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Chapter 24 : Protein Transport Pathways in : a Genome-Based Road Map

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Abstract:

This chapter on protein transport pathways in : a genome-based road map, discusses the properties of distinct classes of amino-terminal signal peptides, which label proteins for passage through the various pathways, as well as the major components of each pathway. The cell wall of contains about 9% of the total cellular protein content, analogous to the periplasm of gram-negative eubacteria. The proteins retained in the wall include DNases, RNases, proteases, penicillin-binding proteins, and cell wall hydrolases. Presumably, to prevent their loss in the environment, the mature parts of 12 proteins with cleavable signal peptides, such as LytB-F, SleB, and WapA, contain potential cell wall retention signals, which consist of a variable number of repeated domains with affinity for certain wall components, such as teichoic acids. Eubacterial Sec-dependent protein export machineries are composed of six types of components: (i) cytoplasmic chaperones or targeting factors, (ii) a translocation motor (SecA), (iii) components of the translocation channel (SecYEG, SecDF-YajC, YidC), (iv) SPases, (v) SPPases, and (vi) folding catalysts. The best-characterized secretion-specific targeting factor of is the GTPase Ffh (fifty-four homologue), a homologue of the 54-kDa subunit of the eukaryotic signal recognition particle (SRP). The expression of components of various protein transport pathways in is regulated in a complex manner, depending on the availability of nutrients, growth phase, and cell density.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24

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Image of FIGURE 1
FIGURE 1

Road map of protein transport pathways in . Ribosomally synthesized proteins can be transported to various extracytoplasmic destinations depending on the presence of an amino-terminal signal peptide (SP) and specific retention signals, such as a lipobox or cell wall binding repeats (CWB). Proteins lacking a signal peptide remain in the cytoplasm. Proteins that have one or more transmembrane segments and lack a signal peptidase recognition site (—AxA) are inserted into the membrane via the Sec pathway or, possibly, the Tat pathway. Proteins that have to be retained at the extracytoplasmic side of the membrane can either be pseudopilins exported by the Com system or lipid-modified proteins ( +lipobox) exported via the Sec pathway. Possibly, some lipid-modified proteins are exported via the Tat pathway. Proteins that are retained in the cell wall (+CWB) can be exported via the Sec or Tat pathways. Proteins can be secreted into the medium via the Sec or Tat pathways or by ABC transporters. Similarly, certain membrane, lipo-, or wall proteins can be released into the growth medium upon cleavage by proteases. Finally, different pathways may be involved in protein transport to the intermembrane space (IMS) of endospores. Notably, signal peptides with a twin-arginine motif (+RR) have the potential to direct proteins into the Tat pathway, but no experimental evidence is presently available showing that integral membrane proteins or lipoproteins are exported via this route.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
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Image of FIGURE 2
FIGURE 2

Model for signal peptide function. During the initiation of protein translocation, positively charged residues in the N domain of a Sec-type signal peptide interact with the translocation machinery (not shown) and negatively charged phospholipids ( ), permitting the hydrophobic H domain to insert loopwise into the membrane. Upon unlooping of the H domain, the first residues of the mature protein are pulled through the membrane ( ), thereby presenting the signal peptidase (SPase) recognition sequence (AXA) to SPase I. Upon processing by SPase I, the cleaved signal peptide is degraded by signal peptide peptidases (SPPases), and the translocated mature protein folds into its native conformation on the extracytoplasmic (out) side of the membrane.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
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Image of FIGURE 3
FIGURE 3

Properties of predicted cleavable amino-terminal signal peptides of . Signal peptides consist of three distinct domains ( ): a positively charged N domain (N; “+”), a hydrophobic H-domain that can adopt an alpha-helical conformation in the membrane (H; gray box), and a C domain (C) that includes the SPase recognition site. Helix-breaking Gly or Pro residues in the middle of the H domain allow the formation of a hairpinlike structure that can insert into the membrane ( ). Helix-breaking residues at the end of the H domain facilitate cleavage by a specific SPase I ( ). To identify exported proteins of , the first 60 residues of all annotated proteins in the SubtiList database (http://bioweb.pasteur.fr/GenoList/SubtiList) were analyzed for the presence of cleavable signal peptides. A distinction between potential secretory proteins and membrane proteins was made by analyzing all protein sequences containing a potential signal peptide for the presence of potential transmembrane segments. All proteins containing additional hydrophobic domains were excluded from the primary set of signal peptides. The remaining signal peptides were searched for the presence of a twin-arginine (RR) motif, a pseudopilin-specific SPase cleavage site, or a lipobox ( ). As the signal peptides of lipoproteins are, in general, shorter than those of secretory proteins, not all lipoproteins were initially recognized. In addition, some lipoproteins, such as CtaC ( ), contain transmembrane segments that were excluded from predictions of the signal peptides of secretory proteins mentioned above. Therefore, additional putative lipoprotein signal peptides were identified through similarity searches in the SubtiList database with signal peptides of known lipoproteins ( ). Finally, the predicted cleavable Sec-type and RR signal peptides were subdivided into three classes: secretory (Sec-type) signal peptides, lipoprotein signal peptides, and twin-arginine (RR) signal peptides. Total numbers of the representatives of each class of signal peptides are indicated. Twin-arginine motifs in the N region, helix-breaking residues in the H domain, consensus SPase recognition sites, and the most frequently occurring residues at the “+1” position of mature proteins are indicated. For each type of signal peptide, the average length of complete signal peptides, N domains, and H domains is indicated, together with the average hydrophobicity of N and H domains (between brackets).

