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一种受TALE启发的针对含有近似串联重复序列的蛋白质的计算筛选方法。

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

作者信息

Perycz Malgorzata, Krwawicz Joanna, Bochtler Matthias

机构信息

Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland.

International Institute of Molecular and Cell Biology in Warsaw, Poland.

出版信息

PLoS One. 2017 Jun 15;12(6):e0179173. doi: 10.1371/journal.pone.0179173. eCollection 2017.

DOI:10.1371/journal.pone.0179173
PMID:28617832
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5472282/
Abstract

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

摘要

转录激活样效应因子（TAL）效应蛋白（TALEs）是细菌分泌到植物细胞中作为转录激活因子的蛋白质。TALEs及相关蛋白（RipTALs、BurrH、MOrTL1和MOrTL2）含有近似串联重复序列，这些重复序列在定义特异性的保守位置上存在差异。我们使用PERL在约4700万个蛋白质序列中筛选具有TALE样结构的序列，其特征为近似串联重复序列（长度在30至43个氨基酸之间）以及保守位置上的序列变异性，且无需与TALEs有序列相似性。候选蛋白根据其核定位倾向、二级结构、重复序列复杂性以及可变残基的共变和预测结构接近性进行评分。通过其他结构域的共现和相互作用组预测初步推断生物学背景。在一种真核植物病原体——栗疫病菌的一种蛋白质中发现了具有值得进行实验表征的TALE样特征的近似重复序列。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/717505c27d73/pone.0179173.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/acb3b37e886c/pone.0179173.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/e10e9a096057/pone.0179173.g002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/00c0206bd0ad/pone.0179173.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/f8129b3b1363/pone.0179173.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/1e22bdb4c5c4/pone.0179173.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/335a3af37c54/pone.0179173.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/ee7f8b7d0468/pone.0179173.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/717505c27d73/pone.0179173.g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/acb3b37e886c/pone.0179173.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/e10e9a096057/pone.0179173.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/fbbe163b6842/pone.0179173.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/00c0206bd0ad/pone.0179173.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/f8129b3b1363/pone.0179173.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/1e22bdb4c5c4/pone.0179173.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/335a3af37c54/pone.0179173.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/ee7f8b7d0468/pone.0179173.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f71/5472282/717505c27d73/pone.0179173.g009.jpg

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Tandem-repeat protein domains across the tree of life.串联重复蛋白结构域遍布生命之树。
PeerJ. 2015 Jan 13;3:e732. doi: 10.7717/peerj.732. eCollection 2015.
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