A new gene inventory of the ubiquitin and ubiquitin-like conjugation pathways in Giardia intestinalis

Memórias do Instituto Oswaldo Cruz
Isabel Cristina CastellanosMoises Wasserman

Abstract

Ubiquitin (Ub) and Ub-like proteins (Ub-L) are critical regulators of complex cellular processes such as the cell cycle, DNA repair, transcription, chromatin remodeling, signal translation, and protein degradation. Giardia intestinalis possesses an experimentally proven Ub-conjugation system; however, a limited number of enzymes involved in this process were identified using basic local alignment search tool (BLAST). This is due to the limitations of BLAST's ability to identify homologous functional regions when similarity between the sequences dips to < 30%. In addition Ub-Ls and their conjugating enzymes have not been fully elucidated in Giardia. To identify the enzymes involved in the Ub and Ub-Ls conjugation processes using intelligent systems based on the hidden Markov models (HMMs). We performed an HMM search of functional Pfam domains found in the key enzymes of these pathways in Giardia's proteome. Each open reading frame identified was analysed by sequence homology, domain architecture, and transcription levels. We identified 118 genes, 106 of which corresponded to the ubiquitination process (Ub, E1, E2, E3, and DUB enzymes). The E3 ligase group was the largest group with 82 members; 71 of which harbored a characterist...Continue Reading

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Citations

Oct 8, 2020·Biomolecules·Maryia Karpiyevich, Katerina Artavanis-Tsakonas

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Datasets Mentioned

BETA
GSE36490
GSE25460

Methods Mentioned

BETA
ubiquitination

Software Mentioned

BLAST
CLUSTAL Omega
Rampage
HMMER
hmmsearch
BLASTP
in
Phyre2
MEGA7
house

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