Martínez-García Pedro Manuel, Ramos Cayo, Rodríguez-Palenzuela Pablo
Área de Genética, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, E-29071, Spain; Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain.
Área de Genética, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, E-29071, Spain.
PLoS One. 2015 Apr 13;10(4):e0119317. doi: 10.1371/journal.pone.0119317. eCollection 2015.
T346Hunter (Type Three, Four and Six secretion system Hunter) is a web-based tool for the identification and localisation of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) clusters in bacterial genomes. Non-flagellar T3SS (NF-T3SS) and T6SS are complex molecular machines that deliver effector proteins from bacterial cells into the environment or into other eukaryotic or prokaryotic cells, with significant implications for pathogenesis of the strains encoding them. Meanwhile, T4SS is a more functionally diverse system, which is involved in not only effector translocation but also conjugation and DNA uptake/release. Development of control strategies against bacterial-mediated diseases requires genomic identification of the virulence arsenal of pathogenic bacteria, with T3SS, T4SS and T6SS being major determinants in this regard. Therefore, computational methods for systematic identification of these specialised machines are of particular interest. With the aim of facilitating this task, T346Hunter provides a user-friendly web-based tool for the prediction of T3SS, T4SS and T6SS clusters in newly sequenced bacterial genomes. After inspection of the available scientific literature, we constructed a database of hidden Markov model (HMM) protein profiles and sequences representing the various components of T3SS, T4SS and T6SS. T346Hunter performs searches of such a database against user-supplied bacterial sequences and localises enriched regions in any of these three types of secretion systems. Moreover, through the T346Hunter server, users can visualise the predicted clusters obtained for approximately 1700 bacterial chromosomes and plasmids. T346Hunter offers great help to researchers in advancing their understanding of the biological mechanisms in which these sophisticated molecular machines are involved. T346Hunter is freely available at http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter.
T346Hunter（三型、四型和六型分泌系统搜寻工具）是一款基于网络的工具，用于识别和定位细菌基因组中的三型、四型和六型分泌系统（分别为T3SS、T4SS和T6SS）簇。非鞭毛T3SS（NF-T3SS）和T6SS是复杂的分子机器，可将效应蛋白从细菌细胞传递到环境中或其他真核或原核细胞中，这对编码它们的菌株的致病性具有重要影响。同时，T4SS是一个功能更为多样的系统，它不仅参与效应蛋白的转运，还参与接合以及DNA摄取/释放。制定针对细菌介导疾病的控制策略需要对病原菌的毒力武器库进行基因组鉴定，在这方面T3SS、T4SS和T6SS是主要决定因素。因此，用于系统识别这些特殊机器的计算方法特别受关注。为便于完成这项任务，T346Hunter提供了一个用户友好的基于网络的工具，用于预测新测序细菌基因组中的T3SS、T4SS和T6SS簇。在查阅了现有的科学文献后，我们构建了一个隐藏马尔可夫模型（HMM）蛋白质谱和序列数据库，这些序列代表了T3SS、T4SS和T6SS的各种组分。T346Hunter针对用户提供的细菌序列搜索这样一个数据库，并定位这三种分泌系统中任何一种的富集区域。此外，通过T346Hunter服务器，用户可以可视化大约1700个细菌染色体和质粒的预测簇。T346Hunter为研究人员深入了解这些复杂分子机器所涉及的生物学机制提供了很大帮助。可通过http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter免费获取T346Hunter。
