33 results on '"Connor A. Olson"'
Search Results
2. Laboratory Evolution, Transcriptomics, and Modeling Reveal Mechanisms of Paraquat Tolerance
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Kevin Rychel, Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Tharwat Tolba Mohamed, Patrick V. Phaneuf, Amitesh Anand, Connor A. Olson, Joon Ho Park, Anand V. Sastry, Laurence Yang, Adam M. Feist, and Bernhard Palsson
- Published
- 2023
3. Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
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Kevin Rychel, Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Tharwat Tolba Mohamed, Patrick V. Phaneuf, Amitesh Anand, Connor A. Olson, Joon Ho Park, Anand V. Sastry, Laurence Yang, Adam M. Feist, and Bernhard O. Palsson
- Abstract
SummaryRelationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data analytic method for characterizing the transcriptome can simplify interpretation by grouping genes into independently modulated sets (iModulons). Here, we demonstrate how iModulons reveal deep understanding of the effects of causal mutations and metabolic rewiring. We use adaptive laboratory evolution to generateE. colistrains that tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulons, and metabolic models to elucidate six interacting stress tolerance mechanisms: 1) modification of transport, 2) activation of ROS stress responses, 3) use of ROS-sensitive iron regulation, 4) motility, 5) broad transcriptional reallocation toward growth, and 6) metabolic rewiring to decrease NADH production. This work thus reveals the genome-scale systems biology of ROS tolerance.Graphical Abstract
- Published
- 2022
4. Use of Riparian Spiders as Sentinels of Persistent and Bioavailable Chemical Contaminants in Aquatic Ecosystems: A Review
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Matthew M. Chumchal, Gale B. Beaubien, Ray W. Drenner, Madeline P. Hannappel, Marc A. Mills, Connor I. Olson, Ryan R. Otter, Andrew C. Todd, and David M. Walters
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Food Chain ,Odonata ,Health, Toxicology and Mutagenesis ,Environmental Chemistry ,Animals ,Humans ,Spiders ,Polychlorinated Biphenyls ,Article ,Ecosystem ,Water Pollutants, Chemical - Abstract
Aquatic ecosystems around the world are contaminated with a wide range of anthropogenic chemicals, including metals and organic pollutants, that originate from point and nonpoint sources. Many of these chemical contaminants have complex environmental cycles, are persistent and bioavailable, can be incorporated into aquatic food webs, and pose a threat to the health of wildlife and humans. Identifying appropriate sentinels that reflect bioavailability is critical to assessing and managing aquatic ecosystems impacted by contaminants. The objective of the present study is to review research on riparian spiders as sentinels of persistent and bioavailable chemical contaminants in aquatic ecosystems. Our review of the literature on riparian spiders as sentinels suggests that significant progress has been made during the last two decades of research. We identified 55 published studies conducted around the world in which riparian spiders (primarily of the families Tetragnathidae, Araneidae, Lycosidae, and Pisauridae) were used as sentinels of chemical contamination of lotic, lentic, and estuarine systems. For several contaminants, such as polychlorinated biphenyls (PCBs), Hg, and Se, it is now clear that riparian spiders are appropriate sentinels. However, many contaminants and factors that could impact chemical concentrations in riparian spiders have not been well characterized. Further study of riparian spiders and their potential role as sentinels is critical because it would allow for development of national-scale programs that utilize riparian spiders as sentinels to monitor chemical contaminants in aquatic ecosystems. A riparian spider sentinel program in the United States would be complementary to existing national sentinel programs, including those for fish and immature dragonflies. Environ Toxicol Chem 2022;41:499-514. © 2021 SETAC.
- Published
- 2022
5. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity
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Amitesh Anand, Arjun Patel, Ke Chen, Connor A. Olson, Patrick V. Phaneuf, Cameron Lamoureux, Ying Hefner, Richard Szubin, Adam M. Feist, and Bernhard O. Palsson
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Electron Transport ,Multidisciplinary ,Proteome ,Affordable and Clean Energy ,Systems Biology ,Respiratory System ,Escherichia coli ,General Physics and Astronomy ,General Chemistry ,Lung ,General Biochemistry, Genetics and Molecular Biology ,Biotechnology - Abstract
Respiration requires organisms to have an electron transport system (ETS) for the generation of proton motive force across the membrane that drives ATP synthase. Although the molecular details of the ETS are well studied and constitute textbook material, few studies have appeared to elucidate its systems biology. The most thermodynamically efficient ETS consists of two enzymes, an NADH: quinone oxidoreductase (NqRED) and a dioxygen reductase (O2RED), which facilitate the shuttling of electrons from NADH to oxygen. However, evolution has produced variations within ETS which modulate the overall energy efficiency of the system even within the same organism 1–3. The system-level impact of these variations and their individual physiological optimality remain poorly determined. To mimic varying ETS efficiency we generated four Escherichia coli deletion strains (named ETS-1H, 2H, 3H, and 4H) harboring unbranched ETS variants that pump 1, 2, 3, or 4 proton(s) per electron respectively. We then used a combination of synergistic methods (laboratory evolution, multi-omic analyses, and computation of proteome allocation) to characterize these ETS variants. We found that: (a) all four ETS variants evolved to a similar optimized growth rate, (b) the evolution of ETS variants was enabled by specific rewiring of major energy-generating pathways that couple to the ETS to optimize their ATP production capability, (c) proteome allocation per ATP generated was the same for all the variants, (d) the aero-type, that designates the overall ATP generation strategy 4 of a variant, remained conserved during its laboratory evolution, with the exception of the ETS-4H variant, and (e) integrated computational analysis of then data supported a proton-to-ATP ratio of 10 protons per 3 ATP for ATP synthase for all four ETS variants. We thus have defined the Aero-Type System (ATS) as a generalization of the aerobic bioenergetics, which is descriptive of the metabolic systems biology of respiration and demonstrates its plasticity.
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- 2022
6. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution
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Connor A. Olson, Bernhard O. Palsson, Richard Szubin, John M. Gladden, Steven W. Singer, Thomas Eng, Bonnie Fong, Harsha D. Magurudeniya, Geovanni Alarcon, Hyun Gyu Lim, Blake A. Simmons, Aindrila Mukhopadhyay, and Adam M. Feist
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0303 health sciences ,Mutation ,biology ,Strain (chemistry) ,030306 microbiology ,Chemistry ,Glyoxylate cycle ,Biomass ,Lignocellulosic biomass ,biology.organism_classification ,medicine.disease_cause ,Pollution ,Hydrolysate ,Pseudomonas putida ,03 medical and health sciences ,Biochemistry ,medicine ,Environmental Chemistry ,Efflux ,030304 developmental biology - Abstract
Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizingPseudomonas putidaKT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA,gacS,oprB/PP_1446,fleQ,tktA, anduvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE,oprD, and PP_5324). We further validated the causality of the PP_5350 andemrEgenes for improved IL toleranceviareverse engineering and transcriptomic analysis. A common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator, was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that theemrEgene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.
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- 2020
7. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States
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Sibei Xu, Richard Szubin, Anand V. Sastry, Amitesh Anand, Troy E. Sandberg, Yara Seif, Laurence Yang, Ke Chen, Bernhard O. Palsson, Connor A. Olson, Edward Catoiu, and Adam M. Feist
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Models, Molecular ,DNA damage ,Protein Conformation ,Biology ,Vibrio natriegens ,medicine.disease_cause ,Transcriptome ,03 medical and health sciences ,Bacterial Proteins ,Catalytic Domain ,Genetics ,medicine ,Escherichia coli ,SOS response ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,adaptive laboratory evolution ,Vibrio ,0303 health sciences ,030306 microbiology ,Escherichia coli Proteins ,systems biology ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Adaptation, Physiological ,Repressor Proteins ,Oxidative Stress ,Oxidative stress ,Mutation ,bacteria ,Repressor lexA ,Directed Molecular Evolution ,Adaptive laboratory evolution ,Systems biology ,Reactive Oxygen Species ,Transcription Factors - Abstract
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, is a common mutational target using bacterial species belonging to two genera, Escherichia coli and Vibrio natriegens, in separate growth conditions implemented during laboratory evolution. The mutations clustered in the redox active site, dimer interface, and flexible redox loop of the protein. These mutations favor the oxidized conformation of OxyR that results in constitutive expression of the genes it regulates. Independent component analysis of the transcriptome revealed that the constitutive activity of OxyR reduces DNA damage from reactive oxygen species, as inferred from the activity of the SOS response regulator LexA. This adaptation to peroxide stress came at a cost of lower growth, as revealed by calculations of proteome allocation using genome-scale models of metabolism and macromolecular expression. Further, identification of similar sequence changes in natural isolates of E. coli indicates that adaptation to oxidative stress through genetic changes in oxyR can be a common occurrence.
