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DNA Research Advance Access originally published online on March 3, 2006
DNA Research 2006 13(1):15-23; doi:10.1093/dnares/dsi027
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© The Author 2006. Kazusa DNA Research Institute
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Genome Sequence of the Cat Pathogen, Chlamydophila felis

Yoshinao Azuma1,* {dagger}, Hideki Hirakawa2 {dagger}, Atsushi Yamashita3 {dagger}, Yan Cai4, Mohd Akhlakur Rahman1, Harumi Suzuki1, Shigeki Mitaku5, Hidehiro Toh1,3, Susumu Goto6, Tomoyuki Murakami7, Kazuro Sugi7, Hideo Hayashi8, Hideto Fukushi4, Masahira Hattori3, Satoru Kuhara2 and Mutsunori Shirai1,*

1 Department of Microbiology, Yamaguchi University School of Medicine 1-1-1, Minamikogushi, Ube, Yamaguchi 755-8505, Japan
2 Graduate School of Genetic Resources Technology, Kyushu University 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
3 Kitasato Institute for Life Sciences, Kitasato University Kitasato 1-15-1, Sagamihara, Kanagawa 228-8555, Japan
4 Department of Veterinary Microbiology, Faculty of Agriculture, Gifu University 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
5 Department of Applied Physics, Graduate School of Engineering, Nagoya University Chikusa-ku, Nagoya Aichi 464-8603, Japan
6 Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan
7 Department of Clinical Research, National Sanyou Hospital Ube Yamaguchi 755-0241, Japan
8 Chugokugakuen University Okayama, Okayama 701-0197, Japan

Received 27 July 2005; revised 6 November 2005


   Abstract
Top
 Abstract
1. Introduction
 2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
 Supplementary Material
 Acknowledgements
 References
 
Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen. The C. felis genome is composed of a circular 1 166 239 bp chromosome encoding 1005 protein-coding genes and a 7552 bp circular plasmid. Comparison of C. felis gene contents with other Chlamydia species shows that 795 genes are common in the family Chlamydiaceae species and 47 genes are specific to C. felis. Phylogenetic analysis of the common genes reveals that most of the orthologue sets exhibit a similar divergent pattern but 14 C. felis genes accumulate more mutations, implicating that these genes may be involved in the evolutional adaptation to the C. felis-specific niche. Gene distribution and orthologue analyses reveal that two distinctive regions, i.e. the plasticity zone and frequently gene-translocated regions (FGRs), may play important but different roles for chlamydial genome evolution. The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution.

Key words: comparative genomics; genome inversion; obligate intercellular bacteria; chlamydia; infectious disease


   1. Introduction
Top
 Abstract
 1. Introduction
2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
 Supplementary Material
 Acknowledgements
 References
 
Chlamydiae are obligate intracellular eubacterial pathogens, including two genera and nine species based on ribosomal RNA gene sequences.1Go The genus Chlamydia includes a human conjunctivitis and sexually transmitted disease agent, C. trachomatis, a mouse pneumonia agent, Chlamydia muridarum and a pig pneumonia agent, Chlamydia suis. The other genus, Chlamydophila, includes a human pneumonia agent, C. pneumoniae and the animal disease or zoonosis agents, Chlamydophila psittaci, Chlamydophila caviae, Chlamydophila pecorum, Chlamydophila abortus and Chlamydophila felis, which infect birds, hamsters, cows, sheep and cats, respectively. The genomic DNA sequences of Chlamydiaceae have been published for five species, C. trachomatis,2Go C. muridarum,3Go C. pneumoniae,3Go–5Go C. caviae,6Go and C. abortus.7Go

Chlamydophila felis strain Fe/C-56, of which the whole genome DNA sequence has been determined in this study, is a frequent cause of infection in cats, largely causing conjunctivitis8Go as well as pneumonitis.9Go Seroepidemiological studies have shown that C. felis is widely spread among cats with prevalence rates of anti-C. felis Fe/Pn1 antibody in {approx}50% of street cats and {approx}20% of domestic cats and in 1.7% of the general human population and 8.8% of veterinarians in small animal clinics in Japan.10Go Although C. felis is a common pathogen in both humans and animals, the infection is rarely identified in humans.11Go,12Go Seroepidemiological data reveals, however, that the infection in humans may be more frequent and are most likely acquired from infected cats.10Go,13Go This suggests that the feline chlamydiosis is widely transmitted to humans when in close contact with infected cats, but it rarely causes any serious illness in humans. In contrast, infection of a taxonomically close chlamydial species, C. pneumoniae, is very frequent in human and is sometimes associated with a serious illness. Moreover, at extremely high frequencies of detection and culturing from atherosclerotic plaques, C. pneumoniae is suspected to involve the development of atherosclerosis.14Go The C. felis genome sequence and the comparative analysis with other chlamydial species will be of importance to investigate the genes relating to their pathogenicity in humans, tropisms in hosts and disease prevention as well as the evolution and intracellular parasitism.

