PMC:3091639 / 6511-8613 JSONTXT

{"project":"2_test","denotations":[{"id":"20646324-10684935-10032175","span":{"begin":194,"end":196},"obj":"10684935"},{"id":"20646324-10684935-10032176","span":{"begin":367,"end":369},"obj":"10684935"},{"id":"20646324-1714846-10032177","span":{"begin":370,"end":372},"obj":"1714846"},{"id":"20646324-9675857-10032177","span":{"begin":370,"end":372},"obj":"9675857"},{"id":"20646324-9784136-10032177","span":{"begin":370,"end":372},"obj":"9784136"},{"id":"20646324-10684935-10032178","span":{"begin":1713,"end":1715},"obj":"10684935"},{"id":"20646324-10871362-10032179","span":{"begin":1727,"end":1729},"obj":"10871362"}],"text":"One of the most striking differences between the C. pneumoniae koala and human genomes were changes associated with the polymorphic membrane proteins (Pmps). Like C. pneumoniae of human origin [25,26], koala LPCoLN is predicted to encode 21 Pmps that are phylogenetically related to one of six basic subtypes (pmpA, B/C, D, E/F, G/I and H; Additional files 3 and 4) [25,27-29]. The organisation of the pmp loci of koala LPCoLN is conserved relative to the C. pneumoniae human isolates. However, where the four human isolates carry several interrupted pmp genes (Additional file 3), koala LPCoLN carries uninterrupted, full-length versions of the same genes, including pmpG3, pmpG4 and pmpE3 (Additional file 3). A global comparison of all pmp sequences reveals a total of 2015 SNPs (of which 994 generated an amino acid change; see Additional file 5 for approximate SNP positions) differentiating koala LPCoLN from the four C. pneumoniae human isolates, with the highest percentage of SNPs observed in pmpE4 (30.46%) and pmpE3 (6.95%). In addition to SNPs, several strain-specific (human versus animal) indels (insertions and deletions) were evident in pmpB, pmpE1, pmpG2, pmpG4, pmpG5, pmpG7, pmpG10, and pmpG13 (Additional file 3). Interestingly, the pmpG5 pseudogene is interrupted by a stop codon in all five strains albeit at different sites: LPCoLN carries a seven nt indel (GAT GTA C) at nt position 332, resulting in a TAA stop codon at nt position 346, while the four human isolates have a SNP (C to T) at nt 1483, resulting in a TAA stop codon (data not shown). Previous analyses of human isolates have revealed variable numbers of 393 nt tandem repeat segments in pmpG6, including two repeats in AR39 [25] and J138 [30], and three repeats in TW183 (Geng MM, Schuhmacher A, Muehldorfer I, Bensch KW, Schaefer KP, Schneider S, Pohl T, Essig A, Marre R, Melchers K: The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis, submitted) and CWL029 [26]. The LPCoLN genome carries three variable tandem repeats in pmpG6."}