Novel overlapping coding sequences in Chlamydia trachomatis

Klaus Thorleif Jensen; Lise Petersen; Søren Falk; Pernille Iversen; Peter Andersen; Michael Theisen; A. Krogh

doi:10.1111/j.1574-6968.2006.00480.x

Novel overlapping coding sequences in Chlamydia trachomatis

Klaus Thorleif Jensen, Lise Petersen, Søren Falk, Pernille Iversen, Peter Andersen, Michael Theisen, A. Krogh

Functional genomics

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

15 Citationer (Scopus)

Abstract

Udgivelsesdato: December 2006

Originalsprog	Engelsk
Tidsskrift	FEMS Microbiology Reviews
Vol/bind	265
Udgave nummer	1
Sider (fra-til)	106-17
ISSN	0168-6445
DOI	https://doi.org/10.1111/j.1574-6968.2006.00480.x
Status	Udgivet - 2006

Bibliografisk note

KEYWORDS
Chlamydia trachomatis • gene prediction • overlapping genes

Adgang til dokumentet

10.1111/j.1574-6968.2006.00480.x

Citationsformater

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title = "Novel overlapping coding sequences in Chlamydia trachomatis",

abstract = "Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.",

author = "Jensen, {Klaus Thorleif} and Lise Petersen and S{\o}ren Falk and Pernille Iversen and Peter Andersen and Michael Theisen and A. Krogh",

note = "KEYWORDS Chlamydia trachomatis • gene prediction • overlapping genes",

year = "2006",

doi = "10.1111/j.1574-6968.2006.00480.x",

language = "English",

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T1 - Novel overlapping coding sequences in Chlamydia trachomatis

AU - Jensen, Klaus Thorleif

AU - Petersen, Lise

AU - Falk, Søren

AU - Iversen, Pernille

AU - Andersen, Peter

AU - Theisen, Michael

AU - Krogh, A.

N1 - KEYWORDS Chlamydia trachomatis • gene prediction • overlapping genes

PY - 2006

Y1 - 2006

N2 - Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.

AB - Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.

U2 - 10.1111/j.1574-6968.2006.00480.x

DO - 10.1111/j.1574-6968.2006.00480.x

M3 - Journal article

SN - 0168-6445

VL - 265

SP - 106

EP - 117

JO - FEMS Microbiology Reviews

JF - FEMS Microbiology Reviews

IS - 1

ER -