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Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris.

Zhou L, Vorhölter FJ, He YQ, Jiang BL, Tang JL, Xu Y, Pühler A, He YW - BMC Genomics (2011)

Bottom Line: In the first, putative CDSs encoded in the two genomes were re-predicted using three gene finders, resulting in the identification of 2850 putative new CDSs.In the second, similarity searching was conducted and 278 CDSs were found to have homologs in other bacterial species.Through a combined strategy involving bioinformatic, postgenomic and genetic approaches, a reliable list of 306 new CDSs was identified and a more thorough understanding of some cellular processes was gained.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Molecular Characterization of GMOs and State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

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Functional classification of the new CDSs based on similarity searching.
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Figure 3: Functional classification of the new CDSs based on similarity searching.

Mentions: The majority of these CDSs (240 of 278) encodes conserved hypothetical proteins or hypothetical proteins (Figure 3). Eleven CDSs (Xcc_CDS105, Xcc_CDS107, Xcc_CDS411, Xcc_CDS1381, Xcc_CDS1831, Xcc_CDS2249, Xcc_CDS2324, Xcc_CDS2391, Xcc_CDS2668, Xcc_CDS2723, Xcc_CDS2777) encode putative secreted or exported proteins and three CDSs encode regulatory protein or transcription factors (Figure 3). Xcc_CDS002 encodes a Sir2-like transcriptional silencer protein; Xcc_CDS1553 encodes an ArsR family transcriptional regulator; Xcc_CDS1633 bears similarity to the Homeodomain of POU domain proteins or HTH_XRE domain proteins (Additional file 1). Two CDSs (Xcc_CDS2171 and Xcc_CDS2691) encode putative phenol hydroxylases and another 2 CDSs (Xcc_CDS2201 and Xcc_CDS2211) encode putative 50S ribosomal proteins. The remaining 20 CDSs respectively encode peptidase-like protein (Xcc_CDS073), hemolysin III (Xcc_CDS095), IS480b transposase (Xcc_CDS177), putative cell wall surface anchor family protein (Xcc_CDS346), endonuclease (Xcc_CDS528), chloramphenicol O-acetyltransferase (Xcc_CDS639), outer protein D (Xcc_CDS900), ABC transporter heme permease (Xcc_CDS1309), putative GTPase (Xcc_CDS1342), putative DNA methylase (Xcc_CDS1416), transmembrane protein (Xcc_CDS1446), putative tryptophan-rich sensory protein (Xcc_CDS1617), dihydroxydipicolinate synthase (Xcc_CDS1689), thermoresistant gluconokinase (Xcc_CDS1836), thiopurine methyltransferase (Xcc_CDS1899), putative tryptophan 2,3-dioxygenase oxidoreductase (Xcc_CDS2015), putative Atu protein (Xcc_CDS2546), WD40-like beta propeller (Xcc_CDS2674), ferric pseudobactins receptor protein (Xcc_CDS2714), and restriction endonuclease (Xcc_CDS2849) (Figure 3; Additional file 1).


Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris.

Zhou L, Vorhölter FJ, He YQ, Jiang BL, Tang JL, Xu Y, Pühler A, He YW - BMC Genomics (2011)

Functional classification of the new CDSs based on similarity searching.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3142249&req=5

Figure 3: Functional classification of the new CDSs based on similarity searching.
Mentions: The majority of these CDSs (240 of 278) encodes conserved hypothetical proteins or hypothetical proteins (Figure 3). Eleven CDSs (Xcc_CDS105, Xcc_CDS107, Xcc_CDS411, Xcc_CDS1381, Xcc_CDS1831, Xcc_CDS2249, Xcc_CDS2324, Xcc_CDS2391, Xcc_CDS2668, Xcc_CDS2723, Xcc_CDS2777) encode putative secreted or exported proteins and three CDSs encode regulatory protein or transcription factors (Figure 3). Xcc_CDS002 encodes a Sir2-like transcriptional silencer protein; Xcc_CDS1553 encodes an ArsR family transcriptional regulator; Xcc_CDS1633 bears similarity to the Homeodomain of POU domain proteins or HTH_XRE domain proteins (Additional file 1). Two CDSs (Xcc_CDS2171 and Xcc_CDS2691) encode putative phenol hydroxylases and another 2 CDSs (Xcc_CDS2201 and Xcc_CDS2211) encode putative 50S ribosomal proteins. The remaining 20 CDSs respectively encode peptidase-like protein (Xcc_CDS073), hemolysin III (Xcc_CDS095), IS480b transposase (Xcc_CDS177), putative cell wall surface anchor family protein (Xcc_CDS346), endonuclease (Xcc_CDS528), chloramphenicol O-acetyltransferase (Xcc_CDS639), outer protein D (Xcc_CDS900), ABC transporter heme permease (Xcc_CDS1309), putative GTPase (Xcc_CDS1342), putative DNA methylase (Xcc_CDS1416), transmembrane protein (Xcc_CDS1446), putative tryptophan-rich sensory protein (Xcc_CDS1617), dihydroxydipicolinate synthase (Xcc_CDS1689), thermoresistant gluconokinase (Xcc_CDS1836), thiopurine methyltransferase (Xcc_CDS1899), putative tryptophan 2,3-dioxygenase oxidoreductase (Xcc_CDS2015), putative Atu protein (Xcc_CDS2546), WD40-like beta propeller (Xcc_CDS2674), ferric pseudobactins receptor protein (Xcc_CDS2714), and restriction endonuclease (Xcc_CDS2849) (Figure 3; Additional file 1).

Bottom Line: In the first, putative CDSs encoded in the two genomes were re-predicted using three gene finders, resulting in the identification of 2850 putative new CDSs.In the second, similarity searching was conducted and 278 CDSs were found to have homologs in other bacterial species.Through a combined strategy involving bioinformatic, postgenomic and genetic approaches, a reliable list of 306 new CDSs was identified and a more thorough understanding of some cellular processes was gained.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Molecular Characterization of GMOs and State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Show MeSH
Related in: MedlinePlus