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Membrane topology and predicted RNA-binding function of the 'early responsive to dehydration (ERD4)' plant protein.

Rai A, Suprasanna P, D'Souza SF, Kumar V - PLoS ONE (2012)

Bottom Line: The structure based sequence alignment with the known RNA-binding proteins revealed conservation of two non-canonical ribonucleoprotein sub-motifs in both the putative RNA-recognition domains of the ERD4 protein.The function of highly conserved ERD4 protein may thus be associated with its RNA-binding ability during the stress response.This is the first functional annotation of ERD4 family of proteins that can be useful in designing experiments to unravel crucial aspects of stress tolerance mechanism.

View Article: PubMed Central - PubMed

Affiliation: Nuclear Agricultural & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India.

ABSTRACT
Functional annotation of uncharacterized genes is the main focus of computational methods in the post genomic era. These tools search for similarity between proteins on the premise that those sharing sequence or structural motifs usually perform related functions, and are thus particularly useful for membrane proteins. Early responsive to dehydration (ERD) genes are rapidly induced in response to dehydration stress in a variety of plant species. In the present work we characterized function of Brassica juncea ERD4 gene using computational approaches. The ERD4 protein of unknown function possesses ubiquitous DUF221 domain (residues 312-634) and is conserved in all plant species. We suggest that the protein is localized in chloroplast membrane with at least nine transmembrane helices. We detected a globular domain of 165 amino acid residues (183-347) in plant ERD4 proteins and expect this to be posited inside the chloroplast. The structural-functional annotation of the globular domain was arrived at using fold recognition methods, which suggested in its sequence presence of two tandem RNA-recognition motif (RRM) domains each folded into βαββαβ topology. The structure based sequence alignment with the known RNA-binding proteins revealed conservation of two non-canonical ribonucleoprotein sub-motifs in both the putative RNA-recognition domains of the ERD4 protein. The function of highly conserved ERD4 protein may thus be associated with its RNA-binding ability during the stress response. This is the first functional annotation of ERD4 family of proteins that can be useful in designing experiments to unravel crucial aspects of stress tolerance mechanism.

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Amino acid composition of presequences.Analysis of the amino acid composition of the N-terminal sixteen residues (%MOL-16), N-terminal sixty residues (%MOL-60) and full-length proteins (%MOL-all) (A) analysis of the 123 chloroplast envelope proteins of A. thaliana (B) analysis of plant ERD4 orthologs.
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pone-0032658-g003: Amino acid composition of presequences.Analysis of the amino acid composition of the N-terminal sixteen residues (%MOL-16), N-terminal sixty residues (%MOL-60) and full-length proteins (%MOL-all) (A) analysis of the 123 chloroplast envelope proteins of A. thaliana (B) analysis of plant ERD4 orthologs.

Mentions: It has been earlier shown that N-terminal sixty residues contain signal sequence for chloroplastic localization, sixteen of which could be used to discriminate between mitochondrial and chloroplastic localization [20]. In order to get detailed information on the amino acid composition of presequences for chloroplast envelope targeting, we analyzed experimentally validated chloroplastic envelope proteins of A. thaliana. An overall amino acid composition and N-terminal sequence logo plots of the 123 selected proteins (ENV dataset) from Arabidopsis proteome [19] were analyzed. The positional abundance of amino acids in sequence logos showed abundance of Ser residues and underrepresentation of Arg residues in the ENV dataset. However, no clear position-specific pattern was observed in sequence logo plots. Similar trends have earlier been observed for the total chloroplast proteins, including stroma proteins [20], [21]. The amino acid composition analysis also showed much higher abundance of Ser, Ala and Leu residues in the N-terminal sixteen residues as compared to the full-length proteins (Fig. 3A). Also, the percentage of Arg residues in the N-terminal sixteen residues was observed to be lower than that observed in full-length or N-terminal sixty residues. The analysis of the N-terminal sixteen residues of the ERD4 orthologs also showed similar trends; higher abundance of potentially hydroxylated Ser/Thr residues and of hydrophobic Phe/Ile residues. The N-terminal sixteen residues also showed high differences in the abundance of Arg and Lys residues, as compared to the N-terminal sixty and overall composition of these proteins. These positively charged residues are underrepresented in the N-terminal sixteen residues of the ERD4 orthologs (Fig. 3B). The lower abundance of Arg and Lys residues in the N-terminal sixteen residues of chloroplast proteins, compared to mitochondrial proteins, has been earlier observed by Bhushan et al. [20]. The low percentages of the positively charged Arg/Lys residues and significantly higher percentage of Ser residues in the N-terminal sixteen residues of ERD4 proteins thus corroborated experimental determination of the ERD4 protein in A. thaliana chloroplast envelope proteome.


