Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents

Petrovski, Steve; Tillett, Daniel; Seviour, Robert J.

doi:10.1128/aem.05584-11

Cited by 34 publications

(31 citation statements)

References 50 publications

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“…Similar repeat structures have been observed in Tsukamurella phage TPA2 (15) as well as in other mycolata phages (21), where similar hypotheses have been proposed for their possible functions.…”

Section: Resultssupporting

confidence: 56%

“…A similar level of stringent strain specificity has been observed in other actinophages (15)(16)(17)(18)(19)(20)(21)27). Possible explanations include an absence of a compatible receptor site in the resistant host cell, absence of appropriate molecular machinery to support infection, or possession of phage resistance systems like clustered regularly interspersed repeat (CRISPR) systems, restriction modification (RM) systems, and abortive infection (Abi) systems (28).…”

Section: Resultsmentioning

confidence: 89%

“…Thomas et al (14) proposed that a phage therapy biocontrol approach might be an attractive option for treating this global operational problem and successfully isolated 17 phages infective for foaming mycolata from Australian wastewater treatment plants. More mycolata phages have been isolated and described since then (15)(16)(17)(18)(19)(20)(21). Among them is the TPA2 phage, infective for members of the genus Tsukamurella (15).…”

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confidence: 99%

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Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4

Dyson

Tucci

Seviour

et al. 2015

Appl Environ Microbiol

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bThree Tsukamurella phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these Siphoviridae viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described Gordonia phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of Siphoviridae phages. All three phages appeared highly virulent on strains of Tsukamurella inchonensis and Tsukamurella paurometabola. The genus Tsukamurella contains Gram-positive organisms in the Corynebacteriales (1) and currently includes 11 species (2). Members of this genus are strictly aerobic and weakly/variably acid-fast, nonmotile, non-spore-forming organisms whose cell envelopes contain long-chain unsaturated mycolic acids (3-8).Together with other mycolic acid-producing genera, including Mycobacterium, Millisia, Nocardia, Rhodococcus, Williamsia, Rhodococcus, and Gordonia, they are often referred to collectively as the mycolata, a group of organisms whose mycolic acids render their cells highly hydrophobic (9, 10).The high hydrophobicity and the biosurfactants produced by the mycolata implicate them as stabilizing agents of foams in activated sludge plants (9, 11). Several Tsukamurella species including T. spumae (12), T. sunchonensis (13), and T. pseudospumae (12) have been isolated from these foams. Stable foams complicate sludge management, have a negative impact on plant esthetics, and increase maintenance costs (9).Several opportunistic Tsukamurella pathogens are known to exist, thus posing a potential health hazard to plant operators from aerosol foam dispersal (9). Thomas et al. (14) proposed that a phage therapy biocontrol approach might be an attractive option for treating this global operational problem and successfully isolated 17 phages infective for foaming mycolata from Australian wastewater treatment plants. More mycolata phages have been isolated and described since then (15-21). Among them is the TPA2 phage, infective for members of the genus Tsukamurella (15).As of March 2015, genomes of 228 phages infective for members of the closely related genus Mycobacterium have been sequenced. To better understand their genomics, Hatfull et al. (22) devised a clustering system that claimed to reveal insights into their evolutionary interrelationships. In this system, TPA2 phage would be placed into their cluster B as its genome organization is similar to that of the Mycobacterium phage Rosebush (15). Despite this similarity between TPA2 and Mycobacterium phages, little else is known about the exte...

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Section: Resultssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 89%

mentioning

confidence: 99%

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Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4

Dyson

Tucci

Seviour

et al. 2015

Appl Environ Microbiol

Self Cite

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“…However, they were considered a single product since the concatenated gene products present homology with single proteins from other systems. It was recently suggested that they were once encoded by a single gene or possibly fused in other systems (97). Second, the phages Enterococcus phiEf11, Microcystis Ma-LMM01, Streptococcus M102, Thermus P23-77, and Synechococcus CBS2 and SPM2 encode two predicted endolysins often found in adjacent genes and proximate to the putative holin ORF.…”

Section: Resultsmentioning

confidence: 99%

Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

Oliveira

Melo

Santos

et al. 2013

J Virol

239

247

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Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted with a rigid cell wall that hinders their release into the environment and the opportunity to start a new infection cycle. Consequently, phages encode hydrolytic enzymes, called endolysins, to digest the peptidoglycan. In this work, we bring to light all phage endolysins found in completely sequenced double-stranded nucleic acid phage genomes and uncover clues that explain the phage-endolysin-host ecology that led phages to recruit unique and specialized endolysins.

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“…Regarding the use of phages in engineered applications, phages may be an advantageous option for inactivating the filamentous bacteria responsible for foaming and sludge bulking, because they can specifically target the desired organisms (Choi et al, 2011;Petrovski et al, 2012;Thomas et al, 2002). Since phages are autocatalytic, and the phage concentration increases after cellular lysis, the return sludge may be used to produce a continual supply of phages, which may control the long-term overgrowth of filamentous bacteria.…”

Section: Introductionmentioning

confidence: 98%