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The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance.

Kunze M, Berger J - Front Physiol (2015)

Bottom Line: The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments.Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals.Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria.

ABSTRACT
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.

No MeSH data available.


Related in: MedlinePlus

Comparison of the structural properties of N-terminal targeting signals and their interaction with the receptor proteins. (A–D)Schematic representation of the N-terminal amino acid sequences encoding different targeting signals: (A) the peroxisomal PTS2 forming an α-helical domain encoding the consensus sequence, which is followed by an unstructured sequence element; (B) the mitochondrial presequence is enriched for positive charges and forms an amphipathic α-helical domain, (C) the chloroplast transit peptide sequence is enriched in hydroxylated amino acids; and (D) the signal peptide for the ER is composed of a positively charged (n)-domain, a hydrophobic (h)-domain, and a polar (p)-domain. +, positive charges; OH, hydroxylated residues; Φ, hydrophobic residues; orange, hydrophobic side; blue, hydrophilic side of the helix. (E–H)Helical wheel depiction of typical N-terminal targeting signals: (E) the PTS2 of yeast thiolase (ScFox3), (F) the presequence of rat aldehyde dehydrogenase (RnAldh2), (G) the transit peptide of pea ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (PsprSSU), and (H) the signal peptide of bovine preprolactin (BtPRL). The amino acid sequences depicted in the α-helical wheel projections are indicated above using the numbering of the primary sequence; amino acids of the central turn are indicated by larger letters; residues of the PTS2 consensus sequence, residues of the presequence interacting with Tom20, the hydroxylated residues of the transit peptide and the hydrophobic patch of the signal sequence are indicated bold and boxed. The color code for the physical properties of the residues is as follows: acidic red, basic blue, hydrophobic yellow, polar basic bluish gray and polar neutral green. The arrows indicate the progression of the amino acid sequence within the α-helical wheel. (I–K)3D structure of the receptor protein and the α-helix of the targeting signal:(I) the N-terminus of yeast Fox3 involving a PTS2 (yellow) together with the receptor protein Pex7 (green), (J) the presequence of rat Aldh2 (yellow) together with the soluble domain of Tom20 (red), (K) the leader peptide of yeast dipeptidylpeptidase B (yellow) together with the cargo binding domain of archeal Srp54. The structures have been generated by the program visual molecular dynamics (VMD) (Humphrey et al., 1996) based on the datasets PDB:3W15 (Pan et al., 2013) (I), PDB:1OM2 (Abe et al., 2000) (J) and PDB:3KL4 (Janda et al., 2010) (K).
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Figure 2: Comparison of the structural properties of N-terminal targeting signals and their interaction with the receptor proteins. (A–D)Schematic representation of the N-terminal amino acid sequences encoding different targeting signals: (A) the peroxisomal PTS2 forming an α-helical domain encoding the consensus sequence, which is followed by an unstructured sequence element; (B) the mitochondrial presequence is enriched for positive charges and forms an amphipathic α-helical domain, (C) the chloroplast transit peptide sequence is enriched in hydroxylated amino acids; and (D) the signal peptide for the ER is composed of a positively charged (n)-domain, a hydrophobic (h)-domain, and a polar (p)-domain. +, positive charges; OH, hydroxylated residues; Φ, hydrophobic residues; orange, hydrophobic side; blue, hydrophilic side of the helix. (E–H)Helical wheel depiction of typical N-terminal targeting signals: (E) the PTS2 of yeast thiolase (ScFox3), (F) the presequence of rat aldehyde dehydrogenase (RnAldh2), (G) the transit peptide of pea ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (PsprSSU), and (H) the signal peptide of bovine preprolactin (BtPRL). The amino acid sequences depicted in the α-helical wheel projections are indicated above using the numbering of the primary sequence; amino acids of the central turn are indicated by larger letters; residues of the PTS2 consensus sequence, residues of the presequence interacting with Tom20, the hydroxylated residues of the transit peptide and the hydrophobic patch of the signal sequence are indicated bold and boxed. The color code for the physical properties of the residues is as follows: acidic red, basic blue, hydrophobic yellow, polar basic bluish gray and polar neutral green. The arrows indicate the progression of the amino acid sequence within the α-helical wheel. (I–K)3D structure of the receptor protein and the α-helix of the targeting signal:(I) the N-terminus of yeast Fox3 involving a PTS2 (yellow) together with the receptor protein Pex7 (green), (J) the presequence of rat Aldh2 (yellow) together with the soluble domain of Tom20 (red), (K) the leader peptide of yeast dipeptidylpeptidase B (yellow) together with the cargo binding domain of archeal Srp54. The structures have been generated by the program visual molecular dynamics (VMD) (Humphrey et al., 1996) based on the datasets PDB:3W15 (Pan et al., 2013) (I), PDB:1OM2 (Abe et al., 2000) (J) and PDB:3KL4 (Janda et al., 2010) (K).

