#synbiosky hashtag - Bluesky

@emmseveri.bsky.social

3 weeks ago

A modular biodevice assembly tool kit for combinatorial screening and benchmarking multiple cell surface display platforms in Escherichia coli - Journal of Biological Engineering Journal of Biological Engineering - Bacterial cell surface display is a versatile platform technology for synthetic biology applications. A successful display platform often requires ad hoc testing...

#microsky #synbiosky

link.springer.com/article/10.1...

1 1 0 0

Emmanuele Severi

@emmseveri.bsky.social

3 weeks ago

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products Molecular biology; Molecular genetics; Molecular mechanism of gene regulation; Molecular microbiology

#microsky #synbiosky

www.cell.com/iscience/ful...

7 0 0 0

Emmanuele Severi

@emmseveri.bsky.social

1 month ago

The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering Rapp et al. combine genome-scale CRISPRi and metabolomics in E. coli. CRISPRi of enzymes enforces metabolite accumulation, which leads to regulatory crosstalk and side reactions. This suggests that ma...

#microsky #synbiosky

www.cell.com/cell-systems...

6 1 0 0

Emmanuele Severi

@emmseveri.bsky.social

1 month ago

#microsky #synbiosky

Transporters matter!

www.nature.com/articles/s41...

4 2 0 0

Emmanuele Severi

@emmseveri.bsky.social

1 month ago

An Engineered Variant of E. coli Nissle 1917 with Enhanced Transformation Efficiency and Robustness The gut microbiome and its effects on human health have generated considerable scientific, veterinary, and medical interest in recent years. Several gut bacterial species have emerged as potential cha...

#microsky #synbiosky #microbiomesky

pubs.acs.org/doi/10.1021/...

6 1 0 0

Emmanuele Severi

@emmseveri.bsky.social

1 month ago

Rapid directed evolution guided by protein language models and epistatic interactions Protein engineering is limited by the inefficient search through a high-dimensional sequence space to find combinations of synergistic mutations. Traditional approaches use stepwise mutation stacking,...

#synbio #synbiosky

www.science.org/doi/10.1126/...

3 1 1 0

Emmanuele Severi

@emmseveri.bsky.social

2 months ago

Engineering plasmids with synthetic origins of replication - Nature Communications The reliance on natural plasmid replication mechanisms limits plasmid tunability, compatibility, and modularity. Here the authors refactor the natural pMB1 origin and create plasmids with customizable...

#microsky #synbiosky

A set of compatible, copy number-controllable plasmids for E. coli:

www.nature.com/articles/s41...

9 2 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

2 months ago

#microsky #synbiosky #microbiomesky

1 0 0 0

Emmanuele Severi

@emmseveri.bsky.social

2 months ago

Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms - Nature Catalysis Light-driven enzymatic catalysis has enabled important abiological transformations in vitro. Now a cellular ene-reductase photoenzyme is integrated with a de novo-designed olefin biosynthetic pathway ...

#microsky #synbiosky

www.nature.com/articles/s41...

10 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

2 months ago

🤯🤯
#microsky #Phagesky #synbiosky

24 4 0 0

Emmanuele Severi

@emmseveri.bsky.social

2 months ago

Refactored genetic parts for modular assembly of the E. coli MccV type I secretion system used to screen class II microcin candidates from plant-associated bacteria Background Microcins are small antibacterial proteins secreted by gram-negative bacteria. The activities of new microcins discovered using bioinformatic searches need to be validated and characterized to understand how they mediate competition in microbiomes and to evaluate their potential as new therapeutics for combating antibiotic resistance. Engineered plasmids containing the type I secretion system associated with Escherichia coli Microcin V (MccV) can secrete heterologous proteins, including other class II microcins, and this system functions in other bacterial hosts. However, existing microcin secretion constructs are not designed for easily swapping components — such as origins of replication, resistance genes, promoters, and signal peptides — that may need to be changed for compatibility with other chassis. Results We refactored the E. coli MccV type I secretion system into genetic parts compatible with a modular Golden Gate assembly scheme and used these parts to construct two-plasmid microcin secretion systems. In our design, one plasmid encodes the type I secretion system proteins, and the other encodes a signal peptide fused to the cargo protein that will be secreted. We tested two versions of a system with inducible promoters separately controlling expression of the components on each plasmid. One used plasmids that replicate in E. coli and its close relatives. The other used broad-host-range plasmids. When induced to secrete MccV, both versions produced similar zones of inhibition against a susceptible strain of E. coli . Next, we identified putative class II microcins in genomes of bacteria from plant-associated genera ( Pantoea , Erwinia , and Xanthomonas ) using an existing bioinformatics pipeline. We screened 23 of these putative microcins for E. coli self-inhibition. Seven exhibited some inhibition, mostly later in growth curves, but none had effects that were comparable in strength to MccV. Conclusions The genetic parts we created can be assembled in various combinations into tailored systems for secreting small proteins from diverse bacterial chassis. These systems can be used to further characterize the targets of novel microcins and to secrete these or other small proteins for various applications. For example, beneficial bacteria used in crop protection could be engineered to secrete microcins that kill or inhibit plant pathogens to increase their efficacy. ### Competing Interest Statement JKP is a co-inventor on patent application US-20250340892-A1 (Gram-Negative Bacteria Containing Peptide Secretion System). United States Army Research Office, W911NF-20-1-0195 U.S. National Science Foundation, IOS-2103208 United States Department of Agriculture, 2024-67013-42304

#microsky #synbiosky

Transporters matter:

www.biorxiv.org/content/10.6...

2 0 0 0

Emmanuele Severi

@emmseveri.bsky.social

2 months ago

Unlocking Bacterial Cellulose Functionalisation: Comparative Genetic and Co-Culture Strategies in Komagataeibacter Bacterial cellulose (BC) is produced by diverse bacterial species, including members of the genus Komagataeibacter, and has emerged as a potential sustainable alternative to conventional materials suc...

