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Cavuzic MT, de Sousa AS, Lohman JR, Waldrop GL. Kinetic characterization of the C-terminal domain of Malonyl-CoA reductase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141033. [PMID: 39019246 DOI: 10.1016/j.bbapap.2024.141033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/28/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Malonyl-CoA reductase utilizes two equivalents of NADPH to catalyze the reduction of malonyl-CoA to 3-hydroxypropionic acid (3HP). This reaction is part of the carbon fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus. The enzyme is composed of two domains. The C-terminal domain catalyzes the reduction of malonyl-CoA to malonic semialdehyde, while the N-terminal domain catalyzes the reduction of the aldehyde to 3HP. The two domains can be produced independently and retain their enzymatic activity. This report focuses on the kinetic characterization of the C-terminal domain. Initial velocity patterns and inhibition studies showed the kinetic mechanism is ordered with NADPH binding first followed by malonyl-CoA. Malonic semialdehyde is released first, while CoA and NADP+ are released randomly. Analogs of malonyl-CoA showed that the thioester carbon is reduced, while the carboxyl group is needed for proper positioning. The enzyme transfers the pro-S hydrogen of NADPH to malonyl-CoA and pH rate profiles revealed that a residue with a pKa value of about 8.8 must be protonated for activity. Kinetic isotope effects indicated that NADPH is not sticky (that is, NADPH dissociates from the enzyme faster than the rate of product formation) and product release is partially rate-limiting. Moreover, the mechanism is stepwise with the pH dependent step occurring before or after hydride transfer. The findings from this study will aid in the development of an eco-friendly biosynthesis of 3HP which is an industrial chemical used in the production of plastics and adhesives.
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Affiliation(s)
- Mirela Tkalcic Cavuzic
- Department of Biological Sciences, Louisiana State University; Baton Rouge, LA 70803, USA.
| | - Amanda Silva de Sousa
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824, USA.
| | - Jeremy R Lohman
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824, USA.
| | - Grover L Waldrop
- Department of Biological Sciences, Louisiana State University; Baton Rouge, LA 70803, USA.
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2
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Nguyen N, Forstater JH, McIntosh JA. Decarboxylation in Natural Products Biosynthesis. JACS AU 2024; 4:2715-2745. [PMID: 39211618 PMCID: PMC11350588 DOI: 10.1021/jacsau.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms and act on a large variety of substrates, making them appealing in terms of biotechnological applications. This Perspective focuses on the occurrence of decarboxylation reactions in natural product biosynthesis and provides a perspective on their applications in biocatalysis for fine chemicals and pharmaceuticals.
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3
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Chen R, Zhu H, Zhang X, Li L, Xu J, Tan Z, Su J, Feng K, Chen K, Xu H. Characterization and Functional Analysis of the 17-Beta Hydroxysteroid Dehydrogenase 2 ( hsd17b2) Gene during Sex Reversal in the Ricefield Eel ( Monopterus albus). Int J Mol Sci 2024; 25:9063. [PMID: 39201749 PMCID: PMC11354438 DOI: 10.3390/ijms25169063] [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: 06/28/2024] [Revised: 08/03/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
In mammals, 17-beta hydroxysteroid dehydrogenase 2 (Hsd17b2) enzyme specifically catalyzes the oxidation of the C17 hydroxyl group and efficiently regulates the activities of estrogens and androgens to prevent diseases induced by hormone disorders. However, the functions of the hsd17b2 gene involved in animal sex differentiation are still largely unclear. The ricefield eel (Monopterus albus), a protogynous hermaphroditic fish with a small genome size (2n = 24), is usually used as an ideal model to study the mechanism of sex differentiation in vertebrates. Therefore, in this study, hsd17b2 gene cDNA was cloned and its mRNA expression profiles were determined in the ricefield eel. The cloned cDNA fragment of hsd17b2 was 1230 bp, including an open reading frame of 1107 bp, encoding 368 amino acid residues with conserved catalytic subunits. Moreover, real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis showed that hsd17b2 mRNA expressed strongly in the ovaries at early developmental stages, weakly in liver and intestine, and barely in testis and other tissues. In particular, hsd17b2 mRNA expression was found to peak in ovaries of young fish and ovotestis at the early stage, and eventually declined in gonads from the late ovotestis to testis. Likewise, chemical in situ hybridization results indicated that the hsd17b2 mRNA signals were primarily detected in the cytoplasm of oogonia and oocytes at stage I-II, subsequently concentrated in the granulosa cells around the oocytes at stage Ⅲ-Ⅳ, but undetectable in mature oocytes and male germ cells. Intriguingly, in ricefield eel ovaries, hsd17b2 mRNA expression could be significantly reduced by 17β-estradiol (E2) or tamoxifen (17β-estradiol inhibitor, E2I) induction at a low concentration (10 ng/mL) and increased by E2I induction at a high concentration (100 ng/mL). On the other hand, both the melatonin (MT) and flutamide (androgen inhibitor, AI) induction could significantly decrease hsd17b2 mRNA expression in the ovary of ricefield eel. This study provides a clue for demonstrating the mechanism of sexual differentiation in fish. The findings of our study imply that the hsd17b2 gene could be a key regulator in sexual differentiation and modulate sex reversal in the ricefield eel and other hermaphroditic fishes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kaili Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, Southwest University, Chongqing 402460, China; (R.C.); (H.Z.); (X.Z.); (L.L.); (J.X.); (Z.T.); (J.S.); (K.F.)
