1
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Barkman TJ. Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230348. [PMID: 39343033 PMCID: PMC11439504 DOI: 10.1098/rstb.2023.0348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 10/01/2024] Open
Abstract
Studies of enzymes in modern-day plants have documented the diversity of metabolic activities retained by species today but only provide limited insight into how those properties evolved. Ancestral sequence reconstruction (ASR) is an approach that provides statistical estimates of ancient plant enzyme sequences which can then be resurrected to test hypotheses about the evolution of catalytic activities and pathway assembly. Here, I review the insights that have been obtained using ASR to study plant metabolism and highlight important methodological aspects. Overall, studies of resurrected plant enzymes show that (i) exaptation is widespread such that even low or undetectable levels of ancestral activity with a substrate can later become the apparent primary activity of descendant enzymes, (ii) intramolecular epistasis may or may not limit evolutionary paths towards catalytic or substrate preference switches, and (iii) ancient pathway flux often differs from modern-day metabolic networks. These and other insights gained from ASR would not have been possible using only modern-day sequences. Future ASR studies characterizing entire ancestral metabolic networks as well as those that link ancient structures with enzymatic properties should continue to provide novel insights into how the chemical diversity of plants evolved. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Todd J. Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI49008, USA
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2
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Kelley EH, Osipiuk J, Korbas M, Endres M, Bland A, Ehrman V, Joachimiak A, Olsen KW, Becker DP. N α -acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification. Front Chem 2024; 12:1415644. [PMID: 39055043 PMCID: PMC11270798 DOI: 10.3389/fchem.2024.1415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 07/27/2024] Open
Abstract
Bacteria are becoming increasingly resistant to antibiotics, therefore there is an urgent need for new classes of antibiotics to fight antibiotic resistance. Mammals do not express N ɑ -acetyl-L-ornithine deacetylase (ArgE), an enzyme that is critical for bacterial survival and growth, thus ArgE represents a promising new antibiotic drug target, as inhibitors would not suffer from mechanism-based toxicity. A new ninhydrin-based assay was designed and validated that included the synthesis of the substrate analog N 5, N 5-di-methyl N α-acetyl-L-ornithine (kcat/Km = 7.32 ± 0.94 × 104 M-1s-1). This new assay enabled the screening of potential inhibitors that absorb in the UV region, and thus is superior to the established 214 nm assay. Using this new ninhydrin-based assay, captopril was confirmed as an ArgE inhibitor (IC50 = 58.7 μM; Ki = 37.1 ± 0.85 μM), and a number of phenylboronic acid derivatives were identified as inhibitors, including 4-(diethylamino)phenylboronic acid (IC50 = 50.1 μM). Selected inhibitors were also tested in a thermal shift assay with ArgE using SYPRO Orange dye against Escherichia coli ArgE to observe the stability of the enzyme in the presence of inhibitors (captopril Ki = 35.9 ± 5.1 μM). The active site structure of di-Zn EcArgE was confirmed using X-ray absorption spectroscopy, and we reported two X-ray crystal structures of E. coli ArgE. In summary, we describe the development of a new ninhydrin-based assay for ArgE, the identification of captopril and phenylboronic acids as ArgE inhibitors, thermal shift studies with ArgE + captopril, and the first two published crystal structures of ArgE (mono-Zn and di-Zn).
