Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
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Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. / Chhabra, Swapnil R; Joachimiak, Marcin P; Petzold, Christopher J; Zane, Grant M; Price, Morgan N; Reveco, Sonia A; Fok, Veronica; Johanson, Alyssa R; Batth, Tanveer S; Singer, Mary; Chandonia, John-Marc; Joyner, Dominique; Hazen, Terry C; Arkin, Adam P; Wall, Judy D; Singh, Anup K; Keasling, Jay D.
In: PLOS ONE, Vol. 6, No. 6, 2011, p. e21470.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
AU - Chhabra, Swapnil R
AU - Joachimiak, Marcin P
AU - Petzold, Christopher J
AU - Zane, Grant M
AU - Price, Morgan N
AU - Reveco, Sonia A
AU - Fok, Veronica
AU - Johanson, Alyssa R
AU - Batth, Tanveer S
AU - Singer, Mary
AU - Chandonia, John-Marc
AU - Joyner, Dominique
AU - Hazen, Terry C
AU - Arkin, Adam P
AU - Wall, Judy D
AU - Singh, Anup K
AU - Keasling, Jay D
PY - 2011
Y1 - 2011
N2 - Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.
AB - Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.
KW - Bacterial Proteins/metabolism
KW - Desulfovibrio vulgaris/metabolism
KW - Escherichia coli/metabolism
KW - Mass Spectrometry
KW - Protein Binding
U2 - 10.1371/journal.pone.0021470
DO - 10.1371/journal.pone.0021470
M3 - Journal article
C2 - 21738675
VL - 6
SP - e21470
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 6
ER -
ID: 204047364