Isolation, characterization, and complete genome analysis of P1312, a thermostable bacteriophage that infects Thermobifida fusca

Abstract

Thermobifida fusca is a moderately thermophilic and cellulolytic actinobacterium. It is of particular interest due to its ability to not only produce a variety of biotechnologically relevant enzymes but also serve as an alternative host for metabolic engineering for the production of valuable chemicals from lignocellulosic agricultural wastes. No bacteriophage that infects T. fusca has been reported, despite its potential impacts on the utilization of T. fusca. In this study, an extremely thermostable bacteriophage P1312 that infects T. fusca was isolated from manure compost. Electron microscopy showed that P1312 has an icosahedral head and a long flexible non-contractile tail, a characteristic of the family Siphoviridae. P1312 has a double-stranded DNA genome of 60,284 bp with 93 potential ORFs. Thirty-one ORFs encode proteins having putative biological functions. The genes involved in phage particle formation cluster together in a region of approximately 16 kb, followed by a segment containing genes presumably for DNA degradation/modification and cell wall disruption. The genes required for DNA replication and transcriptional control are dispersed within the rest of the genome. Phylogenetic analysis of large terminase subunit suggests that P1312 is a headful packaging phage containing a chromosome with circularly permuted direct terminal repeats.

Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage

“…Genomes that have single-stranded cohesive ends and are enzyme digested will produce fragments with cos sites. Gradual temperature cooling will allow these fragments to join together and appear as a larger band on a gel ( Paul et al, 2005 ; Cheepudom et al, 2015 ). No change in the Xho I restriction pattern of SU57 resulting from different cooling processes (gradual or rapid) was observed, excluding the genomic presence of cos sites.…”

Characterization of vB_Kpn_F48, a Newly Discovered Lytic Bacteriophage for Klebsiella pneumoniae of Sequence Type 101

“…Morphological characterization performed by TEM showed that vB_Kpn_F48 is a member of the family Myoviridae , order Caudovirales . Results of phylogenetic analysis performed using markers previously employed in several phylogenetic studies of the T4- and T7-like phages [ 56 , 57 , 58 , 59 ], strongly suggested that vB_Kpn_F48 is a member of a novel genus of the Tevenvirinae subfamily. This finding is also supported by the phylogenetic analysis of the whole phage genome which shows a full consistency of the obtained trees and current ICTV taxonomy, with very high bootstrap values, and again confirmed that vB_Kpn_F48 forms a distinct clade of the Tevenvirinae subfamily.…”

Characterization and genomic analyses of two newly isolated Morganella phages define distant members among Tevenvirinae and Autographivirinae subfamilies

“…These genes have been previously used as marker in several phylogenetic studies of the T4- and T7-like phages58596061. The phylogenetic tree was constructed with all phages currently annotated as Tevenvirinae and Autographivirinae subfamilies along with MP1 and MP2.…”