title: Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains.
abstract: Escherichia coli typically secretes many proteins into the periplasmic space, and the periplasmic proteins have been used for the secretory production of various proteins by the biotechnology industry. However, the identity of all of the E. coli periplasmic proteins remains unknown. Here, high-resolution periplasmic proteome reference maps of the E. coli K-12 and B strains were constructed and compared. Of the 145 proteins identified by tandem mass spectrometry, 61 proteins were conserved in the two strains, whereas 11 and 12 strain-specific proteins were identified for the E. coli K-12 and B strains, respectively. In addition, 27 proteins exhibited differences in intensities greater than 2-fold between the K-12 and B strains. The periplasmic proteins MalE and OppA were the most abundant proteins in the two E. coli strains. Distinctive differences between the two strains included several proteins that were caused by genetic variations, such as CybC, FliC, FliY, KpsD, MglB, ModA, and Ybl119, hydrolytic enzymes, particularly phosphatases, glycosylases, and proteases, and many uncharacterized proteins. Compared to previous studies, the localization of many proteins, including 30 proteins for the K-12 strain and 53 proteins for the B strain, was newly identified as periplasmic. This study identifies the largest number of proteins in the E. coli periplasm as well as the dynamics of these proteins. Additionally, these findings are summarized as reference proteome maps that will be useful for studying protein secretion and may provide new strategies for the enhanced secretory production of recombinant proteins.
authors.affiliation: Department of Biomolecular and Chemical Engineering, Dongyang University, 145 Dongyang-daero, Punggi-eup, Yeongju, Gyeongbuk 750-711, Republic of Korea. Electronic address: mjhan75@dyu.ac.kr.
authors.forename: Mee-Jung
authors.initials: MJ
authors.lastname: Han
authors.affiliation: Mass Spectrometry Research Center, Korea Basic Science Institute, 804-1 Yangcheong-Ri, Ochang-eup, Cheongwon-Gun, Chungbuk 863-883, Republic of Korea.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Mass Spectrometry Research Center, Korea Basic Science Institute, 804-1 Yangcheong-Ri, Ochang-eup, Cheongwon-Gun, Chungbuk 863-883, Republic of Korea.
authors.forename: Jung A
authors.initials: JA
authors.lastname: Kim
mesh_terms: D017124:Conserved Sequence; D004926:Escherichia coli / Q000145:classification / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000166:cytology / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017353:Gene Deletion; D019897:Periplasm / Q000378:metabolism*; D033903:Periplasmic Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012016:Reference Values; D013045:Species Specificity; D053719:Tandem Mass Spectrometry
chemical_list: D029968:Escherichia coli Proteins; D033903:Periplasmic Proteins; D020543:Proteome
keywords: Escherichia coli; Periplasmic fractionation; Periplasmic proteins; Proteome; Secretion