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McNaught KJ, Kuatsjah E, Zahn M, Prates ÉT, Shao H, Bentley GJ, Pickford AR, Gruber JN, Hestmark KV, Jacobson DA, Poirier BC, Ling C, San Marchi M, Michener WE, Nicora CD, Sanders JN, Szostkiewicz CJ, Veličković D, Zhou M, Munoz N, Kim YM, Magnuson JK, Burnum-Johnson KE, Houk KN, McGeehan JE, Johnson CW, Beckham GT. Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440. Metab Eng 2023; 76:193-203. [PMID: 36796578 DOI: 10.1016/j.ymben.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both the engineering of bacterial hosts to produce fatty acid-derived molecules and the development of new antibiotics. However, gaps in our understanding of the initiation of fatty acid biosynthesis remain. Here, we demonstrate that the industrially relevant microbe Pseudomonas putida KT2440 contains three distinct pathways to initiate fatty acid biosynthesis. The first two routes employ conventional β-ketoacyl-ACP synthase III enzymes, FabH1 and FabH2, that accept short- and medium-chain-length acyl-CoAs, respectively. The third route utilizes a malonyl-ACP decarboxylase enzyme, MadB. A combination of exhaustive in vivo alanine-scanning mutagenesis, in vitro biochemical characterization, X-ray crystallography, and computational modeling elucidate the presumptive mechanism of malonyl-ACP decarboxylation via MadB. Given that functional homologs of MadB are widespread throughout domain Bacteria, this ubiquitous alternative fatty acid initiation pathway provides new opportunities to target a range of biotechnology and biomedical applications.
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Affiliation(s)
- Kevin J McNaught
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Érica T Prates
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Huiling Shao
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Gayle J Bentley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Josephine N Gruber
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelley V Hestmark
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Daniel A Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Brenton C Poirier
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Myrsini San Marchi
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Caralyn J Szostkiewicz
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nathalie Munoz
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Young-Mo Kim
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jon K Magnuson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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Klocko AD, Summers CA, Glover ML, Parrish R, Storck WK, McNaught KJ, Moss ND, Gotting K, Stewart A, Morrison AM, Payne L, Hatakeyama S, Selker EU. Selection and Characterization of Mutants Defective in DNA Methylation in Neurospora crassa. Genetics 2020; 216:671-688. [PMID: 32873602 PMCID: PMC7648584 DOI: 10.1534/genetics.120.303471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 01/05/2023] Open
Abstract
DNA methylation, a prototypical epigenetic modification implicated in gene silencing, occurs in many eukaryotes and plays a significant role in the etiology of diseases such as cancer. The filamentous fungus Neurospora crassa places DNA methylation at regions of constitutive heterochromatin such as in centromeres and in other A:T-rich regions of the genome, but this modification is dispensable for normal growth and development. This and other features render N. crassa an excellent model to genetically dissect elements of the DNA methylation pathway. We implemented a forward genetic selection on a massive scale, utilizing two engineered antibiotic-resistance genes silenced by DNA methylation, to isolate mutants d efective i n m ethylation (dim). Hundreds of potential mutants were characterized, yielding a rich collection of informative alleles of 11 genes important for DNA methylation, most of which were already reported. In parallel, we characterized the pairwise interactions in nuclei of the DCDC, the only histone H3 lysine 9 methyltransferase complex in Neurospora, including those between the DIM-5 catalytic subunit and other complex members. We also dissected the N- and C-termini of the key protein DIM-7, required for DIM-5 histone methyltransferase localization and activation. Lastly, we identified two alleles of a novel gene, dim-10 - a homolog of Clr5 in Schizosaccharomyces pombe - that is not essential for DNA methylation, but is necessary for repression of the antibiotic-resistance genes used in the selection, which suggests that both DIM-10 and DNA methylation promote silencing of constitutive heterochromatin.
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Affiliation(s)
- Andrew D Klocko
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Calvin A Summers
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Marissa L Glover
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Robert Parrish
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - William K Storck
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Nicole D Moss
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kirsten Gotting
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Aurelian Stewart
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Ariel M Morrison
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Laurel Payne
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Shin Hatakeyama
- Laboratory of Genetics, Faculty of Science, Shimo-ohkubo 255, Saitama University, Sakura-ward, 338-8570, JAPAN
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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Jamieson K, Wiles ET, McNaught KJ, Sidoli S, Leggett N, Shao Y, Garcia BA, Selker EU. Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome Res 2015; 26:97-107. [PMID: 26537359 PMCID: PMC4691754 DOI: 10.1101/gr.194555.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 11/04/2015] [Indexed: 12/25/2022]
Abstract
Methylated lysine 27 on histone H3 (H3K27me) marks repressed “facultative heterochromatin,” including developmentally regulated genes in plants and animals. The mechanisms responsible for localization of H3K27me are largely unknown, perhaps in part because of the complexity of epigenetic regulatory networks. We used a relatively simple model organism bearing both facultative and constitutive heterochromatin, Neurospora crassa, to explore possible interactions between elements of heterochromatin. In higher eukaryotes, reductions of H3K9me3 and DNA methylation in constitutive heterochromatin have been variously reported to cause redistribution of H3K27me3. In Neurospora, we found that elimination of any member of the DCDC H3K9 methylation complex caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3, while regions that are normally marked by H3K9me3 became methylated at H3K27. Elimination of DNA methylation had no obvious effect on the distribution of H3K27me. Elimination of HP1, which “reads” H3K9me3, also caused major changes in the distribution of H3K27me, indicating that HP1 is important for normal localization of facultative heterochromatin. Because loss of HP1 caused redistribution of H3K27me2/3, but not H3K9me3, these normally nonoverlapping marks became superimposed. Indeed, mass spectrometry revealed substantial cohabitation of H3K9me3 and H3K27me2 on H3 molecules from an hpo strain. Loss of H3K27me machinery (e.g., the methyltransferase SET-7) did not impact constitutive heterochromatin but partially rescued the slow growth of the DCDC mutants, suggesting that the poor growth of these mutants is partly attributable to ectopic H3K27me. Altogether, our findings with Neurospora clarify interactions of facultative and constitutive heterochromatin in eukaryotes.
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Affiliation(s)
- Kirsty Jamieson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Elizabeth T Wiles
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics and the Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA
| | - Neena Leggett
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Yanchun Shao
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics and the Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
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