Mentions: The observation that a peroxisomal targeting signal is encoded in proximity to the N-terminus of the rat peroxisomal enzyme thiolase led to the identification of the PTS2 (Osumi et al., 1991; Swinkels et al., 1991), which was later also identified in yeast and plants (Gietl et al., 1994; Glover et al., 1994). The consensus sequence has originally been described as (R/K)-(L/V/I)-X5-(Q/H)-(L/A)4 (Figure 2A) highlighting two conserved dipeptide motifs separated by five arbitrary amino acids, which are sensitive to different point mutations (Glover et al., 1994; Tsukamoto et al., 1994). Later on, this motif was extended to R-(L/V/I/Q)-X-X-(L/V/I/H)-(L/S/G/A)-X-(H/Q)-(L/A) based on a compilation of the most common PTS2 variants (Petriv et al., 2004). This suggested a previously unrecognized conservation at the central amino acid X3, which was consistently found to present with large and hydrophobic properties (Petriv et al., 2002; Reumann, 2004; Kunze et al., 2011). In a reporter construct harboring the N-terminus of rat thiolase, the functionality of the PTS2 was destroyed by a substitution of residue X3 with a negatively or positively charged amino acid (Kunze et al., 2011). Based on the sequence of charged/polar and hydrophobic residues, an α-helical structure with two turns was suggested, which orients all key residues of the consensus sequence toward one side of this helix (Figure 2E). Moreover, PTS2 motifs are highly enriched in amino acids overrepresented in helical structures and the introduction of the helix-breaking amino acid proline at the least conserved position of a prototypical PTS2 abrogated its functionality (Kunze et al., 2011). This was in line with previous suggestions of a helical structure for PTS2 motifs based on the paucity of proline residues within PTS2 motifs (Reumann, 2004) and the observation that a PTS2-destroying point mutation in the rat thiolase N-terminus generated a mitochondrial targeting signal de novo (Osumi et al., 1992). Finally, this suggestion was confirmed by the elucidation of the 3D structure of the N-terminus of the yeast ortholog of thiolase (Fox3) in a receptor bound state, in which the PTS2 non-apeptide presented as α-helix (Pan et al., 2013). Altogether, the linear PTS2 non-apeptide corresponds to an α-helix, in which one flank is occupied by the key residues that align amino acids of the same property. When comparing the N-terminal sequences of PTS2-containing proteins, the region upstream of the PTS2 was found enriched in acidic residues (Reumann, 2004; Kunze et al., 2011), whereas the region downstream of the PTS2 contains many amino acids, which are typical for unstructured stretches (Kunze et al., 2011). The latter probably reflects a linker domain, which serves the exposure of the PTS2 helix from the fully folded core protein. Accordingly, a similar linker domain has been described next to the PTS1 (Neuberger et al., 2003c), but was not observed in proteins that are imported in an unfolded state into other organelles. In addition, the flexible linker domain of PTS2-carrying proteins could also be necessary for the exposition of the processing site toward the peptidase inside peroxisomes.