| | - Hongyan Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, Southwest University, Chongqing 402460, China; (R.C.); (H.Z.); (X.Z.); (L.L.); (J.X.); (Z.T.); (J.S.); (K.F.)
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4
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Walker MA, Tian R. NAD metabolism and heart failure: Mechanisms and therapeutic potentials. J Mol Cell Cardiol 2024; 195:45-54. [PMID: 39096536 DOI: 10.1016/j.yjmcc.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 08/05/2024]
Abstract
Nicotinamide adenine dinucleotide provides the critical redox pair, NAD+ and NADH, for cellular energy metabolism. In addition, NAD+ is the precursor for de novo NADP+ synthesis as well as the co-substrates for CD38, poly(ADP-ribose) polymerase and sirtuins, thus, playing a central role in the regulation of oxidative stress and cell signaling. Declines of the NAD+ level and altered NAD+/NADH redox states have been observed in cardiometabolic diseases of various etiologies. NAD based therapies have emerged as a promising strategy to treat cardiovascular disease. Strategies that reduce NAD+ consumption or promote NAD+ production have repleted intracellular NAD+ or normalized NAD+/NADH redox in preclinical studies. These interventions have shown cardioprotective effects in multiple models suggesting a great promise of the NAD+ elevating therapy. Mechanisms for the benefit of boosting NAD+ level, however, remain incompletely understood. Moreover, despite the robust pre-clinical studies there are still challenges to translate the therapy to clinic. Here, we review the most up to date literature on mechanisms underlying the NAD+ elevating interventions and discuss the progress of human studies. We also aim to provide a better understanding of how NAD metabolism is changed in failing hearts with a particular emphasis on types of strategies employed and methods to target these pathways. Finally, we conclude with a comprehensive assessment of the challenges in developing NAD-based therapies for heart diseases, and to provide a perspective on the future of the targeting strategies.
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Affiliation(s)
- Matthew A Walker
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| | - Rong Tian
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington School of Medicine, Seattle, WA, USA.
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5
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Bhargavi G, Mallakuntla MK, Kale D, Tiwari S. Rv0687 a Putative Short-Chain Dehydrogenase Is Required for In Vitro and In Vivo Survival of Mycobacterium tuberculosis. Int J Mol Sci 2024; 25:7862. [PMID: 39063103 PMCID: PMC11277061 DOI: 10.3390/ijms25147862] [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: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), a successful human pathogen, resides in host sentinel cells and combats the stressful intracellular environment induced by reactive oxygen and nitrogen species during infection. Mtb employs several evasion mechanisms in the face of the host as a survival strategy, including detoxifying enzymes as short-chain dehydrogenases/reductases (SDRs) to withstand host-generated insults. In this study, using specialized transduction, we have generated a Rv0687 deletion mutant and its complemented strain and investigated the functional role of Rv0687, a member of SDRs family genes in Mtb pathogenesis. A wildtype (WT) and a mutant Mtb strain lacking Rv0687 (RvΔ0687) were tested for the in vitro stress response and in vivo survival in macrophages and mice models of infection. The study demonstrates that the deletion of Rv0687 elevated the sensitivity of Mtb to oxidative and nitrosative stress-inducing agents. Furthermore, the lack of Rv0687 compromised the survival of Mtb in primary bone marrow macrophages and led to an increase in the levels of the secreted proinflammatory cytokines TNF-α and MIP-1α. Interestingly, the growth of WT and RvΔ0687 was similar in the lungs of infected immunocompromised mice; however, a significant reduction in RvΔ0687 growth was observed in the spleen of immunocompromised Rag-/- mice at 4 weeks post-infection. Moreover, Rag-/- mice infected with RvΔ0687 survived longer compared to those infected with the WT Mtb strain. Additionally, we observed a significant reduction in the bacterial burden in the spleens and lungs of immunocompetent C57BL/6 mice infected with RvΔ0687 compared to those infected with complemented and WT Mtb strains. Collectively, this study reveals that Rv0687 plays a role in Mtb pathogenesis.