#microsky #synbiosky

From Tom Ellis lab featuring @northumbriauni.bsky.social ‘s Meng Zhang (co-corresponding) & Katie Gilmour (co-first)

👏❤️

www.biorxiv.org/content/10.6...

6 3 0 0

Emmanuele Severi

@emmseveri.bsky.social

2 months ago

Validate User

#microsky #synbiosky

Bxb1 variants recognising shorter landing pads

academic.oup.com/nar/article/...

0 0 0 0

Emmanuele Severi

@emmseveri.bsky.social

3 months ago

Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing Whole-genome screening reveals strategies to boost CRISPR-associated transposase genome editing efficiency.

#microsky #synbiosky

www.science.org/doi/10.1126/...

22 12 0 0

Emmanuele Severi

@emmseveri.bsky.social

3 months ago

Autonomous biogenesis of all thirty proteins of the Escherichia coli translation machinery - Nature Communications The cell-free biogenesis of the protein translation machinery is essential for the creation of a self-regenerating synthetic cell. Here the authors synthesise all 30 E. coli translation proteins in a ...

#microsky #synbiosky

www.nature.com/articles/s41...

3 1 1 0

Vivek Mutalik

@vivekmutalik.bsky.social

3 months ago

Generating functional plasmid origins with OriGen Abstract. While generative artificial intelligence has shown promise for biological design, no computational system has yet created sequences proven capabl

#microsky #synbiosky

academic.oup.com/nar/article/...

5 1 0 1

Vivek Mutalik

@vivekmutalik.bsky.social

3 months ago

Tunable light-focusing behavior of engineered bacterial microlenses with controllable shapes Recently, engineered bacterial cells have been shown to behave as optically-active photonic devices comparable to industrially fabricated microlenses1. Bacterial cells can be encapsulated within a lay...

😳😳
www.biorxiv.org/content/10.6...

#microsky #synbiosky

1 0 0 0

Emmanuele Severi

@emmseveri.bsky.social

3 months ago

A synthetic cell phage cycle - Nature Communications The reconstitution of complex biological processes in cell-free systems can support the detailed characterisation of biochemical mechanisms which are difficult to probe in vivo. Here authors present a...

#microsky #phagesky #phage #synbiosky

www.nature.com/articles/s41...

10 0 1 0

Vivek Mutalik

@vivekmutalik.bsky.social

3 months ago

Techno-economic assessment-guided biofoundry for microbial strain development A robotics-assisted biofoundry platform was applied to synthetic biology, using robot-assisted module (RAM)-based workflows optimized with the Experiment Price Index (EPI). Demonstrated through the de...

Techno-economic assessment-guided biofoundry for microbial strain development

#synbiosky #microsky

www.cell.com/trends/biote...

1 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

5 months ago

Advances in biosensors for microbial biosynthesis of amino acids and their derivatives Amino acids and their derivatives play pivotal roles across diverse fields including biotechnology, pharmaceuticals, agriculture, and industrial manuf…

#synbiosky #microsky

www.sciencedirect.com/science/arti...

5 1 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

6 months ago

Non-model bacteria as platforms for endogenous gene expression in synthetic biology - Nature Reviews Bioengineering Microbial synthetic biology might greatly benefit from the application of non-model organisms, which have been evolutionarily optimized for the production of specific proteins and metabolites. This Review discusses the design and application of endogenous production in non-model organisms.

#microsky
#synbiosky

Non-model bacteria as platforms for endogenous gene expression in synthetic biology

www.nature.com/articles/s44...

12 2 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

6 months ago

GoldenBraid2.0 E. coli: a comprehensive and characterized toolkit for enterics Abstract. Modular cloning systems streamline laboratory workflows by consolidating genetic ‘parts’ into reusable and modular collections, enabling research

GoldenBraid2.0 E. coli: a comprehensive and characterized toolkit for enterics

#microsky #synbiosky

academic.oup.com/synbio/advan...

10 4 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

6 months ago

#microsky #synbiosky

4 2 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

7 months ago

Love when public benefit tools are created
#microsky #synbiosky

1 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

7 months ago

#microsky #synbiosky

0 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

7 months ago

Engineered bacteria launch and control an oncolytic virus - Nature Biomedical Engineering CAPPSID relies on an engineered S. typhimurium to act as a synthetic ‘capsid’ to transcribe and deliver viral RNA inside cancer cells, launching a virus that can directly lyse surrounding cells.

#microsky #synbiosky

www.nature.com/articles/s41...

7 1 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

7 months ago

❤️

Tagging folks in my reach
#microsky #phage #phagesky #synbiosky #plasmidsky

4 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

7 months ago

#phage #phagesky #microsky #synbiosky

7 2 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

9 months ago

Production of phosphorylated and functional αs1-casein in Escherichia coli The study demonstrates two strategies, phosphorylation of αs1-casein using Bacillus subtilis kinases and phosphomimetic substitution of αs1-casein, to generate functional recombinant αs1-casein in Esc...

Production of phosphorylated and functional αs1-casein in Escherichia coli: Trends in Biotechnology www.cell.com/trends/biote...
#synbiosky #microsky

6 0 0 0

Vivek Mutalik

@vivekmutalik.bsky.social

9 months ago

Fast growth and high-titer bioproduction from renewable formate via metal-dependent formate dehydrogenase in Escherichia coli - Nature Communications Low formate dehydrogenase (FDH) activity limits formate assimilation via the synthetic reductive glycine pathway. In this study, the authors introduce a faster FDH in synthetic formatotrophic E. coli,...

www.nature.com/articles/s41...

#microsky #synbiosky

3 0 0 0