Open Access Research article

Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species

Candice M Mitchell1, Kelley M Hovis2, Patrik M Bavoil2, Garry SA Myers3, Jose A Carrasco2 and Peter Timms1*

Author Affiliations

1 Institute of Health and Biomedical Innovation, Faculty of Science and Technology, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia

2 Department of Microbial Pathogenesis, University of Maryland, Baltimore, Maryland 21201, USA

3 Institute for Genome Sciences, University of Maryland, Baltimore, Maryland 21201, USA

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BMC Genomics 2010, 11:442  doi:10.1186/1471-2164-11-442

Published: 21 July 2010

Additional files

Additional file 1:

Categories of targets for investigation. (1) genes with a prior demonstrated role in chlamydial biology and pathogenicity (n = 49); (2) genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6); (3) extrachromosomal elements, including a plasmid (n = 9) and bacteriophage-related genes (n = 2).

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Additional file 2:

C. pneumoniae-specific genes. A list of C. pneumoniae genes that have no significant similarity to other chlamydial species or organisms. E-value cutoff of 1 × 10-4 with manual curation.

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Additional file 3:

Comparative analysis of the C. pneumoniae polymorphic membrane proteins (Pmps). A comparison of the 21 Pmps revealed a high degree of sequence polymorphism and indels between the koala LPCoLN and human AR39, CWL029 and TW183 isolates. The TW183 and J138 isolates were well-conserved and therefore, TW183 also represents J138 in this figure. Arrows indicate the direction of transcription: green arrows show typical pmp characteristics, red arrows represent pseudogenes (numbers below arrows indicate stop codon position), and white arrows represent proteins with no relation to pmps (note the same orientation as pmpG10). Dashed lines indicate truncated products.

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Additional file 4:

Polymorphic outer membrane protein features of C. pneumoniae.

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Additional file 5:

Polymorphic outer membrane protein SNP position analysis of C. pneumoniae.

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Additional file 6:

T3S ortholog comparisons.

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Additional file 7:

Chlamydia MACPF. A BLAST alignment of the C. pneumoniae MACPF protein. From top to bottom: C. pneumoniae LPCoLN, C. pneumoniae J138, C. pneumoniae CWL029, C. felis FE/C-56, C. trachomatis A/HAR-13, C. trachomatis 6276, C. trachomatis D/UW-3/CX, C. trachomatis 70, C. trachomatis 434/Bu, C. muridarum Nigg, C. pneumoniae CWL029, C. abortus S26/3, C. felis Fe/C-56, Alcanivorax sp. DG881, Saccolglossus kowaleski, Theileria parva strain Muguga....

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Additional file 8:

Chlamydia has lost several steps in the pyrimidine biosynthesis pathway. All chlamydial genomes sequenced thus far, have lost the initial steps involved in pyrimidine biosynthesis. C. pneumoniae (Cpn), C. abortus (Cab), C. caviae (Cav) and C. felis (Cfe) contain a pyrE gene encoding an orotate phosphoribosyltransferase, while C. muridarum (Cmu) and C. trachomatis (Ctr) lack this gene. The next step in the pathway is via pyrF, which is absent from all chlamydial genomes. Interestingly, all six genomes have maintained the last three steps for the conversion of UMP into CTP. Adapted from Koonin and Galperin [66]. Gene names: carA, carbamoyl-phosphate synthase, small subunit; carB, carbamoyl-phosphate synthase, large subunit; pyrB, aspartate carbamoyltransferase; pyrC, dihydroorotase; pyrD, dihydroorotate dehydrogenase; pyrE, orotate phosphoribosyltransferase; pyrF, orotidine 5-phosphate decarboxylase; pyrH, uridylate kinase; ndk, nucleoside diphosphate kinase; pyrG, CTP synthase. Red boxes indicate gene loss, yellow boxes indicate the presence of a gene.

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Additional file 9:

Sequence comparison of the chlamydial plasmid. Multiple sequence alignment of the predicted amino acid sequence from C. pneumoniae koala LPCoLN (pCpnKo), C. pneumoniae horse N16 (pCpnE1), C. psittaci avian N352 (pCpA1), C. felis feline Fe/C-56 (pCfe1), C. caviae guinea pig GPIC (pCpGP1), C. muridarum mouse Nigg (pMoPn) and C. trachomatis human serovars A (pCTA), B (pJALI), E (pSW2) and L1 (pLVG440). The sequences are well-conserved across species, indicating some degree of ancestry among them. The C. pneumoniae plasmid shared a close relationship with C. psittaci, C. caviae and C. felis, while C. muridarum and C. trachomatis were highly conserved. Predicted functions include plasmid replication (ORF1 and ORF2), double-stranded DNA unwinding (ORF3), chlamydial pathogenesis (ORF5) and regulation of partitioning and copy number (ORF7 and ORF8) [34,67]. The functions of ORF4 and ORF6 remain to be determined.

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Additional file 10:

Plasmid similarity scores (%). Plasmid similarity scores based on multiple sequence alignment.

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Additional file 11:

List of C. pneumoniae target genes. Suggested target genes for detection, strain differentiation and plasmid identification in C. pneumoniae. See also reference [68].

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