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Affiliation(s)
| | | | | | - Sangeeta Tiwari
- Department of Biological Sciences, Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
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6
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Serson WR, Gishini MFS, Stupar RM, Stec AO, Armstrong PR, Hildebrand D. Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds. Genes (Basel) 2024; 15:892. [PMID: 39062671 PMCID: PMC11276498 DOI: 10.3390/genes15070892] [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: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes (Glyma.14G101900) may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels.
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Affiliation(s)
- William R. Serson
- Department of Biology, Penn State University, Lehigh Valley, Center Valley, PA 18034, USA
| | | | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Adrian O. Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Paul R. Armstrong
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS 66502, USA
| | - David Hildebrand
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA;
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7
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Zhu C, Wei WP, An JN, Hu JL, Gao CH, Yang M. SdrR, a LysR-type regulator, responds to the mycobacterial antioxidant defense. J Biochem 2024; 176:43-54. [PMID: 38444151 DOI: 10.1093/jb/mvae026] [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: 09/19/2023] [Revised: 01/26/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
Protection against oxidative stress is a vital defense mechanism for Mycobacterium tuberculosis within the host. However, few transcription factors that control bacterial antioxidant defense are known. Here, we present evidence that SdrR, encoded by the MSMEG_5712 (Ms5712) gene, functions as an oxidative stress response regulator in Mycobacterium smegmatis. SdrR recognizes an 11-bp motif sequence in the operon's upstream regulatory region and negatively regulates the expression of short-chain dehydrogenases/reductases (SDR). Overexpressing sdrR inhibited SDR expression, which rendered the strain oxidative more stress-sensitive. Conversely, sdrR knockout alleviates SDR repression, which increases its oxidative stress tolerance. Thus, SdrR responds to oxidative stress by negatively regulating sdr expression. Therefore, this study elucidated an underlying regulatory mechanism behind mycobacterial oxidative stress adaptation.
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Affiliation(s)
- Chen Zhu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Wen-Ping Wei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing-Ning An
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia-Ling Hu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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8
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Zhang L, Sun Z, Xu G, Ni Y. Classification and functional origins of stereocomplementary alcohol dehydrogenases for asymmetric synthesis of chiral secondary alcohols: A review. Int J Biol Macromol 2024; 270:132238. [PMID: 38729463 DOI: 10.1016/j.ijbiomac.2024.132238] [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: 01/28/2024] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Alcohol dehydrogenases (ADHs) mediated biocatalytic asymmetric reduction of ketones have been widely applied in the synthesis of optically active secondary alcohols with highly reactive hydroxyl groups ligated to the stereogenic carbon and divided into (R)- and (S)-configurations. Stereocomplementary ADHs could be applied in the synthesis of both enantiomers and are increasingly accepted as the "first of choice" in green chemistry due to the high atomic economy, low environmental factor, 100 % theoretical yield, and high environmentally friendliness. Due to the equal importance of complementary alcohols, development of stereocomplementary ADHs draws increasing attention. This review is committed to summarize recent advance in discovery of naturally evolved and tailor-made stereocomplementary ADHs, unveil the molecular mechanism of stereoselective catalysis in views of classification and functional basis, and provide guidance for further engineering the stereoselectivity of ADHs for the industrial biosynthesis of chiral secondary alcohol of industrial relevance.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zewen Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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9
