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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 transmembrane regions. Normalized predicted transmembrane helices per 400 amino acids in the studied algae proteomes are presented in (A); Relative percentage of disordered protein content with different numbers of predicted transmembrane helices are presented in (B).
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ijms-16-19812-f005: Correlation between disordered protein content and transmembrane regions. Normalized predicted transmembrane helices per 400 amino acids in the studied algae proteomes are presented in (A); Relative percentage of disordered protein content with different numbers of predicted transmembrane helices are presented in (B).

Mentions: Transmembrane helices in proteins play an important role in the transport of various substances across biological membranes. In the present study, we used the freely available TMHMM tool for transmembrane helix prediction. The content of transmembrane helices varied in the analyzed algae proteomes from approximately 0.6 to 0.8 regions per 400 amino acids (Figure 5A). A negative correlation was observed between the number of predicted transmembrane helices and disordered protein content in all algae proteomes (Figure 5B). The observed correlations of the number of transmembrane helices with disordered protein content were confirmed with the alternative disorder prediction tool, RONN (Figure S6).


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 transmembrane regions. Normalized predicted transmembrane helices per 400 amino acids in the studied algae proteomes are presented in (A); Relative percentage of disordered protein content with different numbers of predicted transmembrane helices are presented in (B).
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-19812-f005: Correlation between disordered protein content and transmembrane regions. Normalized predicted transmembrane helices per 400 amino acids in the studied algae proteomes are presented in (A); Relative percentage of disordered protein content with different numbers of predicted transmembrane helices are presented in (B).
Mentions: Transmembrane helices in proteins play an important role in the transport of various substances across biological membranes. In the present study, we used the freely available TMHMM tool for transmembrane helix prediction. The content of transmembrane helices varied in the analyzed algae proteomes from approximately 0.6 to 0.8 regions per 400 amino acids (Figure 5A). A negative correlation was observed between the number of predicted transmembrane helices and disordered protein content in all algae proteomes (Figure 5B). The observed correlations of the number of transmembrane helices with disordered protein content were confirmed with the alternative disorder prediction tool, RONN (Figure S6).

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