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Affiliation(s)
- Emma H. Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Jerzy Osipiuk
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- eBERlight, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | | | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Alayna Bland
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Victoria Ehrman
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Andrzej Joachimiak
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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3
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Campbell RP, Whittington AC, Zorio DAR, Miller BG. Recruitment of a Middling Promiscuous Enzyme Drives Adaptive Metabolic Evolution in Escherichia coli. Mol Biol Evol 2023; 40:msad202. [PMID: 37708398 PMCID: PMC10519446 DOI: 10.1093/molbev/msad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
A key step in metabolic pathway evolution is the recruitment of promiscuous enzymes to perform new functions. Despite the recognition that promiscuity is widespread in biology, factors dictating the preferential recruitment of one promiscuous enzyme over other candidates are unknown. Escherichia coli contains four sugar kinases that are candidates for recruitment when the native glucokinase machinery is deleted-allokinase (AlsK), manno(fructo)kinase (Mak), N-acetylmannosamine kinase (NanK), and N-acetylglucosamine kinase (NagK). The catalytic efficiencies of these enzymes are 103- to 105-fold lower than native glucokinases, ranging from 2,400 M-1 s-1 for the most active candidate, NagK, to 15 M-1 s-1 for the least active candidate, AlsK. To investigate the relationship between catalytic activities of promiscuous enzymes and their recruitment, we performed adaptive evolution of a glucokinase-deficient E. coli strain to restore glycolytic metabolism. We observed preferential recruitment of NanK via a trajectory involving early mutations that facilitate glucose uptake and amplify nanK transcription, followed by nonsynonymous substitutions in NanK that enhance the enzyme's promiscuous glucokinase activity. These substitutions reduced the native activity of NanK and reduced organismal fitness during growth on an N-acetylated carbon source, indicating that enzyme recruitment comes at a cost for growth on other substrates. Notably, the two most active candidates, NagK and Mak, were not recruited, suggesting that catalytic activity alone does not dictate evolutionary outcomes. The results highlight our lack of knowledge regarding biological drivers of enzyme recruitment and emphasize the need for a systems-wide approach to identify factors facilitating or constraining this important adaptive process.
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Affiliation(s)
- Ryan P Campbell
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Diego A R Zorio
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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4
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Medina-Carmona E, Gutierrez-Rus LI, Manssour-Triedo F, Newton MS, Gamiz-Arco G, Mota AJ, Reiné P, Cuerva JM, Ortega-Muñoz M, Andrés-León E, Ortega-Roldan JL, Seelig B, Ibarra-Molero B, Sanchez-Ruiz JM. Cell Survival Enabled by Leakage of a Labile Metabolic Intermediate. Mol Biol Evol 2023; 40:7036845. [PMID: 36788592 PMCID: PMC9989741 DOI: 10.1093/molbev/msad032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Many metabolites are generated in one step of a biochemical pathway and consumed in a subsequent step. Such metabolic intermediates are often reactive molecules which, if allowed to freely diffuse in the intracellular milieu, could lead to undesirable side reactions and even become toxic to the cell. Therefore, metabolic intermediates are often protected as protein-bound species and directly transferred between enzyme active sites in multi-functional enzymes, multi-enzyme complexes, and metabolons. Sequestration of reactive metabolic intermediates thus contributes to metabolic efficiency. It is not known, however, whether this evolutionary adaptation can be relaxed in response to challenges to organismal survival. Here, we report evolutionary repair experiments on Escherichia coli cells in which an enzyme crucial for the biosynthesis of proline has been deleted. The deletion makes cells unable to grow in a culture medium lacking proline. Remarkably, however, cell growth is efficiently restored by many single mutations (12 at least) in the gene of glutamine synthetase. The mutations cause the leakage to the intracellular milieu of a highly reactive phosphorylated intermediate common to the biosynthetic pathways of glutamine and proline. This intermediate is generally assumed to exist only as a protein-bound species. Nevertheless, its diffusion upon mutation-induced leakage enables a new route to proline biosynthesis. Our results support that leakage of sequestered metabolic intermediates can readily occur and contribute to organismal adaptation in some scenarios. Enhanced availability of reactive molecules may enable the generation of new biochemical pathways and the potential of mutation-induced leakage in metabolic engineering is noted.