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Su F, Koeberle A. Regulation and targeting of SREBP-1 in hepatocellular carcinoma. Cancer Metastasis Rev 2024; 43:673-708. [PMID: 38036934 PMCID: PMC11156753 DOI: 10.1007/s10555-023-10156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is an increasing burden on global public health and is associated with enhanced lipogenesis, fatty acid uptake, and lipid metabolic reprogramming. De novo lipogenesis is under the control of the transcription factor sterol regulatory element-binding protein 1 (SREBP-1) and essentially contributes to HCC progression. Here, we summarize the current knowledge on the regulation of SREBP-1 isoforms in HCC based on cellular, animal, and clinical data. Specifically, we (i) address the overarching mechanisms for regulating SREBP-1 transcription, proteolytic processing, nuclear stability, and transactivation and (ii) critically discuss their impact on HCC, taking into account (iii) insights from pharmacological approaches. Emphasis is placed on cross-talk with the phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt)-mechanistic target of rapamycin (mTOR) axis, AMP-activated protein kinase (AMPK), protein kinase A (PKA), and other kinases that directly phosphorylate SREBP-1; transcription factors, such as liver X receptor (LXR), peroxisome proliferator-activated receptors (PPARs), proliferator-activated receptor γ co-activator 1 (PGC-1), signal transducers and activators of transcription (STATs), and Myc; epigenetic mechanisms; post-translational modifications of SREBP-1; and SREBP-1-regulatory metabolites such as oxysterols and polyunsaturated fatty acids. By carefully scrutinizing the role of SREBP-1 in HCC development, progression, metastasis, and therapy resistance, we shed light on the potential of SREBP-1-targeting strategies in HCC prevention and treatment.
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Affiliation(s)
- Fengting Su
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria.
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10
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Lin YL, Yao T, Wang YW, Zhou ZX, Hong ZC, Shen Y, Yan Y, Li YC, Lin JF. Potential drug targets for gastroesophageal reflux disease and Barrett's esophagus identified through Mendelian randomization analysis. J Hum Genet 2024; 69:245-253. [PMID: 38429412 DOI: 10.1038/s10038-024-01234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
Gastroesophageal reflux disease (GERD) is a prevalent chronic ailment, and present therapeutic approaches are not always effective. This study aimed to find new drug targets for GERD and Barrett's esophagus (BE). We obtained genetic instruments for GERD, BE, and 2004 plasma proteins from recently published genome-wide association studies (GWAS), and Mendelian randomization (MR) was employed to explore potential drug targets. We further winnowed down MR-prioritized proteins through replication, reverse causality testing, colocalization analysis, phenotype scanning, and Phenome-wide MR. Furthermore, we constructed a protein-protein interaction network, unveiling potential associations among candidate proteins. Simultaneously, we acquired mRNA expression quantitative trait loci (eQTL) data from another GWAS encompassing four different tissues to identify additional drug targets. Meanwhile, we searched drug databases to evaluate these targets. Under Bonferroni correction (P < 4.8 × 10-5), we identified 11 plasma proteins significantly associated with GERD. Among these, 7 are protective proteins (MSP, GPX1, ERBB3, BT3A3, ANTR2, CCM2, and DECR2), while 4 are detrimental proteins (TMEM106B, DUSP13, C1-INH, and LINGO1). Ultimately, C1-INH and DECR2 successfully passed the screening process and exhibited similar directional causal effects on BE. Further analysis of eQTLs highlighted 4 potential drug targets, including EDEM3, PBX3, MEIS1-AS3, and NME7. The search of drug databases further supported our conclusions. Our study indicated that the plasma proteins C1-INH and DECR2, along with 4 genes (EDEM3, PBX3, MEIS1-AS3, and NME7), may represent potential drug targets for GERD and BE, warranting further investigation.