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
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Image of FIGURE 4
FIGURE 4

Main components of the Sec-dependent protein export machinery. The SRP-FtsY complex and, possibly, CsaA or SecA (A) keep precursors in a translocation-competent conformation and facilitate their targeting to the preprotein ttanslocase in the membrane. Known components of the translocase are SecA, SecY (Y), SecE (E), SecG (G), and SecDF (DF). SecA acts as a force generator (motor) for protein translocation through cycles of preprotein binding, membrane insertion, preprotein release, and deinsertion from the membrane. Core components of the protein-conducting channel in the membrane are SecY, SecE, and SecG. The cycling of SecA is regulated by ATP binding and hydrolysis. During or shortly after translocation, precursors are processed by one of the type I SPases, SipS, SipT, SipU, SipV, or SipW. Cleaved signal peptides are probably degraded by SppA and, perhaps, TepA. Folding of some mature proteins into their pro-tease-resistant conformation depends on the activity of the lipoprotein PrsA, which is lipid modified and processed by Lgt and SPase II (Lsp), respectively. Other proteins require the thiol-disulfide ox-idoreductases BdbB and BdbC for the formation of disulfide bonds. Upon passage through the wall, mature proteins are secreted into the growth medium. See text for further details. R, ribosome; SP, signal peptide.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
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Tables

Generic image for table
TABLE 1a

Predicted secretory (Sec-type) signal peptides of

Putative Sec-type signal peptides were identified as described in the legend to Fig. 3 . The number of residues in the N and H domains of each signal peptide and the average hydrophobicity (h) of each of these domains, as determined by the algorithms of Kyte and Doolittle ( ), are indicated. Furthermore, the SPase I recognition sites in the C domain (i.e., positions −3 to −1 relative to the predicted SPase cleavage site) are shown.

Proteins containing cell wall binding repeats are marked with a superscript W.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
Generic image for table
TABLE 1b

Predicted secretory (Sec-type) signal peptides of

Putative Sec-type signal peptides were identified as described in the legend to Fig. 3 . The number of residues in the N and H domains of each signal peptide and the average hydrophobicity (h) of each of these domains, as determined by the algorithms of Kyte and Doolittle ( ), are indicated. Furthermore, the SPase I recognition sites in the C domain (i.e., positions −3 to −1 relative to the predicted SPase cleavage site) are shown.

Proteins containing cell wall binding repeats are marked with a superscript W.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
Generic image for table
TABLE 2

Predicted lipoprotein signal peptides

Putative lipoprotein signal peptides were identified as described in the legend to Fig. 3 . The number of residues in the N and H domains of each signal peptide and the average hydrophobicity (h) of each of these domains, as determined by the algorithms of Kyte and Doolittle ( ), are indicated. Furthermore, the SPase II recognition and cleavage site in the C domain (i.e., the lipobox) is shown. The SPase II cleavage site is indicated with a space in the amino acid sequence.

Lipoproteins containing an RR motif in the signal peptide are indicated with a superscript RR, and lipoproteins containing (putative) transmembrane domains in addition to the signal peptide are indicated with a superscript TM. One protein containing cell wall binding repeats is marked with a superscript W. Based on theoretical considerations, the putative start sites of the potential lipoproteins YhaR and YhfQ (indicated with an asterisk) have been modified in a recent update of SubtiList. If the new annotation is correct, it is unlikely that YhaR and YhfQ are lipoproteins.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
Generic image for table
TABLE 3

Predicted twin-arginine (RR) signal peptides of

Amino-terminal RR signal peptides were predicted as described in the legend to Fig. 3 . The listed signal peptides contain, in addition to the twin arginines, at least one other residue of the consensus sequence (R-R-X-#-#, printed in bold; » is a hydrophobic residue). The number of residues in the N and H domains of each signal peptide and the average hydrophobicity (h) of each of these domains, as determined by the algorithms of Kyte and Doolittle ( ), are indicated. Furthermore, the RR motifs in the N domain and SPase I recognition sites in the C domain (i.e., positions −3 to −1 relative to the predicted SPase cleavage site) are shown.

Proteins tacking a (putative) SPase I cleavage site, some of which contain additional transmembrane domains, are indicated with a superscript TM. One protein containing cell wall binding repeats is indicated with a superscript W.

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24
Generic image for table
TABLE 4

Conservation of components of the Sec, Tat, and Com pathways for protein export in the eubacteria and , the archaeon , and the yeast

Sec, Tat, and Com components were identified by amino acid sequence similarity searches via the TIGR microbial database using the sequences of known proteins (see text for details). “+” indicates the presence of orthologous sequences; “—” indicates the absence of orthologous sequences. Note that proteins required for protein transport in mitochondria of were excluded from the comparisons.

Names of orthologues in .

Names of orthologues in ; proteins in the SRP complex are Srp72p, Srp68p, Srp54p, Sec65p, Srp21p, Srpl4p and Srp7p.

It is not known whether orthologues of Hbsu are part of SRP complexes in other organisms.

Names of orthologues in .

Name of orthologue in .

Citation: Van Dijl J, Bolhuis A, Tjalsma H, Jongbloed J, De Jong A, Bron S. 2002. Protein Transport Pathways in : a Genome-Based Road Map, p 337-355. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch24

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