resistance patterns and mechanisms. Methods Whole-genome sequences of 35 CC31 isolates obtained from patient samples, were analyzed against available 210 CC31 genomes in the NCBI database to glean details of resistance, virulence, mobile elements, and phylogenetic markers to study genomic diversity and evolution of CC31 lineage in India. Results Genomic analysis revealed that 35 isolates belonging to CC31 were categorized into 11 sequence types (ST), of which five STs were reported exclusively from India. Phylogenetic analysis classified 245 CC31 isolates into eight distinct clades (I-VIII) and unveiled that NCF isolates are evolving independently from the global cystic fibrosis (CF) isolates forming a distinct clade. The detection rate of seven classes of antibiotic-related genes in 35 isolates was 35 (100%) for tetracyclines, aminoglycosides, and fluoroquinolones; 26 (74.2%) for sulphonamides and phenicols; 7 (20%) for beta-lactamases; and 1 (2.8%) for trimethoprim resistance genes. Additionally, 3 (8.5%) NCF isolates were resistant to disinfecting agents and antiseptics. Antimicrobial susceptibility testing revealed that majority of NCF isolates were resistant to chloramphenicol (77%) and levofloxacin (34%). NCF isolates have a comparable number of virulence genes to CF isolates. A well-studied pathogenicity island of B. cenocepacia, GI11 is present in ST628 and ST709 isolates from the Indian Bcc population. In contrast, genomic island GI15 (highly similar to the island found in B. pseudomallei strain EY1) is exclusively reported in ST839 and ST824 isolates from two different locations in India. Horizontal acquisition of lytic phage ST79 of pathogenic B. pseudomallei is demonstrated in ST628 isolates Bcc1463, Bcc29163, and BccR4654 amongst CC31 lineage. Discussion The study reveals a high diversity of CC31 lineages among B. cenocepacia isolates from India. The extensive information from this study will facilitate the development of rapid diagnostic and novel therapeutic approaches to manage B. cenocepacia infections.
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Affiliation(s)
- Tanu Saroha
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prashant P. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
| | - Rekha Rana
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Kumar
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
| | - Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Vikas Gautam
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
- *Correspondence: Prabhu B. Patil, ; Vikas Gautam,
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- *Correspondence: Prabhu B. Patil, ; Vikas Gautam,
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5
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Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines. Arch Microbiol 2022; 205:25. [PMID: 36515719 DOI: 10.1007/s00203-022-03354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.
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An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis. J Bacteriol 2021; 203:e0068320. [PMID: 33753468 DOI: 10.1128/jb.00683-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacterial genomes can be methylated at particular motifs by methyltransferases (M). This DNA modification allows restriction endonucleases (R) to discriminate between self and foreign DNA. While the accepted primary function of such restriction modification (RM) systems is to degrade incoming foreign DNA, other roles of RM systems and lone R or M components have been found in genome protection, stability and the regulation of various phenotypes. The Burkholderia cepacia complex (Bcc) is a group of closely related opportunistic pathogens with biotechnological potential. Here, we constructed and analysed mutants lacking various RM components in the clinical Bcc isolate Burkholderia cenocepacia H111 and used SMRT sequencing of single mutants to assign the B. cenocepacia H111 Ms to their cognate motifs. DNA methylation is shown to affect biofilm formation, cell shape, motility, siderophore production and membrane vesicle production. Moreover, DNA methylation had a large effect on the maintenance of the Bcc virulence megaplasmid pC3. Our data also suggest that the gp51 M-encoding gene, which is essential in H111 and is located within a prophage, is required for maintaining the bacteriophage in a lysogenic state, thereby ensuring a constant, low level of phage production within the bacterial population.ImportanceWhile genome sequence determines an organism's proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, Ms modify specific nucleotide motifs to allow discrimination of 'self' from 'non-self' DNA, e.g. from bacteriophages. Restriction enzymes detect 'non-self' methylation patterns and cut foreign DNA. Furthermore, methylation of promoter regions can influence gene expression and hence affect various phenotypes. In this study, we determined the methylated motifs of four strains from the Burkholderia cepacia complex of opportunistic pathogens. We deleted all genes encoding the restriction and modification components in one of these strains, Burkholderia cenocepacia H111. It is shown that DNA methylation affects various phenotypic traits, the most noteworthy being lysogenicity of a bacteriophage and maintenance of a virulence megaplasmid.
