1
|
Wang R, Li X, Lv F, He J, Lv R, Wei L. Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems. Microbiol Res 2024; 282:127649. [PMID: 38402727 DOI: 10.1016/j.micres.2024.127649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.
Collapse
Affiliation(s)
- Ruiqing Wang
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China.
| | - Xinsheng Li
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi Province 330200, PR China
| | - Fengjuan Lv
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Junhai He
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Rujie Lv
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China
| | - Lingen Wei
- Soil Fertilizer and Resource Environment Institute, Jiangxi Academy of Agricultural Sciences, No. 602, Nanlian Road, Nanchang, Jiangxi Province 330200, PR China; Key Laboratory of Crop Ecophysiology and Farming System for the Middle and Lower Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, PR China; National Engineering Technology Research Center for Red Soil Improvement, PR China; National Agricultural Experimental Station for Agricultural Environment Yichun, PR China.
| |
Collapse
|
2
|
Romanowski SB, Lee S, Kunakom S, Paulo BS, Recchia MJJ, Liu DY, Cavanagh H, Linington RG, Eustáquio AS. Identification of the lipodepsipeptide selethramide encoded in a giant nonribosomal peptide synthetase from a Burkholderia bacterium. Proc Natl Acad Sci U S A 2023; 120:e2304668120. [PMID: 37812712 PMCID: PMC10589681 DOI: 10.1073/pnas.2304668120] [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: 03/21/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023] Open
Abstract
Bacterial natural products have found many important industrial applications. Yet traditional discovery pipelines often prioritize individual natural product families despite the presence of multiple natural product biosynthetic gene clusters in each bacterial genome. Systematic characterization of talented strains is a means to expand the known natural product space. Here, we report genomics, epigenomics, and metabolomics studies of Burkholderia sp. FERM BP-3421, a soil isolate and known producer of antitumor spliceostatins. Its genome is composed of two chromosomes and two plasmids encoding at least 29 natural product families. Metabolomics studies showed that FERM BP-3421 also produces antifungal aminopyrrolnitrin and approved anticancer romidepsin. From the orphan metabolome features, we connected a lipopeptide of 1,928 Da to an 18-module nonribosomal peptide synthetase encoded as a single gene in chromosome 1. Isolation and structure elucidation led to the identification of selethramide which contains a repeating pattern of serine and leucine and is cyclized at the side chain oxygen of the one threonine residue at position 13. A (R)-3-hydroxybutyric acid moiety decorates the N-terminal serine. Initial attempts to obtain deletion mutants to probe the role of selethramide failed. After acquiring epigenome (methylome) data for FERM BP-3421, we employed a mimicry by methylation strategy that improved DNA transfer efficiency. Mutants defective in selethramide biosynthesis showed reduced surfactant activity and impaired swarming motility that could be chemically complemented with selethramide. This work unveils a lipopeptide that promotes surface motility, establishes improved DNA transfer efficiency, and sets the stage for continued natural product identification from a prolific strain.