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- 2019
8. Mercury in soils of the conterminous United States: patterns and pools
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Connor I Olson, Benjamin M Geyman, Colin P Thackray, David P Krabbenhoft, Michael T Tate, Elsie M Sunderland, and Charles T Driscoll
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Renewable Energy, Sustainability and the Environment ,Public Health, Environmental and Occupational Health ,General Environmental Science - Abstract
Soils account for the largest global mercury reservoirs, but observations are sparse in many regions. The accumulation and turnover of mercury in soils determines whether they act as an atmospheric source or sink. Here, we present a spatial analysis of soil mercury from a large soil survey (three horizons, ∼4800 sites) across the conterminous United States conducted by the U.S. Geological Survey. Soil mercury pools were calculated for 11 layers, cumulatively representing the top 1 m of soil, and totaling 158 ± 2 Gg (±SD) of mercury (20.3 ± 0.2 mg m−2). Mercury areal density was greatest in mixed forest (27.3 ± 0.5 mg m−2), cropland (25.3 ± 0.3 mg m−2), and deciduous forest (25.6 ± 0.5 mg m−2) ecosystems and lowest in barren (13.5 ± 0.3 mg m−2) and shrubland (12.6 ± 0.2 mg m−2) ecosystems. Assessment of the provenance of soil mercury using bedrock titanium normalization suggests that 62%–95% of soil mercury is unexplained by parental sources.
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- 2022
9. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
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Richard Szubin, Yara Seif, Ying Hefner, George Sakoulas, Adam M. Feist, Bernhard O. Palsson, Connor A. Olson, Henrique Machado, Amitesh Anand, Victor Nizet, and Ying Jones
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Staphylococcus aureus ,QH301-705.5 ,Evolution ,Medicine (miscellaneous) ,Biology ,medicine.disease_cause ,Antimicrobial resistance ,General Biochemistry, Genetics and Molecular Biology ,Treatment failure ,Article ,Microbiology ,Evolution, Molecular ,Bacterial evolution ,03 medical and health sciences ,Genes, Regulator ,medicine ,Genetics ,Humans ,2.1 Biological and endogenous factors ,Biology (General) ,Allele ,Aetiology ,Gene ,030304 developmental biology ,Vancomycin resistance ,0303 health sciences ,030306 microbiology ,Regulator ,Molecular ,Vancomycin Resistance ,biochemical phenomena, metabolism, and nutrition ,Phenotype ,Regulon ,Emerging Infectious Diseases ,Infectious Diseases ,Experimental evolution ,Genes ,Mutation ,Vancomycin ,Antimicrobial Resistance ,General Agricultural and Biological Sciences ,medicine.drug - Abstract
While microbiological resistance to vancomycin in Staphylococcus aureus is rare, clinical vancomycin treatment failures are common, and methicillin-resistant S. aureus (MRSA) strains isolated from patients after prolonged vancomycin treatment failure remain susceptible. Adaptive laboratory evolution was utilized to uncover mutational mechanisms associated with MRSA vancomycin resistance in a physiological medium as well as a bacteriological medium used in clinical susceptibility testing. Sequencing of resistant clones revealed shared and media-specific mutational outcomes, with an overlap in cell wall regulons (walKRyycHI, vraSRT). Evolved strains displayed similar properties to resistant clinical isolates in their genetic and phenotypic traits. Importantly, resistant phenotypes that developed in physiological media did not translate into resistance in bacteriological media. Further, a bacteriological media-specific mechanism for vancomycin resistance associated with a mutated mprF was confirmed. This study bridges the gap between the understanding of clinical and microbiological vancomycin resistance in S. aureus and expands the number of allelic variants (18 ± 4 mutations for the top 5 mutated genes) that result in vancomycin resistance phenotypes., Henrique Machado et al. describe mutational mechanisms associated with MRSA vancomycin resistance in Staphylococcus aureus using adaptive laboratory evolution experiments focused on tolerance. Their results reveal environment-dependent mutational strategies to vancomycin tolerization and the impact of mutations in regulatory genes, providing insight into the development of antibiotic resistance under multiple conditions.
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- 2021
10. Mercury Accumulation in Millipedes (Narceus spp.) Living Adjacent to a Southern Appalachian Mountain Stream (USA)
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Gale B. Beaubien, Connor I. Olson, Ryan R. Otter, and Jaylen L. Sims
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Insecta ,Health, Toxicology and Mutagenesis ,Zoology ,chemistry.chemical_element ,Forests ,010501 environmental sciences ,Toxicology ,01 natural sciences ,Rivers ,Animals ,Arthropods ,0105 earth and related environmental sciences ,Salvelinus ,biology ,Millipede ,Narceus ,Mercury ,04 agricultural and veterinary sciences ,General Medicine ,Methylmercury Compounds ,Plant litter ,biology.organism_classification ,Bioaccumulation ,Tennessee ,Pollution ,Mercury (element) ,Trout ,chemistry ,Oncorhynchus mykiss ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Rainbow trout ,Water Pollutants, Chemical ,Environmental Monitoring - Abstract
Millipedes are among the most important processors of leaf litter in temperate forests. Through consumption of leaf litter, millipedes may be exposed to mercury that accumulates in leaf tissues prior to senescence. To investigate mercury uptake in millipedes, Narceus spp. were collected from a remote site in the southern Appalachian Mountains, an area known to receive high mercury deposition. Additionally, aquatic primary consumers (larval caddisflies and stoneflies), brook trout (Salvelinus fontinalis) and rainbow trout (Oncorhynchus mykiss) were collected from the same site for comparisons of mercury concentrations and percent methylmercury. Bioaccumulation factors for millipedes were 18.5 and 20.2 for total and methylmercury, respectively. At this site, the mean THg concentration in millipedes was ~ 10 × greater than both brook trout and rainbow trout and ~ 200 × greater than that of aquatic primary consumers. Millipede THg concentrations ranged from 222 to 1620 ng/g ww in an area where EPA fish consumption criteria (300 ng/g MeHg in fish tissue, ww) were not exceeded. The mean percent methylmercury in millipedes was 1.4%, suggesting these animals were accumulating large quantities of inorganic mercury.
