Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): Examining the role of niche-specific genes in the evolution of the Chlamydiaceae

Read, TD; Myers, GSA; Brunham, RC; Nelson, WC; Paulsen, IT; Heidelberg, J; Holtzapple, E; Khouri, H; Federova, NB; Carty, HA; Umayam, LA; Haft, DH; Peterson, J; Beanan, MJ; White, O; Salzberg, SL; Hsia, RC; McClarty, G; Rank, RG; Bavoil, PM; Fraser, CM

Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): Examining the role of niche-specific genes in the evolution of the Chlamydiaceae

Read, TD Myers, GSA

Brunham, RC Nelson, WC Paulsen, IT Heidelberg, J Holtzapple, E Khouri, H Federova, NB Carty, HA Umayam, LA Haft, DH Peterson, J Beanan, MJ White, O Salzberg, SL Hsia, RC McClarty, G Rank, RG Bavoil, PM Fraser, CM

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Publication Type:: Journal Article
Citation:: Nucleic Acids Research, 2003, 31 (8), pp. 2134 - 2147
Issue Date:: 2003-04-15

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Field	Value	Language
dc.contributor.author	Read, TD	en_US
dc.contributor.author	Myers, GSA https://orcid.org/0000-0002-4756-4810	en_US
dc.contributor.author	Brunham, RC	en_US
dc.contributor.author	Nelson, WC	en_US
dc.contributor.author	Paulsen, IT	en_US
dc.contributor.author	Heidelberg, J	en_US
dc.contributor.author	Holtzapple, E	en_US
dc.contributor.author	Khouri, H	en_US
dc.contributor.author	Federova, NB	en_US
dc.contributor.author	Carty, HA	en_US
dc.contributor.author	Umayam, LA	en_US
dc.contributor.author	Haft, DH	en_US
dc.contributor.author	Peterson, J	en_US
dc.contributor.author	Beanan, MJ	en_US
dc.contributor.author	White, O	en_US
dc.contributor.author	Salzberg, SL	en_US
dc.contributor.author	Hsia, RC	en_US
dc.contributor.author	McClarty, G	en_US
dc.contributor.author	Rank, RG	en_US
dc.contributor.author	Bavoil, PM	en_US
dc.contributor.author	Fraser, CM	en_US
dc.date.issued	2003-04-15	en_US
dc.identifier.citation	Nucleic Acids Research, 2003, 31 (8), pp. 2134 - 2147	en_US
dc.identifier.issn	0305-1048	en_US
dc.identifier.uri	http://hdl.handle.net/10453/39766
dc.description.abstract	The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.	en_US
dc.relation.ispartof	Nucleic Acids Research	en_US
dc.relation.isbasedon	10.1093/nar/gkg321	en_US
dc.subject.classification	Developmental Biology	en_US
dc.subject.mesh	Chromosomes, Bacterial	en_US
dc.subject.mesh	Chlamydiaceae	en_US
dc.subject.mesh	Chlamydophila psittaci	en_US
dc.subject.mesh	Adhesins, Bacterial	en_US
dc.subject.mesh	Escherichia coli Proteins	en_US
dc.subject.mesh	Carrier Proteins	en_US
dc.subject.mesh	DNA, Bacterial	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Virulence	en_US
dc.subject.mesh	Amino Acid Sequence	en_US
dc.subject.mesh	Sequence Homology, Amino Acid	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Plasmids	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.title	Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): Examining the role of niche-specific genes in the evolution of the Chlamydiaceae	en_US
dc.type	Journal Article
utslib.citation.volume	8	en_US
utslib.citation.volume	31	en_US
utslib.for	05 Environmental Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.issue	8	en_US
pubs.publication-status	Published	en_US
pubs.volume	31	en_US

Abstract:

The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.

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http://hdl.handle.net/10453/39766