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Affiliation(s)
- Yun-Lu Lin
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Tao Yao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Ying-Wei Wang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Zhi-Xiang Zhou
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Ze-Chao Hong
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yu Shen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yu Yan
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yue-Chun Li
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Jia-Feng Lin
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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11
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Samson N, Bosoi CR, Roy C, Turcotte L, Tribouillard L, Mouchiroud M, Berthiaume L, Trottier J, Silva HCG, Guerbette T, Plata-Gómez AB, Besse-Patin A, Montoni A, Ilacqua N, Lamothe J, Citron YR, Gélinas Y, Gobeil S, Zoncu R, Caron A, Morissette M, Pellegrini L, Rochette PJ, Estall JL, Efeyan A, Shum M, Audet-Walsh É, Barbier O, Marette A, Laplante M. HSDL2 links nutritional cues to bile acid and cholesterol homeostasis. SCIENCE ADVANCES 2024; 10:eadk9681. [PMID: 38820148 PMCID: PMC11141617 DOI: 10.1126/sciadv.adk9681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
In response to energy and nutrient shortage, the liver triggers several catabolic processes to promote survival. Despite recent progress, the precise molecular mechanisms regulating the hepatic adaptation to fasting remain incompletely characterized. Here, we report the identification of hydroxysteroid dehydrogenase-like 2 (HSDL2) as a mitochondrial protein highly induced by fasting. We show that the activation of PGC1α-PPARα and the inhibition of the PI3K-mTORC1 axis stimulate HSDL2 expression in hepatocytes. We found that HSDL2 depletion decreases cholesterol conversion to bile acids (BAs) and impairs FXR activity. HSDL2 knockdown also reduces mitochondrial respiration, fatty acid oxidation, and TCA cycle activity. Bioinformatics analyses revealed that hepatic Hsdl2 expression positively associates with the postprandial excursion of various BA species in mice. We show that liver-specific HSDL2 depletion affects BA metabolism and decreases circulating cholesterol levels upon refeeding. Overall, our report identifies HSDL2 as a fasting-induced mitochondrial protein that links nutritional signals to BAs and cholesterol homeostasis.
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Affiliation(s)
- Nolwenn Samson
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
| | - Cristina R. Bosoi
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
| | - Christian Roy
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
| | - Laurie Turcotte
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
| | - Laura Tribouillard
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
| | - Mathilde Mouchiroud
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
| | - Line Berthiaume
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
| | - Jocelyn Trottier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
| | - Heitor C. G. Silva
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Thomas Guerbette
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Ana Belén Plata-Gómez
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Aurèle Besse-Patin
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Alicia Montoni
- Axe Médecine régénératrice, Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec, QC, Canada
| | - Nicolò Ilacqua
- Faculté de médecine, Université Laval, Québec, QC, Canada
- Centre de recherche CERVO, Québec, QC, Canada
| | - Jennifer Lamothe
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
| | - Yemima R. Citron
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA, USA
| | - Yves Gélinas
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
| | | | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA, USA
| | - Alexandre Caron
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Faculté de Pharmacie, Université Laval, Québec, QC, Canada
| | - Mathieu Morissette
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Luca Pellegrini
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, QC, Canada
| | - Patrick J. Rochette
- Faculté de médecine, Université Laval, Québec, QC, Canada
- Axe Médecine régénératrice, Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec, QC, Canada
- Département d’Ophtalmologie et ORL – chirurgie cervico-faciale, Université Laval, Québec, QC, Canada
| | - Jennifer L. Estall
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Faculté de médecine, Université de Montréal, Montréal, QC, Canada
| | - Alejo Efeyan
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michael Shum
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Étienne Audet-Walsh
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Olivier Barbier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Endocrinologie et néphrologie, Québec, QC, Canada
- Faculté de Pharmacie, Université Laval, Québec, QC, Canada
| | - André Marette
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Mathieu Laplante
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, QC, Canada
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, Canada
- Faculté de médecine, Université Laval, Québec, QC, Canada
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12
