Indicators from archaeal secretomes

Saleh, Mazen; Song, Catharine; Nasserulla, Sabah; Leduc, L.G.

doi:10.1016/j.micres.2008.03.002

Cited by 18 publications

(23 citation statements)

References 51 publications

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“…Interest in archaeal protein secretion has resulted in studies of various important aspects, including the roles of the Sec and Tat pathways (16,27), the mechanism of action of the various signal peptidases (15,26), numerous attempts to analyze and define archaeal signal peptides (2,5,8), and examination of the archaeal secretome (14,28). Still, the best studied of the archaeal signal peptidases are the type IV prepilin-like peptidases and their role in assembly of archaeal appendages like flagella and pili.…”

Section: Discussionmentioning

confidence: 99%

Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD

VanDyke

Chaban

et al. 2009

J Bacteriol

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In Archaea, the preflagellin peptidase (a type IV prepilin-like peptidase designated FlaK in Methanococcus voltae and Methanococcus maripaludis) is the enzyme that cleaves the N-terminal signal peptide from preflagellins. In methanogens and several other archaeal species, the typical flagellin signal peptide length is 11 to 12 amino acids, while in other archaea preflagellins possess extremely short signal peptides. A systematic approach to address the signal peptide length requirement for preflagellin processing is presented in this study. M. voltae preflagellin FlaB2 proteins with signal peptides 3 to 12 amino acids in length were generated and used as a substrate in an in vitro assay utilizing M. voltae membranes as an enzyme source. Processing by FlaK was observed in FlaB2 proteins containing signal peptides shortened to 5 amino acids; signal peptides 4 or 3 amino acids in length were unprocessed. In the case of Sulfolobus solfataricus, where the preflagellin peptidase PibD has broader substrate specificity, some predicted substrates have predicted signal peptides as short as 3 amino acids. Interestingly, the shorter signal peptides of the various mutant FlaB2 proteins not processed by FlaK were processed by PibD, suggesting that some archaeal preflagellin peptidases are likely adapted toward cleaving shorter signal peptides. The functional complementation of signal peptidase activity by FlaK and PibD in an M. maripaludis ⌬flaK mutant indicated that processing of preflagellins was detected by complementation with either FlaK or PibD, yet only FlaK-complemented cells were flagellated. This suggested that a block in an assembly step subsequent to signal peptide removal occurred in the PibD complementation.The bacterial type IV prepilin peptidase (TFPP) is a wellcharacterized enzyme belonging to a family of novel aspartic acid proteases (20). It is responsible for the cleavage of Nterminal signal peptides from prepilins and pseudopilins, prior to their incorporation into the type IV pilus structure (22,30,31). The prepilin peptidase is also responsible for the processing of prepilin-like proteins needed for type II secretion (22). In Archaea, the existence of bacterial TFPP-like enzymes has also been reported, and they have been most extensively studied in relation to the assembly of the archaeal flagellum. In the euryarchaeotes Methanococcus maripaludis and Methanococcus voltae, the preflagellin peptidase FlaK was demonstrated to be responsible for cleaving the N-terminal signal peptide from the preflagellin prior to its incorporation into the growing flagellar filament, a step essential to flagellar assembly (6, 7, 26). In Sulfolobus solfataricus, an acidophilic crenarchaeote, the equivalent enzyme, PibD, was also shown to process preflagellins (4). Site-directed mutagenesis of FlaK and PibD demonstrated that both aspartic acid residues that aligned with aspartic acid residues essential for bacterial TFPP activity were also essential in the archaeal enzymes (6, 32), indicating that the two archaeal peptidases...

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Section: Discussionmentioning

confidence: 99%

Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD

VanDyke

Chaban

et al. 2009

J Bacteriol

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“…For example, PSORTb predicts the cellular localization of a protein and SignalP predicts the likelihood that a protein contains a signal peptide [57, 58]. By means of these prediction programs, various in silico secretomes of archaea have been drafted [30, 46, 59–61]. These vary from 1.2 up to 19% of the total proteome depending on the specific program, stringency of criteria, and the archaeal species analyzed.…”

Section: Signal Peptides and Secretomesmentioning

confidence: 99%

Shaping the Archaeal Cell Envelope

Ellen

Zolghadr

Driessen

et al. 2010

Archaea

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“…Protein secretion mechanisms through this unusual cell membrane have been mainly addressed by way of comparative genomics studies (10 -12) and by genomic identification and characterization of signal peptidases (13,14). Archaeal extracellular and cell membrane proteins have been predicted because of the presence of a tripartite N-terminal signal motif essential for protein secretion and subsequently cleaved by signal peptidases from the protein (11,14,15). In archaea three different signal peptidases have been identified and characterized so far (13): signal peptidase I is responsible for the cleavage of secretory signal peptides from the majority of secreted proteins, class III signal peptidase is responsible for processing signal peptides from preflagellins and some sugar-binding proteins (11), and signal peptide peptidase is responsible for the hydrolysis of signal peptides following protein secretion.…”

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confidence: 99%

“…Despite the similarities in protein translocation mechanisms between the three domains of life, genome analyses also shed light on unique archaeal characteristics, suggesting that our current knowledge regarding secreted proteins and secretion mechanisms in archaea remains limited (10). It is apparent that the lack of experimental data at the proteome level has become the bottleneck for the further understanding of the existence of novel secretion mechanisms in archaea (15).…”

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Outside the Unusual Cell Wall of the Hyperthermophilic Archaeon Aeropyrum pernix K1

Palmieri

Cannio

Fiume

et al. 2009

Molecular & Cellular Proteomics

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In contrast to the extensively studied eukaryal and bacterial protein secretion systems, comparatively less is known about how and which proteins cross the archaeal cell membrane. To identify secreted proteins of the hyperthermophilic archaeon Aeropyrum pernix K1 we used a proteomics approach to analyze the extracellular and cell surface protein fractions. The experimentally obtained data comprising 107 proteins were compared with the in silico predicted secretome. Because of the lack of signal peptide and cellular localization prediction tools specific for archaeal species, programs trained on eukaryotic and/or Gram-positive and Gram-negative bacterial signal peptide data sets were used. PSortB Gram-negative and Gram-positive analysis predicted 21 (1.2% of total ORFs) and 24 (1.4% of total ORFs) secreted proteins, respectively, from the entire A. pernix K1 proteome, 12 of which were experimentally identified in this work. Six additional proteins were predicted to follow non-classical secretion mechanisms using SecP algorithms. According to at least one of the two PSortB predictions, 48 proteins identified in the two fractions possess an unknown localization site. In addition, more than half of the proteins do not contain signal peptides recognized by current prediction programs. This suggests that known mechanisms only partly describe archaeal protein secretion. The most striking characteristic of the secretome was the high number of transportrelated proteins identified from the ATP-binding cassette (ABC), tripartite ATP-independent periplasmic, ATPase, small conductance mechanosensitive ion channel (MscS), and dicarboxylate amino acid-cation symporter transporter families. In particular, identification of 21 solute-binding receptors of the ABC superfamily of the 24 predicted in silico confirms that ABCmediated transport represents the most frequent strategy adopted by A. pernix for solute translocation across the cell membrane.

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Indicators from archaeal secretomes

Cited by 18 publications

References 51 publications

Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD

Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD

Shaping the Archaeal Cell Envelope

Outside the Unusual Cell Wall of the Hyperthermophilic Archaeon Aeropyrum pernix K1

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