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Article ; Online: Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment.

Choe, Donghui / Olson, Connor A / Szubin, Richard / Yang, Hannah / Sung, Jaemin / Feist, Adam M / Palsson, Bernhard O

2024 Volume 15, Issue 1, Page(s) 2356

Abstract: Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The identification of ... ...

Abstract	Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The identification of iModulons enables accurate identification of genes necessary and sufficient for cross-species transfer of cellular functions. We demonstrate cross-species transfer of: 1) the biotransformation of vanillate to protocatechuate, 2) a malonate catabolic pathway, 3) a catabolic pathway for 2,3-butanediol, and 4) an antimicrobial resistance to ampicillin found in multiple Pseudomonas species to Escherichia coli. iModulon-based engineering is a transformative strategy as it includes all genes comprising the transferred cellular function, including genes without functional annotation. Adaptive laboratory evolution was deployed to optimize the cellular function transferred, revealing mutations in the host. Combining big data analytics and laboratory evolution thus enhances the level of understanding of systems biology, and synthetic biology for strain design and development.
MeSH term(s)	Synthetic Biology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Genes, Bacterial ; Pseudomonas/genetics
Language	English
Publishing date	2024-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46486-3
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Article ; Online: Engineering Pseudomonas putida for improved utilization of syringyl aromatics.

Mueller, Joshua / Willett, Howard / Feist, Adam M / Niu, Wei

Biotechnology and bioengineering

2022 Volume 119, Issue 9, Page(s) 2541–2550

Abstract: Lignin is a largely untapped source for the bioproduction of value-added chemicals. Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic ... ...

Abstract	Lignin is a largely untapped source for the bioproduction of value-added chemicals. Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic capabilities, and genetic amenability. Here we demonstrate the engineering of P. putida for the ability to metabolize syringic acid, one of the major products that comes from the breakdown of the syringyl component of lignin. The rational design was first applied for the construction of strain Sy-1 by overexpressing a native vanillate demethylase. Subsequent adaptive laboratory evolution (ALE) led to the generation of mutations that achieved robust growth on syringic acid as a sole carbon source. The best mutant showed a 30% increase in the growth rate over the original engineered strain. Genomic sequencing revealed multiple mutations repeated in separate evolved replicates. Reverse engineering of mutations identified in agmR, gbdR, fleQ, and the intergenic region of gstB and yadG into the parental strain recaptured the improved growth of the evolved strains to varied extent. These findings thus reveal the ability of P. putida to utilize lignin more fully as a feedstock and make it a more economically viable chassis for chemical production.
MeSH term(s)	Base Sequence ; Carbon/metabolism ; Lignin/metabolism ; Metabolic Engineering ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism
Chemical Substances	Carbon (7440-44-0) ; Lignin (9005-53-2)
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	280318-5
ISSN	1097-0290 ; 0006-3592
ISSN (online)	1097-0290
ISSN	0006-3592
DOI	10.1002/bit.28131
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Article ; Online: Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments.

Carpenter, Alexander C / Feist, Adam M / Harrison, Fergus S M / Paulsen, Ian T / Williams, Thomas C

Metabolic engineering communications

2023 Volume 17, Page(s) e00227

Abstract: Adaptive Laboratory Evolution (ALE) is a powerful tool for engineering and understanding microbial physiology. ALE relies on the selection and enrichment of mutations that enable survival or faster growth under a selective condition imposed by the ... ...

