Project description:After the prophages of the Vibrio natriegens strain were deleted, RNA-seq experiments were conducted to obtain DGE-profiles in the presence and absence of the two prophages VNP1 and VNP2 in the exponential growth phase.
Project description:Vibrio natriegens strain ATCC 14048 is a salt marsh isolate with a notably rapid growth rate that has garnered considerable interest for biotechnological applications. We used systems-level tools (i.e. metabolomics, transcriptomics, proteomics) to characterize its physiological response to different salinities and temperatures that are relevant not only to its natural environment but also to planned scalable culturing processes. We found organic osmolyte synthesis and membrane transporters were most responsive to changes in salinity. The osmolytes glutamate, glutamine and ectoine responded to salinity across temperature treatments. However, when media was supplemented with choline, glycine betaine appeared to replace ectoine. These results provide a baseline data set for metabolic activity under a variety of conditions that will influence future basic and applied V. natriegens research.
Project description:After the wild type strain of Vibrio natriegens ATCC 14048 (BioSample Nr. NCBI: SAMN03178087) was cured from prophages (as described in the material and methods section), the genomes of the resulted strains dvnp1, dvnp2 and vnp12 were sequenced. As a control, the genome of the wild type strain was also prepared and used for sequencing. The aim of the sequencing was to verify the deleted regions and to screen the genome for new mutations.
Project description:DNA replication prior to cell division is essential for the proliferation of all cells. Bacterial chromosomes are replicated bidirectionally from a single origin of replication, with replication proceeding at about 1000 bp per second. For the best-studied model organism, Escherichia coli, this translates into a replication time of about 40 min for its 4.6 Mb chromosome. Nevertheless, E. coli can propagate by overlapping replication cycles with a maximum short doubling time of 20 min. The fastest growing bacterium known today, Vibrio natriegens, is able to replicate with a generation time of less than 10 min. It has a bipartite genome with chromosome sizes of 3.2 and 1.9 Mb. Is simultaneous replication from two origins a prerequisite for its rapid growth? We fused the two chromosomes of V. natriegens to create a strain carrying a 5.2 Mb chromosome with a single origin of replication. Compared to the wild-type, this strain showed little deviation in growth rate. This suggests that the split genome is not a prerequisite for rapid growth, and that DNA replication is not an important growth rate-limiting factor.
Project description:Vibrio natriegens is a rapidly growing salt marsh bacterium that is being developed as a synthetic biology chassis. We characterized its physiological response to different salinities and temperatures in order to optimize culturing conditions and understand its adaptations to a salt marsh environment. Using metabolomics, transcriptomics, and proteomics we determined what pathways respond to these environmental parameters. We found that organic osmolyte synthesis and membrane transporters were most responsive to changes in salinity. The primary osmolytes were glutamate, glutamine, and ectoine, responding to salinity across temperature treatments. However, when media was supplemented with choline, glycine betaine seemed to mostly replace ectoine. These results provide a baseline dataset of metabolic activity under a variety of conditions that will inform decisions made about culturing and genome engineering for future applications.
