Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae

Muhammad Ibrahim, Yu Shi, Hui Qiu, Bin Li, Amara Jabeen, Liping Li, He Liu, Michael Kube, Guanlin Xie, Yanli Wang, Guochang Sun

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.
LanguageEnglish
Article numbere49657
Pages1-10
Number of pages10
JournalPLoS ONE
Volume7
Issue number11
DOIs
Publication statusPublished - 15 Nov 2012
Externally publishedYes

Fingerprint

Acidovorax avenae subsp. avenae
Comamonadaceae
Membrane Proteins
Membranes
outer membrane proteins
Proteins
Computer Simulation
proteins
Virulence
Proteomics
Endopeptidase Clp
pathogenicity
ATP-Dependent Proteases
Lipoprotein Receptors
Pathogens
rice
proteomics
Flagellin
Porins
Plant Proteins

Bibliographical note

Copyright the Author(s) 2012. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Cite this

Ibrahim, Muhammad ; Shi, Yu ; Qiu, Hui ; Li, Bin ; Jabeen, Amara ; Li, Liping ; Liu, He ; Kube, Michael ; Xie, Guanlin ; Wang, Yanli ; Sun, Guochang. / Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae. In: PLoS ONE. 2012 ; Vol. 7, No. 11. pp. 1-10.
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abstract = "Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.",
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Ibrahim, M, Shi, Y, Qiu, H, Li, B, Jabeen, A, Li, L, Liu, H, Kube, M, Xie, G, Wang, Y & Sun, G 2012, 'Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae', PLoS ONE, vol. 7, no. 11, e49657, pp. 1-10. https://doi.org/10.1371/journal.pone.0049657

Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae. / Ibrahim, Muhammad; Shi, Yu; Qiu, Hui; Li, Bin; Jabeen, Amara; Li, Liping; Liu, He; Kube, Michael; Xie, Guanlin ; Wang, Yanli; Sun, Guochang.

In: PLoS ONE, Vol. 7, No. 11, e49657, 15.11.2012, p. 1-10.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae

AU - Ibrahim, Muhammad

AU - Shi, Yu

AU - Qiu, Hui

AU - Li, Bin

AU - Jabeen, Amara

AU - Li, Liping

AU - Liu, He

AU - Kube, Michael

AU - Xie, Guanlin

AU - Wang, Yanli

AU - Sun, Guochang

N1 - Copyright the Author(s) 2012. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2012/11/15

Y1 - 2012/11/15

N2 - Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.

AB - Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium.

U2 - 10.1371/journal.pone.0049657

DO - 10.1371/journal.pone.0049657

M3 - Article

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