Vibrio natriegens as a fast-growing host for molecular biology

Weinstock, Matthew T.; Hesek, Eric D; Wilson, Christopher M.; Gibson, Daniel G.

doi:10.1038/nmeth.3970

Cited by 215 publications

(343 citation statements)

References 35 publications

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“…In adaptively evolved E. coli , mutations in global regulation are frequently observed which shift gene expression toward catabolic processes at the expense of stress response functions (LaCroix et al, 2015; Utrilla et al, 2016). There is some evidence of less robust stress responses already, with the observation of substantially lower intrinsic catalase activity in V. natriegens than in E. coli (Weinstock et al, 2016). Other molecular mechanisms may also be investigated, such as the DNA replication and protein synthesis machinery (the high RNA content measured is believed to be related to high rRNA levels and ribosome number (Aiyar et al, 2002)).…”

Section: Discussionmentioning

confidence: 99%

“…To achieve even faster conversion rates, scientists are now interested in identifying alternative fast-growing organisms to replace E. coli as the workhorse host (Lee et al, 2016; Weinstock et al, 2016). One such organism is the Gram-negative, non-pathogenic marine bacterium Vibrio natriegens , which is commonly found in marine and coastal waters and sediments, and has a reported doubling time of 10 minutes or less when cultured under ideal conditions in rich medium (Eagon, 1962).…”

Section: Introductionmentioning

confidence: 99%

“…Two annotated genomes are available for V. natriegens , for strains ATCC 12048 (Wang et al, 2013) and DSMZ 759 (Maida et al, 2013). Recently, a wide range of genetic tools were developed and described to engineer V. natriegens (Weinstock et al, 2016), and the fast growth of this species was shown to reduce the time needed to execute common cloning pipelines, which has clear advantages in highly iterative strain building efforts (Weinstock et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

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Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis

Long

Gonzalez

Cipolla

et al. 2017

Metabolic Engineering

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Vibrio natriegens is a fast-growing, non-pathogenic bacterium that is being considered as the next-generation workhorse for the biotechnology industry. However, little is known about the metabolism of this organism which is limiting our ability to apply rational metabolic engineering strategies. To address this critical gap in current knowledge, here we have performed a comprehensive analysis of V. natriegens metabolism. We constructed a detailed model of V. natriegens core metabolism, measured the biomass composition, and performed high-resolution 13C metabolic flux analysis (13C-MFA) to estimate intracellular fluxes using parallel labeling experiments with the optimal tracers [1,2-13C]glucose and [1,6-13C]glucose. During exponential growth in glucose minimal medium, V. natriegens had a growth rate of 1.70 1/h (doubling time of 24 min) and a glucose uptake rate of 3.90 g/g/h, which is more than two 2-fold faster than E. coli, although slower than the fast-growing thermophile Geobacillus LC300. 13C-MFA revealed that the core metabolism of V. natriegens is similar to that of E. coli, with the main difference being a 33% lower normalized flux through the oxidative pentose phosphate pathway. Quantitative analysis of co-factor balances provided additional insights into the energy and redox metabolism of V. natriegens. Taken together, the results presented in this study provide valuable new information about the physiology of V. natriegens and establish a solid foundation for future metabolic engineering efforts with this promising microorganism.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis

Long

Gonzalez

Cipolla

et al. 2017

Metabolic Engineering

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“…NEB Turbo TM ) grown in the same culture conditions. The genome of V. natriegens has been recently sequenced (Maida et al, 2013;Lee et al, 2016) and, in an attempt to develop this host as a functional chassis for bioproduction, a number of techniques and tools have been tested and developed, including expression vectors, protocols for DNA transformation, synthetic promoters covering a range of expression strengths and tools for manipulating gene expression levels via CRISPRi (Lee et al, 2016;Weinstock et al, 2016). The fast growth of this bacterium allows for a significant speed-up of laboratory cloning procedures, as colonies are already visible on a plate after a mere six-h post-transformation incubation.…”

Section: Vibrio Natriegensmentioning

confidence: 99%

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Calero

Nikel

2018

Microbial Biotechnology

229

184

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The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

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“…Comparison to other organisms with distinct environmental niches and evolutionary histories will also be quite interesting. For example, are the marine strain Vibrio natriegens [47,48] or the thermophile Geobacillus LC300 [49,50] able to further improve upon their exceptional rates of growth, or are they already ‘optimal’ for growth on glucose? Are these microbes less adaptable than E. coli to alternative substrates or harsher culture conditions?…”

Section: Future Directions and Opportunitiesmentioning

confidence: 99%

How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook

Long

Antoniewicz

2018

Current Opinion in Chemical Engineering

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Adaptive laboratory evolution (ALE) has emerged as a powerful tool in basic microbial research and strain development. In the context of metabolic science and engineering, it has been applied to study gene knockout responses, expand substrate ranges, improve tolerance to process conditions, and to improve productivity via designed growth coupling. In recent years, advancements in ALE methods and systems biology measurement technologies, particularly genome sequencing and 13C metabolic flux analysis (13C-MFA), have enabled detailed study of the mechanisms and dynamics of evolving metabolism. In this review, we discuss a range of studies that have applied flux analysis to adaptively evolved strains, as well as modeling frameworks developed to predict and interpret evolved fluxes. These efforts link mutations to fitness-enhanced phenotypes, identify bottlenecks and approaches to resolve them, and address systems concepts such as optimality.

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Vibrio natriegens as a fast-growing host for molecular biology

Cited by 215 publications

References 35 publications

Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis

Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook

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