Home LiteratureArticle Details
PMID: 15231807 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Validation Study

Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: transcriptome flexibility at diverse growth modes.

Journal of bacteriology ·Vol. 186 ·No. 14 ·2004-07-00 ·Pages 4748-58

Pappas CT, Sram J, Moskvin OV, Ivanov PS, Mackenzie RC, Choudhary M, Land ML, Larimer FW, Kaplan S, Gomelsky M

Abstract

A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes--aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis--were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirrored known functional changes, suggesting that massive changes in gene expression are the major means used by R. sphaeroides in adaptation to diverse conditions. Differential expression was observed for genes encoding putative new participants in these pathways (additional photosystem genes, duplicate NADH dehydrogenase, ATP synthases), whose functionality has yet to be investigated. The DNA microarray data correlated well with data derived from quantitative reverse transcription-PCR, as well as with data from the literature, thus validating the R. sphaeroides genechip as a powerful and reliable tool for studying unprecedented metabolic versatility of this bacterium.

MeSH Terms
Adaptation, Physiological Aerobiosis Anaerobiosis DNA, Intergenic Energy Metabolism/genetics Gene Expression Profiling Genes, Bacterial Genes, rRNA Oligonucleotide Array Sequence Analysis Oxidation-Reduction Photosynthesis Polymerase Chain Reaction/methods RNA, Bacterial/analysis RNA, Messenger/analysis RNA, Transfer/analysis Reproducibility of Results Rhodobacter sphaeroides/genetics,growth & development,metabolism Transcription, Genetic
Chemicals
DNA, Intergenic RNA, Bacterial RNA, Messenger RNA, Transfer
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Pappas Christopher T
Department of Molecular Biology, University of Wyoming, 1000 E. University Ave., Dept. 3944, Laramie, WY 82071, USA.
Sram Jakub
Moskvin Oleg V
Ivanov Pavel S
Mackenzie R Christopher
Choudhary Madhusudan
Land Miriam L
Larimer Frank W
Kaplan Samuel
Gomelsky Mark
References (39)
39 references, click to expand
  1. RNA expression analysis using an antisense Bacillus subtilis genome array.
    J Bacteriol. 2001 Dec;183(24):7371-80 PMID: 11717296
  2. A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides.
    Mol Microbiol. 2002 Aug;45(3):827-36 PMID: 12139627
  3. KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res. 2000 Jan 1;28(1):27-30 PMID: 10592173
  4. Cascade regulation of dimethyl sulfoxide reductase (dor) gene expression in the facultative phototroph Rhodobacter sphaeroides 2.4.1T.
    J Bacteriol. 1998 Jun;180(11):2924-30 PMID: 9603883
  5. Link between the membrane-bound pyridine nucleotide transhydrogenase and glutathione-dependent processes in Rhodobacter sphaeroides.
    J Bacteriol. 2002 Jan;184(2):400-9 PMID: 11751816
  6. Expression of the Rhodobacter sphaeroides cytochrome c2 structural gene.
    J Bacteriol. 1989 Jan;171(1):360-8 PMID: 2536660
  7. A novel cytochrome c oxidase from Rhodobacter sphaeroides that lacks CuA.
    Biochemistry. 1994 Mar 15;33(10):3113-9 PMID: 8130226
  8. Generalized approach to the regulation and integration of gene expression.
    Mol Microbiol. 2001 Mar;39(5):1116-23 PMID: 11251830
  9. Transcript abundance in yeast varies over six orders of magnitude.
    J Biol Chem. 2002 Apr 26;277(17):14363-6 PMID: 11882647
  10. Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1.
    J Bacteriol. 1997 Jan;179(1):128-34 PMID: 8981989
  11. Roles of CfxA, CfxB, and external electron acceptors in regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase expression in Rhodobacter sphaeroides.
    J Bacteriol. 1990 Apr;172(4):1736-48 PMID: 2108123
  12. The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1.
    Photosynth Res. 2001;70(1):19-41 PMID: 16228360
  13. Effects of light, oxygen, and substrates on steady-state levels of mRNA coding for ribulose-1,5-bisphosphate carboxylase and light-harvesting and reaction center polypeptides in Rhodopseudomonas sphaeroides.
    J Bacteriol. 1985 Jun;162(3):925-32 PMID: 2581935
  14. Correlation between Bacillus subtilis scoC phenotype and gene expression determined using microarrays for transcriptome analysis.