Herein, we determined the complete sequence of C. felis genome and present the comparative analyses with other Chlamydia genome DNA sequences, especially to that of C. pneumoniae.


   2. Materials and Methods
Top
 Abstract
 1. Introduction
 2. Materials and Methods
4. Results and Discussion
 5. Conclusions
 Supplementary Material
 Acknowledgements
 References
 
2.1. Strain and culturing
Chlamydophila felis Japanese strain Fe/C-56 was originally isolated from conjunctival mucus of an infected 5-year-old female cat.8Go The genomic DNA for sequencing was prepared from C. felis elementary bodies in the culture medium of the fourth passage with McCoy cells, following five passages with fertile hens' eggs. Chlamydial culturing and detection were performed as described previously.15Go The nomenclature Chlamydophila felis is in dispute, but it is used here instead of the formerly used ‘a cat pneumonitis agent of Chlamydia psittaci’.1Go

2.2. DNA sequencing, assembling and gene prediction
The DNA sequencing was performed by a method using the whole genome shotgun.16Go The total 24 194 sequence reads gave an 11-fold coverage as average. The sequences were assembled and edited using the Phred/Phrap/Consed package software (University of Washington).17Go Protein-coding genes were first predicted using the combination of three programs, GenomeGambler,18Go GeneHacker plus19Go and Glimmer2.0,20Go and at last manually determined. Annotation for each genes was carried out by using programs BLASTP21Go and FASTA322Go against the non-redundant protein database. Transmembrane protein and tRNA genes were predicted using SOSUI23Go and tRNAscan-SE,24Go respectively. Putative inc genes werepredicted by informatics analysis using hydropathy.25Go,26Go

2.3. Data analysis
C. pneumoniae J138 genomic DNA sequence4Go was used for intra-genus comparative analyses. Genomic DNA sequences of other C. pneumoniae strains,3Go,5Go C. trachomatis2Go and C. muridarum3Go were used for inter-genera comparisons. C. caviae6Go and C. abortus7Go were used for analysis within evolutionarily closed species. The gene annotation was performed by homology search using FASTA3,22Go in which the similarity with the expectation values <10–4 was defined significant. Two genes conserved most reciprocally in two different organisms were assigned as orthologous genes using FASTA3. Classification of C. felis genes into Bacteria, Eucarya or Archaea is carried out based on no chlamydial orthologues, described previously.27Go The genes which were categorized into Eucarya and Archaea were confirmed by phylogenetic analyses using CLUSTALW.28Go The detail results for gene annotation, classification, gene divergence patterns and gene content comparisons are available in the Supplementary Tables 1–5 are available at www.dnares.oxfordjournals.org. The sequences in this paper have been deposited in the DDBJ/EMBL/GenBank database (accession; chromosome, AP006861, plasmid, AP006862).


   4. Results and Discussion
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 4. Results and Discussion
5. Conclusions
 Supplementary Material
 Acknowledgements
 References
 
4.1. Genome structure
The Chlamydophila felis Fe/C-56 contains a circular chromosome consisting of 1 166 239 bp and 1005 protein-coding genes (Table 1). The C. felis also harbors a 7552 bp plasmid, pCfe1, with eight genes and the copy number of the plasmid per chromosome is approximately 4.5 (Table 1). The overall G+C contents are 39.4 and 33.9% for the chromosome and plasmid, respectively. The G+C content and gene density appear to be uniform in the genome (Fig. 1). The putative replication origin (Ori) of the chromosome was determined based on comparisons with other chlamydial predicted Ori sequences, the GC skew and the assumed DnaA binding sequences. The replication terminal was determined at a maximum point, 583 kb from the Ori, in a curve of the cumulative GC skew.29Go There is no strong correlation between the directions of transcription and replication, except from the 880 kb position to the Ori observed slightly positive association. Many of the essential genes for transcription, translation and replication are located in a large region around the Ori.5Go


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  		Table 1. General features of C. felis Fe/C-56 chromosome and plasmid.