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- 2019
11. Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
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Ye Gao, Nathan Mih, Amitesh Anand, Ke Chen, Troy E. Sandberg, Connor A. Olson, Bernhard O. Palsson, and Maranas, Costas D
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Protein Folding ,Proteome ,Fitness landscape ,Proteomes ,Enzyme Metabolism ,Plant Science ,Genome ,Biochemistry ,Plant Energy Production ,Protein expression ,Mathematical Sciences ,Adenosine Triphosphate ,Models ,Macromolecular Structure Analysis ,Biology (General) ,Enzyme Chemistry ,Ecology ,Organic Compounds ,Plant Biochemistry ,Escherichia coli Proteins ,Systems Biology ,Monosaccharides ,Bacterial ,Biological Sciences ,Phenotype ,Enzymes ,Chemistry ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Research Article ,Protein Structure ,Evolution ,Bioinformatics ,QH301-705.5 ,Systems biology ,1.1 Normal biological development and functioning ,Carbohydrates ,Computational biology ,Biology ,Microbiology ,Bacterial genetics ,Evolution, Molecular ,Cellular and Molecular Neuroscience ,Genetic ,Underpinning research ,Information and Computing Sciences ,Escherichia coli ,Genetics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Bacterial Evolution ,Nitrates ,Models, Genetic ,Organic Chemistry ,Human Genome ,Chemical Compounds ,Biology and Life Sciences ,Proteins ,Molecular ,Bacteriology ,Phenotypic trait ,Gene Expression Regulation, Bacterial ,Organismal Evolution ,Glucose ,Gene Expression Regulation ,Microbial Evolution ,Enzymology ,Genetic Fitness ,Genome, Bacterial - Abstract
The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution of Escherichia coli phenotypes on the rate-yield plane. We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape. Systems analysis of the ME-model simulations suggest that this stratification results from discrete ATP generation strategies. Accordingly, we define “aero-types”, a phenotypic trait that characterizes how a balanced proteome can achieve a given growth rate by modulating 1) the relative utilization of oxidative phosphorylation, glycolysis, and fermentation pathways; and 2) the differential employment of electron-transport-chain enzymes. This global, quantitative, and mechanistic systems biology interpretation of fitness landscape formed upon proteome allocation offers a fundamental understanding of bacterial physiology and evolution dynamics., Author summary Genome-scale models enable quantitative prediction of bacterial phenotypes and a fine-grained description of the underlying optimal proteome allocation. Thus, we can now analyze the phenotypic potential of a large number of Escherichia coli genotypes grown under different conditions, which leads to the discovery of a stratified distribution of phenotypes. The observed distribution is determined by distinct ATP generation strategies, defined as “aero-types”, associated with optimal proteome allocation modulated upon differential usage of the electron-transport-chain enzymes. This mechanistic approach offers us a genome-scale understanding of the fitness landscape, and a fundamental interpretation of bacterial physiology and evolution dynamics.
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- 2021
12. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media
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Hannah Tsunemoto, Nicholas Dillon, Anne Lamsa, Adam M. Feist, Victor Nizet, Jonathan M. Monk, Joseph Sugie, Saugat Poudel, Rob Knight, Yara Seif, Joe Pogliano, Alison Vrbanac, Richard Szubin, Connor A. Olson, Pieter C. Dorrestein, Bernhard O. Palsson, Akanksha Rajput, Samira Dahesh, and Michael J. Meehan
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Methicillin-Resistant Staphylococcus aureus ,medicine.drug_class ,AcademicSubjects/SCI02254 ,Antibiotics ,Health Informatics ,Microbial Sensitivity Tests ,Biology ,medicine.disease_cause ,Data Note ,Health care associated ,Microbiology ,03 medical and health sciences ,Vancomycin ,medicine ,Humans ,030304 developmental biology ,Vancomycin resistance ,0303 health sciences ,030306 microbiology ,Prevention ,biochemical phenomena, metabolism, and nutrition ,Staphylococcal Infections ,Methicillin-resistant Staphylococcus aureus ,Computer Science Applications ,Emerging Infectious Diseases ,Infectious Diseases ,Staphylococcus aureus ,AcademicSubjects/SCI00960 ,Antimicrobial Resistance ,Infection ,Delivery of Health Care ,medicine.drug - Abstract
Background The evolving antibiotic-resistant behavior of health care–associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern. They are resistant to a broad class of antibiotics such as macrolides, aminoglycosides, fluoroquinolones, and many more. Findings The selection of appropriate antibiotic susceptibility examination media is very important. Thus, we use bacteriological (cation-adjusted Mueller-Hinton broth) as well as physiological (R10LB) media to determine the effect of vancomycin on USA100 strains. The study includes the profiling behavior of HA-MRSA USA100 D592 and D712 strains in the presence of vancomycin through various high-throughput assays. The US100 D592 and D712 strains were characterized at sub-inhibitory concentrations through growth curves, RNA sequencing, bacterial cytological profiling, and exo-metabolomics high throughput experiments. Conclusions The study reveals the vancomycin resistance behavior of HA-MRSA USA100 strains in dual media conditions using wide-ranging experiments.
- Published
- 2021
13. Revealing 29 sets of independently modulated genes in
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Saugat, Poudel, Hannah, Tsunemoto, Yara, Seif, Anand V, Sastry, Richard, Szubin, Sibei, Xu, Henrique, Machado, Connor A, Olson, Amitesh, Anand, Joe, Pogliano, Victor, Nizet, and Bernhard O, Palsson
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Staphylococcus aureus ,Virulence ,Sequence Analysis, RNA ,Virulence Factors ,Sigma Factor ,Gene Expression Regulation, Bacterial ,Staphylococcal Infections ,Biological Sciences ,Microbiology ,DNA-Binding Proteins ,Repressor Proteins ,Bacterial Proteins ,transcriptional regulatory network ,Gene Regulatory Networks ,Transcriptome ,metabolism ,Metabolic Networks and Pathways - Abstract
Significance Staphylococcus aureus infections impose an immense burden on the healthcare system. To establish a successful infection in a hostile host environment, S. aureus must coordinate its gene expression to respond to a wide array of challenges. This balancing act is largely orchestrated by the transcriptional regulatory network. Here, we present a model of 29 independently modulated sets of genes that form the basis for a segment of the transcriptional regulatory network in clinical USA300 strains of S. aureus. Using this model, we demonstrate the concerted role of various cellular systems (e.g., metabolism, virulence, and stress response) underlying key physiological responses, including response during blood infection., The ability of Staphylococcus aureus to infect many different tissue sites is enabled, in part, by its transcriptional regulatory network (TRN) that coordinates its gene expression to respond to different environments. We elucidated the organization and activity of this TRN by applying independent component analysis to a compendium of 108 RNA-sequencing expression profiles from two S. aureus clinical strains (TCH1516 and LAC). ICA decomposed the S. aureus transcriptome into 29 independently modulated sets of genes (i-modulons) that revealed: 1) High confidence associations between 21 i-modulons and known regulators; 2) an association between an i-modulon and σS, whose regulatory role was previously undefined; 3) the regulatory organization of 65 virulence factors in the form of three i-modulons associated with AgrR, SaeR, and Vim-3; 4) the roles of three key transcription factors (CodY, Fur, and CcpA) in coordinating the metabolic and regulatory networks; and 5) a low-dimensional representation, involving the function of few transcription factors of changes in gene expression between two laboratory media (RPMI, cation adjust Mueller Hinton broth) and two physiological media (blood and serum). This representation of the TRN covers 842 genes representing 76% of the variance in gene expression that provides a quantitative reconstruction of transcriptional modules in S. aureus, and a platform enabling its full elucidation.
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- 2020
14. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus
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Connor A. Olson, George Sakoulas, Adam M. Feist, Yara Seif, Bernhard O. Palsson, Victor Nizet, Richard Szubin, and Henrique Machado
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Vancomycin resistance ,Susceptibility testing ,biochemical phenomena, metabolism, and nutrition ,Biology ,medicine.disease_cause ,Phenotype ,Treatment failure ,Microbiology ,Regulon ,Staphylococcus aureus ,medicine ,Vancomycin ,Allele ,medicine.drug - Abstract
While microbiological resistance to vancomycin in Staphylococcus aureus is rare, clinical vancomycin treatment failures are common, and methicillin-resistant S. aureus (MRSA) strains isolated from patients after prolonged vancomycin treatment failure remain susceptible. Adaptive laboratory evolution was utilized to uncover mutational mechanisms associated with MRSA vancomycin resistance in a bacteriological medium used in clinical susceptibility testing and a physiological medium. Sequencing of resistant clones revealed shared and media-specific mutational outcomes, with an overlap in cell wall regulons (walKRyycHI, vraSRT). Evolved strains displayed similar genetic and phenotypic traits to resistant clinical isolates. Importantly, resistant phenotypes that developed in physiological media did not translate into resistance in bacteriological media. Further, a bacteriological media-specific mechanism for vancomycin resistance enabled by a mutated mprF was confirmed. This study bridges the gap of understanding between clinical and microbiological vancomycin resistance in S. aureus and expands the number of allelic variants that result in vancomycin resistance phenotypes.
