Abstract
Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO 2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 7005-7015 |
| Number of pages | 11 |
| Journal | Journal of Bacteriology |
| Volume | 188 |
| Issue number | 19 |
| DOIs | |
| State | Published - Oct 2006 |
| Externally published | Yes |
Fingerprint
ASJC Scopus subject areas
- Applied Microbiology and Biotechnology
- Immunology
Cite this
Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions. / Beller, Harry R.; Letain, Tracy E.; Chakicherla, Anu; Kane, Staci R.; Legler, Tina C.; Coleman, Matthew A.
In: Journal of Bacteriology, Vol. 188, No. 19, 10.2006, p. 7005-7015.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions
AU - Beller, Harry R.
AU - Letain, Tracy E.
AU - Chakicherla, Anu
AU - Kane, Staci R.
AU - Legler, Tina C.
AU - Coleman, Matthew A
PY - 2006/10
Y1 - 2006/10
N2 - Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO 2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.
AB - Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO 2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.
UR - http://www.scopus.com/inward/record.url?scp=33749341500&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33749341500&partnerID=8YFLogxK
U2 - 10.1128/JB.00568-06
DO - 10.1128/JB.00568-06
M3 - Article
C2 - 16980503
AN - SCOPUS:33749341500
VL - 188
SP - 7005
EP - 7015
JO - Journal of Bacteriology
JF - Journal of Bacteriology
SN - 0021-9193
IS - 19
ER -