 

Figure 1
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  		Figure 1. Circular exhibition of the Chlamydophila felis Fe/C-56 genome. The outermost scale is marked for nucleic acid position in base pair. The track 1, gene positions and directions, clockwise in red and anti-clockwise in blue; track 2, common genes in three chlamydiae, C. felis, C. pneumoniae J1384Go and C. trachomatis2Go in gray; track 3, common genes in only two chlamydiae C. felis and C. pneumoniae in yellow, C. felis and C. trachomatis in light blue, C. felis specific in violet; track 4, paralogous genes in orange; track 5, gene origin classification, gram positive in dark blue, gram negative in violet, Archaea in green, Eukaryote in light purple; track 6, transmembrane proteins, inc family in pink, omp/pmp (outer membrane proteins or polymorphic outer membrane proteins) family in light green; track 7, total transmembrane proteins in orange; track 8, virulent factors; track 9, tRNA in light purple, rRNA in dark green; track 10, GC content, a radius is the average of genome GC content. Red and blue bars illustrate for plus and minus from the average (radius: 100%); innermost, respectively, GC skew, outside and inside of green circle indicate values>0 and values<0 calculated by (G–C/G+C).29Go Based on cumulus of the GC skew values and putative DnaA binding sites, a hypothetical origin, shown as Ori, is determined and the base numbers are counted from the origin in the direction settled arbitrarily.

 
4.2. Plasticity zone
To figure out C. felis Fe/C-56 genome characteristics, genome structure and gene contents of C. felis were compared with those of C. pneumoniae J138.4Go Although C. felis and C. pneumoniae relatively diverged far from each other, the two species share 879 orthologous genes and overall high synteny is exhibited, except a region surrounding the Ter, termed the plasticity zone.3Go,30Go Synteny of the orthologous genes between C. felis and C. pneumoniae are displayed in a concentric presentation (Fig. 2A). In this report, C. felis plasticity zone was assigned from 491 to 596 kb (CF0398-0484: 87 genes) including the Ter region.6Go In the C. felis plasticity zone, C. felis genes without C. pneumoniae J138 orthologues (C. felis no-C.pn-genes) are enriched with up to 30 genes out of the total 126 C. felis no-C.pn-genes on the chromosome (Fig. 2B). While 48 genes are functionally annotated out of 87 genes in the plasticity zone, C. felis no-C.pn-genes are 14 out of the 48 genes. The ratio (14:48) is much higher than the one in the C. felis chromosome (46:684). Most of the annotated genes in C. felis are conserved in some other organisms and thus the annotated no-C.pn-genes are thought to have dropped out of C. pneumoniae genome.3Go,6Go


Figure 2
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  		Figure 2. Analyses of the orthologous genes between Chlamydophila felis and Chlamydophila pneumoniae J138. (A), Circular presentation of locations of orthologous genes on whole chromosomes. Two orthologues are linked between C. felis (outer in green) and C. pneumoniae J1384Go (inner in blue). FGR1 and FGR2 indicate the ‘frequently gene-translocated regions’. (B), Gene distributions for C. felis genes without C. pneumoniae orthologues (C. felis no-C.pn-genes: blue), hypothetical genes (yellow) and omp/pmp genes (green) on the genome are calculated at window: 100 genes and step: 10 genes. The red line indicates a ratio of annotated C. felis no-C.pn-genes per annotated genes excepting omp/pmp. (C), Schematic orthologous linkages in the FGRs. Arrows in each chromosome exhibit omp/pmp genes in blue, annotated and conserved genes in green, annotated but specific to each species in gray, not-annotated and conserved genes in purple, not-annotated and specific to each species in red. Arrows outside the chromosomes show tRNA genes, directions of replication and C. pneumoniae seven repetitive sequences are indicated in yellow, orange and blue, respectively.