Abstract	Adaptive Laboratory Evolution (ALE) is a powerful tool for engineering and understanding microbial physiology. ALE relies on the selection and enrichment of mutations that enable survival or faster growth under a selective condition imposed by the experimental setup. Phenotypic fitness landscapes are often underpinned by complex genotypes involving multiple genes, with combinatorial positive and negative effects on fitness. Such genotype relationships result in mutational fitness landscapes with multiple local fitness maxima and valleys. Traversing local maxima to find a global maximum often requires an individual or sub-population of cells to traverse fitness valleys. Traversing involves gaining mutations that are not adaptive for a given local maximum but are necessary to 'peak shift' to another local maximum, or eventually a global maximum. Despite these relatively well understood evolutionary principles, and the combinatorial genotypes that underlie most metabolic phenotypes, the majority of applied ALE experiments are conducted using constant selection pressures. The use of constant pressure can result in populations becoming trapped within local maxima, and often precludes the attainment of optimum phenotypes associated with global maxima. Here, we argue that oscillating selection pressures is an easily accessible mechanism for traversing fitness landscapes in ALE experiments, and provide theoretical and practical frameworks for implementation.
Language	English
Publishing date	2023-07-13
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2821894-2
ISSN	2214-0301 ; 2214-0301
ISSN (online)	2214-0301
ISSN	2214-0301
DOI	10.1016/j.mec.2023.e00227
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Article ; Online: TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent

Goel, Nikita / Srivastav, Stuti / Patel, Arjun / Shirsath, Akshay / Panda, Tushar Ranjan / Patra, Malay / Feist, Adam M / Anand, Amitesh

Microbiology spectrum

2023 Volume 11, Issue 6, Page(s) e0222523

Abstract: Importance: Energy generation pathways are a potential avenue for the development of novel antibiotics. However, bacteria possess remarkable resilience due to the compensatory pathways, which presents a challenge in this direction. NADH, the primary ... ...

Abstract	Importance: Energy generation pathways are a potential avenue for the development of novel antibiotics. However, bacteria possess remarkable resilience due to the compensatory pathways, which presents a challenge in this direction. NADH, the primary reducing equivalent, can transfer electrons to two distinct types of NADH dehydrogenases. Type I NADH dehydrogenase is an enzyme complex comprising multiple subunits and can generate proton motive force (PMF). Type II NADH dehydrogenase does not pump protons but plays a crucial role in maintaining the turnover of NAD+. To study the adaptive rewiring of energy metabolism, we evolved an
MeSH term(s)	NADH Dehydrogenase/genetics ; NADH Dehydrogenase/metabolism ; Proton Pumps/metabolism ; Escherichia coli/metabolism ; Protons ; NAD/metabolism ; Bacteria/metabolism
Chemical Substances	NADH Dehydrogenase (EC 1.6.99.3) ; Proton Pumps ; Protons ; NAD (0U46U6E8UK)
Language	English
Publishing date	2023-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02225-23
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Article ; Online: Adaptive evolution of a minimal organism with a synthetic genome.

Sandberg, Troy E / Wise, Kim S / Dalldorf, Christopher / Szubin, Richard / Feist, Adam M / Glass, John I / Palsson, Bernhard O

iScience

2023 Volume 26, Issue 9, Page(s) 107500

Abstract: The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from ... ...

Abstract	The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107500
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Article ; Online: Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

Park, Mee‐Rye / Gauttam, Rahul / Fong, Bonnie / Chen, Yan / Lim, Hyun Gyu / Feist, Adam M. / Mukhopadhyay, Aindrila / Petzold, Christopher J. / Simmons, Blake A. / Singer, Steven W.

Environmental Microbiology. 2023 Feb., v. 25, no. 2 p.493-504

2023

Abstract: The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to ... ...

Abstract	The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well‐characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth‐promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
Keywords	Pseudomonas putida ; arabinose ; biofuels ; bioremediation ; catabolism ; glucose ; growth promotion ; hemicellulose ; microbiology ; new species ; oxidation ; oxidoreductases ; pentoses ; phytomass ; plant growth ; xylose
Language	English
Dates of publication	2023-02
Size	p. 493-504.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16296
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Article ; Online: Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration.

Kim, Han Sol / Noh, Myung Hyun / White, Evan M / Kandefer, Michael V / Wright, Austin F / Datta, Debika / Lim, Hyun Gyu / Smiggs, Ethan / Locklin, Jason J / Rahman, Md Arifur / Feist, Adam M / Pokorski, Jonathan K

Nature communications

2024 Volume 15, Issue 1, Page(s) 3338

Abstract: The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered ... ...