Collapse
Affiliation(s)
- Sean B. Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL60607
| | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5H 1S6, Canada
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL60607
| | - Bruno S. Paulo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL60607
| | | | - Dennis Y. Liu
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5H 1S6, Canada
| | - Hannah Cavanagh
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5H 1S6, Canada
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5H 1S6, Canada
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL60607
| |
Collapse
|
3
|
Zhou Y, Wei Y, Jiang L, Zhang Y, Jiao X. A ( S)-3-Hydroxybutyrate Dehydrogenase Belonging to the 3-Hydroxyacyl-CoA Dehydrogenase Family Facilitates Hydroxyacid Degradation in Anaerobic Bacteria. Appl Environ Microbiol 2023; 89:e0036623. [PMID: 37255440 PMCID: PMC10305046 DOI: 10.1128/aem.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Ketone bodies, including acetoacetate, 3-hydroxybutyrate, and acetone, are produced in the liver of animals during glucose starvation. Enzymes for the metabolism of (R)-3-hydroxybutyrate have been extensively studied, but little is known about the metabolism of its enantiomer (S)-3-hydroxybutyrate. Here, we report the characterization of a novel pathway for the degradation of (S)-3-hydroxybutyrate in anaerobic bacteria. We identify and characterize a stereospecific (S)-3-hydroxylbutyrate dehydrogenase (3SHBDH) from Desulfotomaculum ruminis, which catalyzes the reversible NAD(P)H-dependent reduction of acetoacetate to form (S)-3-hydroxybutyrate. 3SHBDH also catalyzes oxidation of d-threonine (2R, 3S) and l-allo-threonine (2S, 3S), consistent with its specificity for β-(3S)-hydroxy acids. Isothermal calorimetry experiments support a sequential mechanism involving binding of NADH prior to (S)-3-hydroxybutyrate. Homologs of 3SHBDH are present in anaerobic fermenting and sulfite-reducing bacteria, and experiments with Clostridium pasteurianum showed that 3SHBDH, acetate CoA-transferase (YdiF), and (S)-3-hydroxybutyryl-CoA dehydrogenase (Hbd) are involved together in the degradation of (S)-3-hydroxybutyrate as a carbon and energy source for growth. (S)-3-hydroxybutyrate is a human metabolic marker and a chiral precursor for chemical synthesis, suggesting potential applications of 3SHBDH in diagnostics or the chemicals industry. IMPORTANCE (R)-3-hydroxybutyrate is well studied as a component of ketone bodies produced by the liver and of bacterial polyesters. However, the biochemistry of its enantiomer (S)-3-hydroxybutyrate is poorly understood. This study describes the identification and characterization of a stereospecific (S)-3-hydroxylbutyrate dehydrogenase and its function in a metabolic pathway for the degradation of (S)-3-hydroxybutyrate as a carbon and energy source in anaerobic bacteria. (S)-3-hydroxybutyrate is a mammalian metabolic marker and a precursor for chemical synthesis and bioplastics, suggesting potential applications of these enzymes in diagnostics and biotechnology.
Collapse
Affiliation(s)
- Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality (Ministry of Agriculture of China), Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality (Ministry of Agriculture of China), Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| |
Collapse
|
4
|
Olavarria K, Pijman YO, Cabrera R, van Loosdrecht MCM, Wahl SA. Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions. Sci Rep 2022; 12:3757. [PMID: 35260659 PMCID: PMC8904767 DOI: 10.1038/s41598-022-07663-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories.
Collapse
Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH, Wageningen, The Netherlands.
| | - Yared O Pijman
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| |
Collapse
|
5
|
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nat Biotechnol 2022; 40:335-344. [DOI: 10.1038/s41587-021-01195-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
|
6
|
Dong H, Chang MCY. Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hongjun Dong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720-3200, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
| |
Collapse
|
7
|
Orrego AH, Andrés-Sanz D, Velasco-Lozano S, Sanchez-Costa M, Berenguer J, Guisan JM, Rocha-Martin J, López-Gallego F. Self-sufficient asymmetric reduction of β-ketoesters catalysed by a novel and robust thermophilic alcohol dehydrogenase co-immobilised with NADH. Catal Sci Technol 2021; 11:3217-3230. [PMID: 34094502 PMCID: PMC8111925 DOI: 10.1039/d1cy00268f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/04/2022]
Abstract
β-Hydroxyesters are essential building blocks utilised by the pharmaceutical and food industries in the synthesis of functional products. Beyond the conventional production methods based on chemical catalysis or whole-cell synthesis, the asymmetric reduction of β-ketoesters with cell-free enzymes is gaining relevance. To this end, a novel thermophilic (S)-3-hydroxybutyryl-CoA dehydrogenase from Thermus thermophilus HB27 (Tt27-HBDH) has been expressed, purified and biochemically characterised, determining its substrate specificity towards β-ketoesters and its dependence on NADH as a cofactor. The immobilization of Tt27-HBDH on agarose macroporous beads and its subsequent coating with polyethyleneimine has been found the best strategy to increase the stability and workability of the heterogeneous biocatalyst. Furthermore, we have embedded NADH in the cationic layer attached to the porous surface of the carrier. Since Tt27-HBDH catalyses cofactor recycling through 2-propanol oxidation, we achieve a self-sufficient heterogeneous biocatalyst where NADH is available for the immobilised enzymes but its lixiviation to the reaction bulk is avoided. Taking advantage of the autofluorescence of NADH, we demonstrate the activity of the enzyme towards the immobilised cofactor through single-particle analysis. Finally, we tested the operational stability in the asymmetric reduction of β-ketoesters in batch, succeeding in the reuse of both the enzyme and the co-immobilised cofactor up to 10 reaction cycles.