 
4.3. Frequently gene-translocated regions (FGRs)
When two orthologous genes between C. felis and C. pneumoniae J138 are linked on whole chromosomes shown with two concentric circles, segmental genome translocations are observed as sheaves of parallel lines horizontally crossing the origin-terminal axis between C. felis and C. pneumoniae (Fig. 2A). The regions with translocated genes in the C. felis genome are from 355 to 359 kb (CP0307-311) and from 759 to 878 kb (CP0654-0739, 86 genes), ones in C. pneumoniae J138 genome are from 1200 to 87 kb (Cpj1051-0072, connected at the termini of the genomic sequence) and from 485 to 550 kb (Cpj439-474) (Fig. 2C). The regions, termed frequently gene-translocated regions (FGRs) here, seems to have been formed by the genomic inversion events across the whole genome with the replication terminal region. When Chlamydophila felis genome is compared with Chlamydia trachomatis one, the same phenomenon for the gene translocation is observed in similar regions but the translocation between C. felis and C. trachomatis is more frequent than one between C. felis and C. pneumoniae (data not shown). The FGRs, which include the region reported as a hyper variable region31Go or tmh/Inc locus,7Go exhibit distinctive characteristics of the plasticity zone or the other regions of genome; (i) Out of 49 polymorphic outer membrane proteins genes omp/pmp (described below) in the C. felis chromosome, 22 omp/pmp genes are in the FGRs, whereas interestingly the plasticity zone contains no omp/pmp (Fig. 2B). (ii) Total 22 omp/pmp genes are conserved in C. pneumoniae J138, but in the FGRs only eight out of the 22 omp/pmp are conserved (P < 0.01). (iii) The omp/pmp and hypothetical genes are tandemly localized in the FGRs and seven repetitive sequences in C. pneumoniae genome contain omp/pmp genes, however C. felis genome lacks such repetitive sequences31Go (Fig. 2C). (iv) C. felis no-C.pn-genes are enriched (27 genes) in the FGRs similarly to the plasticity zone. But ratio of annotated C. felis no-C.pn-genes per annotated genes in the FGRs (2:57) is almost equal to the one in the whole chromosome (30:684), when the omp/pmp genes are excluded from the annotated genes. (v) Of the 66 total inc genes (described below), 16 inc genes are enriched in the plasticity zone (P < 0.01) but only 6 in the FGRs (P = 0.5).

Those characteristics implicate that the FGRs may assume a role for the multiplication of the omp/pmp genes rather than for genome reduction and inc genes may be on the verge of gene loss in the plasticity zone. Relationship between the gene translocation (or genome inversion) and gene multiplication are unknown, however it should be noted here that chlamydial genomes conserve an almost complete set of DNA recombination, repair genes and tRNA genes located in or near FGRs may be involved in the inversion fashion32Go (Fig. 2C). The characteristics observed in the FGRs of C. felis and C. pneumoniae are detected as well as in the FGRs of C. trachomatis.

4.4. Comparison within the family Chlamydiaceae
Four Chlamydiaceae species, i.e., C. felis, C. pneumoniae (three strains),3Go–5Go C. trachomatis2Go and C. muridarum3Go share 795 common genes (Fig. 3A), 104 genes are specific to C. felis. Adding, C. caviae6Go and C. abortus,7Go formerly belonging to C. psittaci as strains, to this analysis, 47 genes are specific to C. felis including an extra adenylate kinase gene (CF265) and 8 polymorphic outer membrane protein genes (CF379, 380, 718, 719, 723, 724, 728, 735).


Figure 3
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  		Figure 3. Orthologue comparison within the family Chlamydiaceae. (A) Numbers of orthologous and species specific genes represented in Venn diagrams, using Chlamydophila felis (this work), C. pneumoniae J138, AR39 and CWL029,3Go,5Go Chlamydia trachomatis2Go and C. muridarum.3Go (B) Divergence pattern for all orthologous gene sets, except two, CF0973 and CF0599. (C) A schematic branching pattern for an orthologous gene set showing C. felis-specific evolution. Based on the multiple alignment and phylogenic analysis of orthologues using CLUSTALW,28Go divergent distance is calculated as a branch length for an orthologous gene of each species. Genes are chosen for C. felis when the length of C. felis branch is longer than one of any other branch. (D) Numbers of genes exhibiting species specific evolution for C. felis, C. pneumoniae and C. trachomatis within the common 795 genes in Fig 3A.

 
All of the orthologue sets, except two, surprisingly illustrate the similar phylogenetic patterns, in which the genes from the C. felis and C. pneumoniae and those from C. trachomatis and C. muridarum, are closest (Fig. 3B). The two exceptional genes, CF0973 and CF0599, are too highly conserved to statistically draw relevant phylogenetic trees. Thus, no inter-genus gene exchanges are detected during the chlamydial species establishment in this method.

Regardless of the same phylogenetic pattern illustrated with orthologue sets, the lengths of C. felis divergence branches among the phylogenetic trees varied. To figure out C. felis genes which accumulate mutations more than the orthologous genes, the gene categorization was carried out using the definition that in the phylogenetic tree with C. felis, C. pneumoniae and C. trachomatis, a branch of C. felis gene from the divergent point is longest amongst three branches (Fig. 3C). Similar categorization was used for C. pneumoniae and C. trachomatis (Fig. 3D). Fourteen C. felis genes, such as four hypothetical genes (CF0008, CF0256, CF0470, CF0615), six genes encoding nucleic acid associating proteins (CF0085, CF0313, CF0899, CF0909, CF0925, CF0947) and four genes encoding membrane proteins including IncB (CF0032, CF0329, CF0415, CF0516) are categorized here as genes on faster evolution, implicating that these genes may be devoted for adaptation to the niche of C. felis.

