Date of Award
2015
Document Type
Open Access Dissertation
Department
Biomedical Science
First Advisor
Bert Ely
Abstract
The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 48°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 genome and the Caulobacter crescentus NA1000 genome, the representative strain and most well studied isolate of the Caulobacter genus, revealed extensive rearrangements of gene order suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80 – 95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.
The genomes of type B3 bacteriophage of Caulobacter crescentus are among the largest phage genomes thus far deposited into GenBank with sizes over 200 kb. The bacteriophage samples of our collection where first isolated by graduate students of Dr. Ely’s lab in 1977 in an project aimed at discovering transducing bacteriophages of Caulobacter crescentus (Johnson 1977). We began our genomic characterization of these bacteriophages in hopes of finding genomic rearrangements as observed in the host NA1000 and possibly a more clear understanding of the phenomenon. However, no major rearrangements were discovered and we changed our direction to be more of an evolutionary analysis of this group of bacteriophages. We introduce six new bacteriophage genomes which were obtained from phage collected from various water systems in the southeastern United States and from tropical locations across the globe. Evolutionary analysis of the genomes reveal a “core genome” which accounts for roughly 1/3 of the bacteriophage genomes and is predominately localized to the head, tail, and lysis gene regions. Despite being isolated from geographically distinct locations, the genomes of these bacteriophages were highly conserved in genome sequence and gene order. Here we present the results of our analysis which identify the insertions, deletions, translocations, and horizontal gene transfer events which are responsible for the genomic diversity of this group of bacteriophages.
Rights
© 2015, Kurt Taylor Ash
Recommended Citation
Ash, K. T.(2015). Extensive Genome Rearrangements of Caulobacter K31 and Genomic Diversity of type B3 Bacteriophages of Caulobacter Crescentus. (Doctoral dissertation). Retrieved from https://scholarcommons.sc.edu/etd/3638