Automated in vivo enzyme engineering accelerates biocatalyst optimization

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 24, 2024

Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization engineering is mostly low throughput labor-intensive. Therefore, strategies for increasing while diminishing manual labor are gaining momentum, such as vivo screening evolution campaigns. Computational tools like machine learning further support efforts by widening the explorable design space. Here, we propose an integrated solution to challenges whereby ML-guided, automated workflows (including library generation, implementation hypermutation systems, adapted laboratory evolution, growth-coupled selection) could be realized accelerate pipelines towards superior

Language: Английский

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Comprehensive assessment of biorefinery potential for biofuels production from macroalgal biomass: Towards a sustainable circular bioeconomy and greener future

Chemosphere, Journal Year: 2023, Volume and Issue: 339, P. 139724 - 139724

Published: Aug. 2, 2023

Language: Английский

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Practical Applications of Minichromosomes in Modern Agriculture for Better Crops

Published: Jan. 1, 2025

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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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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Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(5), P. 1537 - 1548

Published: May 8, 2024

Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in ocean. They becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth versatile low-copy-number plasmids, ability produce secondary metabolites. However, molecular tools engineering strains this bacterial lineage limited. Here, we expand genetic toolbox by establishing standardized, modular repABC-based plasmid vectors four well-characterized compatibility groups from Roseobacter group applicable Rhodobacterales, likely further orders (Hyphomicrobiales, Rhodospirillales, Caulobacterales). We confirmed replication these newly constructed pABC two members namely, Dinoroseobacter shibae DFL 12 Rhodobacter capsulatus B10S, as well Hyphomicrobiales (synonym: Rhizobiales; Ensifer meliloti 2011 "Agrobacterium fabrum" C58). Maintenance biotechnologically valuable facilitates shuttling constructs between genera orders. Additionally, was verified one member Rhodospirillales (Rhodospirillum rubrum S1) Caulobacterales (Caulobacter vibrioides CB15N). The construction usage compatible systems, which allows coexistence a host cell, advantageous features future implementations designed synthetic pathways. vector applicability demonstrated functional complementation nitrogenase mutant phenotype complementary pABC-based plasmids R. capsulatus.

Language: Английский

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Blue valorization of lignin-derived monomers via reprogramming marine bacterium Roseovarius nubinhibens

Applied and Environmental Microbiology, Journal Year: 2024, Volume and Issue: 90(7)

Published: June 28, 2024

Biological valorization of lignin, the second most abundant biopolymer on Earth, is an indispensable sector to build a circular economy and net-zero future. However, lignin recalcitrant bioupcycling, demanding innovative solutions. We report here biological lignin-derived aromatic carbon value-added chemicals without requesting extra organic freshwater via reprogramming marine

Language: Английский

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

Biotechnology Advances, Journal Year: 2024, Volume and Issue: 77, P. 108464 - 108464

Published: Oct. 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.

Language: Английский

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Pollutant Tracing in Marine Biota: The Role of Nuclear Technique and Indonesia Nuclear Policy to Enhance Blue Economy

Published: Jan. 1, 2024

Language: Английский

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