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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

Evaluation of global protein disorder in algae proteomes. (A) Predicted disordered protein content in the studied algae proteomes computed with DISOPRED; (B) Results of a pairwise correlation analysis between the disorder content and the total number of amino acids in a proteome.
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ijms-16-19812-f001: Evaluation of global protein disorder in algae proteomes. (A) Predicted disordered protein content in the studied algae proteomes computed with DISOPRED; (B) Results of a pairwise correlation analysis between the disorder content and the total number of amino acids in a proteome.

Mentions: We prepared non-redundant sequence sets from 20 algae whole-protein sequences using the OrthoMCL tool [30] to remove sequences with >90% identity (for details, see Experimental Section 4.1). The number of sequences in the analyzed algae proteomes varied greatly from approximately 4800 in Cyanidioschyzon merolae to 20,000 in Fragilariopsis cylindrus (Table S1). Disordered protein content was determined using DISOPRED [31], which ranged from approximately 20% in Pyropia yezoensis to 35% in Chlamydomonas reinhardtii (Figure 1A). A similar trend was observed with another disorder prediction tool, RONN [32] (Figure S1). Additionally, we found that there was a correlation between disordered protein content and the total number of amino acids among the algae proteomes (Figure 1B).


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

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

Evaluation of global protein disorder in algae proteomes. (A) Predicted disordered protein content in the studied algae proteomes computed with DISOPRED; (B) Results of a pairwise correlation analysis between the disorder content and the total number of amino acids in a proteome.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-19812-f001: Evaluation of global protein disorder in algae proteomes. (A) Predicted disordered protein content in the studied algae proteomes computed with DISOPRED; (B) Results of a pairwise correlation analysis between the disorder content and the total number of amino acids in a proteome.
Mentions: We prepared non-redundant sequence sets from 20 algae whole-protein sequences using the OrthoMCL tool [30] to remove sequences with >90% identity (for details, see Experimental Section 4.1). The number of sequences in the analyzed algae proteomes varied greatly from approximately 4800 in Cyanidioschyzon merolae to 20,000 in Fragilariopsis cylindrus (Table S1). Disordered protein content was determined using DISOPRED [31], which ranged from approximately 20% in Pyropia yezoensis to 35% in Chlamydomonas reinhardtii (Figure 1A). A similar trend was observed with another disorder prediction tool, RONN [32] (Figure S1). Additionally, we found that there was a correlation between disordered protein content and the total number of amino acids among the algae proteomes (Figure 1B).

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