Collapse
Affiliation(s)
- Alejandro H Orrego
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Daniel Andrés-Sanz
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
| | - Mercedes Sanchez-Costa
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
| | - José Berenguer
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology Severo-Ochoa (UAM-CSIC) Nicolás Cabrera 1 28049 Madrid Spain
| | - José M Guisan
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
| | - Javier Rocha-Martin
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC Campus UAM, Cantoblanco 28049 Madrid Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 182 Donostia San Sebastián Spain
- IKERBASQUE, Basque Foundation for Science María Díaz de Haro 3 48013 Bilbao Spain
| |
Collapse
|
8
|
Drufva EE, Spengler NR, Hix EG, Bailey CB. Site-Directed Mutagenesis of Modular Polyketide Synthase Ketoreductase Domains for Altered Stereochemical Control. Chembiochem 2020; 22:1122-1150. [PMID: 33185924 DOI: 10.1002/cbic.202000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Indexed: 12/18/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
Collapse
Affiliation(s)
- Erin E Drufva
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Nolan R Spengler
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Elijah G Hix
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| |
Collapse
|
9
|
Olavarria K, Carnet A, van Renselaar J, Quakkelaar C, Cabrera R, Guedes da Silva L, Smids AL, Villalobos PA, van Loosdrecht MCM, Wahl SA. An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in Escherichia coli. J Biotechnol 2020; 325:207-216. [PMID: 33122026 DOI: 10.1016/j.jbiotec.2020.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
Oxygen supply implies higher production cost and reduction of maximum theoretical yields. Thus, generation of fermentation products is more cost-effective. Aiming to find a key piece for the production of (poly)-3-hydroxybutyrate (PHB) as a fermentation product, here we characterize an acetoacetyl-CoA reductase, isolated from a Candidatus Accumulibacter phosphatis-enriched mixed culture, showing a (kcatNADH/KMNADH)/(kcatNADPH/KMNADPH)>500. Further kinetic analyses indicate that, at physiological concentrations, this enzyme clearly prefers NADH, presenting the strongest NADH preference so far observed among the acetoacetyl-CoA reductases. Structural and kinetic analyses indicate that residues between E37 and P41 have an important role for the observed NADH preference. Moreover, an operon was assembled combining the phaCA genes from Cupriavidus necator and the gene encoding for this NADH-preferring acetoacetyl-CoA reductase. Escherichia coli cells expressing that assembled operon showed continuous accumulation of PHB under oxygen limiting conditions and PHB titer increased when decreasing the specific oxygen consumption rate. Taken together, these results show that it is possible to generate PHB as a fermentation product in E. coli, opening opportunities for further protein/metabolic engineering strategies envisioning a more efficient anaerobic production of PHB.
Collapse
Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Alexandre Carnet
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Joachim van Renselaar
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Caspar Quakkelaar
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile.
| | - Leonor Guedes da Silva
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Aron L Smids
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - Pablo Andres Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile.
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Netherlands.
