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HECTAR: a method to predict subcellular targeting in heterokonts.

Gschloessl B, Guermeur Y, Cock JM - BMC Bioinformatics (2008)

Bottom Line: The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95.It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts.A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism.

View Article: PubMed Central - HTML - PubMed

Affiliation: UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, F 29682, Roscoff, France. gschloesslb@gmail.com

ABSTRACT

Background: The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem.

Results: HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine.

Conclusion: The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism. Both HECTAR and HECTARSEC are available as a web application at the following address: http://www.sb-roscoff.fr/hectar/.

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Primary and secondary endosymbiosis. part A: Primary endosymbiosis is proposed to have involved the capture of a cyanobacterium (green elipse) by a eukaryotic heterotroph (red elipse). The cyanobacterium would then have been modified during evolution to give rise to a plastid with two surrounding membranes. part B: The secondary endosymbiotic event that gave rise to the heterokonts is proposed to have involved the engulfment of a red algae with a chloroplast (green elipse inside a red elipse) by a eukaryotic heterotroph (brown elipse). The red alga would have become the heterokont plastid with four surrounding membranes.
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Figure 1: Primary and secondary endosymbiosis. part A: Primary endosymbiosis is proposed to have involved the capture of a cyanobacterium (green elipse) by a eukaryotic heterotroph (red elipse). The cyanobacterium would then have been modified during evolution to give rise to a plastid with two surrounding membranes. part B: The secondary endosymbiotic event that gave rise to the heterokonts is proposed to have involved the engulfment of a red algae with a chloroplast (green elipse inside a red elipse) by a eukaryotic heterotroph (brown elipse). The red alga would have become the heterokont plastid with four surrounding membranes.

Mentions: The heterokonts are a diverse evolutionary group that includes diatoms, brown algae, and oomycete plant pathogens such as potato late blight [21]. The plastids of the photosynthetic members of this group are thought to be derived from a secondary endosymbiotic event involving a red alga and a eukaryotic heterotroph (Fig. 1). The enslavement of the endosymbiont involved alterations to its structure and most of the endosymbiont's genes were transfered to the host nucleus or lost [22,23]. As a result, present day heterokonts possess plastids with a complex structure. These organelles are surrounded by four concentric membranes and the nuclear-encoded proteins that function in these plastids have to be transported into the organelle through these four membranes. This is mediated by bipartite, N-terminal targeting sequences consisting of a leading signal peptide followed by a chloroplast transit peptide (Fig. 2). Kilian and Kroth [24] have identified a conserved motif (ASAFAP) at the cleavage site of the signal peptide in heterokont plastid targeted proteins. This motif includes the alanine (A) residues at positions -1 and -3 relative to the cleavage site that are commonly found in all signal peptides [25]. The phenylalanine (F) residue just after the cleavage site is highly conserved, it occurs in almost all heterokont chloroplast targeted proteins, being only rarely replaced by tryptophan, tyrosine or leucine [26]. The ASAFAP motif was shown to be essential for import into the plastid in experiments that involved transforming the diatom Phaeodactylum tricornutum with constructs encoding modified plastid target peptides fused to green fluorescent proteins (GFP) [24,26].


HECTAR: a method to predict subcellular targeting in heterokonts.

Gschloessl B, Guermeur Y, Cock JM - BMC Bioinformatics (2008)

Primary and secondary endosymbiosis. part A: Primary endosymbiosis is proposed to have involved the capture of a cyanobacterium (green elipse) by a eukaryotic heterotroph (red elipse). The cyanobacterium would then have been modified during evolution to give rise to a plastid with two surrounding membranes. part B: The secondary endosymbiotic event that gave rise to the heterokonts is proposed to have involved the engulfment of a red algae with a chloroplast (green elipse inside a red elipse) by a eukaryotic heterotroph (brown elipse). The red alga would have become the heterokont plastid with four surrounding membranes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567999&req=5

Figure 1: Primary and secondary endosymbiosis. part A: Primary endosymbiosis is proposed to have involved the capture of a cyanobacterium (green elipse) by a eukaryotic heterotroph (red elipse). The cyanobacterium would then have been modified during evolution to give rise to a plastid with two surrounding membranes. part B: The secondary endosymbiotic event that gave rise to the heterokonts is proposed to have involved the engulfment of a red algae with a chloroplast (green elipse inside a red elipse) by a eukaryotic heterotroph (brown elipse). The red alga would have become the heterokont plastid with four surrounding membranes.
Mentions: The heterokonts are a diverse evolutionary group that includes diatoms, brown algae, and oomycete plant pathogens such as potato late blight [21]. The plastids of the photosynthetic members of this group are thought to be derived from a secondary endosymbiotic event involving a red alga and a eukaryotic heterotroph (Fig. 1). The enslavement of the endosymbiont involved alterations to its structure and most of the endosymbiont's genes were transfered to the host nucleus or lost [22,23]. As a result, present day heterokonts possess plastids with a complex structure. These organelles are surrounded by four concentric membranes and the nuclear-encoded proteins that function in these plastids have to be transported into the organelle through these four membranes. This is mediated by bipartite, N-terminal targeting sequences consisting of a leading signal peptide followed by a chloroplast transit peptide (Fig. 2). Kilian and Kroth [24] have identified a conserved motif (ASAFAP) at the cleavage site of the signal peptide in heterokont plastid targeted proteins. This motif includes the alanine (A) residues at positions -1 and -3 relative to the cleavage site that are commonly found in all signal peptides [25]. The phenylalanine (F) residue just after the cleavage site is highly conserved, it occurs in almost all heterokont chloroplast targeted proteins, being only rarely replaced by tryptophan, tyrosine or leucine [26]. The ASAFAP motif was shown to be essential for import into the plastid in experiments that involved transforming the diatom Phaeodactylum tricornutum with constructs encoding modified plastid target peptides fused to green fluorescent proteins (GFP) [24,26].

Bottom Line: The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95.It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts.A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism.

View Article: PubMed Central - HTML - PubMed

Affiliation: UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, F 29682, Roscoff, France. gschloesslb@gmail.com

ABSTRACT

Background: The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem.

Results: HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine.

Conclusion: The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism. Both HECTAR and HECTARSEC are available as a web application at the following address: http://www.sb-roscoff.fr/hectar/.

Show MeSH
Related in: MedlinePlus