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PMID: 12682364 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

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

Nucleic acids research ·Vol. 31 ·No. 8 ·2003-04-15 ·Pages 2134-47

Read TD, Myers GS, 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

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.

MeSH Terms
Adhesins, Bacterial/genetics Amino Acid Sequence Carrier Proteins/genetics Chlamydiaceae/genetics Chlamydophila psittaci/genetics Chromosomes, Bacterial/genetics DNA, Bacterial/chemistry,genetics Escherichia coli Proteins Evolution, Molecular Genome, Bacterial Molecular Sequence Data Plasmids/genetics Sequence Analysis, DNA Sequence Homology, Amino Acid Virulence/genetics
Chemicals
Adhesins, Bacterial Carrier Proteins DNA, Bacterial Escherichia coli Proteins invasin, Yersinia eaeA protein, E coli
Authors & Affiliations
21 authors, click to expand affiliations / ORCID
Read T D
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. [email protected]
Myers G S A
Brunham R C
Nelson W C
Paulsen I T
Heidelberg J
Holtzapple E
Khouri H
Federova N B
Carty H A
Umayam L A
Haft D H
Peterson J
Beanan M J
White O
Salzberg S L
Hsia R-c
McClarty G
Rank R G
Bavoil P M
Fraser C M
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg321
Email
[email protected]
Published
2003-04-15
Pages
2134-47
Language
English
Region
England
NLM ID
0411011
PMCID
PMC153749
Subset
IM
Grants
NIAID NIH HHS · AI43359 · United States
Databases
GENBANK
AE015925, AE015926
External Links
PubMed source DOI: 10.1093/nar/gkg321 PMC Full Text View journal details
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