| |
Collapse
|
10
|
Dong H, Liffland S, Hillmyer MA, Chang MCY. Engineering in Vivo Production of α-Branched Polyesters. J Am Chem Soc 2019; 141:16877-16883. [DOI: 10.1021/jacs.9b08585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Stephanie Liffland
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Marc A. Hillmyer
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | |
Collapse
|
11
|
Singh A, Das M, Grover A. Molecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428. J Biomol Struct Dyn 2019; 38:827-840. [PMID: 30836854 DOI: 10.1080/07391102.2019.1590239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polyhydroxyalkanoates are gaining importance due to their biodegradable nature and close analogy to plastics. Polyhydroxybutyrate (PHB) is the most widely used bioplastic from polyalkanoate family, which is produced by a legion of bacterial species via phbCAB operon encoding β-ketothiolase (PhaA), NADPH-dependent acetoacetyl-coenzyme A (acetoacetyl-CoA) reductase (PhaB) and polyhydroxyalkanoate synthase (PhaC). Augmentation in the activity of these enzymes is promising for increased PHB production which is achieved by enzyme engineering strategies including non-structural and structural approaches. Our study is deployed on directed evolution-based experimentally reported mutants of PhaB enzyme with increased efficiency due to impact on critical structural factors. We have analyzed and compared the native PhaB with two of its variants Q47L and T173S in complex with their cofactor i.e. NADPH as well as the substrate i.e. acetoacetyl-CoA, via long range molecular dynamics simulations. Interaction profile, MMPBSA, essential dynamics, and free energy landscape analysis revealed that the enzyme efficiency is critically affected by cofactor interactions. It was also observed that mutants have higher equilibrium constant with lesser but optimal affinity for substrate and cofactor than the wild type, which might be the reason for increased efficiency of the mutants via enhanced substrate and cofactor exchange rate. Our study provides insights into the cofactor and substrate binding affinities to PhaB enzyme at atomistic level, which will facilitate designing of highly efficient PhaB enzymes for increased PHB production. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, New Delhi, India
| | - Mriganko Das
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
12
|
Valencia LE, Zhang Z, Cepeda AJ, Keatinge-Clay AT. Seven-enzyme in vitro cascade to (3R)-3-hydroxybutyryl-CoA. Org Biomol Chem 2019; 17:1375-1378. [PMID: 30652175 DOI: 10.1039/c8ob02858c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Economical and environmentally-friendly routes to convert feedstock chemicals like acetate into valuable chiral products such as (R)-3-hydroxybutyrate are in demand. Here, seven enzymes (CoaA, CoaD, CoaE, ACS, BktB, PhaB, and GDH) are employed in a one-pot, in vitro, biocatalytic synthesis of (3R)-3-hydroxybutyryl-CoA, which was readily isolated. This platform generates not only chiral diketide building blocks but also desirable CoA derivatives.
Collapse
Affiliation(s)
- Luis E Valencia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | | | | | | |
Collapse
|
13
|
Segawa M, Wen C, Orita I, Nakamura S, Fukui T. Two NADH-dependent (S)-3-hydroxyacyl-CoA dehydrogenases from polyhydroxyalkanoate-producing Ralstonia eutropha. J Biosci Bioeng 2018; 127:294-300. [PMID: 30243533 DOI: 10.1016/j.jbiosc.2018.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/28/2022]
Abstract
Ralstonia eutropha H16 contains both NADH- and NADPH-dependent reduction activities to acetoacetyl-CoA, and the NADPH-dependent activity is mediated by PhaB paralogs with (R)-stereospecificity providing (R)-3-hydroxybutyryl (3HB)-CoA monomer for poly((R)-3-hydroxybutyrate) synthesis. In contrast, the gene encoding the NADH-dependent enzyme has not been identified to date. This study focused on the NADH-dependent dehydrogenase with (S)-stereospecificity in R. eutropha, as the (S)-specific reduction of acetoacetyl-CoA potentially competed with the polyester biosynthesis via (R)-3HB-CoA. The NADH-dependent reduction activity decreased to one-half when the gene for H16_A0282 (PaaH1), one of two homologs of clostridial NADH-3HB-CoA dehydrogenase, was deleted. The enzyme responsible for the remaining activity was partially purified and identified as H16_A0602 (Had) belonging to a different family from PaaH1. Gene disruption analysis elucidated that most of the NADH-dependent activity was mediated by PaaH1 and Had. The kinetic analysis using the recombinant enzymes indicated that PaaH1 and Had were both NADH-dependent 3-hydroxyacyl-CoA dehydrogenases with rather broad substrate specificity to 3-oxoacyl-CoAs of C4 to C8. The deletion of had in the R. eutropha strain previously engineered for biosynthesis of poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) led to decrease in the C6 composition of the copolyester synthesized from soybean oil, suggesting the role of Had in (S)-specific reduction of 3-oxohexanoyl-CoA with reverse β-oxidation direction. Crotonase ((S)-specific enoyl-CoA hydratase) in R. eutropha H16 was also partially purified and identified as H16_A3307.