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- 2020
15. The Spider Exposure Pathway and the Potential Risk to Arachnivorous Birds
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Gale B. Beaubien, Connor I. Olson, Ryan R. Otter, and Andrew C. Todd
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0106 biological sciences ,Health, Toxicology and Mutagenesis ,Population ,Wildlife ,Zoology ,010501 environmental sciences ,complex mixtures ,010603 evolutionary biology ,01 natural sciences ,Risk Assessment ,Birds ,Rivers ,biology.animal ,Metals, Heavy ,Environmental Chemistry ,Animals ,education ,0105 earth and related environmental sciences ,Riparian zone ,Spider ,geography ,education.field_of_study ,Appalachian Region ,geography.geographical_feature_category ,biology ,Potential risk ,Aquatic ecosystem ,Spiders ,Methylmercury Compounds ,Animal Feed ,Passerine ,Taxon ,Environmental Monitoring - Abstract
There is growing concern over the health of North American birds, with evidence suggesting substantial population declines. Spiders are prominent dietary items for many bird species and mediate the transfer of contaminants to arachnivorous birds that consume them. Few studies have investigated the potential risk the spider exposure pathway poses to these birds because most studies have focused on piscivores. In the present study, we developed new chronic and acute As, Cd, Cu, Pb, Ni, Se, Zn, and MeHg spider-based avian wildlife values (SBAWVs) for multiple adult and nestling birds (primarily passerines) and then used the newly generated SBAWVs to characterize the risk to birds across 2 study areas: 1) 5 reaches in the southern Appalachian Mountains, an area with substantial mercury deposition but minimal anthropogenic impact, and 2) 4 reaches adjacent to the Emory River, an area impacted by the largest fly coal-ash spill in US history. We identified MeHg and Cu, Pb, Se, and Zn as contaminants of potential concern (COPC) at the Appalachian Mountain and Emory River study areas, respectively, based on dietary exposure of aquatic contaminants via riparian spiders. The identification of COPC at both study areas due to dietary spider exposure is notable not only because the spider exposure pathway has largely been uninvestigated at these sites but also because the aquatic systems in both areas have been studied extensively. Significant differences in MeHg concentrations were detected among spider taxa and suggest that the selection of spider taxa can impact risk characterization. These results indicate that the spider exposure pathway is important to consider when assessing potential risk, particularly for passerine birds. Environ Toxicol Chem 2020;39:2314-2324. © 2020 SETAC.
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- 2020
16. Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media
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Akanksha Rajput, Saugat Poudel, Hannah Tsunemoto, Michael Meehan, Richard Szubin, Connor A. Olson, Yara Seif, Anne Lamsa, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Rob Knight, Joe Pogliano, Victor Nizet, Adam M. Feist, and Bernhard O. Palsson
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Vancomycin resistance ,0303 health sciences ,030306 microbiology ,medicine.drug_class ,Antibiotics ,Biology ,medicine.disease_cause ,3. Good health ,Microbiology ,03 medical and health sciences ,Antibiotic resistance ,Staphylococcus aureus ,medicine ,Vancomycin ,030304 developmental biology ,medicine.drug - Abstract
Healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern due to their evolving antibiotic resistant. They are resistant to a broad class of antibiotics like macrolides, aminoglycosides, fluoroquinolones, and many more. The selection of appropriate antibiotic susceptibility examination media is very important. Thus, we use bacteriological (CA-MHB) as well as physiological (R10LB) media to determine the effect of vancomycin on USA100 strains. The study includes the profiling behaviour of HA-MRSA USA100 D592 and D712 strains in the presence of vancomycin through various high-throughput assays. The US100 D592 and D712 strains were characterized at sub-inhibitory concentrations through growth curves, RNA sequencing, bacterial cytological profiling, and exo-metabolomics high throughput experiments. The study reveals the vancomycin resistance behavior of USA100 strains in dual media conditions using wide-ranging experiments.
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- 2020
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17. Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media
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Akanksha Rajput, Saugat Poudel, Rob Knight, Michael J. Meehan, Adam M. Feist, Alison Vrbanac, Nicholas Dillon, Connor A. Olson, Jonathan M. Monk, Joe Pogliano, Hannah Tsunemoto, Pieter C. Dorrestein, Geovanni Alarcon, Bernhard O. Palsson, Anne Lamsa, Joseph Sugie, Victor Nizet, Yara Seif, Richard Szubin, and Samira Daesh
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0303 health sciences ,biology ,030306 microbiology ,medicine.drug_class ,business.industry ,Antibiotics ,Human pathogen ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Antimicrobial ,medicine.disease_cause ,3. Good health ,Microbiology ,03 medical and health sciences ,Tissue culture ,In vivo ,Staphylococcus aureus ,medicine ,Nafcillin ,business ,Bacteria ,030304 developmental biology ,medicine.drug - Abstract
Staphylococcus aureus is a leading human pathogen associated with both hospital-acquired and community-acquired infections. The bacterium has steadily gained resistance to β-lactams and other important first-line antibiotics culminating in its categorization as an urgent threat by the U.S. Centers for Disease Control and Prevention. Observations of a varying response to antimicrobial exposure as a function of media type has revealed that clinical susceptibility testing performed in standard bacteriological media might not adequately represent pharmacological responses in the patient. Such observations have encouraged research designed to identify media types that more closely mimic the in vivo environment. In this study, we examine the response of a hospital-acquired USA100 lineage methicillin-resistant, vancomycin-intermediate S. aureus (MRSA/VISA) strain (D592) to nafcillin in a bacteriological compared to a more physiological tissue culture-based medium. We performed multi-dimensional analysis including growth and bacterial cytological profiling, RNA sequencing, and exo-metabolomics measurements (both HPLC and LC/MS) to shed light on the media-dependent activity of the commonly prescribed β-lactam antibiotic nafcillin.
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- 2020
18. Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses
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Saugat Poudel, Sibei Xu, Victor Nizet, Hannah Tsunemoto, Bernhard O. Palsson, Henrique Machado, Anand V. Sastry, Joe Pogliano, Yara Seif, Connor A. Olson, Richard Szubin, and Amitesh Anand
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0303 health sciences ,Multidisciplinary ,030306 microbiology ,Virulence ,Computational biology ,Biology ,medicine.disease_cause ,3. Good health ,Transcriptome ,03 medical and health sciences ,chemistry.chemical_compound ,chemistry ,Staphylococcus aureus ,Gene expression ,CCPA ,medicine ,Gene ,Transcription factor ,Function (biology) ,030304 developmental biology - Abstract
The ability of Staphylococcus aureus to infect many different tissue sites is enabled, in part, by its Transcriptional Regulatory Network (TRN) that coordinates its gene expression to respond to different environments. We elucidated the organization and activity of this TRN by applying Independent Component Analysis (ICA) to a compendium of 108 RNAseq expression profiles from two S. aureus clinical strains (TCH1516 and LAC). ICA decomposed the S. aureus transcriptome into 29 independently modulated sets of genes (i-modulons) that revealed (1) high confidence associations between 21 i-modulons and known regulators; (2) an association between an i-modulon and σS, whose regulatory role was previously undefined; (3) the regulatory organization of 65 virulence factors in the form of three i-modulons associated with AgrR, SaeR and Vim-3, (4) the roles of three key transcription factors (codY, Fur and ccpA) in coordinating the metabolic and regulatory networks; and (5) a low dimensional representation, involving the function of few transcription factors, of changes in gene expression between two laboratory media (RPMI, CAMHB) and two physiological media (blood and serum). This representation of the TRN covers 842 genes representing 76% of the variance in gene expression that provides a quantitative reconstruction of transcriptional modules in S. aureus, and a platform enabling its full elucidation.Significance StatementStaphylococcus aureus infections impose an immense burden on the healthcare system. To establish a successful infection in a hostile host environment, S. aureus must coordinate its gene expression to respond to a wide array of challenges. This balancing act is largely orchestrated by the Transcriptional Regulatory Network (TRN). Here, we present a model of 29 independently modulated sets of genes that form the basis for a segment of the TRN in clinical USA300 strains of S. aureus. Using this model, we demonstrate the concerted role of various cellular systems (e.g. metabolism, virulence and stress response) underlying key physiological responses, including response during blood infection.