The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance.

Kunze M, Berger J - Front Physiol (2015)

Comparison of the structural properties of N-terminal targeting signals and their interaction with the receptor proteins. (A–D)Schematic representation of the N-terminal amino acid sequences encoding different targeting signals: (A) the peroxisomal PTS2 forming an α-helical domain encoding the consensus sequence, which is followed by an unstructured sequence element; (B) the mitochondrial presequence is enriched for positive charges and forms an amphipathic α-helical domain, (C) the chloroplast transit peptide sequence is enriched in hydroxylated amino acids; and (D) the signal peptide for the ER is composed of a positively charged (n)-domain, a hydrophobic (h)-domain, and a polar (p)-domain. +, positive charges; OH, hydroxylated residues; Φ, hydrophobic residues; orange, hydrophobic side; blue, hydrophilic side of the helix. (E–H)Helical wheel depiction of typical N-terminal targeting signals: (E) the PTS2 of yeast thiolase (ScFox3), (F) the presequence of rat aldehyde dehydrogenase (RnAldh2), (G) the transit peptide of pea ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (PsprSSU), and (H) the signal peptide of bovine preprolactin (BtPRL). The amino acid sequences depicted in the α-helical wheel projections are indicated above using the numbering of the primary sequence; amino acids of the central turn are indicated by larger letters; residues of the PTS2 consensus sequence, residues of the presequence interacting with Tom20, the hydroxylated residues of the transit peptide and the hydrophobic patch of the signal sequence are indicated bold and boxed. The color code for the physical properties of the residues is as follows: acidic red, basic blue, hydrophobic yellow, polar basic bluish gray and polar neutral green. The arrows indicate the progression of the amino acid sequence within the α-helical wheel. (I–K)3D structure of the receptor protein and the α-helix of the targeting signal:(I) the N-terminus of yeast Fox3 involving a PTS2 (yellow) together with the receptor protein Pex7 (green), (J) the presequence of rat Aldh2 (yellow) together with the soluble domain of Tom20 (red), (K) the leader peptide of yeast dipeptidylpeptidase B (yellow) together with the cargo binding domain of archeal Srp54. The structures have been generated by the program visual molecular dynamics (VMD) (Humphrey et al., 1996) based on the datasets PDB:3W15 (Pan et al., 2013) (I), PDB:1OM2 (Abe et al., 2000) (J) and PDB:3KL4 (Janda et al., 2010) (K).
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Figure 2: Comparison of the structural properties of N-terminal targeting signals and their interaction with the receptor proteins. (A–D)Schematic representation of the N-terminal amino acid sequences encoding different targeting signals: (A) the peroxisomal PTS2 forming an α-helical domain encoding the consensus sequence, which is followed by an unstructured sequence element; (B) the mitochondrial presequence is enriched for positive charges and forms an amphipathic α-helical domain, (C) the chloroplast transit peptide sequence is enriched in hydroxylated amino acids; and (D) the signal peptide for the ER is composed of a positively charged (n)-domain, a hydrophobic (h)-domain, and a polar (p)-domain. +, positive charges; OH, hydroxylated residues; Φ, hydrophobic residues; orange, hydrophobic side; blue, hydrophilic side of the helix. (E–H)Helical wheel depiction of typical N-terminal targeting signals: (E) the PTS2 of yeast thiolase (ScFox3), (F) the presequence of rat aldehyde dehydrogenase (RnAldh2), (G) the transit peptide of pea ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (PsprSSU), and (H) the signal peptide of bovine preprolactin (BtPRL). The amino acid sequences depicted in the α-helical wheel projections are indicated above using the numbering of the primary sequence; amino acids of the central turn are indicated by larger letters; residues of the PTS2 consensus sequence, residues of the presequence interacting with Tom20, the hydroxylated residues of the transit peptide and the hydrophobic patch of the signal sequence are indicated bold and boxed. The color code for the physical properties of the residues is as follows: acidic red, basic