Collapse
Affiliation(s)
- Mutsumi Segawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Cheng Wen
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
14
|
Engineering NADH/NAD + ratio in Halomonas bluephagenesis for enhanced production of polyhydroxyalkanoates (PHA). Metab Eng 2018; 49:275-286. [PMID: 30219528 DOI: 10.1016/j.ymben.2018.09.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022]
Abstract
Halomonas bluephagenesis has been developed as a platform strain for the next generation industrial biotechnology (NGIB) with advantages of resistances to microbial contamination and high cell density growth (HCD), especially for production of polyhydroxyalkanoates (PHA) including poly(3-hydroxybutyrate) (PHB), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). However, little is known about the mechanism behind PHA accumulation under oxygen limitation. This study for the first time found that H. bluephagenesis utilizes NADH instead of NADPH as a cofactor for PHB production, thus revealing the rare situation of enhanced PHA accumulation under oxygen limitation. To increase NADH/NAD+ ratio for enhanced PHA accumulation under oxygen limitation, an electron transport pathway containing electron transfer flavoprotein subunits α and β encoded by etf operon was blocked to increase NADH supply, leading to 90% PHB accumulation in the cell dry weight (CDW) of H. bluephagenesis compared with 84% by the wild type. Acetic acid, a cost-effective carbon source, was used together with glucose to balance the redox state and reduce inhibition on pyruvate metabolism, resulting in 22% more CDW and 94% PHB accumulation. The cellular redox state changes induced by the addition of acetic acid increased 3HV ratio in its copolymer PHBV from 4% to 8%, 4HB in its copolymer P34HB from 8% to 12%, respectively, by engineered H. bluephagenesis. The strategy of systematically modulation on the redox potential of H. bluephagenesis led to enhanced PHA accumulation and controllable monomer ratios in PHA copolymers under oxygen limitation, reducing energy consumption and scale-up complexity.
Collapse
|
15
|
Sagong HY, Son HF, Choi SY, Lee SY, Kim KJ. Structural Insights into Polyhydroxyalkanoates Biosynthesis. Trends Biochem Sci 2018; 43:790-805. [PMID: 30139647 DOI: 10.1016/j.tibs.2018.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/04/2018] [Indexed: 12/25/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are diverse biopolyesters produced by numerous microorganisms and have attracted much attention as a substitute for petroleum-based polymers. Despite several decades of study, the detailed molecular mechanisms of PHA biosynthesis have remained unknown due to the lack of structural information on the key PHA biosynthetic enzyme PHA synthase. The recently determined crystal structure of PHA synthase, together with the structures of acetyl-coenzyme A (CoA) acetyltransferase and reductase, have changed this situation. Structural and biochemical studies provided important clues for the molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis from acetyl-CoA. This new information and knowledge is expected to facilitate production of designed novel PHAs and also enhanced production of PHAs.
Collapse
Affiliation(s)
- Hye-Young Sagong
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
| |
Collapse
|
16
|
Domain swapping between FabGs deciphers the structural determinant for in-solution oligomerization and substrate binding. Biophys Chem 2018; 237:9-21. [PMID: 29625337 DOI: 10.1016/j.bpc.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 01/02/2023]
|
17
|
Liu C, Yuan M, Xu X, Wang L, Keatinge-Clay AT, Deng Z, Lin S, Zheng J. Substrate-bound structures of a ketoreductase from amphotericin modular polyketide synthase. J Struct Biol 2018; 203:135-141. [PMID: 29626512 DOI: 10.1016/j.jsb.2018.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 11/29/2022]
Abstract
Ketoreductase (KR) domains of modular polyketide synthases (PKSs) control the stereochemistry of C2 methyl and C3 hydroxyl substituents of polyketide intermediates. To understand the molecular basis of stereocontrol exerted by KRs, the crystal structure of a KR from the second module of the amphotericin PKS (AmpKR2) complexed with NADP+ and 2-methyl-3-oxopentanoyl-pantetheine was solved. This first ternary structure provides direct evidence to the hypothesis that a substrate enters into the active site of an A-type KR from the side opposite the coenzyme to generate an L-hydroxyl substituent. A comparison with the ternary complex of a G355T/Q364H mutant sheds light on the structural basis for stereospecificity toward the substrate C2 methyl substituent. Functional assays suggest the pantetheine handle shows obvious influence on the catalytic efficiency and the stereochemical outcome. Together, these findings extend our current understanding of the stereochemical control of PKS KR domains.
