Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria.

Gayatri Ramakrishnan,Narayanaswamy Srinivasan,Abha Jain,Nagasuma Chandra

doi:10.1186/s13062-016-0130-9

Gayatri Ramakrishnan, Narayanaswamy Srinivasan + Show 2 more

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https://doi.org/10.1186/s13062-016-0130-9

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Journal: Biology Direct	Publication Date: May 31, 2016
Citations: 3	License type: cc-by

Affiliation: Indian Institute of Science Bangalore

Abstract

Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed analyses of sequence and structural features resulted in the recognition of potential cyclase function conferring residues and presence of signature topological motif (βααββαβ) in the uncharacterized set of bacterial proteins. Lack of transmembrane domains and signal peptide cleavage sites is suggestive of their cytosolic subcellular localization. Furthermore, analysis on evolutionarily conserved gene clusters of the predicted nucleotide cyclase-like proteins and their evolutionary relationship with nucleotide cyclases suggest their participation in cellular signalling events. Our analyses suggest expansion of class III nucleotide cyclases.ReviewersThis article was reviewed by Eugene Koonin and Michael Gromiha.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0130-9) contains supplementary material, which is available to authorized users.

Highlights

The development of powerful homology recognition techniques over the past decade has aided in the establishment of protein structure-function and evolutionary relationships using sequence information alone
The effectiveness of AlignHUSH is reflected in the recognition of relationship between a domain family of unknown function DUF2652 and nucleotide cyclase family, which forms the focus of this study
We have presented analyses on probable structure and function acquired by a set of uncharacterised bacterial proteins on the basis of recognition of their evolutionary relationship with nucleotide cyclases

Summary

Introduction

The development of powerful homology recognition techniques over the past decade has aided in the establishment of protein structure-function and evolutionary relationships using sequence information alone. Sensitive search procedures that employ sequence-based and structure-based profiles have been shown to be effective in the reliable detection of remote evolutionary relationships, and are, extensively used in protein structure and function prediction/recognition [1]. An in-house algorithm developed in the past, AlignHUSH, employs highly sensitive profile-profile alignment coupled with information on secondary structure probabilities and hydrophobicity of amino acids to recognise evolutionarily related protein families with reasonable accuracy [2]. This approach has been useful in deriving potential relationships between sequence and structural families, which is comprehended in our inhouse database SUPFAM (http://supfam.mbu.iisc.erne t.in/) [3, 4]. The effectiveness of AlignHUSH is reflected in the recognition of relationship between a domain family of unknown function DUF2652 and nucleotide cyclase family, which forms the focus of this study

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Conclusion