Membrane topology and predicted RNA-binding function of the 'early responsive to dehydration (ERD4)' plant protein.

Rai A, Suprasanna P, D'Souza SF, Kumar V - PLoS ONE (2012)

Amino acid composition of presequences.Analysis of the amino acid composition of the N-terminal sixteen residues (%MOL-16), N-terminal sixty residues (%MOL-60) and full-length proteins (%MOL-all) (A) analysis of the 123 chloroplast envelope proteins of A. thaliana (B) analysis of plant ERD4 orthologs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303787&req=5

pone-0032658-g003: Amino acid composition of presequences.Analysis of the amino acid composition of the N-terminal sixteen residues (%MOL-16), N-terminal sixty residues (%MOL-60) and full-length proteins (%MOL-all) (A) analysis of the 123 chloroplast envelope proteins of A. thaliana (B) analysis of plant ERD4 orthologs.
Mentions: It has been earlier shown that N-terminal sixty residues contain signal sequence for chloroplastic localization, sixteen of which could be used to discriminate between mitochondrial and chloroplastic localization [20]. In order to get detailed information on the amino acid composition of presequences for chloroplast envelope targeting, we analyzed experimentally validated chloroplastic envelope proteins of A. thaliana. An overall amino acid composition and N-terminal sequence logo plots of the 123 selected proteins (ENV dataset) from Arabidopsis proteome [19] were analyzed. The positional abundance of amino acids in sequence logos showed abundance of Ser residues and underrepresentation of Arg residues in the ENV dataset. However, no clear position-specific pattern was observed in sequence logo plots. Similar trends have earlier been observed for the total chloroplast proteins, including stroma proteins [20], [21]. The amino acid composition analysis also showed much higher abundance of Ser, Ala and Leu residues in the N-terminal sixteen residues as compared to the full-length proteins (Fig. 3A). Also, the percentage of Arg residues in the N-terminal sixteen residues was observed to be lower than that observed in full-length or N-terminal sixty residues. The analysis of the N-terminal sixteen residues of the ERD4 orthologs also showed similar trends; higher abundance of potentially hydroxylated Ser/Thr residues and of hydrophobic Phe/Ile residues. The N-terminal sixteen residues also showed high differences in the abundance of Arg and Lys residues, as compared to the N-terminal sixty and overall composition of these proteins. These positively charged residues are underrepresented in the N-terminal sixteen residues of the ERD4 orthologs (Fig. 3B). The lower abundance of Arg and Lys residues in the N-terminal sixteen residues of chloroplast proteins, compared to mitochondrial proteins, has been earlier observed by Bhushan et al. [20]. The low percentages of the positively charged Arg/Lys residues and significantly higher percentage of Ser residues in the N-terminal sixteen residues of ERD4 proteins thus corroborated experimental determination of the ERD4 protein in A. thaliana chloroplast envelope proteome.

Bottom Line: The structure based sequence alignment with the known RNA-binding proteins revealed conservation of two non-canonical ribonucleoprotein sub-motifs in both the putative RNA-recognition domains of the ERD4 protein.The function of highly conserved ERD4 protein may thus be associated with its RNA-binding ability during the stress response.This is the first functional annotation of ERD4 family of proteins that can be useful in designing experiments to unravel crucial aspects of stress tolerance mechanism.

View Article: PubMed Central - PubMed

Affiliation: Nuclear Agricultural & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India.

ABSTRACT
Functional annotation of uncharacterized genes is the main focus of computational methods in the post genomic era. These tools search for similarity between proteins on the premise that those sharing sequence or structural motifs usually perform related functions, and are thus particularly useful for membrane proteins. Early responsive to dehydration (ERD) genes are rapidly induced in response to dehydration stress in a variety of plant species. In the present work we characterized function of Brassica juncea ERD4 gene using computational approaches. The ERD4 protein of unknown function possesses ubiquitous DUF221 domain (residues 312-634) and is conserved in all plant species. We suggest that the protein is localized in chloroplast membrane with at least nine transmembrane helices. We detected a globular domain of 165 amino acid residues (183-347) in plant ERD4 proteins and expect this to be posited inside the chloroplast. The structural-functional annotation of the globular domain was arrived at using fold recognition methods, which suggested in its sequence presence of two tandem RNA-recognition motif (RRM) domains each folded into βαββαβ topology. The structure based sequence alignment with the known RNA-binding proteins revealed conservation of two non-canonical ribonucleoprotein sub-motifs in both the putative RNA-recognition domains of the ERD4 protein. The function of highly conserved ERD4 protein may thus be associated with its RNA-binding ability during the stress response. This is the first functional annotation of ERD4 family of proteins that can be useful in designing experiments to unravel crucial aspects of stress tolerance mechanism.

Show MeSH
Related in: MedlinePlus