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Affiliation(s)
- Encarnación Medina-Carmona
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain.,School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Luis I Gutierrez-Rus
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Fadia Manssour-Triedo
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Matilda S Newton
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,BioTechnology Institute, University of Minnesota, St Paul, MN
| | - Gloria Gamiz-Arco
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Antonio J Mota
- Departamento de Quimica Inorganica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Pablo Reiné
- Departamento de Quimica Organica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Juan Manuel Cuerva
- Departamento de Quimica Organica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Quimica Organica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina "Lopez Neyra", CSIC, Armilla, Granada, Spain
| | | | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,BioTechnology Institute, University of Minnesota, St Paul, MN
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada, Spain
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5
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Pramanik SK, Das A. Small luminescent molecular probe for developing as assay for alkaline phosphatase. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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6
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Mudi PK, Mahato RK, Joshi M, Paul S, Choudhury AR, Biswas B. Synthesis and structural characterization of a linkage isomer to a mononuclear Nickel(II) complex: Experimental and computational depiction of phosphoesterase efficiency. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019; 37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
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8
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Dong WF, Zhang H, Wang RM, Pan HC. Molecular cloning, antiserum preparation and expression analysis during head regeneration of α-crystallin type heat shock protein in Hydra vulgaris. J Genet 2018; 97:911-924. [PMID: 30262703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Our previous study based on the transcriptome profiling indicated that a fragment of α-crystallin type heat shock protein (α-Hsp) gene was one of the numerous cDNA sequences expressed differentially at various stages of head regeneration in Hydra vulgaris. To further investigate the role that which α-Hsp plays during hydra regeneration, a full-length cDNA of α-Hsp gene of H. vulgaris was isolated by the rapid amplification of cDNA ends (RACE) technique. The full-length cDNA of α-Hsp gene was 1156 bp, containing a 765 bp open-reading frame (ORF), which encodes a polypeptide of 254 amino acid residues with a molecular weight of 29.27 kDa. Further, the ORF was subcloned into the plasmid pET-42a(+), and the recombinant plasmid pET-42a(+)-α- Hsp was transformed to Escherichia coli BL21(DE3), then the fusion protein GST-α-Hsp was expressed mainly in the form of a soluble molecule after induction by isopropyl-β-d-thiogalactopyranoside. In addition, BALB/Cmice were immunized with the fusion protein to prepare the polyclonal antiserum which was used as the primary antibody for whole-mount immunohistochemical assay. The results from the immunohistochemical assay showed that α-Hsp had expressedmainly at the wound site and nearby area of hydra after decapitation operation, and both quantitative real-time polymerase chain reaction (qPCR) analysis and immunohistochemical assay revealed that the expression level of α-Hsp increased gradually during the early period of hydra regeneration, then reached a peak at 24 h after decapitation operation, while decreased during the late regeneration period. Moreover, it indicated an important role of α-Hsp gene in hydra head regeneration that RNA interference (RNAi)-mediated α-Hsp silencing led to the obvious delay of the regeneration of head structures in H. vulgaris. In conclusion, our results gave the hint that α-Hsp could be related to wound healing and tissue remodelling at early regeneration stages, and may lay the foundation for further studies about the physiological function and role of α-Hsp during hydra regeneration.
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Affiliation(s)
- Wen-Fang Dong
- Provincial Key Laboratory of Conservation and Exploitation of Biological Resources in Anhui, Provincial Key Laboratory of Biotic, Environment and Ecological, Safety in Anhui, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui Province, People's Republic of China.
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9
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Dong WF, Zhang H, Wang RM, Pan HC. Molecular cloning, antiserum preparation and expression analysis during head regeneration of
$$\upalpha $$
α
-crystallin type heat shock protein in Hydra vulgaris. J Genet 2018. [DOI: 10.1007/s12041-018-0982-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Proc Natl Acad Sci U S A 2018; 115:E7293-E7302. [PMID: 30012610 DOI: 10.1073/pnas.1607817115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme-substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate (βleavinggroup from -1.08 to -0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.
