Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
15 Oct 2024
Historique:
received: 15 04 2024
accepted: 03 10 2024
medline: 16 10 2024
pubmed: 16 10 2024
entrez: 15 10 2024
Statut: epublish

Résumé

Promiscuous enzymes often serve as the starting point for the evolution of novel functions. Yet, the extent to which the promiscuity of an individual enzyme can be harnessed several times independently for different purposes during evolution is poorly reported. Here, we present a case study illustrating how NAD(P)

Identifiants

pubmed: 39406738
doi: 10.1038/s41467-024-53156-x
pii: 10.1038/s41467-024-53156-x
doi:

Substances chimiques

Succinate-Semialdehyde Dehydrogenase EC 1.2.1.24
Pyridoxal Phosphate 5V5IOJ8338
Escherichia coli Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

8898

Subventions

Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 862087
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 862087

Informations de copyright

© 2024. The Author(s).

Références

Khersonsky, O. & Tawfik, D. S. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem. 79, 471–505 (2010).
doi: 10.1146/annurev-biochem-030409-143718
Copley, S. D., Newton, M. S. & Widney, K. A. How to recruit a promiscuous enzyme to serve a new function. Biochemistry 62, 300–308 (2023).
doi: 10.1021/acs.biochem.2c00249
Kirchberger, P. C., Schmidt, M. L. & Ochman, H. The ingenuity of bacterial genomes. Annu. Rev. Microbiol. 74, 815–834 (2020).
doi: 10.1146/annurev-micro-020518-115822
Näsvall, J., Sun, L., Roth, J. R. & Andersson, D. I. Real-time evolution of new genes by innovation, amplification, and divergence. Science 338, 384–387 (2012).
doi: 10.1126/science.1226521
Kim, J. et al. Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc. Natl Acad. Sci. USA 116, 24164–24173 (2019).
doi: 10.1073/pnas.1915569116
Cotton, C. A. et al. Underground isoleucine biosynthesis pathways in E. coli. eLife 9, e54207 (2020).
doi: 10.7554/eLife.54207
Pontrelli, S. et al. Metabolic repair through emergence of new pathways in Escherichia coli. Nat. Chem. Biol. 14, 1005–1009 (2018).
doi: 10.1038/s41589-018-0149-6
Fuhrer, T., Chen, L., Sauer, U. & Vitkup, D. Computational prediction and experimental verification of the gene encoding the NAD
doi: 10.1128/JB.01027-07
Shortall, K., Djeghader, A., Magner, E. & Soulimane, T. Insights into aldehyde dehydrogenase enzymes: a structural perspective. Front. Mol. Biosci. 8, 659550 (2021).
Donnelly, M. I. & Cooper, R. A. Two succinic semialdehyde dehydrogenases are induced when Escherichia coli K-12 Is grown on γ-aminobutyrate. J. Bacteriol. 145, 1425–1427 (1981).
doi: 10.1128/jb.145.3.1425-1427.1981
Park, J. & Rhee, S. Structural basis for a cofactor-dependent oxidation protection and catalysis of cyanobacterial succinic semialdehyde dehydrogenase. J. Biol. Chem. 288, 15760–15770 (2013).
doi: 10.1074/jbc.M113.460428
Donnelly, M. I. & Cooper, R. A. Succinic Semialdehyde Dehydrogenases of Escherichia coli. Eur. J. Biochem. 113, 555–561 (1981).
doi: 10.1111/j.1432-1033.1981.tb05098.x
Kurihara, S., Kato, K., Asada, K., Kumagai, H. & Suzuki, H. A Putrescine-Inducible Pathway Comprising PuuE-YneI in Which γ-Aminobutyrate Is Degraded into Succinate in Escherichia coli K-12. J. Bacteriol. 192, 4582–4591 (2010).
doi: 10.1128/JB.00308-10
Knorr, S. et al. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat. Commun. 9, 5071 (2018).
doi: 10.1038/s41467-018-07563-6
Zhang, M. et al. Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat. Commun. 9, 2114 (2018).
doi: 10.1038/s41467-018-04513-0
Zhang, S. & Bryant, D. A. The tricarboxylic acid cycle in cyanobacteria. Science 334, 1551–1553 (2011).
doi: 10.1126/science.1210858
Lee, H. H. C., McGinty, G. E., Pearl, P. L. & Rotenberg, A. Understanding the molecular mechanisms of succinic semialdehyde dehydrogenase deficiency (SSADHD): Towards the development of SSADH-targeted medicine. Int. J. Mol. Sci. 23, 2606 (2022).
doi: 10.3390/ijms23052606
Toyokura, K. et al. Succinic semialdehyde dehydrogenase is involved in the robust patterning of arabidopsis leaves along the adaxial–abaxial axis. Plant Cell Physiol. 52, 1340–1353 (2011).
doi: 10.1093/pcp/pcr079
Bouché, N., Fait, A., Bouchez, D., Møller, S. G. & Fromm, H. Mitochondrial succinic-semialdehyde dehydrogenase of the γ-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. Proc. Natl Acad. Sci. USA 100, 6843–6848 (2003).
doi: 10.1073/pnas.1037532100