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diCenzo GC, Mengoni A, Perrin E. Chromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae. Mol Biol Evol 2019; 36:562-574. [PMID: 30608550 DOI: 10.1093/molbev/msy248] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Almost all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that interreplicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicated a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also overrepresented on the chromosomes of the environmental genera (Paraburkholderia and Cupriavidus) compared with the pathogenic genera (Burkholderia and Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in replicons enriched in genes associated with adaptation to novel environments.
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Affiliation(s)
- George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Elena Perrin
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
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8
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Richter AM, Fazli M, Schmid N, Shilling R, Suppiger A, Givskov M, Eberl L, Tolker-Nielsen T. Key Players and Individualists of Cyclic-di-GMP Signaling in Burkholderia cenocepacia. Front Microbiol 2019; 9:3286. [PMID: 30687272 PMCID: PMC6335245 DOI: 10.3389/fmicb.2018.03286] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Burkholderia cenocepacia H111 is an opportunistic pathogen associated with chronic lung infections in cystic fibrosis patients. Biofilm formation, motility and virulence of B. cenocepacia are regulated by the second messenger cyclic di-guanosine monophosphate (c-di-GMP). In the present study, we analyzed the role of all 25 putative c-di-GMP metabolizing proteins of B. cenocepacia H111 with respect to motility, colony morphology, pellicle formation, biofilm formation, and virulence. We found that RpfR is a key regulator of c-di-GMP signaling in B. cenocepacia, affecting a broad spectrum of phenotypes under various environmental conditions. In addition, we identified Bcal2449 as a regulator of B. cenocepacia virulence in Galleria mellonella larvae. While Bcal2449 consists of protein domains that may catalyze both c-di-GMP synthesis and degradation, only the latter was essential for larvae killing, suggesting that a decreased c-di-GMP level mediated by the Bcal2449 protein is required for virulence of B. cenocepacia. Finally, our work suggests that some individual proteins play a role in regulating exclusively motility (CdpA), biofilm formation (Bcam1160) or both (Bcam2836).
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Affiliation(s)
- Anja M Richter
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mustafa Fazli
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadine Schmid
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Rebecca Shilling
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Angela Suppiger
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Leo Eberl
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Jenul C, Sieber S, Daeppen C, Mathew A, Lardi M, Pessi G, Hoepfner D, Neuburger M, Linden A, Gademann K, Eberl L. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat Commun 2018; 9:1297. [PMID: 29602945 PMCID: PMC5878181 DOI: 10.1038/s41467-018-03690-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 03/05/2018] [Indexed: 11/23/2022] Open
Abstract
Members of the diazeniumdiolate class of natural compounds show potential for drug development because of their antifungal, antibacterial, antiviral, and antitumor activities. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. A subset of the fragin biosynthetic genes is involved in the synthesis of a previously undescribed cell-to-cell signal molecule, valdiazen. RNA-Seq analyses reveal that valdiazen controls fragin biosynthesis and affects the expression of more than 100 genes. Homologs of the valdiazen biosynthesis genes are found in various bacteria, suggesting that valdiazen-like compounds may constitute a new class of signal molecules. We use structural information, in silico prediction of enzymatic functions and biochemical data to propose a biosynthesis route for fragin and valdiazen. Fragin is a diazeniumdiolate metabolite with antifungal activity, produced by some bacteria. Here, Jenul et al. show that metal chelation is the molecular basis of fragin’s antifungal activity, and that a gene cluster directing fragin biosynthesis is also involved in the synthesis of a signal molecule.
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Affiliation(s)
- Christian Jenul
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Christophe Daeppen
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Markus Neuburger
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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10
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Roux D, Schaefers M, Clark BS, Weatherholt M, Renaud D, Scott D, LiPuma JJ, Priebe G, Gerard C, Yoder-Himes DR. A putative lateral flagella of the cystic fibrosis pathogen Burkholderia dolosa regulates swimming motility and host cytokine production. PLoS One 2018; 13:e0189810. [PMID: 29346379 PMCID: PMC5773237 DOI: 10.1371/journal.pone.0189810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023] Open
Abstract
Burkholderia dolosa caused an outbreak in the cystic fibrosis clinic at Boston Children's Hospital and was associated with high mortality in these patients. This species is part of a larger complex of opportunistic pathogens known as the Burkholderia cepacia complex (Bcc). Compared to other species in the Bcc, B. dolosa is highly transmissible; thus understanding its virulence mechanisms is important for preventing future outbreaks. The genome of one of the outbreak strains, AU0158, revealed a homolog of the lafA gene encoding a putative lateral flagellin, which, in other non-Bcc species, is used for movement on solid surfaces, attachment to host cells, or movement inside host cells. Here, we analyzed the conservation of the lafA gene and protein sequences, which are distinct from those of the polar flagella, and found lafA homologs to be present in numerous β-proteobacteria but notably absent from most other Bcc species. A lafA deletion mutant in B. dolosa showed a greater swimming motility than wild-type due to an increase in the number of polar flagella, but did not appear to contribute to biofilm formation, host cell invasion, or murine lung colonization or persistence over time. However, the lafA gene was important for cytokine production in human peripheral blood mononuclear cells, suggesting it may have a role in recognition by the human immune response.
