Vibrio phages and uses therof

Tuan Son Le; Paul C Southgate; D Ipek Kurtboke

The present invention broadly provides isolated viral particles. The invention also broadly provides isolated proteins and isolated nucleic acids of, derived from, or corresponding to, those of isolated viral particles. In a first aspect, the invention provides an isolated protein comprising an amino acid sequence set forth in SEQ ID NOS:1-1062, or a fragment, variant, or derivative thereof. In an embodiment, the isolated protein comprises an amino acid sequence set forth in SEQ ID NOS:1-210. In an embodiment, the isolated protein comprises an amino acid sequence set forth in SEQ ID NOS:211-427. In an embodiment, the isolated protein comprises an amino acid sequence set forth in SEQ ID NOS:428-638. In an embodiment, the isolated protein comprises an amino acid sequence set forth in SEQ ID NOS:639-850. In an embodiment, the isolated protein comprises an amino acid sequence set forth in SEQ ID NOS:851-1061. In an embodiment, the isolated protein comprises an amino acid sequence selected from two or more of (a)-(e): (a) an amino acid sequence set forth in SEQ ID NOS:1-210; (b) an amino acid sequence set forth in SEQ ID NOS:211-427; (c) an amino acid sequence set forth in SEQ ID NOS:428-638; (d) an amino acid sequence set forth in SEQ ID NOS:639-850; and (e) an amino acid sequence set forth in SEQ ID NOS:851-1061. A second aspect of the invention provides an isolated nucleic acid encoding the amino acid sequence of the isolated protein of the first aspect, or a fragment or variant thereof. In embodiments, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1062-2128. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1062 or 1067-1276. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1063 or 1277-1493. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1064 or 1494-1704. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1065 or 1705-1916. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence set forth in SEQ ID NOS:1066 or 1917-2127. In an embodiment, the isolated nucleic acid comprises a nucleotide sequence selected from two or more of (a)-(e): (a) a nucleotide sequence set forth in SEQ ID NOS:1062 or 1067-1276; (b) a nucleotide sequence set forth in SEQ ID NO:1063 or 1277-1493; (c) a nucleotide sequence set forth in SEQ ID NO:1064 or 1494-1704; (d) a nucleotide sequence set forth in SEQ ID NO:1065 or 1705-1916; and (e) a nucleotide sequence set forth in SEQ ID NO:1066 or 1917-2127. In embodiments, the isolated protein of the first aspect or the isolated nucleic acid of the second aspect is of, or corresponds to, a protein or nucleic acid of a virus. In embodiments, the virus is a bacteriophage. In an embodiment, the bacteriophage is of the order Caudovirales. In an embodiment, the bacteriophage is of the family Myoviridae. In embodiments, the isolated protein of the first aspect or the isolated nucleic acid of the second aspect is of, or corresponds to, a protein or nucleic acid of a bacteriophage capable of infecting bacteria of the family Vibrionaceae. In an embodiment, the bacteriophage is capable of infecting bacteria of the genus Vibrio. In an embodiment, the bacteriophage is capable of infecting Vibrio alginolyticus. In an embodiment, the bacteriophage is capable of infecting Vibrio harveyi. In embodiments, the isolated protein of the first aspect or the isolated nucleic acid of the second aspect is of, or corresponds to, a protein or nucleic acid of a bacteriophage selected from the group consisting of phage ïª-1, phage ïª-2, phage ïª-3, phage ïª-4, phage ïª-5, phage ïª-6, and phage ïª-7. In a third aspect, the invention provides an isolated viral particle. In embodiments of the third aspect, the isolated particle comprises the isolated protein of the first aspect. In embodiments the isolated viral particle further comprises the isolated nucleic acid of the second aspect. In embodiments, the isolated viral particle of the third aspect is capable of infecting and/or replicating in a host cell. In embodiments, the host cell is a bacterial cell. In embodiments, the bacterial is of the family Vibrionaceae. In an embodiment, the bacteria is of the genus Vibrio. In an embodiment, the bacteria is of the species Vibrio alginolyticus. In an embodiment, the bacteria is of the species Vibrio harveyi. In an embodiment of the third aspect, the isolated viral particle is, or is of, a bacteriophage selected from the group of consisting of phage ïª-1, phage ïª-2, phage ïª-3, phage ïª-4, phage ïª-5, phage ïª-6, and phage ïª-7. A fourth aspect of the invention provides a nucleic acid construct comprising the isolated nucleic acid of the second aspect. A fifth aspect of the invention provides a vector comprising the construct of the fourth aspect. In embodiments, the nucleic acid construct of the fourth aspect or the vector of the fifth aspect is capable of expressing the isolated viral particle of the third aspect. In a six aspect, the invention provides a host cell comprising the construct of the fourth aspect or the vector of the fifth aspect. In an embodiment, the host cell is a bacterial cell. A seventh aspect of the invention provides a method of producing the isolated protein of the first aspect; the isolated nucleic acid of the second