Gene variation of tryptophan biosynthesis is one of the most remarkable features in the comparison of chlamydial gene repertories. C. trachomatis and C. pneumoniae, worldwide common parasites to humans but not to animals, contain partial and no tryptophan biosynthesis genes in the genomes, respectively. On the other hand, the genomes of the animal pathogens, C. felis and C. caviae, surprisingly not C. abortus, conserve the tryptophan operon consisting of trpA, B, F, C, D and R and related genes, kynU (CF0435-CF0440 and CF0434, respectively) are conserved.6Go,7Go,33Go Tryptophan depletion by IFN-{gamma} is thought as a crucial host defense mechanism against chlamydiae. On the contrary the chlamydial tryptophan biosynthesis gene is thought to be directly involved in chlamydial resistance against IFN-{gamma}.3Go,5Go,34Go IFN-{gamma} treatment of host cells was performed to show how susceptible C. felis is against IFN-{gamma} comparing with other chlamydial species without a complete tryptophan synthesis pathway. Neither inhibition of inclusion body formation nor reduction in the size of inclusion bodies on average were observed for C. felis in the tests with concentrations of up to 10 ng/ml of human IFN-{gamma}, while both the infection and growth of C. pneumoniae J38 and C. trachomatis were reduced under the same experimental conditions.34Go Tryptophan might play a key role for the molecular basis of host–parasite interaction in terms of IFN-{gamma} resistance, the gene repertories of tryptophan biosynthesis cannot explain all about host tropisms of individual chlamydial species. However, tryptophan utilization evokes all evolutional relationships between host defense and parasite infection, leading to chlamydial host and tissue tropisms.

4.5. Horizontal gene transfer
One of most interesting characteristics of chlamydial genome constituents is that a few percentages of the total genes are similar to genes of taxonomical distinctive organisms.2Go,35Go To figure out such genes in the C. felis genome, sequence-based gene classification was performed as a screening of the horizontal gene transfer from non-chlamydial organisms to the C. felis genome. Of the total of 1005 protein-coding genes of C. felis, 537, 59 and 5 genes may be derived from bacterial, eukaryotic and archaeal origins, respectively (Fig. 1). The numbers of chlamydial specific and ambiguous genes are 323 and 81, respectively. All the eukaryotic and archaeal origin genes in C. felis, except CF0874, are conserved and exhibit synteny in C. pneumoniae, C. trachomatis and C. muridarum. Based on phylogenetic analysis, the CF0874 coding a pyrimidine metabolism enzyme, orotate phosphoribosyl transferase, is seemed to be lost from C. trachomatis and C. muridarum. It is possible that the eukaryotic and archaeal genes in C. felis were laterally transferred before the genera divergence.2Go However, no further proof such as different G+C contents or genome structures is observed to show that the genes have been derived from taxonomical distinctive organisms.

4.6. Plasmid
Chlamydophila felis and many other chlamydial species carry a plasmid, pCf01, similar to other chlamydial plasmids.36Go Interestingly, two genes, pCf07 and pCf08, on the plasmid exhibit high similarities to CF0055 and CF0056 on C. felis chromosome, respectively. The CF0056 and pCf08 gene products show significant similarities to parA and minD gene products conserved widely among bacterial genomes. The phylogenetic analysis of the parA/minD family has illustrated that the chlamydial chromosome and plasmid genes form independent groups, both of which are separated from the other bacterial genes. Moreover, the divergent patterns in each chlamydial group are analogous (Fig. 4). It implies that the chlamydial plasmid had already been presented in an ancient chlamydia before the two genera divergence and that no intra-genus plasmid exchanges and no parA/minD gene exchanges between the chromosome and plasmid occurred after the divergence.


Figure 4
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  		Figure 4. Phylogenetic tree of parA/minD genes. The parA/minD genes used here are for chlamydial chromosome; Chlamydophila pneumoniae J138 (Accession: AP002548-9), Chlamydophila felis Fe/C-56 (CF0056), Chlamydophila caviae GPIC (AE016997-167), Chlamydia muridarum (AE002353-7) and Chlamydia trachomatis D/UW-3/CX (AE001329-1) and plasmid; Chlamydophila pneumoniae N16 pCpnE1 (X82078 [GenBank] -9), Chlamydophila felis Fe/C-56 pCfe1 (pCf08), Chlamydophila caviae GPIC pCpA1 (AE016997-168), Chlamydia muridarum pMoPn (AE002162 [GenBank] -6) and Chlamydia trachomatis pCHL1 (J03321 [GenBank] -7) and for other bacterial genes; Lactobacillus plantarum WCFS1 (AL935261 [GenBank] -129), Treponema pallidum Nichols (AE001208-8), Bacillus subtilis168 (Z99124 [GenBank] -191), Listeria monocytogenes EGD-e (AL591984 [GenBank] -146), Vibrio parahaemolyticus O3:K6 (AP005076-8), Vibrio cholerae N16961 (AE004271 [GenBank] -9), Buchnera aphidicola Sg (Schizaphisgraminum) (AE014108-5), Buchnera aphidicola APS (Acyrthosiphon pisum) (AP001119-13), Yersinia pestis CO92 (AJ414151-83), Salmonella enterica Typhi (AL627272-29) and Escherichia coli K12 (AE000216-6).