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Affiliation(s)
- Damien Roux
- INSERM, IAME, UMR 1137, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
- AP-HP, Louis Mourier Hospital, Intensive Care Unit, Colombes, France
| | - Matthew Schaefers
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bradley S. Clark
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Molly Weatherholt
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Diane Renaud
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - David Scott
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - John J. LiPuma
- Division of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregory Priebe
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig Gerard
- Division of Respiratory Diseases, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Deborah R. Yoder-Himes
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail:
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11
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Perrin E, Fondi M, Bosi E, Mengoni A, Buroni S, Scoffone VC, Valvano M, Fani R. Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance. BMC Genomics 2017; 18:834. [PMID: 29084524 PMCID: PMC5663151 DOI: 10.1186/s12864-017-4222-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/17/2017] [Indexed: 01/09/2023] Open
Abstract
Background Antibiotic resistance is a major problem for human health. Multidrug resistance efflux pumps, especially those of the Resistance-Nodulation-Cell Division (RND) family, are major contributors to high-level antibiotic resistance in Gram-negative bacteria. Most bacterial genomes contain several copies of the different classes of multidrug resistance efflux pumps. Gene duplication and gain of function by the duplicate copies of multidrug resistance efflux pump genes plays a key role in the expansion and diversification of drug-resistance mechanisms. Results We used two members of the Burkholderia RND superfamily as models to understand how duplication events affect the antibiotic resistance of these strains. First, we analyzed the conservation and distribution of these two RND systems and their regulators across the Burkholderia genus. Through genetic manipulations, we identified both the exact substrate range of these transporters and their eventual interchangeability. We also performed a directed evolution experiment, combined with next generation sequencing, to evaluate the role of antibiotics in the activation of the expression of these systems. Together, our results indicate that the first step to diversify the functions of these pumps arises from changes in their regulation (subfunctionalization) instead of functional mutations. Further, these pumps could rewire their regulation to respond to antibiotics, thus maintaining high genomic plasticity. Conclusions Studying the regulatory network that controls the expression of the RND pumps will help understand and eventually control the development and expansion of drug resistance. Electronic supplementary material The online version of this article (10.1186/s12864-017-4222-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Emanuele Bosi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Miguel Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Rd, Belfast, BT9 7BL, UK
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy.
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12
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The Essential Genome of Burkholderia cenocepacia H111. J Bacteriol 2017; 199:JB.00260-17. [PMID: 28847919 DOI: 10.1128/jb.00260-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/19/2017] [Indexed: 12/31/2022] Open
Abstract
The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5% O2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera.IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of "core essential genes" that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.
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13
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Price EP, Sarovich DS, Webb JR, Hall CM, Jaramillo SA, Sahl JW, Kaestli M, Mayo M, Harrington G, Baker AL, Sidak-Loftis LC, Settles EW, Lummis M, Schupp JM, Gillece JD, Tuanyok A, Warner J, Busch JD, Keim P, Currie BJ, Wagner DM. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Negl Trop Dis 2017; 11:e0005928. [PMID: 28910350 PMCID: PMC5614643 DOI: 10.1371/journal.pntd.0005928] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/26/2017] [Accepted: 09/03/2017] [Indexed: 01/02/2023] Open
Abstract
The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc) species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.
