Non-classical protein secretion in bacteria

被引:562
作者
Bendtsen, JD [1 ]
Kiemer, L [1 ]
Fausboll, A [1 ]
Brunak, S [1 ]
机构
[1] Tech Univ Denmark, Bioctr DTU, Ctr Biol Sequence Anal, DK-2800 Lyngby, Denmark
关键词
D O I
10.1186/1471-2180-5-58
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Background: We present an overview of bacterial non-classical secretion and a prediction method for identification of proteins following signal peptide independent secretion pathways. We have compiled a list of proteins found extracellularly despite the absence of a signal peptide. Some of these proteins also have known roles in the cytoplasm, which means they could be so-called "moon-lightning" proteins having more than one function. Results: A thorough literature search was conducted to compile a list of currently known bacterial non-classically secreted proteins. Pattern finding methods were applied to the sequences in order to identify putative signal sequences or motifs responsible for their secretion. We have found no signal or motif characteristic to any majority of the proteins in the compiled list of non-classically secreted proteins, and conclude that these proteins, indeed, seem to be secreted in a novel fashion. However, we also show that the apparently non-classically secreted proteins are still distinguished from cellular proteins by properties such as amino acid composition, secondary structure and disordered regions. Specifically, prediction of disorder reveals that bacterial secretory proteins are more structurally disordered than their cytoplasmic counterparts. Finally, artificial neural networks were used to construct protein feature based methods for identification of non-classically secreted proteins in both Gram-positive and Gram-negative bacteria. Conclusion: We present a publicly available prediction method capable of discriminating between this group of proteins and other proteins, thus allowing for the identification of novel non-classically secreted proteins. We suggest candidates for non-classically secreted proteins in Escherichia coli and Bacillus subtilis. The prediction method is available online.
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页数:13
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共 58 条
[1]   Adaptation of protein surfaces to subcellular location [J].
Andrade, MA ;
O'Donoghue, SI ;
Rost, B .
JOURNAL OF MOLECULAR BIOLOGY, 1998, 276 (02) :517-525
[2]   A proteomic view on genome-based signal peptide predictions [J].
Antelmann, H ;
Tjalsma, H ;
Voigt, B ;
Ohlmeier, S ;
Bron, S ;
van Dijl, JM ;
Hecker, M .
GENOME RESEARCH, 2001, 11 (09) :1484-1502
[3]   The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 [J].
Bairoch, A ;
Apweiler, R .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :45-48
[4]   Catalase-peroxidases of Legionella pneumophila:: Cloning of the katA gene and studies of KatA function [J].
Bandyopadhyay, P ;
Steinman, HM .
JOURNAL OF BACTERIOLOGY, 2000, 182 (23) :6679-6686
[5]   Prediction of twin-arginine signal peptides [J].
Bendtsen, JD ;
Nielsen, H ;
Widdick, D ;
Palmer, T ;
Brunak, S .
BMC BIOINFORMATICS, 2005, 6 (1)
[6]   Feature-based prediction of non-classical and leaderless protein secretion [J].
Bendtsen, JD ;
Jensen, LJ ;
Blom, N ;
von Heijne, G ;
Brunak, S .
PROTEIN ENGINEERING DESIGN & SELECTION, 2004, 17 (04) :349-356
[7]   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
[8]   The Tat protein export pathway [J].
Berks, BC ;
Sargent, F ;
Palmer, T .
MOLECULAR MICROBIOLOGY, 2000, 35 (02) :260-274
[9]   A common export pathway for proteins binding complex redox cofactors? [J].
Berks, BC .
MOLECULAR MICROBIOLOGY, 1996, 22 (03) :393-404
[10]   SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis [J].
Braunstein, M ;
Espinosa, BJ ;
Chan, J ;
Belisle, JT ;
Jacobs, WR .
MOLECULAR MICROBIOLOGY, 2003, 48 (02) :453-464