Genomic and proteomic features of mycobacteriophage SWU1 isolated from China soil

Abstract

Mycobacteriophage SWU1 is a newly isolated phage from soil sample collected in Sichuan province, China using Mycobacterium smegmatis mc(2)155 as host. Plaque, phage morphology and one-step growth curve were characterized. The complete genomic sequence of phage SWU1 was determined by shotgun sequencing. The ends of SWU1 were determined. Structural proteins of SWU1 were analyzed by NanoLC-ESI-MS/MS. Seven ORFs were identified as structural protein encoded by SWU1 genome. The genetic basis underlying the SWU1 plaque was explored using comparative genomics. Prophages homologous to SWU1 were identified in two pathogens, Segniliparus rugosus ATCC BAA-974 and Mycobacterium rhodesiae JS60. Genus Segniliparus is a member of the order Corynebacteriales. To our knowledge, this is the first report of Mycobacterium prophages in different genera.

Keywords: Electron microscopy; Genome; Mycobacteriophage; Plaque; Proteome.

Fig. 1

The plaques and morphology of SWU1. A) Plaque of SWU1 presents a characteristic bull’s eye when plated it on M. smegmatis mc2155 lawn and the juncture of neighboring plaques forms line style lawn. B) Electron micrograph shows that SWU1 has an isometric, icosahedral head and a long flexible tail. Scale bar = 100 nm.

Fig. 2

One-step growth curve of phage SWU1. Experiments were repeated three times with duplicate samples. The Y-axis shows the plaque forming units per milliliter (PFU/ml). The X-axis indicates the time.

Fig. 3

Organization of the mycobacteriophage SWU1 genome.

Fig. 4

Identification of SWU1 genome ends. A) PCR diagram: primers A and B are designed close to the two ends of the genome and PCR results in amplified products as shown after agarose gel electrophoresis. B) Lane 1, the PCR product. Lane 2, DL2000 marker, the size of the bands is indicated on the right. C) The cohesive end sequence in bold was identified by comparing the two end fragment sequences with the PCR fragment.

Fig. 5

Global comparison of SWU1 and L5. A) Two segments of genomic differences are present. There are a lot of insertions, deletions, and substitutions. B and C) We note that SWU1 contains genes that L5 does not: gene 57, 53, 52 and 39; L5 gp40 and gp 45 are not present in SWU1.