Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation

Molecular Systems Biology, Год журнала: 2023, Номер 19(4)

Опубликована: Фев. 27, 2023

Abstract Vibrio natriegens is a Gram‐negative bacterium with an exceptional growth rate that has the potential to become standard biotechnological host for laboratory and industrial bioproduction. Despite this burgeoning interest, current lack of organism‐specific qualitative quantitative computational tools hampered community's ability rationally engineer bacterium. In study, we present first genome‐scale metabolic model (GSMM) V. . The GSMM (iLC858) was developed using automated draft assembly extensive manual curation validated by comparing predicted yields, central fluxes, viable carbon substrates, essential genes empirical data. Mass spectrometry‐based proteomics data confirmed translation at least 76% enzyme‐encoding be expressed during aerobic in minimal medium. iLC858 subsequently used carry out comparison between organism Escherichia coli , leading analysis architecture ' respiratory ATP‐generating system discovery role sodium‐dependent oxaloacetate decarboxylase pump. were further investigate additional halophilic adaptations Finally, utilized create Resource Balance Analysis study allocation resources. Taken together, models presented provide useful guide engineering efforts

Язык: Английский

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Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects

Biotechnology Advances, Год журнала: 2024, Номер 72, С. 108319 - 108319

Опубликована: Янв. 26, 2024

Язык: Английский

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DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates

Briefings in Bioinformatics, Год журнала: 2023, Номер 25(1)

Опубликована: Ноя. 22, 2023

Abstract The enzyme turnover rate, ${k}_{cat}$, quantifies kinetics by indicating the maximum efficiency of catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because cost experimental measurements. To predict and account strong temperature dependence, DLTKcat was developed this study demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared 0.66) than previously published models. Through two case studies, showed ability to effects protein sequence mutations changes on values. Although quantitative accuracy is not high enough yet model responses cellular metabolism changes, has potential eventually become a computational tool describe dependence biological systems.

Язык: Английский

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Antibacterial and antibiofilm activity of halogenated phenylboronic acids against Vibrio parahaemolyticus and Vibrio harveyi

Frontiers in Cellular and Infection Microbiology, Год журнала: 2024, Номер 14

Опубликована: Март 28, 2024

Vibrios are associated with live seafood because they part of the indigenous marine microflora. In Asia, foodborne infections caused by Vibrio spp. common. recent years, V. parahaemolyticus has become leading cause all reported food poisoning outbreaks. Therefore, halogenated acid and its 33 derivatives were investigated for their antibacterial efficacy against . The compounds 3,5-diiodo-2-methoxyphenylboronic (DIMPBA) 2-fluoro-5-iodophenylboronic (FIPBA) exhibited antibiofilm activity. DIMPBA FIPBA had minimum inhibitory concentrations 100 μg/mL planktonic cell growth prevented biofilm formation in a dose-dependent manner. Both iodo-boric acids could diminish several virulence factors influencing motility, agglutination fimbria, hydrophobicity, indole synthesis. Consequently, these two active hampered proliferation cells. Moreover, have potential to effectively inhibit presence on surface both squid shrimp models.

Язык: Английский

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Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens

Chemosphere, Год журнала: 2024, Номер 350, С. 141177 - 141177

Опубликована: Янв. 9, 2024

Язык: Английский

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Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover–Design–Build–Test–Learn Cycle

ACS Synthetic Biology, Год журнала: 2024, Номер 13(9), С. 2684 - 2692

Опубликована: Авг. 20, 2024

Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments field across discover–design–build–test–learn cycle of bioengineering, from recent progress computational tools for AI-supported mining, enzyme pathway engineering, compound identification to novel host systems new techniques improving production levels, place these trends context responsible research innovation, emphasizing importance anticipatory analysis at early stages process development.

Язык: Английский

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Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering

Metabolic Engineering, Год журнала: 2024, Номер 84, С. 34 - 47

Опубликована: Май 31, 2024

Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress of Vibrio natriegens supplied nutrients, aiming enhance engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across comprehensive transcriptomics dataset containing broad array nutrient conditions. Our approach led the i) identification novel transporter systems substrates, ii) detailed understanding how trace elements affect metabolism growth, iii) extensive characterization nutrient-induced responses, including osmotic stress, low glycolytic flux, proteostasis, altered protein expression. By clarifying relationship between acetate-associated regulon flux status various have showcased its vital role directing optimal carbon source selection. findings offer deep insights into transcriptional landscape nutrition underscore significance tailoring strain strategies, thereby facilitating development more efficient robust biotechnological applications.

Язык: Английский

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Graded-CRISPRi, a Tool for Tuning the Strengths of CRISPRi-Mediated Knockdowns in Vibrio natriegens Using gRNA Libraries

ACS Synthetic Biology, Год журнала: 2024, Номер 13(7), С. 2091 - 2104

Опубликована: Июнь 25, 2024

In recent years, the fast-growing bacterium Vibrio natriegens has gained increasing attention as it potential to become a next-generation chassis for synthetic biology. A wide range of genetic parts and genome engineering methods have already been developed. However, there is still need well-characterized tool effectively gradually reduce expression levels native genes. To bridge this gap, we created graded-CRISPRi, system utilizing gRNA variants that lead varying repression strength. By incorporating multiple sequences into our design, successfully extended concept simultaneously repress four distinct reporter Furthermore, demonstrated capability using graded-CRISPRi target genes, thereby examining effect various knockdown on growth.

Язык: Английский

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Unraveling the impact of pH, sodium concentration, and medium osmolality on Vibrio natriegens in batch processes

BMC Biotechnology, Год журнала: 2024, Номер 24(1)

Опубликована: Сен. 23, 2024

Vibrio natriegens, a halophilic marine γ-proteobacterium, holds immense biotechnological potential due to its remarkably short generation time of under ten minutes. However, the highest growth rates have been primarily observed on complex media, which often suffer from batch-to-batch variability affecting process stability and performance. Consistent bioprocesses necessitate use chemically defined are usually optimized for fermenters with pH dissolved oxygen tension (DOT) regulation, both not applied during early-stage cultivations in shake flasks or microtiter plates. Existing studies V. natriegens' mineral media report partially conflicting results, comprehensive study examining combined effects buffering, sodium concentration, medium osmolality is lacking.

Язык: Английский

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The new chassis in the flask: Advances in Vibrio natriegens biotechnology research

Biotechnology Advances, Год журнала: 2024, Номер 77, С. 108464 - 108464

Опубликована: Окт. 9, 2024

Biotechnology has been built on the foundation of a small handful well characterized and well-engineered organisms. Recent years have seen breakout performer gain attention as new entrant into bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts making V. natriegens biotechnology platform, using large language model (LLM) knowledge graph to expedite literature survey process. Scientists made advancements in pertaining fundamental metabolic characteristics natriegens, development characterization synthetic biology tools, systems analysis modeling, bioproduction engineering, microbial ecology. Each these subcategories relevance future for applications. In this review, we cover offer context impact they may field, highlighting benefits drawbacks organism. From examining research, it appears that is precipice becoming platform bacterium biotechnology.

Язык: Английский

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