 
4.7. Inclusion membrane proteins (Incs)
Two hundred and sixty five genes in the C. felis genome contain transmembrane domain(s). The ratio of the number of transmembrane genes per the total number of genes in C. felis agrees with the finding in most bacteria,37Go but the distribution of the number of transmembrane domains is different from non-chlamydial bacteria. Noticeably, C. felis contains 75 genes coding two transmembrane domains, which is twice as many as some non-chlamydial bacteria. Informatics analysis25Go has revealed a total of 63 putative inc genes in the 75 genes. In addition, three more genes similar to eukaryotic myosin heavy chain genes have been classified as inc because four other genes partially similar to myosin heavy chain genes are categorized into the putative inc genes and two myosin heavy chain like protein of the C. pneumoniae J138 were experimentally shown to localize on inclusion bodies (data not shown). However, the functions of Inc proteins are still largely unknown. Forty-six putative inc genes are identified by the same method for C. felis inc identification in the genome of Parachlamydia amoebophila UWE25, which is diverged at about 700 million years ago from the last common ancestor with the family Chlamydiaceae38Go (data not shown). It indicates that before the divergence of the two chlamydial families, inc gene family has already expanded in the common ancestor genome.

4.8. Polymorphism membrane proteins (PMPs)
The omp/pmp genes, which encode outer membrane proteins or polymorphic membrane proteins, compose the most important and characteristic gene family in chlamydia. OMP/PMPs are reported to conserve N-terminal repeat motives, GGAI (or variants) and FXXN and terminate in a phenylanine residue.4Go,7Go,39Go In chlamydial genomes such as C. pneumoniae strains, C. trachomatis, C. muridarum, C. caviae and C. abortus, 18, 21, 9, 9, 17 and 18 omp/pmp genes are identified, respectively.2Go–7Go FASTA analysis with the all chlamydial omp/pmp genes reveals that in the C. felis genome 39 genes are similar to omp/pmp genes. Of the 39 putative omp/pmp genes, 18 genes (CF0209, CF0379, CF0721, CF0722, CF0725-CF0732, CF0735-CF0737, CF0801, CF0802, CF0992) conserve the N-terminal repeat motives and phenylanine at C-termini and 4 (CF0380, CF0719, CF0723, CF0733) and 6 (CF0101, CF0525, CF0720, CF0724, CF0734, CF0958) genes conserve only the N-terminal repeat motives or phenylanine at C-termini, respectively. No-C. felis genes are identified as new omp/pmp genes by the motif analysis. Gene expression of those genes and utilization of the gene products should be tested further.


   5. Conclusions
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
Supplementary Material
 Acknowledgements
 References
 
Here we exhibit genome analyses of a worldwide spread pathogen for pneumonia9Go and conjunctivitis8Go in cats, Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent). C. felis infection is rarely identified in humans while a few were reported,11Go,12Go but seroepidemiological study revealed that the prevalence rates of anti-C. felis Fe/Pn1 antibodies (1.7% and 8.8% for the general human population and veterinarians in small animal clinics in Japan, respectively) are rather higher than expected.10Go Thus the genome data of C. felis must be a useful tool to understand chlamydial tropism and pathogenicities, or to aid in the detection and prevention of C. felis causing diseases in both human and animals.


   Supplementary Material
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
 Supplementary Material
Acknowledgements
 References
 
Supplementary material is available online at www.dnaresearch.oxfordjournals.org.


   Acknowledgements
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
 Supplementary Material
 Acknowledgements
References
 
We thank A. Ishihama and P. Reay for reading of the manuscript; A. Nakazawa, K. Furuya and C. Yoshino for technical assistance. This study was supported by the Japan Society for the Promotion of Science, Research for the Future Program (JSPS-RETF 00L01411), a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan (KAKENHI: 14013043, 15019069, 16012245) and the Venture Business Laboratory, Yamaguchi University.