Fitzpatrick, T. B. et al. Two independent routes of de novo vitamin B
doi: 10.1042/BJ20070765
Rosenberg, J., Ischebeck, T. & Commichau, F. M. Vitamin B6 metabolism in microbes and approaches for fermentative production. Biotechnol. Adv. 35, 31–40 (2017).
doi: 10.1016/j.biotechadv.2016.11.004
Percudani, R. & Peracchi, A. A genomic overview of pyridoxal-phosphate-dependent enzymes. EMBO Rep. 4, 850–854 (2003).
doi: 10.1038/sj.embor.embor914
Tramonti, A. et al. Knowns and unknowns of vitamin B
doi: 10.1128/ecosalplus.ESP-0004-2021
Zhao, G., Pease, A. J., Bharani, N. & Winkler, M. E. Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5’-phosphate biosynthesis. J. Bacteriol. 177, 2804–2812 (1995).
doi: 10.1128/jb.177.10.2804-2812.1995
Yang, Y., Zhao, G., Man, T.-K. & Winkler, M. E. Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. J. Bacteriol. 180, 4294–4299 (1998).
doi: 10.1128/JB.180.16.4294-4299.1998
Jensen, S. I., Lennen, R. M., Herrgard, M. J. & Nielsen, A. T. Seven gene deletions in seven days: fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Sci. Rep. 5, 17874 (2015).
doi: 10.1038/srep17874
Richts, B. & Commichau, F. M. Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis. Appl. Microbiol. Biotechnol. 105, 2297–2305 (2021).
doi: 10.1007/s00253-021-11199-w
Barrick, J. E. et al. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genom. 15, 1039 (2014).
doi: 10.1186/1471-2164-15-1039
Kuznetsova, E. et al. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281, 36149–36161 (2006).
doi: 10.1074/jbc.M605449200
Davidi, D., Longo, L. M., Jablonska, J., Milo, R. & Tawfik, D. S. A bird’s-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations. Chem. Rev. 118, 8786–8797 (2018).
doi: 10.1021/acs.chemrev.8b00039
Park, J. O. et al. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat. Chem. Biol. 12, 482–489 (2016).
doi: 10.1038/nchembio.2077
Nöh, K. et al. Metabolic flux analysis at ultra short time scale: Isotopically non-stationary
doi: 10.1016/j.jbiotec.2006.11.015
Boschi-Muller, S., Azza, S., Pollastro, D., Corbier, C. & Branlant, G. Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase. J. Biol. Chem. 272, 15106–15112 (1997).
doi: 10.1074/jbc.272.24.15106
Kim, J., Kershner, J. P., Novikov, Y., Shoemaker, R. K. & Copley, S. D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis. Mol. Syst. Biol. 6, 436 (2010).
doi: 10.1038/msb.2010.88
Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Escherichia coli ‘Marionette’ strains with 12 highly optimized small-molecule sensors. Nat. Chem. Biol. 15, 196–204 (2019).
doi: 10.1038/s41589-018-0168-3
Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I
doi: 10.1093/nar/25.6.1203
Schuster, L. A. & Reisch, C. R. Plasmids for controlled and tunable high-level expression in E. coli. Appl. Environ. Microbiol. 88, e00939–22 (2022).
doi: 10.1128/aem.00939-22
Bennett, B. D. et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593–599 (2009).
doi: 10.1038/nchembio.186
Kim, J. & Copley, S. D. Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc. Natl Acad. Sci. USA 109, E2856–E2864 (2012).
doi: 10.1073/pnas.1208509109
Scheffen, M. et al. A new-to-nature carboxylation module to improve natural and synthetic CO
doi: 10.1038/s41929-020-00557-y
Aslan, S., Noor, E., Vaquerizo, S. B., Lindner, S. N. & Bar-Even, A. Design and engineering of E. coli metabolic sensor strains with a wide sensitivity range for glycerate. Metab. Eng. 57, 96–109 (2020).
doi: 10.1016/j.ymben.2019.09.002
Starai, V. J. & Escalante-Semerena, J. C. Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica. J. Mol. Biol. 340, 1005–1012 (2004).
doi: 10.1016/j.jmb.2004.05.010
Gao, Y. et al. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Res. 49, 9696–9710 (2021).
doi: 10.1093/nar/gkab735
Rodionova, I. A. et al. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Sci. Rep. 12, 7274 (2022).
doi: 10.1038/s41598-022-11134-7
Gagarinova, A. et al. Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli. Nat. Commun. 13, 4085 (2022).
doi: 10.1038/s41467-022-31819-x
Baugh, A. C., Momany, C. & Neidle, E. L. Versatility and complexity: common and uncommon facets of LysR-type transcriptional regulators. Annu. Rev. Microbiol. 77, 317–339 (2023).
doi: 10.1146/annurev-micro-050323-040543
Matilla, M. A., Velando, F., Martín-Mora, D., Monteagudo-Cascales, E. & Krell, T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol. Rev. 46, fuab043 (2022).
doi: 10.1093/femsre/fuab043