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Pesara P, Szafran K, Nguyen HC, Sirohiwal A, Pantazis DA, Gabruk M. Elucidating substrate binding in the light-dependent protochlorophyllide oxidoreductase. Chem Sci 2024; 15:7767-7780. [PMID: 38784751 PMCID: PMC11110527 DOI: 10.1039/d4sc00923a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) catalyzes a crucial step in chlorophyll biosynthesis: the rare biological photocatalytic reduction of the double C[double bond, length as m-dash]C bond in the precursor, protochlorophyllide (Pchlide). Despite its fundamental significance, limited structural insights into the active complex have hindered understanding of its reaction mechanism. Recently, a high-resolution cryo-EM structure of LPOR in its active conformation challenged our view of pigment binding, residue interactions, and the catalytic process. Surprisingly, this structure contrasts markedly with previous assumptions, particularly regarding the orientation of the bound Pchlide. To gain insights into the substrate binding puzzle, we conducted molecular dynamics simulations, quantum-mechanics/molecular-mechanics (QM/MM) calculations, and site-directed mutagenesis. Two Pchlide binding modes were considered, one aligning with historical proposals (mode A) and another consistent with the recent experimental data (mode B). Binding energy calculations revealed that in contrast to the non-specific interactions found for mode A, mode B exhibits distinct stabilizing interactions that support more thermodynamically favorable binding. A comprehensive analysis incorporating QM/MM-based local energy decomposition unraveled a complex interaction network involving Y177, H319, and the C131 carboxy group, influencing the pigment's excited state energy and potentially contributing to substrate specificity. Importantly, our results uniformly favor mode B, challenging established interpretations and emphasizing the need for a comprehensive re-evaluation of the LPOR reaction mechanism in a way that incorporates accurate structural information on pigment interactions and substrate-cofactor positioning in the binding pocket. The results shed light on the intricacies of LPOR's catalytic mechanism and provide a solid foundation for further elucidating the secrets of chlorophyll biosynthesis.
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Affiliation(s)
- Penelope Pesara
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Katarzyna Szafran
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 30-387 Cracow Poland
| | - Henry C Nguyen
- Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California San Francisco CA USA
| | - Abhishek Sirohiwal
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University 10691 Stockholm Sweden
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Michal Gabruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 30-387 Cracow Poland
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13
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Chen L, Wang X, Zou Y, Tang MC. Genome Mining of a Fungal Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthetase Pathway to Synthesize a Phytotoxic N-Acyl Amino Acid. Org Lett 2024; 26:3597-3601. [PMID: 38661293 DOI: 10.1021/acs.orglett.4c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Guided by the retrobiosynthesis hypothesis, we characterized a fungal polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) hybrid megasynthetase pathway to generate 2-trans-4-trans-2-methylsorbyl-d-leucine (1), a polyketide amino acid conjugate that inhibits Arabidopsis root growth. The biosynthesis of 1 includes a PKS-NRPS enzyme to assemble an N-acyl amino alcohol intermediate, which is further oxidized to an N-acyl amino acid (NAAA), demonstrating a new biosynthetic logic for synthesizing NAAAs and expanding the chemical space of products encoded by fungal PKS-NRPS clusters.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhang jiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
| | - Xin Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Man-Cheng Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhang jiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
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14
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Pu Z, Cao J, Wu W, Song Z, Yang L, Wu J, Yu H. Reconstructing dynamics correlation network to simultaneously improve activity and stability of 2,3-butanediol dehydrogenase by design of distal interchain disulfide bonds. Int J Biol Macromol 2024; 267:131415. [PMID: 38582485 DOI: 10.1016/j.ijbiomac.2024.131415] [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: 01/18/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The complete enzyme catalytic cycle includes substrate binding, chemical reaction and product release, in which different dynamic conformations are adopted. Due to the complex relationship among enzyme activity, stability and dynamics, the directed evolution of enzymes for improved activity or stability commonly leads to a trade-off in stability or activity. It hence remains a challenge to engineer an enzyme to have both enhanced activity and stability. Here, we have attempted to reconstruct the dynamics correlation network involved with active center to improve both activity and stability of a 2,3-butanediol dehydrogenase (2,3-BDH) by introducing inter-chain disulfide bonds. A computational strategy was first applied to evaluate the effect of introducing inter-chain disulfide bond on activity and stability of three 2,3-BDHs, and the N258C mutation of 2,3-BDH from Corynebacterium glutamicum (CgBDH) was proved to be effective in improving both activity and stability. In the results, CgBDH-N258C showed a different unfolding curve from the wild type, with two melting temperatures (Tm) of 68.3 °C and 50.8 °C, 19.7 °C and 2 °C higher than 48.6 °C of the wild type. Its half-life was also improved by 14.8-fold compared to the wild type. Catalytic efficiency (kcat/Km) of the mutant was increased by 7.9-fold toward native substrate diacetyl and 8.8-fold toward non-native substrate 2,5-hexanedione compared to the wild type. Molecular dynamics simulations revealed that an interaction network formed by Cys258, Arg162, Ala144 and the catalytic residues was reconstructed in the mutant and the dynamics change caused by the disulfide bond could be propagated through the interactions network. This improved the enzyme stability and activity by decreasing the flexibility and locking more "reactive" pose, respectively. Further construction of mutations including A144G showing a 44-fold improvement in catalytic efficiency toward meso-2,3-BD confirmed the role of modifying dynamics correlation network in tunning enzyme activity and selectivity. This study provided important insights into the relationship among dynamics, enzyme catalysis and stability, and will be useful in the designing new enzymes with co-evolution of stability, activity and selectivity.
