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RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.

Liu W, Dong H, Li J, Ou Q, Lv Y, Wang X, Xiang Z, He Y, Wu Q - Sci Rep (2015)

Bottom Line: For instance, the virB operon encoding type IV secretion system was significantly down-regulated, and 36 known transcriptional regulators (e.g., vjbR and blxR) were differentially expressed in 16 MΔotpR.Selected RNA-seq results were experimentally confirmed by RT-PCR and RT-qPCR.Overall, these results deciphered differential phenomena associated with virulence, environmental stresses and cell morphology in 16 MΔotpR and 16 M, which provided important information for understanding the detailed OtpR-regulated interaction networks and Brucella pathogenesis.

View Article: PubMed Central - PubMed

Affiliation: 1] Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China [2] Unit for Laboratory Animal Medicine and Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 [3] Center for Computational Medicine and Bioinformatics, The University of Michigan Medical School, Ann Arbor, MI 48109 [4] Beijing Senkang Biotech Development Co., LTD, Beijing 101400, People's Republic of China.

ABSTRACT
The response regulator OtpR is critical for the growth, morphology and virulence of Brucella melitensis. Compared to its wild type strain 16 M, B. melitensis 16 MΔotpR mutant has decreased tolerance to acid stress. To analyze the genes regulated by OtpR under acid stress, we performed RNA-seq whole transcriptome analysis of 16 MΔotpR and 16 M. In total, 501 differentially expressed genes were identified, including 390 down-regulated and 111 up-regulated genes. Among these genes, 209 were associated with bacterial metabolism, including 54 genes involving carbohydrate metabolism, 13 genes associated with nitrogen metabolism, and seven genes associated with iron metabolism. The 16 MΔotpR also decreased capacity to utilize different carbon sources and to tolerate iron limitation in culture experiments. Notably, OtpR regulated many Brucella virulence factors essential for B. melitensis intracellular survival. For instance, the virB operon encoding type IV secretion system was significantly down-regulated, and 36 known transcriptional regulators (e.g., vjbR and blxR) were differentially expressed in 16 MΔotpR. Selected RNA-seq results were experimentally confirmed by RT-PCR and RT-qPCR. Overall, these results deciphered differential phenomena associated with virulence, environmental stresses and cell morphology in 16 MΔotpR and 16 M, which provided important information for understanding the detailed OtpR-regulated interaction networks and Brucella pathogenesis.

No MeSH data available.


Related in: MedlinePlus

Basic metabolism regulated by Brucella OtpR identified in transcriptome analysis.Up-regulated genes in 16 MΔotpR are shown in green and down-regulated genes in 16 MΔotpR are shown in red.
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f2: Basic metabolism regulated by Brucella OtpR identified in transcriptome analysis.Up-regulated genes in 16 MΔotpR are shown in green and down-regulated genes in 16 MΔotpR are shown in red.

Mentions: The transcriptome analysis indicated that many genes associated with carbon and energy metabolism were significantly down-regulated in the otpR mutant under an acid stress. Most interestingly, these included twelve genes involved in the tricarboxylic acid (TCA) cycle (mdh, BMEI0137; sucD, BMEI0138; BMEI0139; sucA, BMEI0140; BMEI0791; gltA, BMEI0836; BMEI0855; BMEI0856; class I fumarate hydratase, BMEI1016; acn, BMEI1855; fumC, BMEII1051; and citrate lyase beta chain, BMEII1074; Fig. 2). The TCA cycle is critical for carbon metabolism and energy generation. The pyruvate metabolism supplies energy to living cells through the TCA cycle when oxygen is present (aerobic respiration), and alternatively through fermentation when oxygen is lacking44. Several genes relating the pyruvate metabolism were down-regulated in the otpR mutant, including mdh (BMEI0137), FAD-linked oxidase (BMEI0599), pdhB (BMEI0855), and aceF (BMEI0856). Furthermore, the entire NADH dehydrogenase operon was down-regulated in 16 MΔotpR. The genes encoding the cytochrome D ubiquinol oxidase subunits I, II, and III (BMEII0759, BMEII0760, BMEI1899, BMEI1900, BMEI1901) were all down-regulated in 16 MΔotpR. The NADH dehydrogenase operon and cytochrome D ubiquinol oxidase subunits participate in the oxidative phosphorylation, an important metabolic process for electron transport and energy release45.


RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.

Liu W, Dong H, Li J, Ou Q, Lv Y, Wang X, Xiang Z, He Y, Wu Q - Sci Rep (2015)

Basic metabolism regulated by Brucella OtpR identified in transcriptome analysis.Up-regulated genes in 16 MΔotpR are shown in green and down-regulated genes in 16 MΔotpR are shown in red.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542472&req=5

f2: Basic metabolism regulated by Brucella OtpR identified in transcriptome analysis.Up-regulated genes in 16 MΔotpR are shown in green and down-regulated genes in 16 MΔotpR are shown in red.
Mentions: The transcriptome analysis indicated that many genes associated with carbon and energy metabolism were significantly down-regulated in the otpR mutant under an acid stress. Most interestingly, these included twelve genes involved in the tricarboxylic acid (TCA) cycle (mdh, BMEI0137; sucD, BMEI0138; BMEI0139; sucA, BMEI0140; BMEI0791; gltA, BMEI0836; BMEI0855; BMEI0856; class I fumarate hydratase, BMEI1016; acn, BMEI1855; fumC, BMEII1051; and citrate lyase beta chain, BMEII1074; Fig. 2). The TCA cycle is critical for carbon metabolism and energy generation. The pyruvate metabolism supplies energy to living cells through the TCA cycle when oxygen is present (aerobic respiration), and alternatively through fermentation when oxygen is lacking44. Several genes relating the pyruvate metabolism were down-regulated in the otpR mutant, including mdh (BMEI0137), FAD-linked oxidase (BMEI0599), pdhB (BMEI0855), and aceF (BMEI0856). Furthermore, the entire NADH dehydrogenase operon was down-regulated in 16 MΔotpR. The genes encoding the cytochrome D ubiquinol oxidase subunits I, II, and III (BMEII0759, BMEII0760, BMEI1899, BMEI1900, BMEI1901) were all down-regulated in 16 MΔotpR. The NADH dehydrogenase operon and cytochrome D ubiquinol oxidase subunits participate in the oxidative phosphorylation, an important metabolic process for electron transport and energy release45.

Bottom Line: For instance, the virB operon encoding type IV secretion system was significantly down-regulated, and 36 known transcriptional regulators (e.g., vjbR and blxR) were differentially expressed in 16 MΔotpR.Selected RNA-seq results were experimentally confirmed by RT-PCR and RT-qPCR.Overall, these results deciphered differential phenomena associated with virulence, environmental stresses and cell morphology in 16 MΔotpR and 16 M, which provided important information for understanding the detailed OtpR-regulated interaction networks and Brucella pathogenesis.

View Article: PubMed Central - PubMed

Affiliation: 1] Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China [2] Unit for Laboratory Animal Medicine and Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 [3] Center for Computational Medicine and Bioinformatics, The University of Michigan Medical School, Ann Arbor, MI 48109 [4] Beijing Senkang Biotech Development Co., LTD, Beijing 101400, People's Republic of China.

ABSTRACT
The response regulator OtpR is critical for the growth, morphology and virulence of Brucella melitensis. Compared to its wild type strain 16 M, B. melitensis 16 MΔotpR mutant has decreased tolerance to acid stress. To analyze the genes regulated by OtpR under acid stress, we performed RNA-seq whole transcriptome analysis of 16 MΔotpR and 16 M. In total, 501 differentially expressed genes were identified, including 390 down-regulated and 111 up-regulated genes. Among these genes, 209 were associated with bacterial metabolism, including 54 genes involving carbohydrate metabolism, 13 genes associated with nitrogen metabolism, and seven genes associated with iron metabolism. The 16 MΔotpR also decreased capacity to utilize different carbon sources and to tolerate iron limitation in culture experiments. Notably, OtpR regulated many Brucella virulence factors essential for B. melitensis intracellular survival. For instance, the virB operon encoding type IV secretion system was significantly down-regulated, and 36 known transcriptional regulators (e.g., vjbR and blxR) were differentially expressed in 16 MΔotpR. Selected RNA-seq results were experimentally confirmed by RT-PCR and RT-qPCR. Overall, these results deciphered differential phenomena associated with virulence, environmental stresses and cell morphology in 16 MΔotpR and 16 M, which provided important information for understanding the detailed OtpR-regulated interaction networks and Brucella pathogenesis.

No MeSH data available.


Related in: MedlinePlus