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Experimental and computational analysis of the secretome of the hyperthermophilic archaeon Pyrococcus furiosus.

Schmid G, Mathiesen G, Arntzen MO, Eijsink VG, Thomm M - Extremophiles (2013)

Bottom Line: Most of the 43 proteins without predicted N-terminal signal sequences are known to have intracellular functions, mainly (70 %) related to intracellular metabolism.In silico analyses indicated that the genome of P. furiosus encodes 145 proteins with N-terminal SPs, including 21 putative lipoproteins and 17 with a class III peptide.The putative lipoprotein signal peptides have a unique sequence motif, distinct from the motifs in bacteria and other archaeal orders.

View Article: PubMed Central - PubMed

Affiliation: Hyperthermics Regensburg GmbH, Josef-Engert-Straße 9, 93053, Regensburg, Germany.

ABSTRACT
Although Pyrococcus furiosus is one of the best studied hyperthermophilic archaea, to date no experimental investigation of the extent of protein secretion has been performed. We describe experimental verification of the extracellular proteome of P. furiosus grown on starch. LC-MS/MS-based analysis of culture supernatants led to the identification of 58 proteins. Fifteen of these proteins had a putative N-terminal signal peptide (SP), tagging the proteins for translocation across the membrane. The detected proteins with predicted SPs and known function were almost exclusively involved in important extracellular functions, like substrate degradation or transport. Most of the 43 proteins without predicted N-terminal signal sequences are known to have intracellular functions, mainly (70 %) related to intracellular metabolism. In silico analyses indicated that the genome of P. furiosus encodes 145 proteins with N-terminal SPs, including 21 putative lipoproteins and 17 with a class III peptide. From these we identified 15 (10 %; 7 SPI, 3 SPIII and 5 lipoproteins) under the specific growth conditions of this study. The putative lipoprotein signal peptides have a unique sequence motif, distinct from the motifs in bacteria and other archaeal orders.

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Frequency plot for signal peptides based on multiple alignment of 16 residues upstream and 10 residues downstream of predicted signal peptide cleavage sites. a A composition map based on 107 predicted SPase I signal sequences identified in the P. furiosus DSM 3638 genome. b A composition map based on 21 predicted lipoprotein signal sequences identified in the P. furiosus DSM 3638 genome. These pictures were made with WebLogo (Crooks et al. 2004)
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Fig2: Frequency plot for signal peptides based on multiple alignment of 16 residues upstream and 10 residues downstream of predicted signal peptide cleavage sites. a A composition map based on 107 predicted SPase I signal sequences identified in the P. furiosus DSM 3638 genome. b A composition map based on 21 predicted lipoprotein signal sequences identified in the P. furiosus DSM 3638 genome. These pictures were made with WebLogo (Crooks et al. 2004)

Mentions: To summarize, the 15 extracellular proteins with signal peptides detected in this study (Tables 1, 3) comprise seven proteins with a predicted SPase I cleavage site, five proteins with a putative SPase II cleavage site (lipoproteins) and three with a predicted SPase III cleavage site. The predicted SPase I signal sequences are very similar in length (24–28 amino acids) and amino acid composition (Table 3). They have two or more lysine or arginine residues at the N-terminus and a distinct hydrophobic region dominated by leucines (Fig. 2a). The signal peptides of the lipoproteins are 18–22 amino acids in length and share the motif ([S(A)]G/CIGG) around the predicted cleavage site (indicated by ‘/’) (Table 3; Fig. 2b).Fig. 2


Experimental and computational analysis of the secretome of the hyperthermophilic archaeon Pyrococcus furiosus.

Schmid G, Mathiesen G, Arntzen MO, Eijsink VG, Thomm M - Extremophiles (2013)

Frequency plot for signal peptides based on multiple alignment of 16 residues upstream and 10 residues downstream of predicted signal peptide cleavage sites. a A composition map based on 107 predicted SPase I signal sequences identified in the P. furiosus DSM 3638 genome. b A composition map based on 21 predicted lipoprotein signal sequences identified in the P. furiosus DSM 3638 genome. These pictures were made with WebLogo (Crooks et al. 2004)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3824201&req=5

Fig2: Frequency plot for signal peptides based on multiple alignment of 16 residues upstream and 10 residues downstream of predicted signal peptide cleavage sites. a A composition map based on 107 predicted SPase I signal sequences identified in the P. furiosus DSM 3638 genome. b A composition map based on 21 predicted lipoprotein signal sequences identified in the P. furiosus DSM 3638 genome. These pictures were made with WebLogo (Crooks et al. 2004)
Mentions: To summarize, the 15 extracellular proteins with signal peptides detected in this study (Tables 1, 3) comprise seven proteins with a predicted SPase I cleavage site, five proteins with a putative SPase II cleavage site (lipoproteins) and three with a predicted SPase III cleavage site. The predicted SPase I signal sequences are very similar in length (24–28 amino acids) and amino acid composition (Table 3). They have two or more lysine or arginine residues at the N-terminus and a distinct hydrophobic region dominated by leucines (Fig. 2a). The signal peptides of the lipoproteins are 18–22 amino acids in length and share the motif ([S(A)]G/CIGG) around the predicted cleavage site (indicated by ‘/’) (Table 3; Fig. 2b).Fig. 2

Bottom Line: Most of the 43 proteins without predicted N-terminal signal sequences are known to have intracellular functions, mainly (70 %) related to intracellular metabolism.In silico analyses indicated that the genome of P. furiosus encodes 145 proteins with N-terminal SPs, including 21 putative lipoproteins and 17 with a class III peptide.The putative lipoprotein signal peptides have a unique sequence motif, distinct from the motifs in bacteria and other archaeal orders.

View Article: PubMed Central - PubMed

Affiliation: Hyperthermics Regensburg GmbH, Josef-Engert-Straße 9, 93053, Regensburg, Germany.

ABSTRACT
Although Pyrococcus furiosus is one of the best studied hyperthermophilic archaea, to date no experimental investigation of the extent of protein secretion has been performed. We describe experimental verification of the extracellular proteome of P. furiosus grown on starch. LC-MS/MS-based analysis of culture supernatants led to the identification of 58 proteins. Fifteen of these proteins had a putative N-terminal signal peptide (SP), tagging the proteins for translocation across the membrane. The detected proteins with predicted SPs and known function were almost exclusively involved in important extracellular functions, like substrate degradation or transport. Most of the 43 proteins without predicted N-terminal signal sequences are known to have intracellular functions, mainly (70 %) related to intracellular metabolism. In silico analyses indicated that the genome of P. furiosus encodes 145 proteins with N-terminal SPs, including 21 putative lipoproteins and 17 with a class III peptide. From these we identified 15 (10 %; 7 SPI, 3 SPIII and 5 lipoproteins) under the specific growth conditions of this study. The putative lipoprotein signal peptides have a unique sequence motif, distinct from the motifs in bacteria and other archaeal orders.

Show MeSH
Related in: MedlinePlus