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SecReT4


NAR Molecular Biology Database Collection entry number 1576
Dexi Bi 1, Linmeng Liu 1, Cui Tai 1, Zixin Deng 1, Kumar Rajakumar 2, Hong-Yu Ou1
1 State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai 200030, China.

2 Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, United Kingdom.

Database Description

Type IV secretion systems (T4SSs) are versatile, bacterial membrane-spanning apparatuses, composed of diverse structural units, which mediate both genetic exchange and the delivery of effector proteins to target eukaryotic cells (1,2). Hence, these secretory organelles play key roles in bacterial genome plasticity and pathogenesis. SecReT4 is an integrated database providing comprehensive information of type IV secretion systems (T4SSs) in bacteria. SecReT4 presents reported and predicted essential components that make up T4SS instruments, and effectors delivered by T4SSs, in Gram-negative and Gram-positive bacteria. All the component data have been curated and re-annotated according to a set of reference T4SSs. Components are not only organized by entire T4SSs but can also be analyzed alongside other components in SecReT4 belonging to the same bit part. SecReT4 has classified all archived T4SSs based on two known classification schemes (3,4). Furthermore, references have been collected, mined and mapped to T4SSs and effectors. The database provides functional descriptions for T4SSs, T4SS components and cognate effectors according to findings reported in the literature. To organize and display these data in an efficient manner, we designed a customized PostgreSQL schema and developed a user-friendly web-interface. The SecReT4 browse module contains detailed information on all archived T4SSs, matching essential component parts and T4SS effector molecules. Users can create maps of T4SS gene clusters, investigate gene loci of interest with the embedded graphic display and search for T4SSs by name, function or host organism. Besides, SecReT4 offers easily accessible tools including BLAST, HMMER, Primer3, and MUSCLE to permit a wide range of analyses. SecReT4 exclusively provides a web tool to identify T4SS components encoded by user-supplied DNA sequences, thus promoting the efficient identification of novel putative T4SSs in newly sequenced genomes.

References

1. Cascales, E. and Christie, P.J. (2003) The versatile bacterial type IV secretion systems. Nat Rev Microbiol, 1(2), 137-149.

2. Fronzes, R., Christie, P.J. and Waksman, G. (2009) The structural biology of type IV secretion systems. Nat Rev Microbiol, 7(10), 703-714.

3. Christie, P.J., Atmakuri, K., Krishnamoorthy, V., Jakubowski, S. and Cascales, E. (2005) Biogenesis, architecture, and function of bacterial type IV secretion systems. Annu Rev Microbiol, 59, 451-485.

4. Lawley, T.D., Klimke, W.A., Gubbins, M.J. and Frost, L.S. (2003) F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett, 224(1), 1-15.



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