GlyGly-CTERM and Rhombosortase: A C-Terminal Protein Processing Signal in a Many-to-One Pairing with a Rhomboid Family Intramembrane Serine Protease

被引:18
作者
Haft, Daniel H. [1 ]
Varghese, Neha [2 ]
机构
[1] J Craig Venter Inst, Dept Bioinformat, Rockville, MD USA
[2] Georgia Inst Technol, Atlanta, GA 30332 USA
来源
PLOS ONE | 2011年 / 6卷 / 12期
基金
美国国家卫生研究院;
关键词
MULTIPLE SEQUENCE ALIGNMENT; BIOLOGICAL FUNCTIONS; SURFACE-PROTEINS; PROTEOLYSIS; GENOMES; MODEL; MOTIF;
D O I
10.1371/journal.pone.0028886
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The rhomboid family of serine proteases occurs in all domains of life. Its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. The model member GlpG from Escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple X-ray crystal studies, yet its relationship to endogenous substrates is not well understood. Here we describe an apparent membrane anchoring C-terminal homology domain that appears in numerous genera including Shewanella, Vibrio, Acinetobacter, and Ralstonia, but excluding Escherichia and Haemophilus. Individual genomes encode up to thirteen members, usually homologous to each other only in this C-terminal region. The domain's tripartite architecture consists of motif, transmembrane helix, and cluster of basic residues at the protein C-terminus, as also seen with the LPXTG recognition sequence for sortase A and the PEP-CTERM recognition sequence for exosortase. Partial Phylogenetic Profiling identifies a distinctive rhomboid-like protease subfamily almost perfectly co-distributed with this recognition sequence. This protease subfamily and its putative target domain are hereby renamed rhombosortase and GlyGly-CTERM, respectively. The protease and target are encoded by consecutive genes in most genomes with just a single target, but far apart otherwise. The signature motif of the Rhombo-CTERM domain, often SGGS, only partially resembles known cleavage sites of rhomboid protease family model substrates. Some protein families that have several members with C-terminal GlyGly-CTERM domains also have additional members with LPXTG or PEP-CTERM domains instead, suggesting there may be common themes to the post-translational processing of these proteins by three different membrane protein superfamilies.
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页数:11
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共 29 条
[1]   Improved prediction of signal peptides: SignalP 3.0 [J].
Bendtsen, JD ;
Nielsen, H ;
von Heijne, G ;
Brunak, S .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 340 (04) :783-795
[2]   A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma [J].
Brossier, F ;
Jewett, TJ ;
Sibley, LD ;
Urban, S .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (11) :4146-4151
[3]   Comparative Bacterial Proteomics: Analysis of the Core Genome Concept [J].
Callister, Stephen J. ;
McCue, Lee Ann ;
Turse, Joshua E. ;
Monroe, Matthew E. ;
Auberry, Kenneth J. ;
Smith, Richard D. ;
Adkins, Joshua N. ;
Lipton, Mary S. .
PLOS ONE, 2008, 3 (02)
[4]   WebLogo: A sequence logo generator [J].
Crooks, GE ;
Hon, G ;
Chandonia, JM ;
Brenner, SE .
GENOME RESEARCH, 2004, 14 (06) :1188-1190
[5]  
Eddy Sean R, 2009, Genome Inform, V23, P205
[6]   MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].
Edgar, RC .
NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797
[7]   The Pfam protein families database [J].
Finn, Robert D. ;
Tate, John ;
Mistry, Jaina ;
Coggill, Penny C. ;
Sammut, Stephen John ;
Hotz, Hans-Rudolf ;
Ceric, Goran ;
Forslund, Kristoffer ;
Eddy, Sean R. ;
Sonnhammer, Erik L. L. ;
Bateman, Alex .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D281-D288
[8]   Rhomboid Proteases and their Biological Functions [J].
Freeman, Matthew .
ANNUAL REVIEW OF GENETICS, 2008, 42 :191-210
[9]   Bacillus anthracis Sortase A (SrtA) anchors LPXTG motif-containing surface proteins to the cell wall envelope [J].
Gaspar, AH ;
Marraffini, LA ;
Glass, EM ;
DeBord, KL ;
Ton-That, H ;
Schneewind, O .
JOURNAL OF BACTERIOLOGY, 2005, 187 (13) :4646-4655
[10]   Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic [J].
Haft, Daniel H. ;
Paulsen, Ian T. ;
Ward, Naomi ;
Selengut, Jeremy D. .
BMC BIOLOGY, 2006, 4 (1)