Collapse
Affiliation(s)
- Chenguang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meijuan Yuan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
18
|
Biernacki M, Riechen J, Hähnel U, Roick T, Baronian K, Bode R, Kunze G. Production of (R)-3-hydroxybutyric acid by Arxula adeninivorans. AMB Express 2017; 7:4. [PMID: 28050847 PMCID: PMC5209319 DOI: 10.1186/s13568-016-0303-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/11/2016] [Indexed: 12/28/2022] Open
Abstract
(R)-3-hydroxybutyric acid can be used in industrial and health applications. The synthesis pathway comprises two enzymes, β-ketothiolase and acetoacetyl-CoA reductase which convert cytoplasmic acetyl-CoA to (R)-3-hydroxybutyric acid [(R)-3-HB] which is released into the culture medium. In the present study we used the non-conventional yeast, Arxula adeninivorans, for the synthesis enantiopure (R)-3-HB. To establish optimal production, we investigated three different endogenous yeast thiolases (Akat1p, Akat2p, Akat4p) and three bacterial thiolases (atoBp, thlp, phaAp) in combination with an enantiospecific reductase (phaBp) from Cupriavidus necator H16 and endogenous yeast reductases (Atpk2p, Afox2p). We found that Arxula is able to release (R)-3-HB used an existing secretion system negating the need to engineer membrane transport. Overexpression of thl and phaB genes in organisms cultured in a shaking flask resulted in 4.84 g L−1 (R)-3-HB, at a rate of 0.023 g L−1 h−1 over 214 h. Fed-batch culturing with glucose as a carbon source did not improve the yield, but a similar level was reached with a shorter incubation period [3.78 g L−1 of (R)-3-HB at 89 h] and the rate of production was doubled to 0.043 g L−1 h−1 which is higher than any levels in yeast reported to date. The secreted (R)-3-HB was 99.9% pure. This is the first evidence of enantiopure (R)-3-HB synthesis using yeast as a production host and glucose as a carbon source.
Collapse
|
19
|
Moretto L, Vance S, Heames B, Broadhurst RW. Dissecting how modular polyketide synthase ketoreductases interact with acyl carrier protein-attached substrates. Chem Commun (Camb) 2017; 53:11457-11460. [PMID: 28980673 PMCID: PMC6038798 DOI: 10.1039/c7cc04625a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/21/2022]
Abstract
Interaction studies using fragments excised from the modular mycolactone polyketide synthase show that ketoreductase domains possess a generic binding site for acyl carrier protein domains and provide evidence that the pendant 5'-phosphopantetheine prosthetic group plays a key role in delivering acyl substrates to the active site in the correct orientation.
Collapse
Affiliation(s)
- Luisa Moretto
- Department of Molecular Biosciences
, The University of Texas at Austin
,
Austin
, TX 78712
, USA
| | - Steven Vance
- Crescendo Biologics Ltd
,
Meditrina Building 260
, Babraham Research Campus
, Cambridge CB22 3AT
, UK
| | - Brennan Heames
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
| | - R. William Broadhurst
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
| |
Collapse
|
20
|
de Las Heras AM, Portugal-Nunes DJ, Rizza N, Sandström AG, Gorwa-Grauslund MF. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact 2016; 15:197. [PMID: 27863495 PMCID: PMC5116212 DOI: 10.1186/s12934-016-0598-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
Background Poly-3-d-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. Results In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. Conclusions This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0598-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Diogo J Portugal-Nunes
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Nathasha Rizza
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Vattenhallen Science Center, John Ericssons väg 1, 223 63, Lund, Sweden
| | - Anders G Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.