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Affiliation(s)
- Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Carina M. Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sierra A. Jaramillo
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Glenda Harrington
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Anthony L. Baker
- Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lindsay C. Sidak-Loftis
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik W. Settles
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Madeline Lummis
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - John D. Gillece
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Warner
- Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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14
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An evolutionary perspective on plasmid lifestyle modes. Curr Opin Microbiol 2017; 38:74-80. [DOI: 10.1016/j.mib.2017.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/19/2022]
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15
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Use of Synthetic Hybrid Strains To Determine the Role of Replicon 3 in Virulence of the Burkholderia cepacia Complex. Appl Environ Microbiol 2017; 83:AEM.00461-17. [PMID: 28432094 DOI: 10.1128/aem.00461-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/12/2017] [Indexed: 01/08/2023] Open
Abstract
The Burkholderia cepacia complex (Bcc) displays a wealth of metabolic diversity with great biotechnological potential, but the utilization of these bacteria is limited by their opportunistic pathogenicity to humans. The third replicon of the Bcc, megaplasmid pC3 (0.5 to 1.4 Mb, previously chromosome 3), is important for various phenotypes, including virulence, antifungal, and proteolytic activities and the utilization of certain substrates. Approximately half of plasmid pC3 is well conserved throughout sequenced Bcc members, while the other half is not. To better locate the regions responsible for the key phenotypes, pC3 mutant derivatives of Burkholderia cenocepacia H111 carrying large deletions (up to 0.58 Mb) were constructed with the aid of the FLP-FRT (FRT, flippase recognition target) recombination system from Saccharomyces cerevisiae The conserved region was shown to confer near-full virulence in both Caenorhabditis elegans and Galleria mellonella infection models. Antifungal activity was unexpectedly independent of the part of pC3 bearing a previously identified antifungal gene cluster, while proteolytic activity was dependent on the nonconserved part of pC3, which encodes the ZmpA protease. To investigate to what degree pC3-encoded functions are dependent on chromosomally encoded functions, we transferred pC3 from Burkholderia cenocepacia K56-2 and Burkholderia lata 383 into other pC3-cured Bcc members. We found that although pC3 is highly important for virulence, it was the genetic background of the recipient that determined the pathogenicity level of the hybrid strain. Furthermore, we found that important phenotypes, such as antifungal activity, proteolytic activity, and some substrate utilization capabilities, can be transferred between Bcc members using pC3.IMPORTANCE The Burkholderia cepacia complex (Bcc) is a group of closely related bacteria with great biotechnological potential. Some strains produce potent antifungal compounds and can promote plant growth or degrade environmental pollutants. However, their agricultural potential is limited by their opportunistic pathogenicity, particularly for cystic fibrosis patients. Despite much study, their virulence remains poorly understood. The third replicon, pC3, which is present in all Bcc isolates and is important for pathogenicity, stress resistance, and the production of antifungal compounds, has recently been reclassified from a chromosome to a megaplasmid. In this study, we identified regions on pC3 important for virulence and antifungal activity and investigated the role of the chromosomal background for the function of pC3 by exchanging the megaplasmid between different Bcc members. Our results may open a new avenue for the construction of antifungal but nonpathogenic Burkholderia hybrids. Such strains may have great potential as biocontrol strains for protecting fungus-borne diseases of plant crops.
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16
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Moreira AS, Lourenço AB, Sá-Correia I. 1H-NMR-Based Endometabolome Profiles of Burkholderia cenocepacia Clonal Variants Retrieved from a Cystic Fibrosis Patient during Chronic Infection. Front Microbiol 2016; 7:2024. [PMID: 28066350 PMCID: PMC5167703 DOI: 10.3389/fmicb.2016.02024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022] Open
Abstract
During cystic fibrosis (CF) chronic lung infections, bacteria of the Burkholderia cepacia complex (Bcc) are exposed for several years to a stressful and changing environment. These environmental challenges results in genetic changes of the initial infecting strain with the consequent diversification of genotypes and phenotypes. The exploitation of functional and comparative genomic approaches has suggested that such diversification is associated with massive metabolic remodeling but these alterations are poorly understood. In the present work, we have explored a high resolution 1H-NMR-based metabolomic approach coupled to multivariate analysis to compare the endometabolome of three B. cenocepacia clonal variants retrieved from a CF patient from the onset of infection (IST439) until death with cepacia syndrome after 3.5 years (IST4113 and IST4134), to complement former proteomic and transcriptomic analyses. A fourth clonal variant (IST4129) retrieved from the same CF patient when the clinical condition worsened during the last months of life, was also examined since it was found to lack the third replicon. The metabolomic profiles obtained, based on the complete 1H-NMR spectra, highlight the separation of the four clonal variants examined, the most distinct profile corresponding to IST4129. Results indicate a variable content of several amino acids in the different isolates examined and suggest that glycolysis and the glyoxylate shunt are favored in late variants. Moreover, the concentration of two metabolites with demonstrated cellular protective functions against stress, glycine-betaine and trehalose, is different in the different isolates examined. However, no clear correlation could be established between their content and stress tolerance. For example, IST4113, previously found to be the most resistant variant to antimicrobials of different classes, exhibits low levels of trehalose and glycine-betaine but the highest resistance to heat and oxidative stress. Also, IST4129, with a high level of glycine-betaine but lacking the third replicon, previously associated with stress resistance and virulence, exhibits the highest susceptibility to all the stresses tested. Taken together, results from this study provide insights into the metabolic diversification of B. cenocepacia clonal variants during long-term infection of the CF airways.