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- 2020
19. Practical Considerations for the Incorporation of Insect-Mediated Contaminant Flux into Ecological Risk Assessments
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Marc A. Mills, Gale B. Beaubien, Ryan R. Otter, David M. Walters, and Connor I. Olson
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Potential risk ,business.industry ,Environmental resource management ,Environmental science ,Ecological risk ,Landscape ecology ,business ,Risk assessment ,Flux (metabolism) - Abstract
Insect-mediated contaminant flux is truly an interdisciplinary concept that merges ideas from many technical areas of science (e.g., environmental chemistry, landscape ecology, and entomology). This chapter introduces risk assessors to this emerging and ecologically relevant concept by distilling the main mechanisms that drive insect-mediated contaminant flux and integrating them together so that more informed decisions can be made on whether the phenomenon presents a potential risk at a site.
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- 2020
20. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration
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Yara Seif, Adam M. Feist, Ke Chen, Saugat Poudel, Bernhard O. Palsson, Richard Szubin, Ying Hefner, Connor A. Olson, Anand V. Sastry, Sibei Xu, Patrick V. Phaneuf, Amitesh Anand, and Laurence Yang
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Cellular respiration ,naphthoquinone ,medicine.disease_cause ,Photosynthesis ,Microbiology ,Electron Transport ,03 medical and health sciences ,chemistry.chemical_compound ,genome-scale model ,medicine ,Escherichia coli ,Aerobic electron transport chain ,030304 developmental biology ,2. Zero hunger ,chemistry.chemical_classification ,0303 health sciences ,Reactive oxygen species ,Multidisciplinary ,030306 microbiology ,Oxo-Acid-Lyases ,Biological Sciences ,equipment and supplies ,Biological Evolution ,Naphthoquinone ,Aerobiosis ,Oxygen ,Oxidative Stress ,chemistry ,Biochemistry ,13. Climate action ,Reactive Oxygen Species ,rpoS ,Anaerobic exercise ,Oxidative stress ,respiration ,Naphthoquinones - Abstract
Significance A vectorial flow of electrons in the membrane generates proton-motive force, which is central to cellular respiration. Organisms, including the last universal common ancestor of living organisms (LUCA), have multiple electron transport systems to use diverse electron donor–acceptor pairs. Such respiratory flexibility enables survival in varying environments. The appearance of oxygen in Earth’s environment due to the Great Oxidation Event (GOE) caused a major transformation in microbial bioenergetics. Here we performed a systems-level analysis to examine the suitability of pre-GOE era respiratory quinone, naphthoquinone, in oxic environments and resource constraint requiring the advent of the high-redox-potential quinone., Evolution fine-tunes biological pathways to achieve a robust cellular physiology. Two and a half billion years ago, rapidly rising levels of oxygen as a byproduct of blooming cyanobacterial photosynthesis resulted in a redox upshift in microbial energetics. The appearance of higher-redox-potential respiratory quinone, ubiquinone (UQ), is believed to be an adaptive response to this environmental transition. However, the majority of bacterial species are still dependent on the ancient respiratory quinone, naphthoquinone (NQ). Gammaproteobacteria can biosynthesize both of these respiratory quinones, where UQ has been associated with aerobic lifestyle and NQ with anaerobic lifestyle. We engineered an obligate NQ-dependent γ-proteobacterium, Escherichia coli ΔubiC, and performed adaptive laboratory evolution to understand the selection against the use of NQ in an oxic environment and also the adaptation required to support the NQ-driven aerobic electron transport chain. A comparative systems-level analysis of pre- and postevolved NQ-dependent strains revealed a clear shift from fermentative to oxidative metabolism enabled by higher periplasmic superoxide defense. This metabolic shift was driven by the concerted activity of 3 transcriptional regulators (PdhR, RpoS, and Fur). Analysis of these findings using a genome-scale model suggested that resource allocation to reactive oxygen species (ROS) mitigation results in lower growth rates. These results provide a direct elucidation of a resource allocation tradeoff between growth rate and ROS mitigation costs associated with NQ usage under oxygen-replete condition.
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- 2019
21. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
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Adam M. Feist, Joe Pogliano, Bernhard O. Palsson, Hannah Tsunemoto, Joseph Sugie, Samira Dahesh, Alison Vrbanac, Saugat Poudel, Rob Knight, Nicholas Dillon, Akanksha Rajput, Anne Lamsa, Connor A. Olson, Jonathan M. Monk, Pieter C. Dorrestein, Michael J. Meehan, Victor Nizet, Yara Seif, and Richard Szubin
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Data Descriptor ,Antibiotics ,Drug Resistance ,Drug resistance ,Antimicrobial resistance ,medicine.disease_cause ,chemistry.chemical_compound ,Drug Resistance, Multiple, Bacterial ,lcsh:Science ,0303 health sciences ,Bacterial ,3. Good health ,Computer Science Applications ,Infectious Diseases ,Staphylococcus aureus ,Vancomycin ,Statistics, Probability and Uncertainty ,Infection ,Sequence Analysis ,Multiple ,medicine.drug ,Information Systems ,Statistics and Probability ,Methicillin-Resistant Staphylococcus aureus ,medicine.drug_class ,Biology ,Library and Information Sciences ,Microbiology ,Education ,Nafcillin ,03 medical and health sciences ,Antibiotic resistance ,medicine ,Metabolomics ,Clinical microbiology ,030304 developmental biology ,Sequence Analysis, RNA ,030306 microbiology ,Prevention ,Bacteriology ,biochemical phenomena, metabolism, and nutrition ,Culture Media ,High-Throughput Screening Assays ,Emerging Infectious Diseases ,chemistry ,Linezolid ,RNA ,lcsh:Q ,Antimicrobial Resistance ,Daptomycin - Abstract
Staphylococcus aureus strains have been continuously evolving resistance to numerous classes of antibiotics including methicillin, vancomycin, daptomycin and linezolid, compounding the enormous healthcare and economic burden of the pathogen. Cation-adjusted Mueller-Hinton broth (CA-MHB) is the standard bacteriological media for measuring antibiotic susceptibility in the clinical lab, but the use of media that more closely mimic the physiological state of the patient, e.g. mammalian tissue culture media, can in certain circumstances reveal antibiotic activities that may be more predictive of effectiveness in vivo. In the current study, we use both types of media to explore antibiotic resistance phenomena in hospital-acquired USA100 lineage methicillin-resistant, vancomycin-intermediate Staphylococcus aureus (MRSA/VISA) strain D712 via multidimensional high throughput analysis of growth rates, bacterial cytological profiling, RNA sequencing, and exo-metabolomics (HPLC and LC-MS). Here, we share data generated from these assays to shed light on the antibiotic resistance behavior of MRSA/VISA D712 in both bacteriological and physiological media., Measurement(s)Antibacterial Response • cDNA • transcription profiling assay • culture medium • organic acidTechnology Type(s)bacterial cytological profiling • RNA sequencing • liquid chromatography-tandem mass spectrometry • high-performance liquid chromatographyFactor Type(s)growth mediumSample Characteristic - OrganismStaphylococcus aureus Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.10283108
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- 2019
22. Adaptive laboratory evolution of
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Bin, Du, Connor A, Olson, Anand V, Sastry, Xin, Fang, Patrick V, Phaneuf, Ke, Chen, Muyao, Wu, Richard, Szubin, Sibei, Xu, Ye, Gao, Ying, Hefner, Adam M, Feist, and Bernhard O, Palsson
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Glucose ,Escherichia coli Proteins ,Gene Expression Profiling ,Mutation ,Escherichia coli ,Gene Expression Regulation, Bacterial ,Acids ,Adaptation, Physiological ,Biological Evolution ,Genome, Bacterial ,Metabolic Networks and Pathways ,Culture Media ,Research Article - Abstract
The ability of Escherichia coli to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strain E. coli K-12 MG1655 at pH 5.5 in glucose minimal medium. After 800 generations, six independent populations under evolution had reached 18.0 % higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains and found that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations in rpoC appearing in five of six sequenced clones; and (2) gene expression profiles revealed different strategies to mitigate acid stress, which are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing and expression profiling revealed, on a genome scale, the strategies that E. coli uses to mitigate acid stress.