| |
Collapse
|
21
|
Abstract
Most of the stereocenters of polyketide natural products are established during assembly line biosynthesis. The body of knowledge for how stereocenters are set is now large enough to begin constructing physical models of key reactions. Interactions between stereocenter-forming enzymes and polyketide intermediates are examined here at atomic resolution, drawing from the most current structural and functional information of ketosynthases (KSs), ketoreductases (KRs), dehydratases (DHs), enoylreductases (ERs), and related enzymes. While many details remain to be experimentally determined, our understanding of the chemical and physical mechanisms utilized by the chirality-molding enzymes of modular PKSs is rapidly advancing.
Collapse
Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA. and Department of Chemistry, The University of Texas at Austin, 105 E 24th St. Stop A5300, Austin, TX 78712, USA
| |
Collapse
|
22
|
Oyserman BO, Moya F, Lawson CE, Garcia AL, Vogt M, Heffernen M, Noguera DR, McMahon KD. Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria. ISME JOURNAL 2016; 10:2931-2945. [PMID: 27128993 PMCID: PMC5148189 DOI: 10.1038/ismej.2016.67] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 12/13/2022]
Abstract
The evolution of complex traits is hypothesized to occur incrementally. Identifying the transitions that lead to extant complex traits may provide a better understanding of the genetic nature of the observed phenotype. A keystone functional group in wastewater treatment processes are polyphosphate accumulating organisms (PAOs), however the evolution of the PAO phenotype has yet to be explicitly investigated and the specific metabolic traits that discriminate non-PAO from PAO are currently unknown. Here we perform the first comprehensive investigation on the evolution of the PAO phenotype using the model uncultured organism Candidatus Accumulibacter phosphatis (Accumulibacter) through ancestral genome reconstruction, identification of horizontal gene transfer, and a kinetic/stoichiometric characterization of Accumulibacter Clade IIA. The analysis of Accumulibacter's last common ancestor identified 135 laterally derived genes, including genes involved in glycogen, polyhydroxyalkanoate, pyruvate and NADH/NADPH metabolisms, as well as inorganic ion transport and regulatory mechanisms. In contrast, pathways such as the TCA cycle and polyphosphate metabolism displayed minimal horizontal gene transfer. We show that the transition from non-PAO to PAO coincided with horizontal gene transfer within Accumulibacter's core metabolism; likely alleviating key kinetic and stoichiometric bottlenecks, such as anaerobically linking glycogen degradation to polyhydroxyalkanoate synthesis. These results demonstrate the utility of investigating the derived genome of a lineage to identify key transitions leading to an extant complex phenotype.
Collapse
Affiliation(s)
- Ben O Oyserman
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Francisco Moya
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Antonio L Garcia
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Vogt
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell Heffernen
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
23
|
Bailey CB, Pasman ME, Keatinge-Clay AT. Substrate structure-activity relationships guide rational engineering of modular polyketide synthase ketoreductases. Chem Commun (Camb) 2016; 52:792-5. [PMID: 26568113 PMCID: PMC4690787 DOI: 10.1039/c5cc07315d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthase ketoreductases can set two chiral centers through a single reduction. To probe the basis of stereocontrol, a structure-activity relationship study was performed with three α-methyl, β-ketothioester substrates and four ketoreductases. Since interactions with the β-ketoacyl moiety were found to be most critical, residues implicated in contacting this moiety were mutated. Two mutations were sufficient to completely reverse the stereoselectivity of the model ketoreductase EryKR1, converting it from an enzyme that generates (2S,3R)-products into one that yields (2S,3S)-products.
