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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 ubiquitination sites or PEST regions. Normalized predicted ubiquitination sites and PEST regions per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; Relative percentage of disordered protein content with different numbers of predicted sites of ubiquitination and predicted regions of PEST are presented in (B,D), respectively.
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ijms-16-19812-f004: Correlation between disordered protein content and ubiquitination sites or PEST regions. Normalized predicted ubiquitination sites and PEST regions per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; Relative percentage of disordered protein content with different numbers of predicted sites of ubiquitination and predicted regions of PEST are presented in (B,D), respectively.

Mentions: Ubiquitination sites and PEST regions within a protein sequence are related to protein degradation [48]. We used the freely available UbPred tool for ubiquitination site prediction and epestfind tool for PEST region prediction [49,50]. The content of ubiquitination sites varied from approximately 0.4 to 1.4 sites per 400 amino acids, and the content of PEST regions varied from approximately 0.2 to 0.5 sites per 400 amino acids in the analyzed algae proteomes (Figure 4A,C). We observed that the predicted presence of both ubiquitination sites and PEST regions were statistically positively correlated to disordered protein content in all algae proteomes (Figure 4B,D) with high correlation coefficients (Table 1). The observed correlations of ubiquitination and PEST with protein disorder were confirmed with the alternative disorder prediction tool, RONN (Figure S5).


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 ubiquitination sites or PEST regions. Normalized predicted ubiquitination sites and PEST regions per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; Relative percentage of disordered protein content with different numbers of predicted sites of ubiquitination and predicted regions of PEST 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-f004: Correlation between disordered protein content and ubiquitination sites or PEST regions. Normalized predicted ubiquitination sites and PEST regions per 400 amino acids in the studied algae proteomes are presented in (A,C), respectively; Relative percentage of disordered protein content with different numbers of predicted sites of ubiquitination and predicted regions of PEST are presented in (B,D), respectively.
Mentions: Ubiquitination sites and PEST regions within a protein sequence are related to protein degradation [48]. We used the freely available UbPred tool for ubiquitination site prediction and epestfind tool for PEST region prediction [49,50]. The content of ubiquitination sites varied from approximately 0.4 to 1.4 sites per 400 amino acids, and the content of PEST regions varied from approximately 0.2 to 0.5 sites per 400 amino acids in the analyzed algae proteomes (Figure 4A,C). We observed that the predicted presence of both ubiquitination sites and PEST regions were statistically positively correlated to disordered protein content in all algae proteomes (Figure 4B,D) with high correlation coefficients (Table 1). The observed correlations of ubiquitination and PEST with protein disorder were confirmed with the alternative disorder prediction tool, RONN (Figure S5).

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