Biology subjects

Son, H.-I.

Publications and source records attributed to Son, H.-I..

5 recordsLinked to original sources

bioRxiv2026

Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli

The laboratory Escherichia coli K-12 strain has doubled no faster than [~]20 minutes for decades. This plateau could reflect a biophysical limit or simply the way batch culture selects on growth rate. Here we show it can be broken through amplified selection with a Red Queen gene circuit, which takes advantage of growth rate heterogeneity in monoclonal populations to selectively suppress slow-growing cells and creates a tunable mapping from intrinsic growth rate to survival. After 70 days ([~]1,000 generations) of amplified selection in MG1655+FHr and subsequent removal of the circuit, a top evolved clone (RQ70) reached a maximum specific growth rate of 2.61 h-{superscript 1} in shake-flask culture. This corresponds to a doubling time of 15.9 minutes, to our knowledge the shortest reported for E. coli K-12, against 18.1 minutes for evolved controls and 20.3 minutes for the ancestor. The gain came at the cost of a [~]3-fold increase in lag time, indicating that the 20-minute plateau is a multi-trait optimum under conventional batch selection rather than an absolute constraint. We argue that synthetic gene circuits can therefore reshape the evolutionary process itself, pushing performance beyond apparent physiological limits.

synthetic biology↗

bioRxiv2024

Scaling laws of plasmids across the microbial tree of life

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

microbiology↗

bioRxiv2024

Antibiotic-mediated microbial community restructuring is dictated by variability in antibiotic susceptibility and population interactions

It is widely known that faster-growing bacterial cells are more susceptible to antibiotics. Given this notion, it appears intuitive that antibiotic treatment would enrich slower-growing cells in a clonal population or slower-growing populations in a microbial community, which has been commonly observed. However, experimental observations also show the enrichment of faster-growing subpopulations under certain conditions. Does this apparent discrepancy suggest uniqueness about different growth environments or the role of additional confounding factors? If so, what could be the major determinant in antibiotic-mediated community restructuring? Combining modeling and quantitative measurements using a barcoded heterogeneous E. coli library, we show that the outcome of antibiotic-mediated community restructuring can be driven by two major factors. One is the variability among the clonal responses of different subpopulations to the antibiotic; the other is their interactions. Our results suggest the importance of quantitative measurements of antibiotic responses in individual clones in predicting community responses to antibiotics and addressing subpopulation interactions.

microbiology↗

bioRxiv2023

Programming dynamic division of labor using horizontal gene transfer

The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.

synthetic biology↗

bioRxiv2019

Discovery and Engineering of a Therapeutic Interfering Particle (TIP): a combination self-renewing antiviral

Population-level control of HIV-1 faces recognized challenges, including the evolution of viral resistance and adherence issues in resource-limited settings. It has long been proposed that viral deletion mutants that conditionally self-renew at the expense of the wild-type virus (i.e., Defective Interfering Particles, DIPs1) could constitute a long-term intervention that circumvents adherence challenges and has a high genetic barrier to resistance, echoing recent approaches2. Theories predict3, 4 that DIPs could be engineered into a therapy for HIV-1 (i.e., Therapeutic interfering particles or TIPs) provided they stably persist in patients (R0>1) by spreading to new cells during active infection (hence, a self-replenishing antiviral). To date, DIPs amenable to such engineering have remained elusive for HIV-1. Here we report the discovery of an HIV-1 DIP and its subsequent engineering into a TIP. The TIP interferes with HIV-1 replication at multiple stages of the viral lifecycle, including genome packaging, virion maturation, and reverse transcription, essentially acting as a combination antiviral. In humanized mice, the TIP suppressed HIV-1 replication by ten-fold and significantly protected CD4+ T cells from HIV-1 mediated depletion. These data provide proof-of-concept for a class of biologic with the potential to circumvent significant barriers to HIV-1 control.

synthetic biology↗