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In silico analysis of ubiquitin/ubiquitin-like modifiers and their conjugating enzymes in Entamoeba species

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Abstract

Covalent modification of proteins by ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) regulates many cellular functions in eukaryotes. These modifications are likely to be associated with pathogenesis, growth, and development of many protozoan parasites but molecular details about this pathway are unavailable for most protozoa. This study presents an analysis of the Ub pathway in three members of the Entamoeba species. Using bioinformatics tools we have identified all Ub and Ubl genes along with their corresponding activating, conjugating, and ligating enzymes (E1, E2s, and E3s) in three Entamoeba species, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens. Phylogenetic trees were established for the identified E2s and RING finger E3s using maximum-likelihood method to infer the relationship among these proteins. In silico co-domain analysis of RING finger E3s implicates these proteins in a variety of functions. Several known and putative regulatory motifs were identified in the upstream regions of RING finger domain containing E3 genes. All E2 and E3 genes were analyzed in genomic context in E. histolytica and E. dispar. Most E2s and E3s were in syntenic positions in the two genomes. Association of these genes with transposable elements (TEs) was compared between E. histolytica and E. dispar. A closer association was found between RING finger E3s with TEs in E. histolytica. In summary, our analyses suggests that the complexity of the Ub pathway in Entamoeba species is close to that observed in higher eukaryotes. This study provides important data for further understanding the role of Ub pathway in the biology of these organisms.

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Abbreviations

APC/C:

Anaphase promoting complex/cyclosome

CRL:

Cullin-RING ligases

HECT:

Homologous to E6-AP C-terminal

RING:

Really interesting new gene

PHD:

Plant homeo domain

TE:

Transposable element

UBC:

Ubiquitin conjugating

Ubl:

Ubiquitin-like

UPP:

Ubiquitin–proteasome pathway

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Acknowledgments

This work was supported by grants from the Department of Science and Technology to ST. SA was supported by fellowship from the University Grants Commission. PG was supported by the Defense Research and Development Organization grant to ST. We thank Dr. Sudha Bhattacharya for sharing the data on transposons. We are grateful to Dr Sudha and Alok Bhattacharya for critical reading of the manuscript and for many stimulating discussions.

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  1. Gaurav Sharma

    Present address: Institute for Microbial Technology, Chandigarh, Punjab, India

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  1. School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India

    Shweta Arya, Gaurav Sharma, Preeti Gupta & Swati Tiwari

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  1. Shweta Arya
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Correspondence to Swati Tiwari.

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Shweta Arya and Gaurav Sharma contributed equally to this work.

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Arya, S., Sharma, G., Gupta, P. et al. In silico analysis of ubiquitin/ubiquitin-like modifiers and their conjugating enzymes in Entamoeba species. Parasitol Res 111, 37–51 (2012). https://doi.org/10.1007/s00436-011-2799-0

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