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Open Access Research article

Genomic sequence of temperate phage Smp131 of Stenotrophomonas maltophilia that has similar prophages in xanthomonads

Chia-Ni Lee1, Tsai-Tien Tseng2, Hsiao-Chuan Chang1, Juey-Wen Lin3 and Shu-Fen Weng1*

Author Affiliations

1 Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan

2 Department of Biology and Chemistry, Southern Polytechnic State University, Marietta, GA 30060, USA

3 Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan

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BMC Microbiology 2014, 14:17  doi:10.1186/1471-2180-14-17

Published: 28 January 2014

Abstract

Background

Stenotrophomonas maltophilia is a ubiquitous Gram-negative bacterium previously named as Xanthomonas maltophilia. This organism is an important nosocomial pathogen associated with infections in immunocompromised patients. Clinical isolates of S. maltophilia are mostly resistant to multiple antibiotics and treatment of its infections is becoming problematic. Several virulent bacteriophages, but not temperate phage, of S. maltophilia have been characterized.

Results

In this study, a temperate myophage of S. maltophilia (Smp131) was isolated and characterized. Sequence analysis showed that its genome is 33,525-bp long with 47 open reading frames (ORFs). Its similarity to P2-like phages and prophages in S. maltophilia and several Xanthomonas pathovars includes genomic organization, arrangement of several operons, and possession of a slippery sequence T7G for translational frameshifting in tail assembly genes. Smp131 encodes a tyrosine family integrase that shares low degrees of similarity with those of other phages and a lysin belonging to family 19 chitinase that is observed in plants and some bacteria, although not in phages. tRNA are the preferred sites for host integration of Smp131 and the related phages: tRNA-Thr for Smp131 and prophage of S. maltophilia K279a; tRNA-Lys for prophages of X. campestris pv. campestris ATCC33913, X. oryzae pv. oryzae strains MAFF311018, and KACC10331; and tRNA-Asn for prophage of X. oryzae pv. oryzae PXO99A and remnant of X. axonopodis pv. citri 306. Regions flanking the prophages are varied highly in nucleotide sequence and rich in transposase genes, suggesting that frequent insertion/excision had occurred.

Conclusions

Prevalence of closely related prophages in Stenotrophomonas and Xanthomonads may have contributed to the diversity of these closely related species owing to possible horizontal gene transfer mediated by the phages.

Keywords:
Genomic sequence; Integration; Prophage; Stenotrophomonas; Temperate phage; Xanthomonas