Limits...
In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

Kurotani A, Sakurai T - Int J Mol Sci (2015)

Bottom Line: In contrast, transmembrane helices were favored in ordered regions.Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae.Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. atsushi.kurotani@riken.jp.

ABSTRACT
Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

No MeSH data available.


Related in: MedlinePlus

Correlation between disordered protein content and glycosylation sites. Normalized predicted O-glycosylation and N-glycosylation sites per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; The relative percentage of disordered protein content with different numbers of predicted O- and N-glycosylation sites are presented in (B,D), respectively.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4581327&req=5

ijms-16-19812-f003: Correlation between disordered protein content and glycosylation sites. Normalized predicted O-glycosylation and N-glycosylation sites per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; The relative percentage of disordered protein content with different numbers of predicted O- and N-glycosylation sites are presented in (B,D), respectively.

Mentions: Protein glycosylation is one of the most common PTMs where the attachment of glycans to specific residues affects protein folding, localization, and stability. Glycosylated proteins play an important role in essential biological functions such as immunogenicity, catalytic activity, viral clearance, and ligand-receptor interactions [34,35,36,37]. Two major types of protein glycosylation exist: O-linked and N-linked. O-glycosylation occurs frequently in eukaryotic cells and is involved in many basic cellular functions. However, significant differences in O-glycosylation patterns between plants and animals have been described, including the sites of glycan addition and glycan composition. O-glycosylation in plants mainly occurs on hydroxylproline (Hyp) residues [38]. The freely available NetOGlyc tool can be used to predict O-glycosylation sites in mammalian proteins [39]. However, there is currently no available prediction tool for O-glycosylation sites for plant proteins. Therefore, in the present study, we designed an original program to predict Hyp-O-linked glycosylation sites utilizing the consensus sequence for Hyp-O-linked glycosylation previously reported for plants [40]. The average abundance of O-glycosylations sites varied in the studied algae proteomes from approximately 0.8 to more than 1.7 sites per protein (Figure 3A). Additionally, we observed that the disordered protein content was positively correlated with the number of O-glycosylation sites (from 0 to ≥7) in every algae proteome analyzed (Figure 3B). The correlation between IDRs and O-glycosylation had high correlation coefficients and were found to be statistically significant (Table 1). The positive correlation between disordered protein content and the number of O-glycosylation sites was confirmed by using the alternative disorder prediction tool, RONN (Figure S4A).


In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

Kurotani A, Sakurai T - Int J Mol Sci (2015)

Correlation between disordered protein content and glycosylation sites. Normalized predicted O-glycosylation and N-glycosylation sites per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; The relative percentage of disordered protein content with different numbers of predicted O- and N-glycosylation sites are presented in (B,D), respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581327&req=5

ijms-16-19812-f003: Correlation between disordered protein content and glycosylation sites. Normalized predicted O-glycosylation and N-glycosylation sites per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; The relative percentage of disordered protein content with different numbers of predicted O- and N-glycosylation sites are presented in (B,D), respectively.
Mentions: Protein glycosylation is one of the most common PTMs where the attachment of glycans to specific residues affects protein folding, localization, and stability. Glycosylated proteins play an important role in essential biological functions such as immunogenicity, catalytic activity, viral clearance, and ligand-receptor interactions [34,35,36,37]. Two major types of protein glycosylation exist: O-linked and N-linked. O-glycosylation occurs frequently in eukaryotic cells and is involved in many basic cellular functions. However, significant differences in O-glycosylation patterns between plants and animals have been described, including the sites of glycan addition and glycan composition. O-glycosylation in plants mainly occurs on hydroxylproline (Hyp) residues [38]. The freely available NetOGlyc tool can be used to predict O-glycosylation sites in mammalian proteins [39]. However, there is currently no available prediction tool for O-glycosylation sites for plant proteins. Therefore, in the present study, we designed an original program to predict Hyp-O-linked glycosylation sites utilizing the consensus sequence for Hyp-O-linked glycosylation previously reported for plants [40]. The average abundance of O-glycosylations sites varied in the studied algae proteomes from approximately 0.8 to more than 1.7 sites per protein (Figure 3A). Additionally, we observed that the disordered protein content was positively correlated with the number of O-glycosylation sites (from 0 to ≥7) in every algae proteome analyzed (Figure 3B). The correlation between IDRs and O-glycosylation had high correlation coefficients and were found to be statistically significant (Table 1). The positive correlation between disordered protein content and the number of O-glycosylation sites was confirmed by using the alternative disorder prediction tool, RONN (Figure S4A).

Bottom Line: In contrast, transmembrane helices were favored in ordered regions.Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae.Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. atsushi.kurotani@riken.jp.

ABSTRACT
Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

No MeSH data available.


Related in: MedlinePlus