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

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(4)

Published: Feb. 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

Language: Английский

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

Biotechnology Advances, Journal Year: 2024, Volume and Issue: 72, P. 108319 - 108319

Published: Jan. 26, 2024

Language: Английский

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

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 25(1)

Published: Nov. 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.

Language: 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, Journal Year: 2024, Volume and Issue: 14

Published: March 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.

Language: Английский

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

Chemosphere, Journal Year: 2024, Volume and Issue: 350, P. 141177 - 141177

Published: Jan. 9, 2024

Language: Английский

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

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(9), P. 2684 - 2692

Published: Aug. 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.

Language: Английский

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Dual roles of glycine betaine (GB), dimethylglycine, and sarcosine as osmoprotectants and nutrient sources forVibrio natriegens

Published: March 18, 2025

ABSTRACT Bacteria respond to osmotic stress by intracellularly accumulating low molecular weight compounds called compatible solutes (CS), also known as osmolytes. Glycine betaine ( N , -trimethylglycine, GB) is a highly effective and widely available osmolyte used bacteria, algae, plants for abiotic protection. Here, we highlight the dual roles of GB, dimethyl glycine (DMG), sarcosine both osmoprotection less role sole carbon sources. First, showed that marine halophile Vibrio natriegens can grow in 1% 7% NaCl biosynthesize ectoine, glutamate, imported DMG, response stress. Betaine-carnitine-choline transporters (BCCTs) uptake GB but not sarcosine, were identified. Bioinformatics analyses uncovered homologs catabolism genes dgcAB_fixAB, gbcA, gbcB, purU, soxBDAG, glyA, glxA ) clustered V. genome these had limited distribution among vibrios. We ATCC 14048 grew on sources gbcA dgcA required growth. A contiguous cluster was present subset fluvialis strains, demonstrated growth 2013V-1197 DMG Phylogenetic analysis revealed did share common ancestor members family Vibrionaceae . IMPORTANCE Compatible are frequently most concentrated organic components organisms allowing them adapt high saline environments well affording protection other stresses. These significant energy stores have been overlooked their potential abundant nutrient bacteria. Our study characterized efficient use halophilic

Language: Английский

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Development of a CRISPR-based cytosine base editor for restriction-modification system inactivation to enhance transformation efficiency in Vibrio sp. dhg

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Background Vibrio sp. dhg is a fast-growing, alginate-utilizing, marine bacterium being developed as platform host for macroalgae biorefinery. To maximize its potential in the production of various value-added products, there need to expand genetic engineering tools versatile editing.Results The CRISPR-based cytosine base editing (CBE) system was established dhg, enabling C:G-to-T:A point mutations multiple genomic loci. This CBE displayed high efficiencies single and targets, reaching up 100%. efficiently introduced premature stop codons, inactivating seven genes encoding putative restriction enzymes restriction-modification two rounds. A resulting engineered strain significantly enhanced transformation efficiency by 55.5-fold.Conclusions Developing highly efficient improving enable manipulation diverse brown bioconversion.

Language: Английский

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Small-scale fed-batch cultivations of Vibrio natriegens: overcoming challenges for early process development

Bioprocess and Biosystems Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Abstract Vibrio natriegens is a fast-growing microbial workhorse with high potential for biotechnological applications. However, handling the bacterium in batch processes challenging due to its overflow metabolism and mixed acid formation under microaerobic conditions. For early process development, technologies enabling small-scale fed-batch cultivation of V. Vmax are needed. In this study, cultivations 96-well microtiter plates were successfully online-monitored first time µTOM device. Using oxygen transfer rate, scale up membrane-based shake flasks was performed. The efficiently minimized by choosing suitable feed rates, prevented. A glucose soft sensor using rate provided accurate estimates consumption throughout fermentation, eliminating need offline sampling. Analyzing impact inducer IPTG on recombinant production enzyme inulosucrase revealed concentration-dependent effects processes. contrast, operating mode resulted activity even without induction. Overall, an titer 80 U/mL achieved. conclusion, advantages supported have been demonstrated development Vmax.

Language: Английский

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Dual roles of glycine betaine, dimethylglycine, and sarcosine as osmoprotectants and nutrient sources for Vibrio natriegens

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 23, 2025

ABSTRACT Bacteria respond to osmotic stress by intracellularly accumulating low molecular weight compounds called compatible solutes, also known as osmolytes. Glycine betaine ( N , -trimethylglycine, GB) is a highly effective and widely available osmolyte used bacteria, algae, plants for abiotic protection. Here, we highlight the dual roles of GB, dimethyl glycine (DMG), sarcosine both osmoprotection less role sole carbon sources. First, showed that marine halophile Vibrio natriegens can grow in 1% 7% NaCl biosynthesize ectoine, glutamate import DMG, response stress. Betaine-carnitine-choline transporters (BCCTs) uptake GB but not sarcosine, were identified. Bioinformatics analyses uncovered homologs catabolism genes dgcAB_fixAB, gbcA, gbcB, purU, soxBDAG, glyA, glxA ) clustered V. genome, these had limited distribution among vibrios. We ATCC 14048 grew on sources, gbcA dgcA required growth. A contiguous cluster was present subset fluvialis strains, demonstrated growth 2013V-1197 DMG Phylogenetic analysis revealed did share common ancestor members family Vibrionaceae . IMPORTANCE Compatible solutes are frequently most concentrated organic components organisms, allowing them adapt high saline environments well affording protection other stresses. These significant energy stores have been overlooked their potential abundant nutrient sources bacteria. Our study characterized (GB), efficient use halophilic

Language: Английский

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