   Footnotes
 
*To whom correspondence should be addressed. Yoshinao Azuma (main corresponding author), Tel. (Japan)-836-22-2227, Fax. (Japan)-836-22-2415, E-mail: yazuma{at}yamaguchi-u.ac.jp. and Mutsunori Shirai, Tel. (Japan)-836-22-2226, Fax. (Japan)-836-22-2415, E-mail: mshirai{at}yamaguchi-u.ac.jp

{dagger}These authors contributed equally to this work.

Data deposition: The sequences reported in this paper have been deposited in the DDBJ/EMBL/GenBank database (accession chromosome, AP006861, plasmid, AP006862).

Communicated by Naotake Ogasawara Back


   References
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 4. Results and Discussion
 5. Conclusions
 Supplementary Material
 Acknowledgements
 References
 

  1. Everett, K. D., Bush, R. M., Andersen, A. A. 1999, Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov, each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms, Int. J. Syst. Bacteriol., 49, 415–440.[CrossRef][Medline]
  2. Stephens, R. S., Kalman, S., Lammel, C., et al. 1998, Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis, Science, 282, 754–759.[Abstract/Free Full Text]
  3. Read, T. D., Brunham, R. C., Shen, C., et al. 2000, Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39, Nucleic Acids Res., 28, 1397–1406.[Abstract/Free Full Text]
  4. Shirai, M., Hirakawa, H., Kimoto, M., et al. 2000, Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA, Nucleic Acids Res., 28, 2311–2314.[Abstract/Free Full Text]
  5. Kalman, S., Mitchell, W., Marathe, R., et al. 1999, Comparative genomes of Chlamydia pneumoniae and C. trachomatis, Nat. Genet., 21, 385–389.[CrossRef][ISI][Medline]
  6. Read, T. D., Myers, G. S., Brunham, R. C., et al. 2003, Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae, Nucleic Acids Res., 31, 2134–2147.[Abstract/Free Full Text]
  7. Thomson, N. R., Yeats, C., Bell, K., et al. 2005, The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation, Genome Res., 15, 629–640.[Abstract/Free Full Text]
  8. Cai, Y., Fukushi, H., Koyasu, S., Kuroda, E., Yamaguchi, T., Hirai, K. 2002, An etiological investigation of domestic cats with conjunctivitis and upper respiratory tract disease in Japan, J. Vet. Med. Sci., 64, 215–219.[CrossRef][ISI][Medline]
  9. Baker, K. A. 1942, A virus from a pneumonia of cats and its possible relation to the cause of a typical pneumonia in man, Science, 96, 475–476.[Free Full Text]
  10. Yan, C., Fukushi, H., Matsudate, H., et al. 2000, Seroepidemiological investigation of feline chlamydiosis in cats and humans in Japan, Microbiol. Immunol., 44, 155–160.[ISI][Medline]
  11. Schachter, J., Ostler, H. B., Meyer, K. F. 1969, Human infection with the agent of feline pneumonitis, Lancet, 1, 1063–1065.[CrossRef][ISI][Medline]
  12. Darougar, S., John, A. C., Viswalingam, M., Cornell, L., Jones, B. R. 1978, Isolation of Chlamydia psittaci from a patient with interstitial keratitis and uveitis associated with otological and cardiovascular lesions, Br. J. Ophthalmol., 62, 709–714.[Abstract/Free Full Text]
  13. Hartley, J. C., Stevenson, S., Robinson, A. J., et al. 2001, Conjunctivitis due to Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) acquired from a cat: case report with molecular characterization of isolates from the patient and cat, J. Infect., 43, 7–11.[ISI][Medline]
  14. Rosenfeld, M. E., Blessing, E., Lin, T. M., Moazed, T. C., Campbell, L. A., Kuo, C. 2000, Chlamydia, inflammation, and atherogenesis, J. Infect. Dis., 181, Suppl 3, S492–S497.
  15. Matsushima, H., Shirai, M., Ouchi, K., et al. 1999, Lymphotoxin inhibits Chlamydia pneumoniae growth in HEp-2 cells, Infect. Immun., 67, 3175–3179.[Abstract/Free Full Text]
  16. Hattori, M., Tsukahara, F., Furuhata, Y., et al. 1997, A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus, Nucleic Acids Res., 25, 1802–1808.[Abstract/Free Full Text]
  17. Gordon, D., Desmarais, C., Green, P. 2001, Automated finishing with autofinish, Genome Res., 11, 614–625.[Abstract/Free Full Text]
