Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Sociality and disease transmission wikipedia , lookup
Quorum sensing wikipedia , lookup
Metagenomics wikipedia , lookup
Marine microorganism wikipedia , lookup
Human microbiota wikipedia , lookup
Magnetotactic bacteria wikipedia , lookup
Bacterial cell structure wikipedia , lookup
Community fingerprinting wikipedia , lookup
Triclocarban wikipedia , lookup
Cross-Domain and Within-Domain Horizontal Gene Transfer: Implications for Bacterial Pathogenicity 1. Pathogenomics Project 2. Cross-Domain Horizontal Gene Transfer Analysis 3. Horizontal Gene Transfer: Identifying Pathogenicity Islands Pathogenomics Goal: Identify previously unrecognized mechanisms of microbial pathogenicity using a combination of informatics, evolutionary biology, microbiology and genetics. Explosion of data 23 of the 37 publicly available microbial genome sequences are for bacterial pathogens Approximately 21,000 pathogen genes with no known function! >95 bacterial pathogen genome projects in progress … The need for new tools Prioritize new genes for further laboratory study Capitalize on the existing genomic data Bacterial Pathogenicity Processes of microbial pathogenicity at the molecular level are still minimally understood Pathogen proteins identified that manipulate host cells by interacting with, or mimicking, host proteins Yersinia Type III secretion system Approach Idea: Could we identify novel virulence factors by identifying bacterial pathogen genes more similar to host genes than you would expect based on phylogeny? Approach Search pathogen genes against databases. Identify those with eukaryotic similarity. Evolutionary significance. - Horizontal transfer? Similar by chance? Prioritize for biological study. - Previously studied in the laboratory? - Can UBC microbiologists study it? - C. elegans homolog? Modify screening method /algorithm Genome data for… Anthrax Cat scratch disease Chancroid Chlamydia Cholera Dental caries Diarrhea (E. coli etc.) Diphtheria Epidemic typhus Mediterranean fever Gastroenteritis Gonorrhea Legionnaires' disease Leprosy Leptospirosis Listeriosis Lyme disease Meliodosis Meningitis Necrotizing fasciitis Paratyphoid/enteric fever Peptic ulcers and gastritis Periodontal disease Plague Pneumonia Salmonellosis Scarlet fever Shigellosis Strep throat Syphilis Toxic shock syndrome Tuberculosis Tularemia Typhoid fever Urethritis Urinary Tract Infections Whooping cough +Hospital-acquired infections Bacterial Pathogens Chlamydophila psittaci Mycoplasma mycoides Mycoplasma hyopneumoniae Pasteurella haemolytica Pasteurella multicoda Ralstonia solanacearum Xanthomonas citri Xylella fastidiosa Respiratory disease, primarily in birds Contagious bovine pleuropneumonia Pneumonia in pigs Cattle shipping fever Cattle septicemia, pig rhinitis Plant bacterial wilt Citrus canker Pierce’s Disease - grapevines Bacterial wilt Approach Prioritized candidates Study function of gene in bacterium. Study function of homolog in model host (C. elegans) Collaborations with others Infection of mutant in model host DATABASE World Research Community C. elegans Interdisciplinary group Informatics/Bioinformatics Evolutionary Theory • BC Genome Sequence Centre • Centre for Molecular Medicine and Therapeutics • Dept of Zoology • Dept of Botany • Canadian Institute for Advanced Research Coordinator Pathogen Functions Host Functions • • • • • Dept. Medical Genetics • C. elegans Reverse Genetics Facility • Dept. Biological Sciences SFU Dept. Microbiology Biotechnology Laboratory Dept. Medicine BC Centre for Disease Control Pathogenomics Database: Bacterial proteins with unusual similarity with Eukaryotic proteins Haemophilus influenzae Rd-KW20 proteins most strongly matching eukaryotic proteins PhyloBLAST – a tool for analysis Brinkman et al. (2001) Bioinformatics. In Press. Trends in the Initial Analysis • Identifies the strongest cases of lateral gene transfer between bacteria and eukaryotes • Most common “cross-domain” horizontal transfers: Bacteria Unicellular Eukaryote • Identifies nuclear genes with potential organelle origins • A control: Method identifies all previously reported Chlamydia trachomatis “eukaryote-like” genes. First case: Bacterium Eukaryote Lateral Transfer Bacillus subtilis Escherichia coli Salmonella typhimurium Staphylococcua aureus Clostridium perfringens Clostridium difficile Trichomonas vaginalis Haemophilus influenzae N-acetylneuraminate lyase (NanA) of the protozoan Trichomonas vaginalis is 92-95% similar to NanA of Pasteurellaceae bacteria. Acinetobacillus actinomycetemcomitans 0.1 Pasteurella multocida de Koning et al. (2000) Mol. Biol. Evol. 17:1769-1773 N-acetylneuraminate lyase – role in pathogenicity? Pasteurellaceae •Mucosal pathogens of the respiratory tract T. vaginalis •Mucosal pathogen, causative agent of the STD Trichomonas N-acetylneuraminate lyase (sialic acid lyase, NanA) Hydrolysis of glycosidic linkages of terminal sialic residues in glycoproteins, glycolipids Sialidase Free sialic acid Transporter Free sialic acid NanA N-acetyl-D-mannosamine + pyruvate Involved in sialic acid metabolism Role in Bacteria: Proposed to parasitize the mucous membranes of animals for nutritional purposes Role in Trichomonas: ? Another case: A Sensor Histidine Kinase for a Two-component Regulation System Signal Transduction Histidine kinases common in bacteria Ser/Thr/Tyr kinases common in eukaryotes Candida However, a histidine kinase was recently identified in fungi, including pathogens Fusarium solani and Candida albicans How did it get there? Streptomyces Histidine Kinase. The Missing Link? Pseudomonas aeruginosa PhoQ 100 100 Xanthomonas campestris RpfC Vibrio cholerae TorS Escherichia coli TorS Escherichia coli RcsC 39 100 100 54 100 Candida albicans CaNIK1 100 Neurospora crassa NIK-1 51Fusarium solani FIK1 Fusarium solani FIK2 Streptomyces coelicolor SC4G10.06c 100 Streptomyces coelicolor SC7C7.03 Pseudomonas aeruginosa GacS 100 100Pseudomonas fluorescens GacS / ApdA Fungi virulence factor ? Pseudomonas tolaasii RtpA / PheN 86 100 0.1 100 100Pseudomonas syringae GacS / LemA Pseudomonas viridiflava RepA Azotobacter vinelandii GacS Erwinia carotovora RpfA / ExpS 100 100 Escherichia coli BarA Salmonella typhimurium BarA virulence = factor Reduced virulence of a Pseudomonas aeruginosa transposon mutant disrupted in the histidine kinase gene gacS Groups of 7-8 neutropenic mice challenged on two separate occasions with doses ranging from 8 to 8 x 106 bacteria Wildtype LD50 = 10 1 bacteria gacS mutant LD50 = 7,500 100 bacteria 750-fold increase Recent report: P. aeruginosa eukaryote-type Phospholipase plays a role in infection Wilderman et al. 2001. Mol Microbiol 39:291-304 • Phospholipase D (PLDs) virtually ubiquitous in eukaryotes (relatively uncommon in prokaryotes) • P. aeruginosa expresses PLD with significant (1e-38 BLAST Expect) similarity to eukaryotic PLDs • Part of a mobile 7 kb genetic element • Role in P. aeruginosa persistence in a chronic pulmonary infection model Eukaryote Bacteria Horizontal Transfer? Rat 0.1 Human Escherichia coli Caenorhabditis elegans Pig roundworm Methanococcus jannaschii Methanobacterium thermoautotrophicum E. coli Guanosine monophosphate reductase 81% similar to corresponding enzyme in humans and rats Bacillus subtilis Streptococcus pyogenes Aquifex aeolicus Acinetobacter calcoaceticus Haemophilus influenzae Chlorobium vibrioforme Role in virulence not yet investigated. Expanding the Cross-Domain Analysis • Identify cross-domain lateral gene transfer between bacteria, archaea and eukaryotes • No obvious correlation seen with protein functional classification • Most cases: no obvious correlation seen between “organisms involved” in potential lateral transfer Exceptions: – Unicellular eukaryotes – “Organelle-like” proteins in Rickettsia and Synechocystis – “Plant-like(?)” genes in the obligate intracellular bacteria Chlamydia “Plant-like” genes in Chlamydia Aquifex aeolicus 96 Haemophilus influenza 100 Escherichia coli Anabaena 100 Synechocystis 100 63 64 83 0.1 Chlamydia trachomatis Enoyl-acyl carrier protein reductase (involved in lipid metabolism) of Chlamydia trachomatis is similar to those of Plants Petunia x hybrida Nicotiana tabacum Brassica napus 99 Arabidopsis thaliana 52 Oryza sativa Organelle relationship? Notably more similar to plants than Synechocystis Eukaryote Top Hits in Bacterial Genomes (after excluding relatives of the same