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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

Correlations between disordered protein content and the number of phosphorylation sites. (A) Normalized predicted Ser (S), Thr (T) and Tyr (Y) phosphorylation sites per 400 amino acids in the studied algae proteomes; The relative percentage of disordered protein content with different numbers of predicted S, T and Y phosphorylation sites are presented in (B–D), respectively.
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ijms-16-19812-f002: Correlations between disordered protein content and the number of phosphorylation sites. (A) Normalized predicted Ser (S), Thr (T) and Tyr (Y) phosphorylation sites per 400 amino acids in the studied algae proteomes; The relative percentage of disordered protein content with different numbers of predicted S, T and Y phosphorylation sites are presented in (B–D), respectively.

Mentions: Recently, the bioinformatics tool Musite was developed for large-scale prediction of phosphorylation sites from protein sequences as a stand-alone application [17]. Therefore, the Musite tool was used to predict phosphorylation sites in the target algae proteomes. The number of predicted phosphorylation sites was normalized to the uniform length of 400 amino acids, rather than per sequence, to account for the difference in the average protein lengths in the datasets. Similarly, we used normalized values in the analyses of the number of glycosylation sites, ubiquitination sites, PEST regions, and transmembrane helices. No trend in the average abundance of phosphorylation sites in algae proteomes was found (Figure 2A). However, a strong positive correlation was observed between protein disorder and phosphorylation. For every algae proteome analyzed, there was a positive correlation between the predicted number (from 0 to ≥7) of Ser, Thr, or Tyr phosphorylation sites and disordered protein content (Figure 2B–D). The correlations between the number of Ser and Thr phosphorylation sites to disordered protein content were statistically significant as determined by one-tailed probability values and false discovery rates controlled by the Benjamini–Hochberg procedure [33] (Table 1). The positive correlation between disordered protein content and the number of phosphorylation sites was confirmed by using the alternative disorder prediction tool, RONN (Figure S3).


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

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

Correlations between disordered protein content and the number of phosphorylation sites. (A) Normalized predicted Ser (S), Thr (T) and Tyr (Y) phosphorylation sites per 400 amino acids in the studied algae proteomes; The relative percentage of disordered protein content with different numbers of predicted S, T and Y phosphorylation 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-f002: Correlations between disordered protein content and the number of phosphorylation sites. (A) Normalized predicted Ser (S), Thr (T) and Tyr (Y) phosphorylation sites per 400 amino acids in the studied algae proteomes; The relative percentage of disordered protein content with different numbers of predicted S, T and Y phosphorylation sites are presented in (B–D), respectively.
Mentions: Recently, the bioinformatics tool Musite was developed for large-scale prediction of phosphorylation sites from protein sequences as a stand-alone application [17]. Therefore, the Musite tool was used to predict phosphorylation sites in the target algae proteomes. The number of predicted phosphorylation sites was normalized to the uniform length of 400 amino acids, rather than per sequence, to account for the difference in the average protein lengths in the datasets. Similarly, we used normalized values in the analyses of the number of glycosylation sites, ubiquitination sites, PEST regions, and transmembrane helices. No trend in the average abundance of phosphorylation sites in algae proteomes was found (Figure 2A). However, a strong positive correlation was observed between protein disorder and phosphorylation. For every algae proteome analyzed, there was a positive correlation between the predicted number (from 0 to ≥7) of Ser, Thr, or Tyr phosphorylation sites and disordered protein content (Figure 2B–D). The correlations between the number of Ser and Thr phosphorylation sites to disordered protein content were statistically significant as determined by one-tailed probability values and false discovery rates controlled by the Benjamini–Hochberg procedure [33] (Table 1). The positive correlation between disordered protein content and the number of phosphorylation sites was confirmed by using the alternative disorder prediction tool, RONN (Figure S3).

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