Abstract	The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
MeSH term(s)	Polyurethanes/chemistry ; Spores, Bacterial ; Biocompatible Materials/chemistry ; Tensile Strength ; Hot Temperature ; Green Fluorescent Proteins/metabolism ; Green Fluorescent Proteins/genetics
Chemical Substances	Polyurethanes ; Biocompatible Materials ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2024-04-30
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47132-8
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Article ; Online: What do cells actually want?

Feist, Adam M / Palsson, Bernhard O

Genome biology

2016 Volume 17, Issue 1, Page(s) 110

Abstract: Genome-scale models require an objective function representing what an organism strives for. A method has been developed to infer this fundamental biological function from data.Please see related Research article: www.dx.doi.org/10.1186/s13059-016-0968-2. ...

Abstract	Genome-scale models require an objective function representing what an organism strives for. A method has been developed to infer this fundamental biological function from data.Please see related Research article: www.dx.doi.org/10.1186/s13059-016-0968-2.
Language	English
Publishing date	2016-05-23
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/s13059-016-0983-3
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Article ; Online: Compensatory evolution of Pseudomonas aeruginosa's slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis.

La Rosa, Ruggero / Rossi, Elio / Feist, Adam M / Johansen, Helle Krogh / Molin, Søren

Nature communications

2021 Volume 12, Issue 1, Page(s) 3186

Abstract: Long-term infection of the airways of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. This reduction has been hypothesised to increase within-patient fitness and overall persistence of ... ...

Abstract	Long-term infection of the airways of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. This reduction has been hypothesised to increase within-patient fitness and overall persistence of the pathogen. Here, we apply adaptive laboratory evolution to revert the slow growth phenotype of P. aeruginosa clinical strains back to a high growth rate. We identify several evolutionary trajectories and mechanisms leading to fast growth caused by transcriptional and mutational changes, which depend on the stage of adaptation of the strain. Return to high growth rate increases antibiotic susceptibility, which is only partially dependent on reversion of mutations or changes in the transcriptional profile of genes known to be linked to antibiotic resistance. We propose that similar mechanisms and evolutionary trajectories, in reverse direction, may be involved in pathogen adaptation and the establishment of chronic infections in the antibiotic-treated airways of cystic fibrosis patients.
MeSH term(s)	Adaptation, Physiological/drug effects ; Adaptation, Physiological/genetics ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics ; Cell Proliferation/drug effects ; Cell Proliferation/genetics ; Cystic Fibrosis/complications ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/immunology ; Cystic Fibrosis/microbiology ; DNA Mutational Analysis ; DNA, Bacterial/genetics ; DNA, Bacterial/isolation & purification ; Directed Molecular Evolution ; Drug Resistance, Microbial/drug effects ; Drug Resistance, Microbial/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genetic Fitness/drug effects ; Genome, Bacterial ; Humans ; Lung/immunology ; Lung/microbiology ; Microbial Sensitivity Tests ; Mutation ; Phenotype ; Pseudomonas Infections/drug therapy ; Pseudomonas Infections/immunology ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/drug effects ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/isolation & purification ; Sputum/microbiology
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; DNA, Bacterial
Language	English
Publishing date	2021-05-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-23451-y
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Article ; Online: Selection for Cell Yield Does Not Reduce Overflow Metabolism in Escherichia coli.

Rabbers, Iraes / Gottstein, Willi / Feist, Adam M / Teusink, Bas / Bruggeman, Frank J / Bachmann, Herwig

Molecular biology and evolution

2021 Volume 39, Issue 1

Abstract: Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates ... ...

Abstract	Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here, we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of Escherichia coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead, the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism, followed by the consumption of the overflow metabolite, can lead to a higher numerical cell yield and therefore a higher fitness compared with full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favorable even in the absence of nutrient competition.
MeSH term(s)	Acetates/metabolism ; Carbon/metabolism ; Escherichia coli/metabolism ; Glucose/metabolism
Chemical Substances	Acetates ; Carbon (7440-44-0) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2021-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msab345
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