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Biology of a novel mycobacteriophage, SWU1, isolated from Chinese soil as revealed by genomic characteristics.

ABSTRACT: Mycobacteriophage SWU1 is a newly isolated phage from a soil sample collected at Gongping village, Pingchang County, Sichuan Province, China, using Mycobacterium smegmatis mc(2)155 as a host. Plaques of SWU1 appear as a unique bull's-eye on an M. smegmatis lawn. In this paper, we report the complete genome sequence of SWU1 and some major findings from the analysis result.

SUBMITTER: Fan X

PROVIDER: S-EPMC3446572 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

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Biology of a novel mycobacteriophage, SWU1, isolated from Chinese soil as revealed by genomic characteristics.

Fan Xiangyu X Teng Tieshan T Wang Honghai H Xie Jianping J

Journal of virology 20120901 18

Mycobacteriophage SWU1 is a newly isolated phage from a soil sample collected at Gongping village, Pingchang County, Sichuan Province, China, using Mycobacterium smegmatis mc(2)155 as a host. Plaques of SWU1 appear as a unique bull's-eye on an M. smegmatis lawn. In this paper, we report the complete genome sequence of SWU1 and some major findings from the analysis result. ...[more]

PMID: 22923793

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Project description:Background: Alterations in MET exon 14 (METex14) and its flanking intronic regions have been identified in a variety of cancers. Patients with METex14 alterations often benefit from MET inhibitors such as crizotinib. Given the unique mutation profiles of Chinese lung cancer patients, it is necessary to investigate the prevalence of METex14 alterations in a large cohort of cancer patients. Patients and methods: Cases carrying METex14 alterations were screened from 26,391 Chinese cancer patients by next-generation sequencing (NGS), and the clinicopathologic and molecular characteristics were reviewed. Results: Compared to Western population (~3%), the frequency of METex14 alterations is much lower in Chinese cancer patients (0.7%, n=184) and lung cancer patients (1.1%, n=175). Seventy-eight distinct METex14 alterations, including several novel alteration types were detected. Concurrent MET copy gain and non-exon14 MET mutations were also found. EGFR copy gain (11%) and mutations (8%), KRAS (5%) and PIK3CA (5%), appeared in a mutually exclusive pattern. Female patients contain much less TP53 mutations than male patients (65% vs. 24%, FDR = 0.01). Co-amplification of CDK4 and MDM2, CDK6 and EGFR were identified, which indicated cell cycle dysregulation and EGFR alteration are important co-occurring features in patients with METex 14 alteration. Of 9 tissue specimens having PD-L1 immunohistochemistry (IHC) results, 5 of them (55.5%) were found PD-L1 positive, which is comparable to other types of tumor. In 14 crizotinib-treated patients, the median progression free survival (mPFS) was 7 months. Upon resistance to crizotinib, two patients acquired secondary mutations in MET and one patient acquired BRAF p.K601E that can be a novel resistance mechanism. Conclusion: Chinese cancer patients have a relatively lower frequency of METex14 alterations compared to Western patients. Patients with METex14 alterations showed distinct molecular characteristics and the representative case study showed responses to MET tyrosine kinase inhibitor (TKI).

Project description:Mycobacteriophages are viruses that specifically infect bacteria of the Mycobacterium genus. A substantial collection of mycobacteriophages has been isolated and characterized, offering valuable insights into their diversity and evolution. This collection also holds significant potential for therapeutic applications, particularly as an alternative to antibiotics in combating drug-resistant bacterial strains. In this study, we report the isolation and characterization of a new mycobacteriophage, Vic9, using Mycobacterium smegmatis mc (2)155 as the host strain. Vic9 has been classified within the B2 subcluster of the B cluster. Morphological analysis revealed that Vic9 has a structure typical of siphophages from this subcluster and forms characteristic plaques. The phage adsorbs onto host strain cells within 30 min, and according to one-step growth experiments, its latent period lasts about 90 min, followed by a growth period of 150 min, with an average yield of approximately 68 phage particles per infected cell. In host range experiments, Vic9 efficiently lysed the host strain and also exhibited the ability to lyse M. tuberculosis H37Rv, albeit with a low efficiency of plating (EOP ≈ 2 × 10-5), a typical feature of B2 phages. No lysis was observed in other tested mycobacterial species. The genome of Vic9 comprises 67,543 bp of double-stranded DNA and encodes 89 open reading frames. Our analysis revealed unique features in Vic9, despite its close relationship to other B2 subcluster phages, highlighting its distinct characteristics even among closely related phages. Particularly noteworthy was the discovery of a distinct 435 bp sequence within the gene cluster responsible for queuosine biosynthesis, as well as a recombination event within the structural cassette region (Vic_0033-Vic_0035) among members of the B1, B2, and B3 subclusters. These genetic features are of interest for further research, as they may reveal new mechanisms of phage-bacteria interactions and their potential for developing novel phage therapy methods.

Dataset Information

Biology of a novel mycobacteriophage, SWU1, isolated from Chinese soil as revealed by genomic characteristics.

Publications

Biology of a novel mycobacteriophage, SWU1, isolated from Chinese soil as revealed by genomic characteristics.

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