A5048081015- Microbial Metabolic Engineering and Bioproduction
- Evolution and Genetic Dynamics
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Photosynthetic Processes and Mechanisms
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related gene regulation
- Metalloenzymes and iron-sulfur proteins
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Evolutionary Algorithms and Applications
- Medical Imaging Techniques and Applications
- Radiopharmaceutical Chemistry and Applications
- Metabolomics and Mass Spectrometry Studies
- Epigenetics and DNA Methylation
- Advanced Glycation End Products research
- Redox biology and oxidative stress
- Fungal and yeast genetics research
- Amino Acid Enzymes and Metabolism
- Mitochondrial Function and Pathology
- Biofuel production and bioconversion
- Microbial Community Ecology and Physiology
University of California, San Diego
2014-2024
La Jolla Bioengineering Institute
2018-2019
California Institute of Technology
2013
University of California, Los Angeles
2012
ABSTRACT Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes their combinatorial effects challenging time-consuming. Understanding how these enable increased can be difficult. A series approaches that address challenges was developed demonstrated using Escherichia coli K-12 MG1655 on glucose minimal...
Full-length human protein arginine methyltransferase 7 (PRMT7) expressed as a fusion in Escherichia coli was initially found to generate only ω-NG-monomethylated residues small peptides, suggesting that it is type III enzyme. A later study, however, characterized proteins of PRMT7 bacterial and mammalian cells II/type I enzyme, capable producing symmetrically dimethylated (type II activity) well amounts asymmetric dimethylarginine activity). We have sought clarify the enzymatic activity...
Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation desired environment. Here, we performed ALE 42 °C of ten parallel populations Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward similar phenotype along distinct genetic paths. Adapted possessed few 6 and many 55...
Catalysis using iron-sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage metalloproteins caused by reactive oxygen species (ROS) prevent cell growth survival when unmanaged, thus eliciting an essential stress response that is fundamental in biology. Here we develop a computable multiscale description of ROS Escherichia coli, called OxidizeME. We use OxidizeME explain four key responses oxidative stress: 1) ROS-induced auxotrophy for...
Adaptive laboratory evolution (ALE) experiments are often designed to maintain a static culturing environment minimize confounding variables that could influence the adaptive process, but dynamic nutrient conditions occur frequently in natural and bioprocessing settings. To study nature of carbon substrate fitness tradeoffs, we evolved batch cultures Escherichia coli via serial propagation into tubes alternating between glucose either xylose, glycerol, or acetate. Genome sequencing revealed...
Report8 April 2019Open Access Transparent process Enzyme promiscuity shapes adaptation to novel growth substrates Gabriela I Guzmán Department of Bioengineering, University California, San Diego, La Jolla, CA, USA Search for more papers by this author Troy E Sandberg orcid.org/0000-0003-3240-3659 Ryan A LaCroix Ákos Nyerges orcid.org/0000-0002-1581-490X Synthetic and Systems Biology Unit, Institute Biochemistry, Biological Research Centre the Hungarian Academy Sciences, Szeged, Hungary...
Abstract Biological regulatory network architectures are multi-scale in their function and can adaptively acquire new functions. Gene knockout (KO) experiments provide an established experimental approach not just for studying gene function, but also unraveling networks which a its product involved. Here we study the architecture of Escherichia coli K-12 MG1655 by applying adaptive laboratory evolution (ALE) to metabolic KO strains. Multi-omic analysis reveal common overall schema describing...
Oxidative stress is concomitant with aerobic metabolism. Thus, bacterial genomes encode elaborate mechanisms to achieve redox homeostasis. Here we report that the peroxide-sensing transcription factor, oxyR, a common mutational target using species belonging two genera, Escherichia coli and Vibrio natriegens, in separate growth conditions implemented during laboratory evolution. The mutations clustered active site, dimer interface, flexible loop of protein. These favor oxidized conformation...
