Computational prediction of secreted proteins in gram-negative bacteria

被引：24

作者：

Hui, Xinjie ^{[1
]}

Chen, Zewei ^{[1
]}

Zhang, Junya ^{[1
]}

Lu, Moyang ^{[3
]}

Cai, Xuxia ^{[1
]}

Deng, Yuping ^{[1
]}

Hu, Yueming ^{[1
]}

Wang, Yejun ^{[1
,2
]}

机构：

[1] Shenzhen Univ, Youth Innovat Team Med Bioinformat, Hlth Sci Ctr, Shenzhen 518060, Peoples R China

[2] Shenzhen Univ, Dept Cell Biol & Genet, Hlth Sci Ctr, Shenzhen 518060, Peoples R China

[3] Army Med Univ, Coll Basic Med Sci, Chongqing 400038, Peoples R China

来源：

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL | 2021年 / 19卷

关键词：

Gram-negative bacteria; Prediction; Secreted protein; Transmembrane protein; Protein secretion system; OUTER-MEMBRANE PROTEINS; SIGNAL PEPTIDE PREDICTION; SUBCELLULAR-LOCALIZATION PREDICTION; ARGININE TRANSLOCATION PATHWAY; AMINO-ACID-COMPOSITION; SPANNING BETA-STRANDS; HIDDEN MARKOV MODEL; III SECRETION; IV SECRETION; ESCHERICHIA-COLI;

D O I：

10.1016/j.csbj.2021.03.019

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

引用

页码：1806 / 1828

页数：23

共 303 条

[1] Identification of protein secretion systems in bacterial genomes [J].

Abby, Sophie S. ;

Cury, Jean ;

Guglielmini, Julien ;

Neron, Bertrand ;

Touchon, Marie ;

Rocha, Eduardo P. C. .

SCIENTIFIC REPORTS, 2016, 6

[2] The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems [J].

Abby, Sophie S. ;

Rocha, Eduardo P. C. .

PLOS GENETICS, 2012, 8 (09)

[3] Type VII secretion - mycobacteria show the way [J].

Abdallah, M. Abdallah ;

Gey Van Pittius, Nicolaas C. ;

Champion, Patricia A. DiGiuseppe ;

Cox, Jeffery ;

Luirink, Joen ;

Vandenbroucke-Grauls, Christina M. J. E. ;

Appelmelk, Ben J. ;

Bitter, Wilbert .

NATURE REVIEWS MICROBIOLOGY, 2007, 5 (11) :883-891

[4] A unified catalog of 204,938 reference genomes from the human gut microbiome [J].

Almeida, Alexandre ;

Nayfach, Stephen ;

Boland, Miguel ;

Strozzi, Francesco ;

Beracochea, Martin ;

Shi, Zhou Jason ;

Pollard, Katherine S. ;

Sakharova, Ekaterina ;

Parks, Donovan H. ;

Hugenholtz, Philip ;

Segata, Nicola ;

Kyrpides, Nikos C. ;

Finn, Robert D. .

NATURE BIOTECHNOLOGY, 2021, 39 (01) :105-114

[5] Multicellular Bacteria Deploy the Type VI Secretion System to Preemptively Strike Neighboring Cells [J].

Alteri, Christopher J. ;

Himpsl, Stephanie D. ;

Pickens, Shannon R. ;

Lindner, Jonathon R. ;

Zora, Jonathan S. ;

Miller, Jessa E. ;

Arno, Peter D. ;

Straight, Samuel W. ;

Mobley, Harry L. T. .

PLOS PATHOGENS, 2013, 9 (09)

[6] Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI [J].

An, Yi ;

Wang, Jiawei ;

Li, Chen ;

Leier, Andre ;

Marquez-Lago, Tatiana ;

Wilksch, Jonathan ;

Zhang, Yang ;

Webb, Geoffrey I. ;

Song, Jiangning ;

Lithgow, Trevor .

BRIEFINGS IN BIOINFORMATICS, 2018, 19 (01) :148-161

[7] A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica [J].

Anderson, DM ;

Schneewind, O .

SCIENCE, 1997, 278 (5340) :1140-1143

[8] Reciprocal secretion of proteins by the bacterial type III machines of plant and animal pathogens suggests universal recognition of mRNA targeting signals [J].

Anderson, DM ;

Fouts, DE ;

Collmer, A ;

Schneewind, O .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (22) :12839-12843

[9] SignalP 5.0 improves signal peptide predictions using deep neural networks [J].

Armenteros, Jose Juan Almagro ;

Tsirigos, Konstantinos D. ;

Sonderby, Casper Kaae ;

Petersen, Thomas Nordahl ;

Winther, Ole ;

Brunak, Soren ;

von Heijne, Gunnar ;

Nielsen, Henrik .

NATURE BIOTECHNOLOGY, 2019, 37 (04) :420-+

[10] Sequence-Based Prediction of Type III Secreted Proteins [J].

Arnold, Roland ;

Brandmaier, Stefan ;

Kleine, Frederick ;

Tischler, Patrick ;

Heinz, Eva ;

Behrens, Sebastian ;

Niinikoski, Antti ;

Mewes, Hans-Werner ;

Horn, Matthias ;

Rattei, Thomas .

PLOS PATHOGENS, 2009, 5 (04)

← 1 2 3 4 5 6 7 8 9 10 →