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Sequencing and Comparative Genomic Analysis of Novel Bacteriophage Isolated from Agrobacterium tumefaciens

Derek Jones UL-Monroe

Dr. Kousoulas LSU

Dr. Chouljenko LSU

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Goals of this Project

Understand protocols for isolating phage DNA and sequencing on Ion Torrent PGM platform
Sequence and annotate the genome of CDLY3, an Agrobacterium tumefaciens phage
Use sequence to determine similarities and differences between CDLY3 and other sequenced Agrobacterium phage

Hypotheses

The sequence for phage CDLY3 will show gene organization similar to other phage isolated from Agrobacterium.
The sequence will also exhibit individual gene/ORF homology to sequenced phage isolated from Agrobacterium.

Summary of:

Agrobacterium tumefaciens

Short, capsule forming, gram-negative, rod shaped
Secretes tumor inducing principle that induces changes in plant hormones contributing to the growth of crown gall

Bacteriophage

Approach

infected bacterial plate

Isolated DNA
Prepared DNA according “Ion Xpress^™Plus gDNA Fragment Library Preparation” protocol
Sequencing performed using default settings for Ion Torrent PGM
Annotation performed using DNA Master v5.22.6

CDLY3

Gene Comparison

Gene product	JP1 Gene List
92	Recombinase A
94	putative VV A18-like helicase
96	DNA primase
100	DNA polymerase 1
101	Helicase
106	HP 7-7-1[Agrobacterium phage 7-7-1]
125	Tail assembly protein
126	Putative phage minor tail protein L
127	Minor tail protein M
128	Putative tail tape measure protein
141	HP AGRO_2649 [Agrobacterium sp. ATCC 31749]
144	phage portal protein, PBSX family
156	HP 7-7-1[Agrobacterium phage 7-7-1]

Gene Product	CDLY 3 Gene List
5	ribonucleotide-diphosphate reductase subunit alpha[Agrobacterium sp. 10MFCol1.1]
82	HP[Agrobacterium tumefaciens]
103	Mu-like phage tail fiber protein[Pseudomonas entomophila L48]
107	HP[Agrobacterium tumefaciens]
110	DNA ligase[Sheqanella woodyi ATCC 51908]
119	HP[Rhizobium giardinii]
121	HP 7-7-1[Agrobacterium phage 7-7-1]
152	transcriptional regulator, AraC family[Oscillatoria nigro-viridi]
181	HP RHEph10[Rhizobium phage RHEph10]
182	HP RHEph10[Rhizobium phage RHEph10]

Gene Product	7-7-1 Gene List
7	baseplate protein; phage P2 GpJ homolog
102	Putative tail fibre
108	Terminase
111	Structural protein
113	Portal protein
114	Prohead protease
115	Major capsid protein
116	Structural protein
118	Structural protein
119	Structural protein
121	Portal protein
122	Prohead protease
124	Structural protein
126	Tail sheath protein
127	Structural protein

HP=Hypothetical Protein

NCBI BLAST

DNA Master v5.22.6 by Dr. Jeffery Lawrence-University of Pittsburgh

Sequence Comparison

Next Steps

Acknowledgments

Questions