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Affiliation(s)
- Ana S Moreira
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa (ULISBOA) Lisbon, Portugal
| | - Artur B Lourenço
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa (ULISBOA) Lisbon, Portugal
| | - Isabel Sá-Correia
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa (ULISBOA) Lisbon, Portugal
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17
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Kanyó I, Molnár LV. Procaryotic species and subspecies delineation using average nucleotide identity and gene order conservation. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67). GENOME ANNOUNCEMENTS 2016; 4:4/6/e01294-16. [PMID: 27856590 PMCID: PMC5114382 DOI: 10.1128/genomea.01294-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the complete annotated genome sequence of the Burkholderia stabilis type strain ATCC BAA-67. There were three circular chromosomes with a combined size of 8,527,947 bp and G+C composition of 66.4%. These characteristics closely resemble the genomes of other sequenced members of the Burkholderia cepacia complex.
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19
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Yong D, Tee KK, Yin WF, Chan KG. Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains. Front Microbiol 2016; 7:1606. [PMID: 27790203 PMCID: PMC5064223 DOI: 10.3389/fmicb.2016.01606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/26/2016] [Indexed: 11/25/2022] Open
Abstract
To date, information on plasmid analysis in Pandoraea spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. namely Pandoraea faecigallinarum DSM 23572T (pPF72-1, pPF72-2), Pandoraea oxalativorans DSM 23570T (pPO70-1, pPO70-2, pPO70-3, pPO70-4), Pandoraea vervacti NS15 (pPV15) and Pandoraea apista DSM 16535T (pPA35) were studied for the first time in this study. The information on plasmid sequences in Pandoraea spp. is useful as the sequences did not match any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA, and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. The observed features in the plasmids shed light on the Pandoraea spp. as opportunistic pathogens.
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Affiliation(s)
- Delicia Yong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
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20
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Moreira AS, Mil-Homens D, Sousa SA, Coutinho CP, Pinto-de-Oliveira A, Ramos CG, Dos Santos SC, Fialho AM, Leitão JH, Sá-Correia I. Variation of Burkholderia cenocepacia virulence potential during cystic fibrosis chronic lung infection. Virulence 2016; 8:782-796. [PMID: 27652671 DOI: 10.1080/21505594.2016.1237334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
During long-term lung infection in cystic fibrosis (CF) patients, Burkholderia cenocepacia faces multiple selective pressures in this highly stressful and fluctuating environment. As a consequence, the initial infecting strain undergoes genetic changes that result in the diversification of genotypes and phenotypes. Whether this clonal expansion influences the pathogenic potential is unclear. The virulence potential of 39 sequential B. cenocepacia (recA lineage IIIA) isolates, corresponding to 3 different clones retrieved from 3 chronically infected CF patients was compared in this study using the non-mammalian infection hosts Galleria mellonella and Caenorhabditis elegans. The isolates used in this retrospective study were picked randomly from selective agar plates as part of a CF Center routine, from the onset of infection until patients' death after 3.5 and 7.5 y or the more recent isolation date after 12.5 y of chronic infection. The infection models proved useful to assess virulence potential diversification, but for some isolates the relative values diverged in C. elegans and G. mellonella. Results also reinforce the concept of the occurrence of clonal diversification and co-existence of multiple phenotypes within the CF lungs, also with respect to pathogenicity. No clear trend of decrease (or increase) of the virulence potential throughout long-term infection was found but there is an apparent tendency for a clone/patient-dependent decrease of virulence when the G. mellonella model was used. The sole avirulent variant in both infection hosts was found to lack the small third replicon previously associated to virulence. Although possible, the in vivo loss of this nonessential megaplasmid was found to be a rare event (1 among a total of 64 isolates examined).
