TY - JOUR
T1 - Comparative temporal proteomics of a response regulator (S02426)-deficient strain and wild-type shewanella oneidensis MR-1 during chromate transformation
AU - Chourey, Karuna
AU - Thompson, Melissa R.
AU - Shah, Manesh
AU - Zhang, Bing
AU - Verberkmoes, Nathan C.
AU - Thompson, Dorothea K.
AU - Hettich, Robert L.
PY - 2009/1
Y1 - 2009/1
N2 - Predicted orphan response regulators encoded in the Shewanella oneidensis MR-1 genome are poorly understood from a cellular function perspective. Our previous transcriptomic and proteomic analyses demonstrated that an annotated DNA-binding response regulator, S02426, was significantly up-regulated in wild-type S. oneidensis cells at both the mRNA and protein levels in response to acute chromate [Cr(VI)] challenge, suggesting a potential regulatory role for this protein in metal stress pathways. To investigate the impact of S02426 activity on chromate stress response at a genome-wide scale, we describe here comparative and temporal proteome characterizations using multidimensional HPLC-MS/MS and statistical analysis to identify differentially expressed proteins in biological replicates of wild-type S. oneidensis MR-1 and a so2426 deletion (Δso2426) strain, which exhibited an impaired Cr(VI) transformation rate compared to that of the parental strain. Global protein profiles were examined at different time intervals (0,1, 3, 4 h) following exogenous chromate challenge. Results indicated that deletion of the so2426 gene negatively affected expression of a small protein subset (27 proteins) including those with annotated functions in siderophore biosynthesis (SO3032), Fe uptake (S04743), intracellular Fe storage (Bfr1), and other transport processes. Cr(VI) exposure and subsequent transformation dramatically increased the number of differentially expressed proteins detected, with up-regulated abundance patterns observed largely for proteins involved in general stress protection and detoxification strategies, cell motility, and protein fate. In addition, the proteome data sets were mined for amino acids with potential post-translational modifications (PTMs) indicative of a level of gene expression regulation extending beyond the transcriptional control imposed by S02426.
AB - Predicted orphan response regulators encoded in the Shewanella oneidensis MR-1 genome are poorly understood from a cellular function perspective. Our previous transcriptomic and proteomic analyses demonstrated that an annotated DNA-binding response regulator, S02426, was significantly up-regulated in wild-type S. oneidensis cells at both the mRNA and protein levels in response to acute chromate [Cr(VI)] challenge, suggesting a potential regulatory role for this protein in metal stress pathways. To investigate the impact of S02426 activity on chromate stress response at a genome-wide scale, we describe here comparative and temporal proteome characterizations using multidimensional HPLC-MS/MS and statistical analysis to identify differentially expressed proteins in biological replicates of wild-type S. oneidensis MR-1 and a so2426 deletion (Δso2426) strain, which exhibited an impaired Cr(VI) transformation rate compared to that of the parental strain. Global protein profiles were examined at different time intervals (0,1, 3, 4 h) following exogenous chromate challenge. Results indicated that deletion of the so2426 gene negatively affected expression of a small protein subset (27 proteins) including those with annotated functions in siderophore biosynthesis (SO3032), Fe uptake (S04743), intracellular Fe storage (Bfr1), and other transport processes. Cr(VI) exposure and subsequent transformation dramatically increased the number of differentially expressed proteins detected, with up-regulated abundance patterns observed largely for proteins involved in general stress protection and detoxification strategies, cell motility, and protein fate. In addition, the proteome data sets were mined for amino acids with potential post-translational modifications (PTMs) indicative of a level of gene expression regulation extending beyond the transcriptional control imposed by S02426.
KW - Chromate challenge
KW - Linear trapping quadrupole
KW - Liquid-chromatography-mass spectrometry
KW - Posttranslational modifications
KW - Response regulator-deficient strain
KW - Shewanella oneidensis
KW - Shotgun proteomics
UR - http://www.scopus.com/inward/record.url?scp=60849130139&partnerID=8YFLogxK
U2 - 10.1021/pr800776d
DO - 10.1021/pr800776d
M3 - Article
C2 - 19118451
AN - SCOPUS:60849130139
SN - 1535-3893
VL - 8
SP - 59
EP - 71
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 1
ER -