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

Zhou L, Vorhölter F-J, He Y-Q, Jiang B-L, Tang J-L, Xu Y, Pühler A, He Y-W (2011)
BMC Genomics 12(1): 359.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ; ;
Abstract
ABSTRACT: One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the gene finding problem and a number of prokaryotic gene-finding software are available, gene recognition in bacteria is far from being always straightforward. This study reported a thorough search for new CDS in the two published Xcc genomes. 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. In the third, oligonucleotide microarray and RT-PCR analysis identified 147 CDSs with detectable mRNA transcripts. Finally, in-frame deletion and subsequent phenotype analysis of confirmed that Xcc_CDS002 encoding a novel SIR2-like domain protein is involved in virulence and Xcc_CDS1553 encoding a ArsR family transcription factor is involved in arsenate resistance. Despite sophisticated approaches available for genome annotation, many cellular transcripts have remained unidentified so far in Xcc genomes. 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.
Publishing Year
ISSN
PUB-ID

Cite this

Zhou L, Vorhölter F-J, He Y-Q, et al. Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics. 2011;12(1):359.
Zhou, L., Vorhölter, F. - J., He, Y. - Q., Jiang, B. - L., Tang, J. - L., Xu, Y., Pühler, A., et al. (2011). Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics, 12(1), 359. doi:10.1186/1471-2164-12-359
Zhou, L., Vorhölter, F. - J., He, Y. - Q., Jiang, B. - L., Tang, J. - L., Xu, Y., Pühler, A., and He, Y. - W. (2011). Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics 12, 359.
Zhou, L., et al., 2011. Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics, 12(1), p 359.
L. Zhou, et al., “Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris”, BMC Genomics, vol. 12, 2011, pp. 359.
Zhou, L., Vorhölter, F.-J., He, Y.-Q., Jiang, B.-L., Tang, J.-L., Xu, Y., Pühler, A., He, Y.-W.: Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics. 12, 359 (2011).
Zhou, Lian, Vorhölter, Frank-Jörg, He, Yong-Qiang, Jiang, Bo-Le, Tang, Ji-Liang, Xu, Yuquan, Pühler, Alfred, and He, Ya-Wen. “Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris”. BMC Genomics 12.1 (2011): 359.
This data publication is cited in the following publications:
This publication cites the following data publications:

20 Citations in Europe PMC

Data provided by Europe PubMed Central.

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
Global Transcriptome Profiling of Xanthomonas oryzae pv. oryzae under in planta Growth and in vitro Culture Conditions.
Lee SE, Gupta R, Jayaramaiah RH, Lee SH, Wang Y, Park SR, Kim ST., Plant Pathol J 33(5), 2017
PMID: 29018309
Angiogenesis is repressed by ethanol exposure during chick embryonic development.
Wang G, Zhong S, Zhang SY, Ma ZL, Chen JL, Lu WH, Cheng X, Chuai M, Lee KK, Lu DX, Yang X., J Appl Toxicol 36(5), 2016
PMID: 26177723
PM2.5 induces embryonic growth retardation: Potential involvement of ROS-MAPKs-apoptosis and G0/G1 arrest pathways.
Yuan X, Wang Y, Li L, Zhou W, Tian D, Lu C, Yu S, Zhao J, Peng S., Environ Toxicol 31(12), 2016
PMID: 26472167
PCDHB14- and GABRB1-like nervous system developmental genes are altered during early neuronal differentiation of NCCIT cells treated with ethanol.
Halder D, Mandal C, Lee BH, Lee JS, Choi MR, Chai JC, Lee YS, Jung KH, Chai YG., Hum Exp Toxicol 34(10), 2015
PMID: 25566775
Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies.
Schmid J, Sieber V, Rehm B., Front Microbiol 6(), 2015
PMID: 26074894
Ethanol-related alterations in gene expression patterns in the developing murine hippocampus.
Mandal C, Park KS, Jung KH, Chai YG., Acta Biochim Biophys Sin (Shanghai) 47(8), 2015
PMID: 26063602
CITED2 mutation and methylation in children with congenital heart disease.
Xu M, Wu X, Li Y, Yang X, Hu J, Zheng M, Tian J., J Biomed Sci 21(), 2014
PMID: 24456003
Long-term genomic and epigenomic dysregulation as a consequence of prenatal alcohol exposure: a model for fetal alcohol spectrum disorders.
Kleiber ML, Diehl EJ, Laufer BI, Mantha K, Chokroborty-Hoque A, Alberry B, Singh SM., Front Genet 5(), 2014
PMID: 24917881
Transcriptional reprogramming and phenotypical changes associated with growth of Xanthomonas campestris pv. campestris in cabbage xylem sap.
Dugé de Bernonville T, Noël LD, SanCristobal M, Danoun S, Becker A, Soreau P, Arlat M, Lauber E., FEMS Microbiol Ecol 89(3), 2014
PMID: 24784488
Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice.
Lossie AC, Muir WM, Lo CL, Timm F, Liu Y, Gray W, Zhou FC., Front Genet 5(), 2014
PMID: 24966868
Neuronal development genes are key elements mediating the reinforcing effects of methamphetamine, amphetamine, and methylphenidate.
Dela Peña I, Jeon SJ, Lee E, Ryu JH, Shin CY, Noh M, Cheong JH., Psychopharmacology (Berl) 230(3), 2013
PMID: 23783774
DNA methylation program during development.
Zhou FC., Front Biol (Beijing) 7(6), 2012
PMID: 23687512

41 References

Data provided by Europe PubMed Central.

Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins.
Frye RA., Biochem. Biophys. Res. Commun. 273(2), 2000
PMID: 10873683
Sirtuins: Sir2-related NAD-dependent protein deacetylases.
North BJ, Verdin E., Genome Biol. 5(5), 2004
PMID: 15128440
Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent.
Campbell DR, Chapman KE, Waldron KJ, Tottey S, Kendall S, Cavallaro G, Andreini C, Hinds J, Stoker NG, Robinson NJ, Cavet JS., J. Biol. Chem. 282(44), 2007
PMID: 17726022
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array.
Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM., Nat. Biotechnol. 18(12), 2000
PMID: 11101804
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.
Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C., Nucleic Acids Res. 30(17), 2002
PMID: 12202758
Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase.
Imai S, Armstrong CM, Kaeberlein M, Guarente L., Nature 403(6771), 2000
PMID: 10693811
The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases.
Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R., Proc. Natl. Acad. Sci. U.S.A. 97(11), 2000
PMID: 10811920
A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family.
Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S, Starai VJ, Avalos JL, Escalante-Semerena JC, Grubmeyer C, Wolberger C, Boeke JD., Proc. Natl. Acad. Sci. U.S.A. 97(12), 2000
PMID: 10841563
Metalloregulation of Soft Metal Resistance Pumps
AUTHOR UNKNOWN, 1999
Understanding how cells allocate metals using metal sensors and metallochaperones.
Tottey S, Harvie DR, Robinson NJ., Acc. Chem. Res. 38(10), 2005
PMID: 16231873
Genome-wide cDNA oligo design and its applications in Schizosaccharomyces pombe
AUTHOR UNKNOWN, 2004

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 21745409
PubMed | Europe PMC

Search this title in

Google Scholar