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Affiliation(s)
- Ana S Moreira
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Dalila Mil-Homens
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Sílvia A Sousa
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Carla P Coutinho
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Ana Pinto-de-Oliveira
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Christian G Ramos
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Sandra C Dos Santos
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Arsénio M Fialho
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Jorge H Leitão
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
| | - Isabel Sá-Correia
- a iBB-Institute for Bioengineering and Biosciences , Department of Bioengineering , Instituto Superior Técnico, Universidade de Lisboa , Lisbon , Portugal
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Toxin-Antitoxin Systems in Clinical Pathogens. Toxins (Basel) 2016; 8:toxins8070227. [PMID: 27447671 PMCID: PMC4963858 DOI: 10.3390/toxins8070227] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022] Open
Abstract
Toxin-antitoxin (TA) systems are prevalent in bacteria and archaea. Although not essential for normal cell growth, TA systems are implicated in multiple cellular functions associated with survival under stress conditions. Clinical strains of bacteria are currently causing major human health problems as a result of their multidrug resistance, persistence and strong pathogenicity. Here, we present a review of the TA systems described to date and their biological role in human pathogens belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and others of clinical relevance (Escherichia coli, Burkholderia spp., Streptococcus spp. and Mycobacterium tuberculosis). Better understanding of the mechanisms of action of TA systems will enable the development of new lines of treatment for infections caused by the above-mentioned pathogens.
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Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315. PLoS Genet 2016; 12:e1006172. [PMID: 27428258 PMCID: PMC4948915 DOI: 10.1371/journal.pgen.1006172] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/15/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315). It comprises an extra replicon (c2) of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1), another extra replicon(c3) of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the choreography of the cell cycle. Unlike higher organisms, bacteria typically carry their genetic information on a single chromosome. But in a few bacterial families the genome includes one to three additional chromosome-like DNA molecules. Because these families are rich in pathogenic and environmentally versatile species, it is important to understand how their split genomes evolved and how their maintenance is managed without confusion. We find that mitotic segregation (partition) of all three chromosomes of the cystic fibrosis type strain, Burkholderia cenocepacia J2315, proceeds from mid-cell to cell quarter positions, but that it occurs in a sequential manner, from largest chromosome to smallest. Positioning of each chromosome is specified solely by its own partition proteins. Nevertheless, the partition system of the largest chromosome appears also to play a global role in the cell cycle, by modulating the timing of initiation of replication. In addition, disrupting the partition systems of all three chromosomes induced specific cell abnormalities. Hence, although such bacteria are governed mainly by the largest, housekeeping chromosome, all the Par systems have insinuated themselves into cell cycle regulation to become indispensable for normal growth. Exploration of the underlying mechanisms should allow us to understand their full importance to bacterial life.
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Carlier A, Fehr L, Pinto-Carbó M, Schäberle T, Reher R, Dessein S, König G, Eberl L. The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environ Microbiol 2016; 18:2507-22. [PMID: 26663534 DOI: 10.1111/1462-2920.13184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
A majority of Ardisia species harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted hereditarily and have not yet been cultured outside of their host. Because the plants cannot develop beyond the seedling stage without their symbionts, the symbiosis is considered obligatory. We sequenced for the first time the genome of Candidatus Burkholderia crenata (Ca. B. crenata), the leaf nodule symbiont of Ardisia crenata. The genome of Ca. B. crenata is the smallest Burkholderia genome to date. It contains a large amount of insertion sequences and pseudogenes and displays features consistent with reductive genome evolution. The genome does not encode functions commonly associated with plant symbioses such as nitrogen fixation and plant hormone metabolism. However, we identified unique genes with a predicted role in secondary metabolism in the genome of Ca. B. crenata. Specifically, we provide evidence that the bacterial symbionts are responsible for the synthesis of compound FR900359, a cyclic depsipeptide with biomedical properties previously isolated from leaves of A. crenata.