blue, hydrophobic yellow, polar basic bluish gray and polar neutral green. The arrows indicate the progression of the amino acid sequence within the α-helical wheel. (I–K)3D structure of the receptor protein and the α-helix of the targeting signal:(I) the N-terminus of yeast Fox3 involving a PTS2 (yellow) together with the receptor protein Pex7 (green), (J) the presequence of rat Aldh2 (yellow) together with the soluble domain of Tom20 (red), (K) the leader peptide of yeast dipeptidylpeptidase B (yellow) together with the cargo binding domain of archeal Srp54. The structures have been generated by the program visual molecular dynamics (VMD) (Humphrey et al., 1996) based on the datasets PDB:3W15 (Pan et al., 2013) (I), PDB:1OM2 (Abe et al., 2000) (J) and PDB:3KL4 (Janda et al., 2010) (K).
Mentions: The observation that a peroxisomal targeting signal is encoded in proximity to the N-terminus of the rat peroxisomal enzyme thiolase led to the identification of the PTS2 (Osumi et al., 1991; Swinkels et al., 1991), which was later also identified in yeast and plants (Gietl et al., 1994; Glover et al., 1994). The consensus sequence has originally been described as (R/K)-(L/V/I)-X5-(Q/H)-(L/A)4 (Figure 2A) highlighting two conserved dipeptide motifs separated by five arbitrary amino acids, which are sensitive to different point mutations (Glover et al., 1994; Tsukamoto et al., 1994). Later on, this motif was extended to R-(L/V/I/Q)-X-X-(L/V/I/H)-(L/S/G/A)-X-(H/Q)-(L/A) based on a compilation of the most common PTS2 variants (Petriv et al., 2004). This suggested a previously unrecognized conservation at the central amino acid X3, which was consistently found to present with large and hydrophobic properties (Petriv et al., 2002; Reumann, 2004; Kunze et al., 2011). In a reporter construct harboring the N-terminus of rat thiolase, the functionality of the PTS2 was destroyed by a substitution of residue X3 with a negatively or positively charged amino acid (Kunze et al., 2011). Based on the sequence of charged/polar and hydrophobic residues, an α-helical structure with two turns was suggested, which orients all key residues of the consensus sequence toward one side of this helix (Figure 2E). Moreover, PTS2 motifs are highly enriched in amino acids overrepresented in helical structures and the introduction of the helix-breaking amino acid proline at the least conserved position of a prototypical PTS2 abrogated its functionality (Kunze et al., 2011). This was in line with previous suggestions of a helical structure for PTS2 motifs based on the paucity of proline residues within PTS2 motifs (Reumann, 2004) and the observation that a PTS2-destroying point mutation in the rat thiolase N-terminus generated a mitochondrial targeting signal de novo (Osumi et al., 1992). Finally, this suggestion was confirmed by the elucidation of the 3D structure of the N-terminus of the yeast ortholog of thiolase (Fox3) in a receptor bound state, in which the PTS2 non-apeptide presented as α-helix (Pan et al., 2013). Altogether, the linear PTS2 non-apeptide corresponds to an α-helix, in which one flank is occupied by the key residues that align amino acids of the same property. When comparing the N-terminal sequences of PTS2-containing proteins, the region upstream of the PTS2 was found enriched in acidic residues (Reumann, 2004; Kunze et al., 2011), whereas the region downstream of the PTS2 contains many amino acids, which are typical for unstructured stretches (Kunze et al., 2011). The latter probably reflects a linker domain, which serves the exposure of the PTS2 helix from the fully folded core protein. Accordingly, a similar linker domain has been described next to the PTS1 (Neuberger et al., 2003c), but was not observed in proteins that are imported in an unfolded state into other organelles. In addition, the flexible linker domain of PTS2-carrying proteins could also be necessary for the exposition of the processing site toward the peptidase inside peroxisomes.

Bottom Line: The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments.Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals.Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria.

ABSTRACT
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.

No MeSH data available.


Related in: MedlinePlus