    J Bacteriol. 2001 Dec;183(24):7329-40 PMID: 11717292
  15. Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches.
    Nucleic Acids Res. 2001 Nov 15;29(22):E112 PMID: 11713332
  16. The cbb3 terminal oxidase of Rhodobacter sphaeroides 2.4.1: structural and functional implications for the regulation of spectral complex formation.
    Biochemistry. 1999 Mar 2;38(9):2688-96 PMID: 10052939
  17. The COG database: new developments in phylogenetic classification of proteins from complete genomes.
    Nucleic Acids Res. 2001 Jan 1;29(1):22-8 PMID: 11125040
  18. Expression of the Rhodobacter sphaeroides hemA and hemT genes, encoding two 5-aminolevulinic acid synthase isozymes.
    J Bacteriol. 1993 Apr;175(8):2292-303 PMID: 8468290
  19. 1-Deoxy-D-xylulose 5-phosphate synthase, the gene product of open reading frame (ORF) 2816 and ORF 2895 in Rhodobacter capsulatus.
    J Bacteriol. 2001 Jan;183(1):1-11 PMID: 11114895
  20. AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides.
    Cell. 2002 Sep 6;110(5):613-23 PMID: 12230978
  21. GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes.
    Mol Microbiol. 2002 Sep;45(5):1277-87 PMID: 12207696
  22. Identification and in vivo characterization of PpaA, a regulator of photosystem formation in Rhodobacter sphaeroides.
    Microbiology. 2003 Feb;149(Pt 2):377-88 PMID: 12624200
  23. Kinetic studies of pigment synthesis by non-sulfur purple bacteria.
    J Cell Physiol. 1957 Feb;49(1):25-68 PMID: 13416343
  24. The molecular regulation of the reductive pentose phosphate pathway in Proteobacteria and Cyanobacteria.
    Arch Microbiol. 1996 Sep;166(3):141-50 PMID: 8703190
  25. The Q gene of Rhodobacter sphaeroides: its role in puf operon expression and spectral complex assembly.
    J Bacteriol. 1994 May;176(10):2946-61 PMID: 8188596
  26. Interdependent expression of the ccoNOQP-rdxBHIS loci in Rhodobacter sphaeroides 2.4.1.
    J Bacteriol. 2002 Oct;184(19):5330-8 PMID: 12218019
  27. Over 1000 genes are involved in the DNA damage response of Escherichia coli.
    Mol Microbiol. 2002 Apr;44(1):89-105 PMID: 11967071
  28. In vivo analysis of puf operon expression in Rhodobacter sphaeroides after deletion of a putative intercistronic transcription terminator.
    J Bacteriol. 1988 Oct;170(10):4681-92 PMID: 2459108
  29. Coding in the noncoding DNA strand: A novel mechanism of gene evolution?
    J Mol Evol. 2000 Dec;51(6):600-6 PMID: 11116333
  30. A second and unusual pucBA operon of Rhodobacter sphaeroides 2.4.1: genetics and function of the encoded polypeptides.
    J Bacteriol. 2003 Oct;185(20):6171-84 PMID: 14526029
  31. Artemis: sequence visualization and annotation.
    Bioinformatics. 2000 Oct;16(10):944-5 PMID: 11120685
  32. Control of photosystem formation in Rhodobacter sphaeroides.
    J Bacteriol. 1998 Jun;180(11):2801-9 PMID: 9603864
  33. BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms.
    Trends Biochem Sci. 2002 Oct;27(10):497-500 PMID: 12368079
  34. The puf operon region of Rhodobacter sphaeroides.
    Photosynth Res. 1988 Jan;19(1-2):39-61 PMID: 24425367
  35. Summaries of Affymetrix GeneChip probe level data.
    Nucleic Acids Res. 2003 Feb 15;31(4):e15 PMID: 12582260
  36. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  37. SMART: a web-based tool for the study of genetically mobile domains.
    Nucleic Acids Res. 2000 Jan 1;28(1):231-4 PMID: 10592234
  38. Photosynthetic electron transport and anaerobic metabolism in purple non-sulfur phototrophic bacteria.
    Antonie Van Leeuwenhoek. 1994;66(1-3):151-64 PMID: 7747929
  39. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays.
    Nucleic Acids Res. 2002 May 15;30(10):e48 PMID: 12000853
Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.186.14.4748-4758.2004
Published
2004-07-00
Pages
4748-58
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC438620
Subset
IM
Grants
NCRR NIH HHS · P20 RR015640 · United States
NIGMS NIH HHS · R01 GM015590 · United States
NIGMS NIH HHS · GM15590 · United States
NCRR NIH HHS · P20 RR15640 · United States
External Links
PubMed source DOI: 10.1128/JB.186.14.4748-4758.2004 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2