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Affiliation(s)
- Aurelien Carlier
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland.,Department of Microbiology, University of Ghent, 9000, Gent, Belgium
| | - Linda Fehr
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Till Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Steven Dessein
- Plant Conservation and Population Biology, KU Leuven, 3001, Leuven, Belgium.,National Botanic Garden of Belgium, 1860, Meise, Belgium
| | - Gabriele König
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
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Miller RR, Hird TJ, Tang P, Zlosnik JEA. Whole-Genome Sequencing of Three Clonal Clinical Isolates of B. cenocepacia from a Patient with Cystic Fibrosis. PLoS One 2015; 10:e0143472. [PMID: 26599356 PMCID: PMC4658001 DOI: 10.1371/journal.pone.0143472] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/05/2015] [Indexed: 11/29/2022] Open
Abstract
Burkholderia cepacia complex bacteria are amongst the most feared of pathogens in cystic fibrosis (CF). The BCC comprises at least 20 distinct species that can cause chronic and unpredictable lung infections in CF. Historically the species B. cenocepacia has been the most prevalent in CF infections and has been associated in some centers with high rates of mortality. Modeling chronic infection by B. cenocepacia in the laboratory is challenging and no models exist which effectively recapitulate CF disease caused by BCC bacteria. Therefore our understanding of factors that contribute towards the morbidity and mortality caused by this organism is limited. In this study we used whole-genome sequencing to examine the evolution of 3 clonal clinical isolates of B. cenocepacia from a patient with cystic fibrosis. The first isolate was from the beginning of infection, and the second two almost 10 years later during the final year of the patients’ life. These isolates also demonstrated phenotypic heterogeneity, with the first isolate displaying the mucoid phenotype (conferred by the overproduction of exopolysaccharide), while one of the later two was nonmucoid. In addition we also sequenced a nonmucoid derivative of the initial mucoid isolate, acquired in the laboratory by antibiotic pressure. Examination of sequence data revealed that the two late stage isolates shared 20 variant nucleotides in common compared to the early isolate. However, despite their isolation within 10 months of one another, there was also considerable variation between the late stage isolates, including 42 single nucleotide variants and three deletions. Additionally, no sequence differences were identified between the initial mucoid isolate and its laboratory acquired nonmucoid derivative, however transcript analysis indicated at least partial down regulation of genes involved in exopolysaccharide production. Our study examines the progression of B. cenocepacia throughout chronic infection, including establishment of sub-populations likely evolved from the original isolate, suggestive of parallel evolution. Additionally, the lack of sequence differences between two of the isolates with differing mucoid phenotypes suggests that other factors, such as gene regulation, come into play in establishing the mucoid phenotype.
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Affiliation(s)
- Ruth R. Miller
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, University of British Columbia, Canada, Vancouver, British Columbia, Canada
| | - Trevor J. Hird
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick Tang
- British Columbia Centre for Disease Control, University of British Columbia, Canada, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - James E. A. Zlosnik
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Torraca V, Masud S, Spaink HP, Meijer AH. Macrophage-pathogen interactions in infectious diseases: new therapeutic insights from the zebrafish host model. Dis Model Mech 2015; 7:785-97. [PMID: 24973749 PMCID: PMC4073269 DOI: 10.1242/dmm.015594] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying macrophage biology in the context of a whole living organism provides unique possibilities to understand the contribution of this extremely dynamic cell subset in the reaction to infections, and has revealed the relevance of cellular and molecular processes that are fundamental to the cell-mediated innate immune response. In particular, various recently established zebrafish infectious disease models are contributing substantially to our understanding of the mechanisms by which different pathogens interact with macrophages and evade host innate immunity. Transgenic zebrafish lines with fluorescently labeled macrophages and other leukocyte populations enable non-invasive imaging at the optically transparent early life stages. Furthermore, there is a continuously expanding availability of vital reporters for subcellular compartments and for probing activation of immune defense mechanisms. These are powerful tools to visualize the activity of phagocytic cells in real time and shed light on the intriguing paradoxical roles of these cells in both limiting infection and supporting the dissemination of intracellular pathogens. This Review will discuss how several bacterial and fungal infection models in zebrafish embryos have led to new insights into the dynamic molecular and cellular mechanisms at play when pathogens encounter host macrophages. We also describe how these insights are inspiring novel therapeutic strategies for infectious disease treatment.
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Affiliation(s)
- Vincenzo Torraca
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Samrah Masud
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Annemarie H Meijer
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00298-14. [PMID: 24723723 PMCID: PMC3983312 DOI: 10.1128/genomea.00298-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Burkholderia cepacia complex (BCC) is a group of related bacterial species that are commonly isolated from environmental samples. Members of the BCC can cause respiratory infections in cystic fibrosis patients and immunocompromised individuals. We report here the genome sequence of Burkholderia cenocepacia H111, a well-studied model strain of the BCC.
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