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- 2019
23. Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance
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Patrick V. Phaneuf, Anand V. Sastry, Richard Szubin, Ying Hefner, Adam M. Feist, Bernhard O. Palsson, Justin Tan, Laurence Yang, Connor A. Olson, and Joon Ho Park
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chemistry.chemical_classification ,Reactive oxygen species ,Experimental evolution ,Superoxide ,Systems biology ,Robustness (evolution) ,Oxidative phosphorylation ,Biology ,medicine.disease_cause ,Cell biology ,chemistry.chemical_compound ,chemistry ,medicine ,Escherichia coli ,Oxidative stress - Abstract
Bacterial response to oxidative stress is of fundamental importance. Oxidative stresses are endogenous, such as reactive oxidative species (ROS) production during respiration, or exogenous in industrial biotechnology, due to culture conditions or product toxicity. The immune system inflicts strong ROS stress on invading pathogens. In this study we make use of Adaptive Laboratory Evolution (ALE) to generate two independent lineages ofEscherichia coliwith increased tolerance to superoxide stress by up to 500% compared to wild type. We found: 1) that the use of ALE reveals the genetic basis for and systems biology of ROS tolerance, 2) that there are only 6 and 7 mutations, respectively, in each lineage, five of which reproducibly occurred in the same genes (iron-sulfur cluster regulatoriscR, putative iron-sulfur repair proteinygfZ, pyruvate dehydrogenase subunit EaceE, succinate dehydrogenasesucA, and glutamine tRNAglnX), and 3) that the transcriptome of the strain lineages exhibits two different routes of tolerance: the direct mitigation and repair of ROS damage and the up-regulation of cell motility and swarming genes mediated through phosphate starvation, which has been linked to biofilm formation and aggregation. These two transcriptomic responses can be interpreted as ‘flight’ and ‘fight’ phenotypes.ImportanceBacteria encounter oxidative stress from multiple sources. During pathogenic infections, our body’s immune system releases ROS as a form of antimicrobial defense whilst bacteria used in industrial biotechnology are frequently exposed to genetic modifications and culture conditions which induce oxidative stress. In order to get around the body’s defences, pathogens have developed various adaptations to tolerate high levels of ROS, and these adaptive mechanisms are not always well understood. At the same time, there is a need to improve oxidative stress tolerance for industrially relevant strains in order to increase robustness and productivity. In this study we generate two strains of superoxide tolerantEscherichia coliand identify several adaptive mechanisms. These findings can be directly applied to improve production strain fitness in an industrial setting. They also provide insight into potential virulence factors in other pathogens, highlighting potential targets for antimicrobial compounds.
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- 2019
24. Adaptive laboratory evolution ofEscherichia coliunder acid stress
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Sibei Xu, Muyao Wu, Patrick V. Phaneuf, Bernhard O. Palsson, Bin Du, Xin Fang, Connor A. Olson, Richard Szubin, Ye Gao, Adam M. Feist, Anand V. Sastry, Ying Hefner, and Ke Chen
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Population ,Computational biology ,Biology ,medicine.disease_cause ,Microbiology ,7. Clean energy ,03 medical and health sciences ,Gene expression ,Escherichia coli ,medicine ,Colonization ,education ,030304 developmental biology ,Acid stress ,Genetics ,Whole genome sequencing ,education.field_of_study ,0303 health sciences ,Strain (chemistry) ,030306 microbiology ,Chemistry ,RNA sequencing ,Gene expression profiling ,Whole genome resequencing ,Adaptive laboratory evolution - Abstract
The ability ofEscherichia colito tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strainE. coliK-12 MG1655 at pH 5.5 in glucose minimal medium. By 800 generations, six independent populations under evolution reached 18.0% higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains to find that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations inrpoCappearing in 5 of 6 sequenced clones; (2) gene expression profiles revealed different strategies to mitigate acid stress, that are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing, and expression profiling reveals, on a genome-scale, the strategies thatE. colideploys to mitigate acid stress.
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- 2019
25. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media
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Joe Pogliano, Adam M. Feist, Hannah Tsunemoto, Bernhard O. Palsson, Anne Lamsa, Richard Szubin, Nicholas Dillon, Jonathan M. Monk, Saugat Poudel, Rob Knight, Connor A. Olson, Pieter C. Dorrestein, Yara Seif, Michael J. Meehan, Joseph Sugie, Victor Nizet, Alison Vrbanac, and Samira Dahesh
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Methicillin-Resistant Staphylococcus aureus ,Statistics and Probability ,Data Descriptor ,010504 meteorology & atmospheric sciences ,medicine.drug_class ,Antibiotics ,Microbial Sensitivity Tests ,Library and Information Sciences ,Biology ,medicine.disease_cause ,01 natural sciences ,Education ,Microbiology ,Nafcillin ,03 medical and health sciences ,Minimum inhibitory concentration ,In vivo ,medicine ,Metabolomics ,lcsh:Science ,030304 developmental biology ,0105 earth and related environmental sciences ,Bacteriological Techniques ,0303 health sciences ,Extramural ,Prevention ,RNA sequencing ,Antimicrobial ,Anti-Bacterial Agents ,Culture Media ,3. Good health ,Computer Science Applications ,Emerging Infectious Diseases ,Infectious Diseases ,Staphylococcus aureus ,lcsh:Q ,Antimicrobial Resistance ,Pathogens ,Statistics, Probability and Uncertainty ,Infection ,Transcriptome ,Information Systems ,medicine.drug - Abstract
Cation adjusted-Mueller Hinton Broth (CA-MHB) is the standard bacteriological medium utilized in the clinic for the determination of antibiotic susceptibility. However, a growing number of literature has demonstrated that media conditions can cause a substantial difference in the efficacy of antibiotics and antimicrobials. Recent studies have also shown that minimum inhibitory concentration (MIC) tests performed in standard cell culture media (e.g. RPMI and DMEM) are more indicative of in vivo antibiotic efficacy, presumably because they are a better proxy for the human host’s physiological conditions. The basis for the bacterial media dependent susceptibility to antibiotics remains undefined. To address this question, we characterized the physiological response of methicillin-resistant Staphylococcus aureus (MRSA) during exposure to sub-inhibitory concentrations of the beta-lactam antibiotic nafcillin in either CA-MHB or RPMI + 10% LB (R10LB). Here, we present high quality transcriptomic, exo-metabolomic and morphological data paired with growth and susceptibility results for MRSA cultured in either standard bacteriologic or more physiologic relevant medium., Design Type(s)replicate design • transcription profiling design • sequence analysis objectiveMeasurement Type(s)transcription profiling assay • cellular morphology • exo-metabolome • growthTechnology Type(s)RNA sequencing • fluorescence microscopy • liquid chromatography-tandem mass spectrometry • high performance liquid chromatography • Optical Density MeasurementFactor Type(s)culture medium • biological replicate • experimental conditionSample Characteristic(s)Staphylococcus aureus • culturing environment Machine-accessible metadata file describing the reported data (ISA-Tab format)
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- 2019
26. Identifying contaminants of potential concern in remote headwater streams of Tennessee’s Appalachian Mountains
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Gale B. Beaubien, A. David McKinney, Ryan R. Otter, and Connor I. Olson
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010504 meteorology & atmospheric sciences ,chemistry.chemical_element ,010501 environmental sciences ,Management, Monitoring, Policy and Law ,01 natural sciences ,chemistry.chemical_compound ,Rivers ,Animals ,Methylmercury ,0105 earth and related environmental sciences ,General Environmental Science ,biology ,Altitude ,Fishes ,Biotic Ligand Model ,General Medicine ,Pesticide ,Contamination ,biology.organism_classification ,Tennessee ,Pollution ,Mercury (element) ,Trout ,chemistry ,Environmental chemistry ,Environmental science ,Water quality ,Acid rain ,Water Pollutants, Chemical ,Environmental Monitoring - Abstract
The susceptibility of Tennessee's Appalachian Mountains to anthropogenic stressors has remained largely uninvestigated likely due to a lack of known point source contamination. However, a growing body of scientific evidence suggests that depositional inputs can lead to concerning levels of contamination, even in remote areas. To investigate potential concerns, water quality parameters, contaminants in water (nitrogen, TSS, and metals), and contaminants in eastern brook trout (mercury, polychlorinated biphenyls [PCBs], organochlorine [OC] pesticides, dioxins, furans, and phthalates) were measured in four Appalachian Mountain streams from 2015 to 2017. Concentrations were compared to literature and/or model-derived (e.g., biotic ligand model) threshold values to determine whether levels exceeded those acceptable for stream health. Dioxins and furans were detectable in fish tissue at all sites with an average 2,3,7,8-tetrachlorodinbenzodioxin toxicity equivalence (TEQ) of 0.0015 ng/kg. Concentrations of PCBs, phthalates, and organochlorine pesticides were never above analytical quantitation limits, although several OC pesticides (e.g., alpha-chlordane) were detectable in fish. Aluminum concentrations in water were found at levels shown previously to cause mortality in brook trout during acidic rain events. The average whole-body methylmercury concentrations in fish among sites were 0.037 ± 0.003 μg/kg and were on average 75 ± 2% of total mercury.
