Signal Peptidase I

Secreted proteins play an important part in the pathogenicity of Mycobacterium tuberculosis, and are the primary source of vaccine and diagnostic candidates. A majority of these proteins are exported via the signal peptidase I-dependent pathway, and have a signal peptide that is cleaved off during the secretion process. Sequence similarities within signal peptides have spurred the development of several algorithms for predicting their presence as well as the respective cleavage sites. For proteins exported via this pathway, algorithms exist for eukaryotes, and for Gram-negative and Gram-positive bacteria. However, the unique structure of the mycobacterial membrane raises the question of whether the existing algorithms are suitable for predicting signal peptides within mycobacterial proteins. In this work, we have evaluated the performance of nine signal peptide prediction algorithms on a positive validation set, consisting of 57 proteins with a verified signal peptide and cleavage site, and a negative set, consisting of 61 proteins that have an N-terminal sequence that confirms the annotated translational start site. We found the hidden Markov model of SignalP v3.0 to be the best-performing algorithm for predicting the presence of a signal peptide in mycobacterial proteins. It predicted no false positives or false negatives, and predicted a correct cleavage site for 45 of the 57 proteins in the positive set. Based on these results, we used the hidden Markov model of SignalP v3.0 to analyse the 10 available annotated proteomes of mycobacterial species, including annotations of M. tuberculosis H37Rv from the Wellcome Trust Sanger Institute and the J. Craig Venter Institute (JCVI). When excluding proteins with transmembrane regions among the proteins predicted to harbour a signal peptide, we found between 7.8 and 10.5 % of the proteins in the proteomes to be putative secreted proteins. Interestingly, we observed a consistent difference in the percentage of predicted proteins between the Sanger Institute and JCVI. We have determined the most valuable algorithm for predicting signal peptidase I-processed proteins of M. tuberculosis, and used this algorithm to estimate the number of mycobacterial proteins with the potential to be exported via this pathway.

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3.4.21.89 Signal Peptidase I

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1995.tb20774.x_3 ◽

1995 ◽

Vol 232 (1) ◽

pp. 1-2

Keyword(s):

Signal Peptidase ◽

Signal Peptidase I

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Putative β-Barrel Outer Membrane Proteins of the Bovine Digital Dermatitis-Associated Treponemes: Identification, Functional Characterization, and Immunogenicity

Infection and Immunity ◽

10.1128/iai.00050-20 ◽

2020 ◽

Vol 88 (5) ◽

Author(s):

G. J. Staton ◽

S. D. Carter ◽

S. Ainsworth ◽

J. Mullin ◽

R. F. Smith ◽

...

Keyword(s):

Membrane Proteins ◽

Outer Membrane ◽

Outer Membrane Proteins ◽

Functional Characterization ◽

Signal Peptidase ◽

Effective Vaccine ◽

Digital Dermatitis ◽

Diverse Range ◽

Content Type ◽

Signal Peptidase I

ABSTRACT Bovine digital dermatitis (BDD), an infectious disease of the bovine foot with a predominant treponemal etiology, is a leading cause of lameness in dairy and beef herds worldwide. BDD is poorly responsive to antimicrobial therapy and exhibits a relapsing clinical course; an effective vaccine is therefore urgently sought. Using a reverse vaccinology approach, the present study surveyed the genomes of the three BDD-associated Treponema phylogroups for putative β-barrel outer membrane proteins and considered their potential as vaccine candidates. Selection criteria included the presence of a signal peptidase I cleavage site, a predicted β-barrel fold, and cross-phylogroup homology. Four candidate genes were overexpressed in Escherichia coli BL21(DE3), refolded, and purified. Consistent with their classification as β-barrel OMPs, circular-dichroism spectroscopy revealed the adoption of a predominantly β-sheet secondary structure. These recombinant proteins, when screened for their ability to adhere to immobilized extracellular matrix (ECM) components, exhibited a diverse range of ligand specificities. All four proteins specifically and dose dependently adhered to bovine fibrinogen. One recombinant protein was identified as a candidate diagnostic antigen (disease specificity, 75%). Finally, when adjuvanted with aluminum hydroxide and administered to BDD-naive calves using a prime-boost vaccination protocol, these proteins were immunogenic, eliciting specific IgG antibodies. In summary, we present the description of four putative treponemal β-barrel OMPs that exhibit the characteristics of multispecific adhesins. The observed interactions with fibrinogen may be critical to host colonization and it is hypothesized that vaccination-induced antibody blockade of these interactions will impede treponemal virulence and thus be of therapeutic value.

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Gut SymbiontBacteroides fragilisSecretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism

mBio ◽

10.1128/mbio.01902-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 15

Author(s):

Maria Chatzidaki-Livanis ◽

Michael J. Coyne ◽

Kevin G. Roelofs ◽

Rahul R. Gentyala ◽

Jarreth M. Caldwell ◽

...

Keyword(s):

Gut Microbiota ◽

Bacteroides Fragilis ◽

Signal Peptidase ◽

Metagenomic Data ◽

Antimicrobial Protein ◽

Secretion Systems ◽

Human Gut ◽

Gene Encoding ◽

Toxic Activity ◽

Signal Peptidase I

ABSTRACTHuman gutBacteroidesspecies produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains ofBacteroides fragilissecrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidalessecreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced byB. fragilisstrain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset ofB. fragilisstrains. The addition ofubbinto a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in theB. fragilisgenome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed thatubbis present in 12% of the metagenomes that have evidence ofB. fragilis. As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40B. fragilisstrains, revealing that 75% ofB. fragilisstrains are targeted by one or the other of these two secreted proteins of strain 638R.IMPORTANCEWe are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundantBacteroidesspecies. Here, we show that some strains ofBacteroides fragilishave acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against otherB. fragilisstains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.