aspect; or the isolated viral particle of the third aspect, including the step of combining the construct of the fourth aspect or the vector of the fifth aspect with a host cell, wherein the isolated protein, isolated nucleic acid, or isolated viral particle is expressed from the construct of the fourth aspect or the vector of the fifth aspect in the host cell. An eighth aspect of the invention provides a method of producing the isolated protein of the first aspect or the isolated nucleic acid of the second aspect, including the step of combining the isolated viral particle of the third aspect with a host cell, wherein the isolated protein or isolated nucleic acid is expressed from the isolated viral particle in the host cell. A ninth aspect of the invention provides a method of produced the isolated protein of the first aspect; the isolated nucleic acid of the second aspect; or the isolated viral particle of the third aspect, including the step of combining the isolated viral particle of the third aspect with a host cell, wherein the isolated particle replicates in the host cell. In embodiments of the eighth or ninth aspect, the step of combining the isolated viral particle of the third aspect with the host cell is or includes infecting the host cell with the viral particle. A tenth aspect of the invention provides an isolated protein or an isolated nucleic acid produced according to the method of the eighth or ninth aspect. An eleventh aspect of the invention provides an isolated viral particle produced according to the method of the ninth aspect. In a twelfth aspect of the invention, there is provided a composition comprising the isolated protein of the first or tenth aspect; the isolated nucleic acid of the second aspect or tenth aspect; the isolated viral particle of the third aspect or eleventh aspect; the isolated construct of the fourth aspect; or the isolated vector of the fifth aspect, and one or more carriers, diluents, or excipients. A thirteenth aspect of the invention provides a method of controlling or killing a bacteria, including the step of combining the isolated protein of the first or tenth aspect; the isolated nucleic acid of the second or tenth aspect; the isolated viral particle of the third or eleventh aspect; the isolated construct of the fourth aspect; the isolated vector of the fifth aspect; or the composition of the twelfth aspect, with the bacteria. In embodiments of the thirteenth aspect, the bacteria that is controlled or killed is of the family Vibrionaceae. In embodiments, the bacteria is of the genus Vibrio. In embodiments, the bacteria is of the species Vibrio alginolyticus. In embodiments, the bacteria is of the species Vibrio harveyi. In a fourteenth aspect the invention provides a method of treating or preventing a bacterial infection in an organism, including the step of administering the isolated protein of the first or tenth aspect; the isolated nucleic acid of the second or tenth aspect; the isolated viral particle of the third or eleventh aspect; the isolated construct of the fourth aspect; the isolated vector of the fifth aspect; or the composition of the twelfth aspect, to the organism. In embodiments of the fourteenth aspect, the bacterial infection is an infection with a bacteria is of the family Vibrionaceae. In embodiments, the bacterial infection is an infection with a bacteria is of the genus Vibrio. In embodiments, the bacterial infection is an infection with a bacteria of the species Vibrio alginolyticus. In embodiments, the bacterial infection is an infection of the species Vibrio harveyi. In a fifteenth aspect the disclosure provides a method of cultivating an organism, including the step of administering the isolated protein of the first or tenth aspect; the isolated nucleic acid of the second or tenth aspect; the isolated viral particle of the third or eleventh aspect; the isolated construct of the fourth aspect; the isolated vector of the fifth aspect; or the composition of the twelfth aspect, to the organism. In embodiments of the fifteenth aspect, the organism is cultivated by aquaculture. In embodiments of the fourteenth or fifteenth aspect, the organism is an aquatic organism. In embodiments, the aquatic organism is a salt water or marine aquatic organism. In embodiments of the fourteenth or fifteenth aspect the organism is a mollusc. In embodiments, the mollusc is a bivalve mollusc. In embodiments, the mollusc is of a family selected from the group consisting of Ostreidae, Pteriidae, Spondylus, and Anomiidae. In embodiments, the mollusc is an oyster. In embodiments, the oyster is of the genus Saccostrea. In embodiments, the oyster is of the species Saccostrea glomerata. It will be appreciated that the indefinite articles "a" and "an" are not to be read as singular indefinite articles or as otherwise excluding more than one or more than a single subject to which the indefinite article refers. For example, "a" protein includes one protein, one or more proteins, or a plurality of proteins. As used herein, unless the context requires otherwise, the words "comprise", "comprises" and "comprising" will be understood to mean the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.

Vibrio phages and uses therof

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