  18. Sakiyama, T., Takami, H., Ogasawara, N., et al. 2000, An automated system for genome analysis to support microbial whole-genome shotgun sequencing, Biosci. Biotechnol. Biochem., 64, 670–673.[CrossRef][Medline]
  19. Yada, T., Nakao, M., Totoki, Y., Nakai, K. 1999, Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models, Bioinformatics, 15, 987–993.[Abstract/Free Full Text]
  20. Delcher, A. L., Harmon, D., Kasif, S., White, O., Salzberg, S. L. 1999, Improved microbial gene identification with GLIMMER, Nucleic Acids Res., 27, 4636–4641.[Abstract/Free Full Text]
  21. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403–410.[CrossRef][ISI][Medline]
  22. Pearson, W. R. and Lipman, D. J. 1988, Improved tools for biological sequence comparison, Proc. Natl Acad. Sci. USA, 85, 2444–2448.[Abstract/Free Full Text]
  23. Hirokawa, T., Boon-Chieng, S., Mitaku, S. 1998, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics, 14, 378–379.[Abstract/Free Full Text]
  24. Lowe, T. M. and Eddy, S. R. 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955–964.[Abstract/Free Full Text]
  25. Toh, H., Miura, K., Shirai, M., Hattori, M. 2003, In silico inference of inclusion membrane protein family in obligate intracellular parasites chlamydiae, DNA Res., 10, 9–17.[Abstract]
  26. Bannantine, J. P., Griffiths, R. S., Viratyosin, W., Brown, W.J., Rockey, D. D. 2000, A secondary structure motif predictive of protein localization to the chlamydial inclusion membrane, Cell Microbiol., 2, 35–47.[CrossRef][ISI][Medline]
  27. Suckow, J. M., Amano, N., Ohfuku, Y., Kakinuma, J., Koike, H., Suzuki, M. 1998, A transcription frame-based analysis of the genomic DNA sequence of a hyper-thermophilic archaeon for the identification of genes, pseudo-genes and operon structures, FEBS Lett., 426, 86–92.[CrossRef][ISI][Medline]
  28. Thompson, J. D., Higgins, D. G., Gibson, T. J. 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673–4680.[Abstract/Free Full Text]
  29. Grigoriev, A. 1998, Analyzing genomes with cumulative skew diagrams, Nucleic Acids Res., 26, 2286–2290.[Abstract/Free Full Text]
  30. Alm, R. A., Ling, L. S., Moir, D. T., et al. 1999, Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori, Nature, 397, 176–180.[CrossRef][Medline]
  31. Daugaard, L., Christiansen, G., Birkelund, S. 2001, Characterization of a hypervariable region in the genome of Chlamydophila pneumoniae, FEMS Microbiol. Lett., 203, 241–248.[CrossRef][ISI][Medline]
  32. Dunham, M. J., Badrane, H., Ferea, T., et al. 2002, Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae, Proc. Natl Acad. Sci. USA, 99, 16144–16149.[Abstract/Free Full Text]
  33. Xie, G., Bonner, C. A., Jensen, R. A. 2002, Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture, Genome Biol., 3, research0051.[Medline]
  34. Rahman, M. A., Azuma, Y., Fukunaga, H., et al. 2005, Serotonin and melatonin, neurohormones for homeostasis, as novel inhibitors of infections by the intracellular parasite Chlamydia, J. Antimicrob. Chemother., 56, 861–868.[Abstract/Free Full Text]
  35. Brinkman, F. S., Blanchard, J. L., Cherkasov, A., et al. 2002, Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast, Genome Res., 12, 1159–1167.[Abstract/Free Full Text]
  36. Thomas, N. S., Lusher, M., Storey, C. C., Clarke, I. N. 1997, Plasmid diversity in Chlamydia, Microbiology, 143, 1847–1854.[Abstract]
  37. Mitaku, S., Ono, M., Hirokawa, T., Boon-Chieng, S., Sonoyama, M. 1999, Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system, Biophys. Chem., 82, 165–171.[CrossRef][ISI][Medline]
  38. Horn, M., Collingro, A., Schmitz-Esser, S., et al. 2004, Illuminating the evolutionary history of chlamydiae, Science, 304, 728–730.[Abstract/Free Full Text]
  39. Grimwood, J. and Stephens, R. S. 1999, Computational analysis of the polymorphic membrane protein superfamily of Chlamydia trachomatis and Chlamydia pneumoniae, Microb. Comp. Genomics, 4, 187–201.[Medline]
  40. Subtil, A. and Dautry-Varsat, A. 2004, Chlamydia: five years A.G. (after genome), Curr. Opin. Microbiol., 7, 85–92.[CrossRef][ISI][Medline]

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