Scaling laws of plasmids across the microbial tree of life DOI Open Access
Rohan Maddamsetti,

Maggie L. Wilson,

Hye-In Son

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 5, 2024

Abstract Plasmids play a critical role in shaping the dynamics and evolution of microbial communities. The capacity plasmid to express genes is constrained by two parameters: length copy number. However, interplay between these parameters their constraints on have remained elusive due absence comprehensive quantitative analyses. To address this gap, we developed Probabilistic Iterative Read Assignment (PIRA), new computational method that overcomes previous bottlenecks, enabling rapid accurate determination numbers at an unprecedented scale. Applying PIRA all genomes NCBI RefSeq database with linked short-read sequencing data Sequencing Archive (SRA), analyzed 4,317 bacterial archaeal encompassing 11,338 plasmids, spanning tree life. Our analysis reveals three scaling laws plasmids: first, inverse power-law correlation number length; second, positive linear protein-coding third, metabolic per length, particularly for large plasmids. These imply fundamental functional organization, indicating as plasmids increase they converge toward chromosomal characteristics content. findings not only advance understanding but also implications evolution, biotechnology, design synthetic Significance By discovering universal developing compute across life, show chromosomes coding properties. This insight principles governing has biotechnology medicine.

Language: Английский

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia DOI Creative Commons

Yue Casey Chen,

Louie Destouches,

Alice Cook

et al.

Journal of Applied Microbiology, Journal Year: 2024, Volume and Issue: 135(7)

Published: June 27, 2024

Abstract Microbiomes, the complex networks of micro-organisms and molecules through which they interact, play a crucial role in health ecology. Over at least past two decades, engineering biology has made significant progress, impacting bio-based industry, health, environmental sectors; but only recently begun to explore microbial ecosystems. The creation synthetic communities presents opportunities help us understand dynamics wild ecosystems, learn how manipulate interact with existing microbiomes for therapeutic other purposes, create entirely new capable undertaking tasks industrial biology. Here, we describe ecosystems can be constructed controlled, focusing on available methods interaction mechanisms facilitate regulation community composition output. While experimental decisions are dictated by intended applications, vast number tools suggests great opportunity researchers develop diverse array novel

Language: Английский

Citations

4
Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover–Design–Build–Test–Learn Cycle DOI Creative Commons

Jonathan Foldi,

Jack A. Connolly, Eriko Takano

et al.

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

Citations

4
Title: Engineering Plasmids with Synthetic Origins of Replication DOI Creative Commons
Baiyang Liu, Xiao Peng, Matthew R. Bennett

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Abstract Plasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity. Here we refactor pMB1 origin create plasmids with customizable copy numbers tuning refactored components. We then compatible origins that use synthetic RNA regulators implement independent control. further demonstrate of (SynORI) can be modularly respond various signals, allowing multiplexed copy-based reporting environmental signals. Lastly, a library 6 orthogonal SynORI is created co-maintained in E. coli week. This work establishes feasibility creating serve as new biotechnology biology.

Language: Английский

Citations

0
A predatory gene drive for targeted control of self-transmissible plasmids DOI Creative Commons
Ryan Tsoi,

Hye-In Son,

Grayson S. Hamrick

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(14)

Published: April 2, 2025

Suppressing plasmid transfer in microbial communities has profound implications due to the role of horizontal gene (HGT) spreading and maintaining diverse functional traits such as metabolic functions, virulence factors, antibiotic resistance. However, existing tools for inhibiting HGT are limited their modes delivery, efficacy, scalability. Here, we present a versatile denial-of-spread (DoS) strategy target eliminate specific conjugative plasmids. Our exploits retrotransfer, whereby an engineered DoS is introduced into host cells containing plasmid. Acting predatory drive, propagates itself at expense plasmid, through competition or active elimination. Once eradicated, removed via induced suicide, resulting community neither The tunable scalable various plasmids, different mechanisms inheritance interruption, environmental contexts. represents new tool precise control persistence communities.

Language: Английский

Citations

0
Why cellular computations challenge our design principles DOI Creative Commons
Lewis Grozinger, Bruno Cuevas-Zuviría, Ángel Goñi‐Moreno

et al.

Seminars in Cell and Developmental Biology, Journal Year: 2025, Volume and Issue: 171, P. 103616 - 103616

Published: May 1, 2025

Biological systems inherently perform computations, inspiring synthetic biologists to engineer biological capable of executing predefined computational functions for diverse applications. Typically, this involves applying principles from the design conventional silicon-based computers create novel systems, such as genetic Boolean gates and circuits. However, natural evolution computation has not adhered these principles, distinction warrants careful consideration. Here, we explore several concepts connecting theory, living cells, computers, which may offer insights into development increasingly sophisticated computations. While approach theoretical limits, solving nearly all problems that are computationally solvable, have opportunity outperform them in specific niches problem domains. Crucially, biocomputation does necessarily need scale rival or replicate capabilities electronic computation. Rather, efforts re-engineer biology must recognise life evolved optimised itself solve using its own principles. Consequently, intelligently designed cellular computations will diverge traditional computing both implementation application.

Language: Английский

Citations

0
Scaling laws of plasmids across the microbial tree of life DOI Open Access
Rohan Maddamsetti,

Maggie L. Wilson,

Hye-In Son

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 5, 2024

Abstract Plasmids play a critical role in shaping the dynamics and evolution of microbial communities. The capacity plasmid to express genes is constrained by two parameters: length copy number. However, interplay between these parameters their constraints on have remained elusive due absence comprehensive quantitative analyses. To address this gap, we developed Probabilistic Iterative Read Assignment (PIRA), new computational method that overcomes previous bottlenecks, enabling rapid accurate determination numbers at an unprecedented scale. Applying PIRA all genomes NCBI RefSeq database with linked short-read sequencing data Sequencing Archive (SRA), analyzed 4,317 bacterial archaeal encompassing 11,338 plasmids, spanning tree life. Our analysis reveals three scaling laws plasmids: first, inverse power-law correlation number length; second, positive linear protein-coding third, metabolic per length, particularly for large plasmids. These imply fundamental functional organization, indicating as plasmids increase they converge toward chromosomal characteristics content. findings not only advance understanding but also implications evolution, biotechnology, design synthetic Significance By discovering universal developing compute across life, show chromosomes coding properties. This insight principles governing has biotechnology medicine.

Language: Английский

Citations

2