Biochemistry and Physiology of Plants, Bielefeld University, 33501, Bielefeld, Germany.
Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.
BMC Bioinformatics. 2020 Oct 31;21(1):490. doi: 10.1186/s12859-020-03749-2.
Post-translational modifications (PTM) of amino acid (AA) side chains in peptides control protein structure and functionality. PTMs depend on the specific AA characteristics. The reactivity of cysteine thiol-based PTMs are unique among all proteinaceous AA. This pipeline aims to ease the identification of conserved AA of polypeptides or protein families based on the phylogenetic occurrence in the plant kingdom. The tool is customizable to include any species. The degree of AA conservation is taken as indicator for structural and functional significance, especially for PTM-based regulation. Further, this pipeline tool gives insight into the evolution of these potentially regulatory important peptides.
The web-based or stand-alone pipeline tool Conserved Cysteine Finder (ConCysFind) was developed to identify conserved AA such as cysteine, tryptophan, serine, threonine, tyrosin and methionine. ConCysFind evaluates multiple alignments considering the proteome of 21 plant species. This exemplar study focused on Cys as evolutionarily conserved target for multiple redox PTM. Phylogenetic trees and tables with the compressed results of the scoring algorithm are generated for each Cys in the query polypeptide. Analysis of 33 translation elongation and release factors alongside of known redox proteins from Arabidopsis thaliana for conserved Cys residues confirmed the suitability of the tool for identifying conserved and functional PTM sites. Exemplarily, the redox sensitivity of cysteines in the eukaryotic release factor 1-1 (eRF1-1) was experimentally validated.
ConCysFind is a valuable tool for prediction of new potential protein PTM targets in a broad spectrum of species, based on conserved AA throughout the plant kingdom. The identified targets were successfully verified through protein biochemical assays. The pipeline is universally applicable to other phylogenetic branches by customization of the database.
氨基酸（AA）侧链的翻译后修饰（PTM）控制着蛋白质的结构和功能。PTM 取决于特定的 AA 特征。基于半胱氨酸巯基的 PTM 的反应性在所有蛋白质 AA 中是独特的。这个流水线旨在根据植物王国中的系统发生出现，轻松识别多肽或蛋白质家族的保守 AA。该工具可定制，可包含任何物种。AA 的保守程度被视为结构和功能重要性的指标，特别是对于基于 PTM 的调节。此外，这个流水线工具可以深入了解这些潜在调节肽的进化。
开发了基于网络或独立的流水线工具保守半胱氨酸查找器（ConCysFind），用于识别保守的 AA，如半胱氨酸、色氨酸、丝氨酸、苏氨酸、酪氨酸和蛋氨酸。ConCysFind 评估了考虑到 21 种植物物种蛋白质组的多重比对。这个示例研究集中在半胱氨酸上，作为多种氧化还原 PTM 的进化保守靶标。为查询多肽中的每个半胱氨酸生成了带有评分算法压缩结果的系统发育树和表。对 33 种翻译延伸和释放因子以及来自拟南芥的已知氧化还原蛋白的保守半胱氨酸残基的分析，证实了该工具用于识别保守和功能 PTM 位点的适用性。作为示例，实验验证了真核释放因子 1-1（eRF1-1）中半胱氨酸的氧化还原敏感性。
ConCysFind 是一种在广泛物种中预测新的潜在蛋白质 PTM 靶标的有价值的工具，这些靶标基于整个植物王国中的保守 AA。通过蛋白质生化测定成功验证了鉴定出的靶标。通过数据库的定制，该流水线可普遍适用于其他系统发育分支。