Mayo-Pérez, S., Gama-Martínez, Y., Dávila, S., Rivera, N. & Hernández-Lucas, I. LysR-type transcriptional regulators: state of the art. Crit. Rev. Microbiol. 0, 1–33 (2023).
Cozzani, I., Fazio, A. M., Felici, E. & Barletta, G. Separation and characterization of NAD- and NADP-specific succinate-semialdehyde dehydrogenase from Escherichia coli K-12 3300. Biochim. Biophys. Acta BBA Enzymol. 613, 309–317 (1980).
doi: 10.1016/0005-2744(80)90085-6
Kopečná, M. et al. The ALDH21 gene found in lower plants and some vascular plants codes for a NADP
doi: 10.1111/tpj.13648
Blank, D., Wolf, L., Ackermann, M. & Silander, O. K. The predictability of molecular evolution during functional innovation. Proc. Natl Acad. Sci. USA 111, 3044–3049 (2014).
doi: 10.1073/pnas.1318797111
Brunner, N. A., Brinkmann, H., Siebers, B. & Hensel, R. NAD
doi: 10.1074/jbc.273.11.6149
Eisenberg, P. et al. The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN is a potential new drug target in Streptococcus pyogenes. Front. Microbiol. 13, 802427 (2022).
Habenicht, A., Hellman, U. & Cerff, R. Non-phosphorylating GAPDH of higher plants is a member of the aldehyde dehydrogenase superfamily with no sequence homology to phosphorylating GAPDH. J. Mol. Biol. 237, 165–171 (1994).
doi: 10.1006/jmbi.1994.1217
Denise, R., Babor, J., Gerlt, J. A. & de Crécy-Lagard, V. Pyridoxal 5’-phosphate synthesis and salvage in bacteria and archaea: predicting pathway variant distributions and holes. Microb. Genom. 9, 000926 (2023).
Helsen, J. et al. Gene loss predictably drives evolutionary adaptation. Mol. Biol. Evol. 37, 2989–3002 (2020).
doi: 10.1093/molbev/msaa172
Kim, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat. Chem. Biol. 16, 538–545 (2020).
doi: 10.1038/s41589-020-0473-5
Wu, T. et al. Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli. Nat. Commun. 14, 8490 (2023).
doi: 10.1038/s41467-023-44247-2
Williams, J. F., Blackmore, P. F., Duke, C. C. & MacLeod, J. K. Fact, uncertainty and speculation concening the biochemistry of D-erythrose-4-phosphate and its metabolic roles. Int. J. Biochem. 12, 339–344 (1980).
doi: 10.1016/0020-711X(80)90112-3
Serianni, A. S., Clark, E. L. & Barker, R. Carbon-13-enriched carbohydrates. Preparation of erythrose, threose, glyceraldehyde, and glycolaldehyde with
doi: 10.1016/S0008-6215(00)83925-7
Wenk, S., Yishai, O., Lindner, S. N. & Bar-Even, A. An engineering approach for rewiring microbial metabolism. In Methods in Enzymology, Vol. 608 329–367 (Academic Press, 2018).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA. 97, 6640–6645 (2000).
doi: 10.1073/pnas.120163297
Krueger, F., James, F., Ewels, P., Afyounian, E. & Schuster-Boeckler, B. FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo. Zenodo https://doi.org/10.5281/zenodo.5127899 (2021).
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. In Engineering and Analyzing Multicellular Systems (eds. Sun, L. & Shou, W.) vol. 1151 165–188 (Springer New York, New York, NY, 2014).
Kabsch, W. XDS. Acta Crystallogr. D. Biol. Crystallogr. 66, 125–132 (2010).
doi: 10.1107/S0907444909047337
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Zheng, H. et al. Structure and activity of the NAD(P)
doi: 10.1002/prot.24227
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Volkmer, B. & Heinemann, M. Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PLoS ONE 6, e23126 (2011).
doi: 10.1371/journal.pone.0023126
Milo, R., Jorgensen, P., Moran, U., Weber, G. & Springer, M. BioNumbers—the database of key numbers in molecular and cell biology. Nucleic Acids Res. 38, D750–D753 (2010).
doi: 10.1093/nar/gkp889
Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41–44 (2020).
doi: 10.1038/s41592-019-0638-x
The UniProt Consortium. et al. UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2023).
doi: 10.1093/nar/gkac1052
Ahrné, E., Molzahn, L., Glatter, T. & Schmidt, A. Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 13, 2567–2578 (2013).
doi: 10.1002/pmic.201300135
Glatter, T. et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11, 5145–5156 (2012).
doi: 10.1021/pr300273g
He, H. Evolutionary trajectories to recruit a promiscuous enzyme for a new function, Created in BioRender. BioRender.com/n42z674 (2024).
Monterrubio, R., Baldoma, L., Obradors, N., Aguilar, J. & Badia, J. A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli. J. Bacteriol. 182, 2672–2674 (2000).
doi: 10.1128/JB.182.9.2672-2674.2000