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- 2019
27. The genetic basis for adaptation of model-designed syntrophic co-cultures
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Zachary A. King, Karenina Sanders, Caitriona Brennan, Jon G. Sanders, Adam M. Feist, Colton J. Lloyd, Patrick V. Phaneuf, Rob Knight, Rodolfo A. Salido, Troy E. Sandberg, Ying Hefner, Gregory Humphrey, Edward J. O’Brien, Connor A. Olson, and Hatzimanikatis, Vassily
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Evolutionary Genetics ,0301 basic medicine ,Auxotrophy ,Enzyme Metabolism ,Mutant ,Biochemistry ,Mathematical Sciences ,0302 clinical medicine ,Glucose Metabolism ,Models ,Metabolites ,Biology (General) ,Enzyme Chemistry ,Protein Metabolism ,2. Zero hunger ,Ecology ,Strain (biology) ,Bacterial ,Biological Sciences ,Adaptation, Physiological ,Biological Evolution ,Mutant Strains ,Computational Theory and Mathematics ,Modeling and Simulation ,Mutation (genetic algorithm) ,Carbohydrate Metabolism ,Algorithms ,Research Article ,Biotechnology ,Evolutionary Processes ,QH301-705.5 ,Bioinformatics ,Physiological ,Niche ,Genomics ,Computational biology ,Biology ,Research and Analysis Methods ,Models, Biological ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,SDG 3 - Good Health and Well-being ,Evolutionary Adaptation ,Information and Computing Sciences ,Escherichia coli ,Genetics ,Adaptation ,Molecular Biology Techniques ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Human evolutionary genetics ,Human Genome ,Biology and Life Sciences ,Biological ,Coculture Techniques ,Metabolism ,030104 developmental biology ,Genes ,Genes, Bacterial ,Mutation ,Enzymology ,030217 neurology & neurosurgery ,Cloning - Abstract
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 the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains—with diverse metabolic deficiencies—were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities., Author summary Many basic characteristics underlying the establishment of cooperative growth in bacterial communities have not been studied in detail. The presented work sought to understand the adaptation of syntrophic communities by first employing a new computational method to generate a comprehensive catalog of E. coli auxotrophic mutants. Many of the knockouts in the catalog had the predicted effect of disabling a major biosynthetic process. As a result, these strains were predicted to be capable of growing when supplemented with many different individual metabolites (i.e., a non-specific auxotroph), but the strains would require a high amount of metabolic cooperation to grow in community. Three such non-specific auxotroph mutants from this catalog were co-cultured with a proven auxotrophic partner in vivo and evolved via adaptive laboratory evolution. In order to successfully grow, each strain in co-culture had to evolve under a pressure to grow cooperatively in its new niche. The non-specific auxotrophs further had to adapt to significant homeostatic changes in cell’s metabolic state caused by knockouts in metabolic genes. The genomes of the successfully growing communities were sequenced, thus providing unique insights into the genetic changes accompanying the formation and optimization of the viable communities. A computational model was further developed to predict how finite protein availability, a fundamental constraint on cell metabolism, could impact the composition of the community (i.e., the relative abundances of each community member).
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- 2019
28. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications
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Richard Szubin, Adam M. Feist, Amitesh Anand, Connor A. Olson, Anand V. Sastry, Laurence Yang, Arjun Patel, and Bernhard O. Palsson
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0301 basic medicine ,System biology ,Bioenergetics ,Transcription, Genetic ,Medical Physiology ,Regulator ,bioenergetics ,medicine.disease_cause ,0302 clinical medicine ,Pyruvic Acid ,Homeostasis ,lcsh:QH301-705.5 ,adaptive laboratory evolution ,Chemistry ,system biology ,Escherichia coli Proteins ,Proteome allocation ,Pyruvate dehydrogenase complex ,Cell biology ,Adaptive laboratory evolution ,Transcription ,Glycolysis ,Oxidation-Reduction ,Citric Acid Cycle ,Electrons ,Pyruvate Dehydrogenase Complex ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Genetic ,transcriptional regulatory network ,Genetics ,medicine ,Escherichia coli ,proteome allocation ,Gene ,Binding Sites ,Ribosomal binding site ,Citric acid cycle ,Emerging Infectious Diseases ,030104 developmental biology ,lcsh:Biology (General) ,Biochemistry and Cell Biology ,Flux (metabolism) ,Ribosomes ,Transcriptional regulatory network ,030217 neurology & neurosurgery - Abstract
SUMMARY Pyruvate dehydrogenase complex (PDC) functions as the main determinant of the respiro-fermentative balance because it converts pyruvate to acetyl-coenzyme A (CoA), which then enters the TCA (tricarboxylic acid cycle). PDC is repressed by the pyruvate dehydrogenase complex regulator (PdhR) in Escherichia coli. The deletion of the pdhR gene compromises fitness in aerobic environments. We evolve the E. coli pdhR deletion strain to examine its achievable growth rate and the underlying adaptive strategies. We find that (1) optimal proteome allocation to PDC is critical in achieving optimal growth rate; (2) expression of PDC in evolved strains is reduced through mutations in the Shine-Dalgarno sequence; (3) rewiring of the TCA flux and increased reactive oxygen species (ROS) defense occur in the evolved strains; and (4) the evolved strains adapt to an efficient biomass yield. Together, these results show how adaptation can find alternative regulatory mechanisms for a key cellular process if the primary regulatory mode fails., Graphical abstract, In brief Anand et al. show that the proximal effect of a proteome imbalance and consequent growth retardation from dysregulated expression of the pyruvate dehydrogenase complex is mitigated by an adaptive alteration in the efficiency of the ribosome recruitment.
