Marx, C. J. | Search bioRxiv

bioRxiv2017

Multiplex genome editing for synthetic biology in Vibrio natriegens

Vibrio natriegens has recently emerged as an alternative to Escherichia coli for molecular biology and biotechnology, but low-efficiency genetic tools hamper its development. Here, we uncover how to induce natural competence in V. natriegens and describe methods for multiplex genome editing by natural transformation (MuGENT). MuGENT promotes integration of large genome edits at high-efficiency on unprecedented timescales, which will extend the utility of this species for diverse applications.\n\nV. natriegens is the fastest growing organism known, with a doubling time of <10 min1,2. With broad metabolic capabilities, lack of pathogenicity, and its rapid growth rate, it is an attractive alternative to E. coli for diverse molecular biology and biotechnology applications3. Methods for classical genetic techniques have been developed for V. natriegens, but these are rel ...

synthetic biology↗

bioRxiv2016

The E. coli molecular phenotype under different growth conditions

Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling of E. coli gene regulation, transcription, and translation.

bioinformatics↗