Auteurs

Hai He (H)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. hai.he@mpi-marburg.mpg.de.

Paul A Gómez-Coronado (PA)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Jan Zarzycki (J)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Sebastian Barthel (S)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Jörg Kahnt (J)

Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Peter Claus (P)

Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Moritz Klein (M)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Melanie Klose (M)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Valérie de Crécy-Lagard (V)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
Genetic Institute, University of Florida, Gainesville, FL, USA.

Daniel Schindler (D)

MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany.

Nicole Paczia (N)

Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Timo Glatter (T)

Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Tobias J Erb (TJ)

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. toerb@mpi-marburg.mpg.de.
LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany. toerb@mpi-marburg.mpg.de.

Articles similaires

T-Lymphocytes, Regulatory Lung Neoplasms Proto-Oncogene Proteins p21(ras) Animals Humans

Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis.

Spencer D Shelton, Sara House, Luiza Martins Nascentes Melo et al.
1.00
DNA, Mitochondrial Humans Melanoma Mutation Neoplasm Metastasis

Prevalence and implications of fragile X premutation screening in Thailand.

Areerat Hnoonual, Sunita Kaewfai, Chanin Limwongse et al.
1.00
Humans Fragile X Mental Retardation Protein Thailand Male Female
Humans Receptors, Antigen, T-Cell Proto-Oncogene Proteins p21(ras) Pancreatic Neoplasms T-Lymphocytes

Classifications MeSH