Homepeptide Repeats: Implications for Protein Structure, Function and Evolution

Muthukumarasamy, Uthayakumar; Benazir, Bowdadu; Patra, Sanjeev; Vaishnavi, Marthandan Kirti; Gurusaran, Manickam; Kanagarajan, Sureka; Jeyakanthan, Jeyaraman; Sekar, K.

doi:10.1016/j.gpb.2012.04.001

Cited by 9 publications

(7 citation statements)

References 51 publications

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“…Our survey of long repeats in a non-redundant set of UniProt sequences has highlighted the occurrence of these repeats that play an important role in the structure and function of domains of the proteins. Previous studies have focused on structural and functional implications of proteins with homo repeats (Uthayakumar et al, 2012), fibrous repeats (Parry, 2005) and different well-characterized repeats of length 5–50 (Andrade et al, 2001). Therefore, an in-depth study of long repeats in UniProt sequences was carried out for a better understanding of the correspondence of repeat sequences with their structures and functions.…”

Section: Discussionmentioning

confidence: 99%

Identification and Analysis of Long Repeats of Proteins at the Domain Level

Rajathei

Parthasarathy

Selvaraj

2019

Front. Bioeng. Biotechnol.

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Amino acid repeats play an important role in the structure and function of proteins. Analysis of long repeats in protein sequences enables one to understand their abundance, structure and function in the protein universe. In the present study, amino acid repeats of length >50 (long repeats) were identified in a non-redundant set of UniProt sequences using the RADAR program. The underlying structures and functions of these long repeats were carried out using the Gene3D for structural domains, Pfam for functional domains and enzyme and non-enzyme functional classification for catalytic and binding of the proteins. From a structural perspective, these long repeats seem to predominantly occur in certain architectures such as sandwich, bundle, barrel, and roll and within these architectures abundant in the superfolds. The lengths of the repeats within each fold are not uniform exhibiting different structures for different functions. We also observed that long repeats are in the domain regions of the family and are involved in the function of the proteins. After grouping based on enzyme and non-enzyme classes, we observed the abundant occurrence of long repeats in specific catalytic and binding of the proteins. In this study, we have analyzed the occurrence of long repeats in the protein sequence universe apart from well-characterized short tandem repeats in sequences and their structures and functions of the proteins at the domain level. The present study suggests that long repeats may play an important role in the structure and function of domains of the proteins.

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Section: Discussionmentioning

confidence: 99%

Identification and Analysis of Long Repeats of Proteins at the Domain Level

Rajathei

Parthasarathy

Selvaraj

2019

Front. Bioeng. Biotechnol.

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“…In general, homopeptides are more conserved in bacteria, than in archaea and eukaryotes, and there is a correlation between repeat length differences and species divergence (Uthayakumar et al 2012). Homopeptides increase the functional versatility of proteins, and facilitate spatial organization of proteins in a repeat-dependent way (Chavali et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome (v0.1)"

2020

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The proteome of the malaria parasite Plasmodium falciparum is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum. Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (<5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (<10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (≥10 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include 'vesicle-mediated transport', and 'DNA-directed 5'-3' RNA polymerase activity', with various categories linked to 'binding' evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near/in IDRs. The implications of these findings are discussed.

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“…Although homopeptides are sites of such polymorphic variation, earlier work showed that some homopeptides are deeply conserved across orthologs from bacteria and eukaryotes, suggesting ancient origin and functional essentiality ( Faux et al, 2005 ). In general, homopeptides are more conserved in bacteria, than in archaea and eukaryotes, and there is a correlation between repeat length differences and species divergence ( Uthayakumar et al, 2012 ). Homopeptides increase the functional versatility of proteins, and facilitate spatial organization of proteins in a repeat-dependent way ( Chavali et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome

Wang

Yang

Harrison

2020

PeerJ

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The proteome of the malaria parasite Plasmodium falciparum is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum. Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (<5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (<10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (≥10 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include “vesicle-mediated transport”, and “DNA-directed 5′-3′ RNA polymerase activity”, with various categories linked to “binding” evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near/in IDRs. The implications of these findings are discussed.

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Homepeptide Repeats: Implications for Protein Structure, Function and Evolution

Cited by 9 publications

References 51 publications

Identification and Analysis of Long Repeats of Proteins at the Domain Level

Identification and Analysis of Long Repeats of Proteins at the Domain Level

Peer Review #1 of "The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome (v0.1)"

The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome

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