Family) No. of Eukaryotic Top Hits 300 Synechocystis 250 200 150 100 50 0 0 1000 2000 3000 4000 No. of Proteins in each Bacterial Genome 5000 6000 Eukaryote Top Hits in Bacterial Genomes (excluding "Family" and Synechocystis ) No. of Eukaryotic Top Hits 80 70 60 50 40 30 Rickettsia and Chlamydia 20 10 0 0 1000 2000 3000 No. of Proteins 4000 5000 6000 Proteins Homologous to Eukaryote Proteins (according to BLAST Exp=1) No of Proteins with Eukaryotic Homology 1800 1600 1400 1200 1000 800 600 400 200 0 0 1000 2000 3000 No. of Proteins 4000 5000 6000 Horizontal Gene Transfer and Bacterial Pathogenicity Transposons: ST enterotoxin genes in E. coli Prophages: Shiga-like toxins in EHEC Diptheria toxin gene, Cholera toxin Botulinum toxins Plasmids: Shigella, Salmonella, Yersinia Horizontal Gene Transfer and Bacterial Pathogenicity Pathogenicity Islands: Uropathogenic and Enteropathogenic E. coli Salmonella typhimurium Yersinia spp. Helicobacter pylori Vibrio cholerae Pathogenicity Islands Associated with – – – – Atypical %G+C tRNA sequences Transposases, Integrases and other mobility genes Flanking repeats IslandPath: Identifying Pathogenicity Islands Yellow circle = high %G+C Pink circle = low %G+C tRNA gene lies between the two dots rRNA gene lies between the two dots Both tRNA and rRNA lie between the two dots Dot is named a transposase Dot is named an integrase Neisseria meningitidis serogroup B strain MC58 Mean %G+C: 51.37 STD DEV: 7.57 %G+C 39.95 51.96 39.13 40.00 42.86 34.74 43.96 40.83 42.34 47.99 45.32 37.14 31.67 37.57 20.38 45.69 51.35 SD -1 -1 -1 -1 -2 -1 -1 -1 -2 -1 -2 Location Strand Product 1834676..1835113 + virulence associated pro. homolog 1835110..1835211 cryptic plasmid A-related 1835357..1835701 + hypothetical 1836009..1836203 + hypothetical 1836558..1836788 + hypothetical 1837037..1837249 + hypothetical 1837432..1838796 + conserved hypothetical 1839157..1839663 + conserved hypothetical 1839826..1841079 + conserved hypothetical 1841404..1843191 put. hemolysin activ. HecB 1843246..1843704 put. toxin-activating 1843870..1844184 hypothetical 1844196..1844495 hypothetical 1844476..1845489 hypothetical 1845558..1845974 hypothetical 1845978..1853522 hemagglutinin/hemolysin-rel. 1854101..1855066 + transposase, IS30 family Variance of the Mean %G+C for all Genes in a Genome: Correlation with bacteria’s clonal nature non-clonal clonal Variance of the Mean %G+C for all Genes in a Genome Is this a measure of clonality of a bacterium? Are intracellular bacteria more clonal because they are ecologically isolated from other bacteria? Pathogenomics Project: Future Developments • Identify eukaryotic motifs and domains in pathogen genes • Threader: Detect proteins with similar tertiary structure • Identify more motifs associated with • Pathogenicity islands • Virulence determinants • Functional tests for new predicted virulence factors • Expand analysis to include viral genomes Peter Wall Major Thematic Grant • Fundamental research • Interdisciplinary • Lack of fit with alternative funding sources Pathogenomics group Ann M. Rose, Yossef Av-Gay, David L. Baillie, Fiona S. L. Brinkman, Robert Brunham, Rachel C. Fernandez, B. Brett Finlay, Hans Greberg, Robert E.W. Hancock, Steven J. Jones, Patrick Keeling, Audrey de Koning, Don G. Moerman, Sarah P. Otto, B. Francis Ouellette, Ivan Wan. www.pathogenomics.bc.ca Universal role of this Histidine Kinase in pathogenicity? Pathogenic Fungi •Senses change in osmolarity of the environment •Role in hyphal formation pathogenicity Pseudomonas species plant pathogens •Role in excretion of secondary metabolites that are virulence factors or antimicrobials Virulence factor for human opportunistic pathogen Pseudomonas aeruginosa? A Histidine Kinase in Streptomyces. The Missing Link? Neurospora crassa NIK-1 Streptomyces coelicolor SC7C7 Fusarium solani FIK Candida albicans CHIK1 Erwinia carotovora EXPS Escherichia coli BARA Pseudomonas aeruginosa LEMA Pseudomonas syringae LEMA Pseudomonas viridiflava LEMA Pseudomonas tolaasii RTPA 0.1 Euykaryotic top hits in bacterial genomes (after excluding "tertiary" relatives) 350 No. of Eukaryote Hits Synechocystis 300 250 200 150 100 Rikettsia 50 0 0 1000 2000 3000 No. of Proteins 4000 5000 6000