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- 2021
29. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
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Adam M. Feist, Chuankai Cheng, Troy E. Sandberg, Ryan A. LaCroix, Zachary A. King, José Utrilla, Douglas McCloskey, Edward J. O’Brien, Bernhard O. Palsson, and Connor A. Olson
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0301 basic medicine ,Proteome ,Proteomes ,Physiology ,Enzyme Metabolism ,Microbial metabolism ,Biochemistry ,0302 clinical medicine ,Glucose Metabolism ,Medicine and Health Sciences ,Growth rate ,Biology (General) ,Enzyme Chemistry ,Overflow metabolism ,Mathematics ,Ecology ,Systems Biology ,Physics ,Enzymes ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Carbohydrate Metabolism ,Metabolic Pathways ,Protons ,Biological system ,Research Article ,Evolutionary Processes ,QH301-705.5 ,Systems biology ,Excretion ,Models, Biological ,Evolution, Molecular ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Bacterial Proteins ,Evolutionary Adaptation ,Genetics ,Escherichia coli ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Nuclear Physics ,Nucleons ,Evolutionary Biology ,Biology and Life Sciences ,Proteins ,Metabolic pathway ,030104 developmental biology ,Metabolism ,Yield (chemistry) ,Enzymology ,Adaptation ,Physiological Processes ,Flux (metabolism) ,030217 neurology & neurosurgery ,Genome, Bacterial ,Adaptive evolution - Abstract
Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach., Author summary This study reconciles multiple existing microbial rate-yield tradeoff theories with experimental data. There is great interest in developing quantitative descriptions of the relationship between growth rate and growth yield [1]. However, some reported experiments [2–4] in the literature do not agree with existing theories [5–7]. Specifically, overflow metabolism in E. coli can either be coupled [5, 8] or decoupled [2–4] from growth rate. We found that adaptive laboratory evolution (ALE) experiments of E. coli reveal a two-dimensional rate-yield tradeoff in adapted strains where the dimensions are (i) a tradeoff between growth rate and growth yield, previously reported by [5], and (ii) a tradeoff between substrate uptake rate and growth yield. The appearance of this two-dimensional tradeoff during adaptation suggests that microorganisms adapting to new environments are subject to a more complex set of rate-yield tradeoffs than previously reported [5, 6]. In this study, the two-dimensional rate-yield tradeoff is quantitatively explained through our multi-scale modeling approach, combining a previously reported small-scale proteome allocation model [5] with a genome-scale model of metabolism and gene-expression (ME-model) [9]. The modeling approach is also instrumental to future studies.
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- 2018
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30. Pseudogene repair driven by selection pressure applied in experimental evolution
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Richard Szubin, Bernhard O. Palsson, Adam M. Feist, Sibei Xu, Connor A. Olson, Troy E. Sandberg, Ying Hefner, Patrick V. Phaneuf, Anand V. Sastry, Amitesh Anand, Kumari Sonal Choudhary, Laurence Yang, and Edward Catoiu
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Microbiology (medical) ,Pseudogene ,Iron ,Immunology ,Computational biology ,Biology ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Microbiology ,Genome ,DNA Mismatch Repair ,Gene product ,Evolution, Molecular ,03 medical and health sciences ,Open Reading Frames ,Genetics ,medicine ,Escherichia coli ,Selection, Genetic ,Cation Transport Proteins ,Selection (genetic algorithm) ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Experimental evolution ,030306 microbiology ,Repertoire ,Escherichia coli Proteins ,Cell Biology ,Open reading frame ,Directed Molecular Evolution ,Pseudogenes - Abstract
Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product non-functional. Pseudogenes are found in many genomes and are not always eliminated, even if they are potentially ‘wasteful’. This raises a fundamental question about their prevalence. Here we report pseudogene efeU repair that restores the iron uptake system of Escherichia coli under a designed selection pressure during adaptive laboratory evolution. Adaptive laboratory evolution experiments in Escherichia coli show that the pseudogene efeU can be repaired to restore the bacterium’s iron uptake system, demonstrating that pseudogenes may serve as an ‘adaptive repertoire’ of selectable traits.
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- 2018
31. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
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Karsten Zengler, Ali Ebrahim, Mahmoud M. Al-Bassam, Connor A. Olson, Pieter C. Dorrestein, Ji-Nu Kim, Alexander A. Aksenov, Colton J. Lloyd, and Joanne K. Liu
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0301 basic medicine ,Glycerol ,Proteome ,Commodity chemicals ,Physiology ,Proteomes ,Gene Expression ,Fructoses ,Biochemistry ,0302 clinical medicine ,Nickel ,Medicine and Health Sciences ,Biology (General) ,Overflow metabolism ,Protein Metabolism ,Ecology ,biology ,Chemistry ,Organic Compounds ,Monosaccharides ,Monomers ,Acetogen ,Bioproduction ,Computational Theory and Mathematics ,Metals ,Modeling and Simulation ,Physical Sciences ,Clostridium ljungdahlii ,Research Article ,Chemical Elements ,QH301-705.5 ,Carbohydrates ,Computational biology ,Models, Biological ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Secretion ,Clostridium ,Ethanol ,Organic Chemistry ,Chemical Compounds ,Proteins ,Reproducibility of Results ,Biology and Life Sciences ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Polymer Chemistry ,Carbon ,Metabolic pathway ,030104 developmental biology ,Metabolism ,Genes, Bacterial ,Alcohols ,Fermentation ,Biocatalysis ,Energy Metabolism ,Physiological Processes ,030217 neurology & neurosurgery - Abstract
The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens., Author summary Acetogens are renowned for their potential biotechnological applications. The model acetogen Clostridium ljungdahlii has been studied intensively for its ability to produce biofuels from sustainable resources, like syngas. We describe a novel genome-scale model of metabolism and gene expression (ME-model) to gain insights into this model acetogen. This first ME-model for a Gram-positive bacterium contains all major metabolic and biosynthetic pathways and calculates accurate proteome allocations under diverse growth conditions, thereby significantly broadening the scope of predictability of metabolic models. Furthermore, the ME-model enables rational medium design for improved production. Our experimental validation implies wide applicability to others strains for rapid improvement of yield and titer in biotechnology-relevant applications.
- Published
- 2018
32. Reframing gene essentiality in terms of adaptive flexibility
- Author
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Edward Catoiu, Adam M. Feist, Patrick V. Phaneuf, Lucas Goldschmidt Micas, Connor A. Olson, Ying Hefner, Lais B. Crepaldi, Gabriela I. Guzman, and Bernhard O. Palsson
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0301 basic medicine ,Population ,Adaptive evolution ,Single-nucleotide polymorphism ,Computational biology ,Biology ,Isozyme ,Genome ,Transcriptome ,Evolution, Molecular ,03 medical and health sciences ,Structural Biology ,Gene duplication ,Escherichia coli ,education ,Molecular Biology ,Gene ,lcsh:QH301-705.5 ,Whole genome sequencing ,education.field_of_study ,Genes, Essential ,Whole Genome Sequencing ,Applied Mathematics ,Gene Expression Profiling ,Genomics ,Adaptation, Physiological ,Computer Science Applications ,Isoenzymes ,Essentiality ,030104 developmental biology ,Genome-scale model ,lcsh:Biology (General) ,Modeling and Simulation ,Mutation ,Research Article - Abstract
Background Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality. Results In this study, we explored the definition of conditional essentiality from a phenotypic and genomic perspective. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing and transcriptome analysis. Of the twenty false positive strains available and confirmed from the Keio single gene knock-out collection, 11 strains were shown to grow with longer incubation periods making these actual true positives. These strains grew reproducibly with a diverse range of growth phenotypes. The lag phase observed for these strains ranged from less than one day to more than 7 days. It was found that 9 out of 11 of the false positive strains that grew acquired mutations in at least one replicate experiment and the types of mutations ranged from SNPs and small indels associated with regulatory or metabolic elements to large regions of genome duplication. Comparison of the detected adaptive mutations, modeling predictions of alternate pathways and isozymes, and transcriptome analysis of KO strains suggested agreement for the observed growth phenotype for 6 out of the 9 cases where mutations were observed. Conclusions Longer-term growth experiments followed by whole genome sequencing and transcriptome analysis can provide a better understanding of conditional gene essentiality and mechanisms of adaptation to such perturbations. Compensatory mutations are largely reproducible mechanisms and are in agreement with genome-scale modeling predictions to loss of function gene deletion events. Electronic supplementary material The online version of this article (10.1186/s12918-018-0653-z) contains supplementary material, which is available to authorized users.
- Published
- 2017
33. Analytic Solution to Verify Code Predictions of Two-Phase Flow in a Boiling Water Reactor Core Channel
- Author
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Kuo-Fu Chen and Connor A. Olson
- Subjects
Core (optical fiber) ,Nuclear and High Energy Physics ,Nuclear Energy and Engineering ,Chemistry ,Code (cryptography) ,Boiling water reactor ,Thermodynamics ,Two-phase flow ,Mechanics ,Condensed Matter Physics ,Analytic solution ,Communication channel - Published
- 1983
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