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11
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Bouzon M, Perret A, Loreau O, Delmas V, Perchat N, Weissenbach J, Taran F, Marlière P. A Synthetic Alternative to Canonical One-Carbon Metabolism. ACS Synth Biol 2017; 6:1520-1533. [PMID: 28467058 DOI: 10.1021/acssynbio.7b00029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One-carbon metabolism is an ubiquitous metabolic pathway that encompasses the reactions transferring formyl-, hydroxymethyl- and methyl-groups bound to tetrahydrofolate for the synthesis of purine nucleotides, thymidylate, methionine and dehydropantoate, the precursor of coenzyme A. An alternative cyclic pathway was designed that substitutes 4-hydroxy-2-oxobutanoic acid (HOB), a compound absent from known metabolism, for the amino acids serine and glycine as one-carbon donors. It involves two novel reactions, the transamination of l-homoserine and the transfer of a one-carbon unit from HOB to tetrahydrofolate releasing pyruvate as coproduct. Since canonical reactions regenerate l-homoserine from pyruvate by carboxylation and subsequent reduction, every one-carbon moiety made available for anabolic reactions originates from CO2. The HOB-dependent pathway was established in an Escherichia coli auxotroph selected for prototrophy using long-term cultivation protocols. Genetic, metabolic and biochemical evidence support the emergence of a functional HOB-dependent one-carbon pathway achieved with the recruitment of the two enzymes l-homoserine transaminase and HOB-hydroxymethyltransferase and of HOB as an essential metabolic intermediate. Escherichia coli biochemical reprogramming was achieved by minimally altering canonical metabolism and leveraging on natural selection mechanisms, thereby launching the resulting strain on an evolutionary trajectory diverging from all known extant species.
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Affiliation(s)
- Madeleine Bouzon
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Alain Perret
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Valérie Delmas
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Nadia Perchat
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | - Jean Weissenbach
- CEA, Genoscope, 2 rue Gaston
Crémieux, 91000 Evry, France
- CNRS UMR8030 Génomique Métabolique, 2 rue Gaston Crémieux, 91000 Evry, France
- Université Evry Val d’Essone, 91000 Evry, France
- Université Paris-Saclay, 91000 Evry, France
| | | | - Philippe Marlière
- Institute of Systems and Synthetic Biology, Génopole, 5 rue Desbruères, 91030 Evry Cedex, France
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12
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Applied evolutionary theories for engineering of secondary metabolic pathways. Curr Opin Chem Biol 2016; 35:133-141. [PMID: 27736648 DOI: 10.1016/j.cbpa.2016.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 11/20/2022]
Abstract
An expanded definition of 'secondary metabolism' is emerging. Once the exclusive provenance of naturally occurring organisms, evolved over geological time scales, secondary metabolism increasingly encompasses molecules generated via human engineered biocatalysts and biosynthetic pathways. Many of the tools and strategies for enzyme and pathway engineering can find origins in evolutionary theories. This perspective presents an overview of selected proposed evolutionary strategies in the context of engineering secondary metabolism. In addition to the wealth of biocatalysts provided via secondary metabolic pathways, improving the understanding of biosynthetic pathway evolution will provide rich resources for methods to adapt to applied laboratory evolution.
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13
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Newton MS, Arcus VL, Patrick WM. Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. J R Soc Interface 2016; 12:rsif.2015.0036. [PMID: 25926697 DOI: 10.1098/rsif.2015.0036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks.
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Affiliation(s)
- Matilda S Newton
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Vickery L Arcus
- School of Biology, University of Waikato, Hamilton, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Colin PY, Kintses B, Gielen F, Miton CM, Fischer G, Mohamed MF, Hyvönen M, Morgavi DP, Janssen DB, Hollfelder F. Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun 2015; 6:10008. [PMID: 26639611 PMCID: PMC4686663 DOI: 10.1038/ncomms10008] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/25/2015] [Indexed: 12/25/2022] Open
Abstract
Unculturable bacterial communities provide a rich source of biocatalysts, but their experimental discovery by functional metagenomics is difficult, because the odds are stacked against the experimentor. Here we demonstrate functional screening of a million-membered metagenomic library in microfluidic picolitre droplet compartments. Using bait substrates, new hydrolases for sulfate monoesters and phosphotriesters were identified, mostly based on promiscuous activities presumed not to be under selection pressure. Spanning three protein superfamilies, these break new ground in sequence space: promiscuity now connects enzymes with only distantly related sequences. Most hits could not have been predicted by sequence analysis, because the desired activities have never been ascribed to similar sequences, showing how this approach complements bioinformatic harvesting of metagenomic sequencing data. Functional screening of a library of unprecedented size with excellent assay sensitivity has been instrumental in identifying rare genes constituting catalytically versatile hubs in sequence space as potential starting points for the acquisition of new functions.