Collapse
Affiliation(s)
- Constance B Bailey
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Marjolein E Pasman
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Adrian T Keatinge-Clay
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA. and Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
| |
Collapse
|
24
|
Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F. Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34. Metallomics 2016; 8:1204-1216. [DOI: 10.1039/c6mt00142d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
25
|
Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME JOURNAL 2015; 10:810-22. [PMID: 26555245 PMCID: PMC4796919 DOI: 10.1038/ismej.2015.155] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 01/08/2023]
Abstract
Previous studies on enhanced biological phosphorus removal (EBPR) have focused on reconstructing genomic blueprints for the model polyphosphate-accumulating organism Candidatus Accumulibacter phosphatis. Here, a time series metatranscriptome generated from enrichment cultures of Accumulibacter was used to gain insight into anerobic/aerobic metabolism and regulatory mechanisms within an EBPR cycle. Co-expressed gene clusters were identified displaying ecologically relevant trends consistent with batch cycle phases. Transcripts displaying increased abundance during anerobic acetate contact were functionally enriched in energy production and conversion, including upregulation of both cytoplasmic and membrane-bound hydrogenases demonstrating the importance of transcriptional regulation to manage energy and electron flux during anerobic acetate contact. We hypothesized and demonstrated hydrogen production after anerobic acetate contact, a previously unknown strategy for Accumulibacter to maintain redox balance. Genes involved in anerobic glycine utilization were identified and phosphorus release after anerobic glycine contact demonstrated, suggesting that Accumulibacter routes diverse carbon sources to acetyl-CoA formation via previously unrecognized pathways. A comparative genomics analysis of sequences upstream of co-expressed genes identified two statistically significant putative regulatory motifs. One palindromic motif was identified upstream of genes involved in PHA synthesis and acetate activation and is hypothesized to be a phaR binding site, hence representing a hypothetical PHA modulon. A second motif was identified ~35 base pairs (bp) upstream of a large and diverse array of genes and hence may represent a sigma factor binding site. This analysis provides a basis and framework for further investigations into Accumulibacter metabolism and the reconstruction of regulatory networks in uncultured organisms.
Collapse
Affiliation(s)
- Ben O Oyserman
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA
| | | | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
| |
Collapse
|
26
|
Structure-directed construction of a high-performance version of the enzyme FabG from the photosynthetic microorganism Synechocystis sp. PCC 6803. FEBS Lett 2015; 589:3052-7. [PMID: 26358291 DOI: 10.1016/j.febslet.2015.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 11/20/2022]
Abstract
PhaB (acetoacetyl-CoA reductase) catalyzes the reduction of acetoacetyl-CoA to (R)-3-hydroxybutyryl-CoA in polyhydroxybutyrate (PHB) synthesis and FabG (3-ketoacyl-acyl-carrier-protein reductase) catalyzes the β-ketoacyl-ACP to yield (R)-3-hydroxyacyl-ACP in fatty acid biosynthesis. Both of them have been classified into the same group EC 1.1.1. PhaB is limited with substrate specificities, while FabG was considered as a potential PhaB due to broad substrate selectivity despite of low activity. Here, X-ray crystal structures of FabG and PhaB from the photosynthetic microorganism Synechocystis sp. PCC 6803 were resolved. Based on them, a high-performance FabG on acyl-CoA directed by structural evolution was constructed that may serve as a critical enzyme to partition carbon flow from fatty acid synthesis to PHA.
Collapse
|
27
|
Kim EJ, Kim KJ. Crystal structure and biochemical characterization of PhaA from Ralstonia eutropha, a polyhydroxyalkanoate-producing bacterium. Biochem Biophys Res Commun 2014; 452:124-9. [DOI: 10.1016/j.bbrc.2014.08.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 08/14/2014] [Indexed: 11/24/2022]
|
28
|
Kim J, Kim KJ. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha H16. Acta Crystallogr F Struct Biol Commun 2014; 70:955-8. [PMID: 25005097 PMCID: PMC4089540 DOI: 10.1107/s2053230x14011881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/22/2014] [Indexed: 11/11/2022] Open
Abstract
The (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha (RePaaH1) is an enzyme used in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to (S)-3-hydroxybutyryl-CoA. The RePaaH1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.6 Å on a synchrotron beamline. The crystal belonged to space group P3221, with unit-cell parameters a=b=135.4, c=97.2 Å. With three molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.68 Å3 Da(-1), which corresponds to a solvent content of approximately 54.1%. The structure was solved by the single-wavelength anomalous dispersion method and refinement of the structure is in progress.
Collapse
Affiliation(s)
- Jieun Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| |
Collapse
|