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Analysis of a Streptococcus pneumoniae gene encoding signal peptidase I and overproduction of the enzyme

Gene ◽

10.1016/s0378-1119(97)00198-4 ◽

1997 ◽

Vol 194 (2) ◽

pp. 249-255 ◽

Cited By ~ 28

Author(s):

Yian-Biao Zhang ◽

Bill Greenberg ◽

Sanford A Lacks

Keyword(s):

Streptococcus Pneumoniae ◽

Signal Peptidase ◽

Gene Encoding ◽

Signal Peptidase I

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Molecular characterization and analysis of a gene encoding the acidic repeat protein (Arp) of Treponema pallidum

Journal of Medical Microbiology ◽

10.1099/jmm.0.46943-0 ◽

2007 ◽

Vol 56 (6) ◽

pp. 715-721 ◽

Cited By ~ 20

Author(s):

Hsi Liu ◽

Berta Rodes ◽

Robert George ◽

Bret Steiner

Keyword(s):

Synthetic Peptides ◽

Treponema Pallidum ◽

Signal Peptidase ◽

Type I ◽

Type Ii ◽

Gene Encoding ◽

Western Blot Assay ◽

Repeat Protein ◽

Signal Peptidase I ◽

Cdc 2

The acidic repeat protein (arp) genes from three subspecies of the treponeme Treponema pallidum (T. pallidum subsp. pallidum, Nichols strain; T. pallidum subsp. pertenue, CDC-1 and CDC-2 strains; and T. pallidum subsp. endemicum, Bosnia A strain) were cloned and sequenced. The predicted protein sequence contained a high percentage of glutamic acid, hence the name acidic repeat protein, or Arp. The protein had a potential membrane-spanning domain and a signal peptidase I site. The gene from the Nichols strain of T. pallidum subsp. pallidum contained a set of 14 nearly identical repeats of a 60 bp sequence, which occupied ∼51 % of the length of the gene. Analyses of arp from laboratory strains showed that the 5′ and 3′ ends of the genes were conserved, but there was considerable heterogeneity in the number of repeats of this 60 bp sequence. Based on amino acid variations, the 14 sequence repeats could be classified into three types, which were named type I, type II and type III repeats. The type II repeat was the most common in the strains examined. The arp gene of the Nichols strain was subsequently cloned into the expression vector pBAD/TOPO ThioFusion. The expressed protein was detected in a Western blot assay using rabbit immune sera produced against T. pallidum, or synthetic peptides derived from the repeat sequences. Using an ELISA, rapid plasma reagin (RPR) test-positive sera reacted with synthetic peptides derived from the repeat region but not with peptides derived from N and C termini of the Arp protein. These results show that the Arp protein is immunogenic and could prove to be a useful target for serological diagnosis of T. pallidum infection.

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Enzyme Handbook 15 ◽

10.1007/978-3-642-58948-5_152 ◽

1998 ◽

pp. 745-752

Author(s):

Dietmar Schomburg ◽

Dörte Stephan

Keyword(s):

Signal Peptidase ◽

Signal Peptidase I

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Molecular and Functional Analysis of the lepB Gene, Encoding a Type I Signal Peptidase from Rickettsia rickettsii and Rickettsia typhi

Journal of Bacteriology ◽

10.1128/jb.185.15.4578-4584.2003 ◽

2003 ◽

Vol 185 (15) ◽

pp. 4578-4584 ◽

Cited By ~ 18

Author(s):

M. Sayeedur Rahman ◽

Jason A. Simser ◽

Kevin R. Macaluso ◽

Abdu F. Azad

Keyword(s):

Spotted Fever ◽

Rocky Mountain ◽

Amino Acid Sequences ◽

Signal Peptidase ◽

Type I ◽

Rocky Mountain Spotted Fever ◽

Rickettsia Typhi ◽

Rickettsia Rickettsii ◽

Signal Peptidase I

ABSTRACT The type I signal peptidase lepB genes from Rickettsia rickettsii and Rickettsia typhi, the etiologic agents of Rocky Mountain spotted fever and murine typhus, respectively, were cloned and characterized. Sequence analysis of the cloned lepB genes from R. rickettsii and R. typhi shows open reading frames of 801 and 795 nucleotides, respectively. Alignment analysis of the deduced amino acid sequences reveals the presence of highly conserved motifs that are important for the catalytic activity of bacterial type I signal peptidase. Reverse transcription-PCR and Northern blot analysis demonstrated that the lepB gene of R. rickettsii is cotranscribed in a polycistronic message with the putative nuoF (encoding NADH dehydrogenase I chain F), secF (encoding protein export membrane protein), and rnc (encoding RNase III) genes in a secF-nuoF-lepB-rnc cluster. The cloned lepB genes from R. rickettsii and R. typhi have been demonstrated to possess signal peptidase I activity in Escherichia coli preprotein processing in vivo by complementation assay.

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