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Affiliation(s)
- Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Balint Kintses
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte M Miton
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Mark F Mohamed
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Diego P Morgavi
- INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle, France.,Clermont Université, VetAgro Sup, UMR Herbivores, BP 10448, F-63000 Clermont-Ferrand, France
| | - Dick B Janssen
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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15
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Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. The Classification and Evolution of Enzyme Function. Biophys J 2015; 109:1082-6. [PMID: 25986631 DOI: 10.1016/j.bpj.2015.04.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/30/2022] Open
Abstract
Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.
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Affiliation(s)
- Sergio Martínez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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Liu C, Zhu J, Li Y, Zhang J, Lu C, Wang H, Shen Y. In Vitro Reconstitution of a PKS Pathway for the Biosynthesis of Galbonolides inStreptomycessp. LZ35. Chembiochem 2015; 16:998-1007. [DOI: 10.1002/cbic.201500017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Indexed: 01/13/2023]
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Araki M, Cox RS, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A. M-path: a compass for navigating potential metabolic pathways. Bioinformatics 2014; 31:905-11. [DOI: 10.1093/bioinformatics/btu750] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chai J, Kora G, Ahn TH, Hyatt D, Pan C. Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. BMC Evol Biol 2014; 14:207. [PMID: 25293379 PMCID: PMC4194380 DOI: 10.1186/s12862-014-0207-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/22/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. RESULTS A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. CONCLUSIONS Our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.
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Affiliation(s)
- Juanjuan Chai
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Guruprasad Kora
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Tae-Hyuk Ahn
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Doug Hyatt
- />BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />Joint Institute for Biological Sciences, University of Tennessee, Knoxville TN, USA
| | - Chongle Pan
- />Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Aerobic biodegradation of 2,4-Dinitroanisole by Nocardioides sp. strain JS1661. Appl Environ Microbiol 2014; 80:7725-31. [PMID: 25281383 DOI: 10.1128/aem.02752-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,4-Dinitroanisole (DNAN) is an insensitive munition ingredient used in explosive formulations as a replacement for 2,4,6-trinitrotoluene (TNT). Little is known about the environmental behavior of DNAN. There are reports of microbial transformation to dead-end products, but no bacteria with complete biodegradation capability have been reported. Nocardioides sp. strain JS1661 was isolated from activated sludge based on its ability to grow on DNAN as the sole source of carbon and energy. Enzyme assays indicated that the first reaction involves hydrolytic release of methanol to form 2,4-dinitrophenol (2,4-DNP). Growth yield and enzyme assays indicated that 2,4-DNP underwent subsequent degradation by a previously established pathway involving formation of a hydride-Meisenheimer complex and release of nitrite. Identification of the genes encoding the key enzymes suggested recent evolution of the pathway by recruitment of a novel hydrolase to extend the well-characterized 2,4-DNP pathway.
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Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res 2014; 42:W389-94. [PMID: 24792156 PMCID: PMC4086079 DOI: 10.1093/nar/gku362] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring, however, the vast possibility of pathways amenable to engineering through heterologous genes expression in a chassis organism is complex and unattainable manually. Here, we present XTMS, a web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity and enzyme efficiency. By answering such critical design points, XTMS not only paves the road toward the rationalization of metabolic engineering, but also opens new processing possibilities for non-natural metabolites and novel enzymatic transformations.
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Affiliation(s)
- Pablo Carbonell
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Pierre Parutto
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Joan Herisson
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | | | - Jean-Loup Faulon
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
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