An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

Zheng, Yuanting; Young, Neil D.; Song, Jiangning; Chang, Bill Chia-Han; Gasser, Robin B.

doi:10.1016/j.csbj.2023.03.025

Cited by 5 publications

(2 citation statements)

References 111 publications

(129 reference statements)

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“…Individual proteins and their gene models were manually inspected and curated [49]. Functional annotation was achieved employing a recently established pipeline, with all proteins being assigned gene ontology (GO) terms [51]. Excretory/secretory (ES) proteins were inferred according to previous studies [43,51].…”

Section: Identification Classification and Annotation Of Proteases An...mentioning

confidence: 99%

“…There have been major advances in the genomics, transcriptomics and proteomics of H. contortus [39][40][41][42][43][44][45][46][47][48], allowing detailed explorations of this parasite at the molecular level and revealing distinct biological mechanisms and/or critical pathways [32,49]. Some recently developed informatic pipelines have demonstrated utility for analyses of molecular data sets [25,50] as well as protein annotation [51] and the prediction of essential genes [52]. In this context, exploring the proteases and associated inhibitors in H. contortus using abundant omics data sets and advanced informatics could contribute to finding parasitespecific targets.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Zheng,

Young,

Song

et al. 2023

IJMS

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Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber’s pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 “mixed” proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host–parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.

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Section: Identification Classification and Annotation Of Proteases An...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Zheng,

Young,

Song

et al. 2023

IJMS

Self Cite

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Unveiling the peptidases of parasites from the office chair – The endothelin-converting enzyme case study

Konečný,

Peterková

2024

Advances in Parasitology

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Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates

Zheng,

Young,

Campos

et al. 2024

International Journal for Parasitology

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An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

Cited by 5 publications

References 111 publications

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

Unveiling the peptidases of parasites from the office chair – The endothelin-converting enzyme case study

Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates

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