13C-Metabolic flux analysis (13C-MFA) traditionally assumes that kinetic isotope effects from isotopically labeled compounds do not appreciably alter cellular growth or metabolism, despite indications some biochemical reactions can be non-negligibly impacted. Here, populations of Escherichia coli were adaptively evolved for ~1000 generations on uniformly 13C-glucose, a commonly used 13C-MFA. Phenotypic characterization these strains revealed ~40% increases in rate, with no significant...
The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with minimized synthetic genome, derived from Mycoplasma mycoides genome and chemically synthesized in vitro. Here, we report experimental evolution syn3.0- strain. Ten independent replicates were evolved for several hundred generations, leading to growth rate improvements > 15%. Endpoint strains possessed an average 8 mutations composed indels SNPs, pronounced C/G- A/T transversion bias. Multiple genes...
Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic quantitative understanding the rate-yield relationship. Studies pairing computational predictions with experiments have shown importance maintenance energy proteome allocation in explaining tradeoffs overflow metabolism. Recently, adaptive evolution Escherichia coli reveal phenotypic diversity beyond what has been explained using simple models growth versus yield. Here, identify two-dimensional...
Abstract Background Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover mutations that confer phenotypic functions of interest. However, the task finding and understanding all beneficial ALE experiment remains open challenge for field. To provide better results than traditional methods mutation analysis, this work applied enrichment described by a multiscale annotation framework consolidated set conditions. A total 25,321 unique genome annotations from...
A mechanistic understanding of how new phenotypes develop to overcome the loss a gene product provides valuable insight on both metabolic and regulatory functions lost gene. The pgi gene, whose catalyzes second step in glycolysis, was deleted growth-optimized Escherichia coli K-12 MG1655 strain. initial knockout (KO) strain exhibited an 80% drop growth rate that largely recovered eight replicate, but phenotypically distinct, cultures after undergoing adaptive laboratory evolution (ALE)....
Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, insights into the systemic function of gene product. Two E. coli knockout strains were constructed: one that blocked Pentose Phosphate Pathway (gnd KO) and decoupled TCA cycle from electron transport (sdhCDAB KO). Despite major perturbations central metabolism, minimal growth rate changes found two strains. More surprisingly, many similarities their...
Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding genetic basis evolutionary strategies underlying formation viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that nascent E. coli can be established where mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to...
The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) study the distribution Escherichia coli phenotypes on rate-yield plane. found that measured distribute non-uniformly form highly stratified landscape. Systems analysis ME-model simulations suggest this stratification results...
A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent study this information. Here, introduce Bitome, a matrix composed of binary digits (bits) representing genomic positions features. We Bitome for Escherichia coli K-12 MG1655. find that: (i) features are encoded unevenly, both spatially categorically; (ii) coding intergenic recapitulated at high resolution; (iii) adaptive mutations skewed towards with fewer features; (iv)...
Abstract Adaptive laboratory evolution (ALE) is able to generate microbial strains which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use ALE evolve Escherichia coli that grow at temperatures as high 45.3°C, a temperature lethal wild type cells. The adopted hypermutator phenotype and employed multiple systems-level adaptations made global analysis of the DNA mutations difficult. Given challenge genomic level, were motivated uncover tolerance...
We report on a radiopharmaceutical imaging platform designed to capture the kinetics of cellular responses drugs. <b>Methods:</b> A portable in vitro molecular system comprising microchip and β-particle camera permitted routine cell-based radioassays small numbers either suspended or adherent cells. investigated model lymphoma glioblastoma cancer cell lines <sup>18</sup>F-FDG uptake after drug exposure. Those were correlated with kinetic changes cycle receptor tyrosine kinase signaling....
Summary Catalysis using iron-sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage metalloproteins caused by reactive oxygen species (ROS) completely inhibit cell growth when unmanaged thus elicits an essential stress response that is fundamental in biology. We develop a computable multi-scale description of ROS Escherichia coli . show this quantitative framework allows for understanding prediction responses at three levels: 1) pathways:...