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Genome-Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species
Published online January 10, 2018
© 2018 The Korean Society of Plant Pathology.

Thao Thi Nguyen1, Hyun-Hee Lee1, Inmyoung Park1,2, and Young-Su Seo1*

1Department of Microbiology, Pusan National University, Busan 46241, Korea
2Department of Asian Food and Culinary Arts, Youngsan University, Busan 48015, Korea
Correspondence to: Phone) +82-51-510-2267, FAX) +82-51-514-1778
E-mail) yseo2011@pusan.ac.kr
Received November 9, 2017; Revised November 28, 2017; Accepted December 4, 2017.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plantassociated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.
Keywords : Burkholderia species, T6SS, type VI effector


December 2017, 33 (6)