Genome-wide identification, characterisation and expression profiling of the ubiquitin-proteasome genes in Biomphalaria glabrata

BACKGROUND Biomphalaria glabrata is the major species used for the study of schistosomiasis-related parasite-host relationships, and understanding its gene regulation may aid in this endeavor. The ubiquitin-proteasome system (UPS) performs post-translational regulation in order to maintain cellular protein homeostasis and is related to several mechanisms, including immune responses. OBJECTIVE The aims of this work were to identify and characterise the putative genes and proteins involved in UPS using bioinformatic tools and also their expression on different tissues of B. glabrata. METHODS The putative genes and proteins of UPS in B. glabrata were predicted using BLASTp and as queries reference proteins from model organism. We characterised these putative proteins using PFAM and CDD software describing the conserved domains and active sites. The phylogenetic analysis was performed using ClustalX2 and MEGA5.2. Expression evaluation was performed from 12 snail tissues using RPKM. FINDINGS 119 sequences involved in the UPS in B. glabrata were identified, which 86 have been related to the ubiquitination pathway and 33 to proteasome. In addition, the conserved domains found were associated with the ubiquitin family, UQ_con, HECT, U-box and proteasome. The main active sites were lysine and cysteine residues. Lysines are responsible and the starting point for the formation of polyubiquitin chains, while the cysteine residues of the enzymes are responsible for binding to ubiquitin. The phylogenetic analysis showed an organised distribution between the organisms and the clades of the sequences, corresponding to the tree of life of the animals, for all groups of sequences analysed. The ubiquitin sequence was the only one with a high expression profile found in all libraries, inferring its wide range of performance. MAIN CONCLUSIONS Our results show the presence, conservation and expression profile of the UPS in this mollusk, providing a basis and new knowledge for other studies involving this system. Due to the importance of the UPS and B. glabrata, this work may influence the search for new methodologies for the control of schistosomiasis.

背景：光滑双脐螺（Biomphalaria glabrata）是研究血吸虫病相关宿主-寄生虫互作关系的核心模式物种，解析其基因调控机制可为该领域研究提供重要助力。泛素-蛋白酶体系统（ubiquitin-proteasome system, UPS）通过翻译后调控维持细胞蛋白质稳态，且与免疫应答等多种生理机制密切相关。
研究目的：本研究旨在通过生物信息学工具鉴定并表征参与泛素-蛋白酶体系统的潜在基因与蛋白，并分析其在光滑双脐螺不同组织中的表达模式。
研究方法：以模式生物的参考蛋白作为查询序列，通过BLASTp算法预测光滑双脐螺体内泛素-蛋白酶体系统的潜在基因与蛋白。利用PFAM与CDD软件对上述潜在蛋白进行保守结构域与活性位点注释，并通过ClustalX2与MEGA5.2软件开展系统发育分析。采用RPKM值对12份螺组织样本的转录组数据进行表达量评估。
研究结果：本研究共鉴定出119个参与光滑双脐螺泛素-蛋白酶体系统的序列，其中86个与泛素化通路相关，33个与蛋白酶体功能相关。此外，鉴定到的保守结构域涵盖泛素家族结构域、UQ_con结构域、HECT结构域、U-box结构域以及蛋白酶体相关结构域。核心活性位点主要为赖氨酸残基与半胱氨酸残基：赖氨酸是多聚泛素链形成的核心位点与起始位点，而酶类的半胱氨酸残基则负责介导泛素结合。系统发育分析显示，各序列在物种间的聚类分布符合动物界的系统发育树拓扑结构，覆盖所有分析的序列组。泛素序列是唯一在所有测序文库中均呈现高表达特征的序列，提示其功能分布的广泛性。
主要结论：本研究结果证实了光滑双脐螺体内泛素-蛋白酶体系统的存在、保守性与表达谱特征，为该系统的后续研究提供了理论基础与新的研究方向。鉴于泛素-蛋白酶体系统与光滑双脐螺的研究重要性，本研究可为血吸虫病防控新方法的开发提供重要参考依据。