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Affiliation(s)
- Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Jiawen Cao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China.
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15
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Zheng S, Lin T, Chen H, Zhang X, Jiang F. Impact of changes in biofilm composition response following chlorine and chloramine disinfection on nitrogenous disinfection byproduct formation and toxicity risk in drinking water distribution systems. WATER RESEARCH 2024; 253:121331. [PMID: 38377929 DOI: 10.1016/j.watres.2024.121331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
In practical drinking water treatment, chlorine and chloramine disinfection exhibit different mechanisms that affect biofilm growth. This study focused on the influence of biofilm composition changes, especially extracellular polymeric substance (EPS) fractions, on the potential formation and toxicity of nitrogenous disinfection by-products (N-DBP). Significant differences in microbial diversity and community structure were observed between the chlorine and chloramine treatments. Notably, the biofilms from the chloramine-treated group had higher microbial dominance and greater accumulation of organic precursors, as evidenced by the semi-quantitative confocal laser-scanning microscopy assay of more concentrated microbial aggregates and polysaccharide proteins in the samples. Additionally, the chloramine-treated group compared with chlorine had a higher EPS matrix content, with a 13.5 % increase in protein. Furthermore, the protein distribution within the biofilm differed; in the chlorine group, proteins were concentrated in the central region, whereas in the chloramine group, proteins were primarily located at the water-biofilm interface. Notably, functional prediction analyses of protein fractions in biofilms revealed specific functional regulation patterns and increased metabolism-related abundance of proteins in the chlorine-treated group. This increase was particularly pronounced for proteins such as dehydrogenases, reductases, transcription factors, and acyl-CoA dehydrogenases. By combining the Fukui function and density functional calculations to further analyse the effect of biofilm component changes on N-DBP production under chlorine/chloramine and by assessing the toxicity risk potential of N-DBP, it was determined that chloramine disinfection is detrimental to biofilm control and the accumulation of protein precursors has a higher formation potential of N-DBPs and toxicity risk, increasing the health risk of drinking water.
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Affiliation(s)
- Songyuan Zheng
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Tao Lin
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Han Chen
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Xue Zhang
- Suzhou Water Supply Company, Suzhou 215002, China
| | - Fuchun Jiang
- Suzhou Water Supply Company, Suzhou 215002, China
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16
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Roth S, Niese R, Müller M, Hall M. Redox Out of the Box: Catalytic Versatility Across NAD(P)H-Dependent Oxidoreductases. Angew Chem Int Ed Engl 2024; 63:e202314740. [PMID: 37924279 DOI: 10.1002/anie.202314740] [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: 10/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
The asymmetric reduction of double bonds using NAD(P)H-dependent oxidoreductases has proven to be an efficient tool for the synthesis of important chiral molecules in research and on industrial scale. These enzymes are commercially available in screening kits for the reduction of C=O (ketones), C=C (activated alkenes), or C=N bonds (imines). Recent reports, however, indicate that the ability to accommodate multiple reductase activities on distinct C=X bonds occurs in different enzyme classes, either natively or after mutagenesis. This challenges the common perception of highly selective oxidoreductases for one type of electrophilic substrate. Consideration of this underexplored potential in enzyme screenings and protein engineering campaigns may contribute to the identification of complementary biocatalytic processes for the synthesis of chiral compounds. This review will contribute to a global understanding of the promiscuous behavior of NAD(P)H-dependent oxidoreductases on C=X bond reduction and inspire future discoveries with respect to unconventional biocatalytic routes in asymmetric synthesis.
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Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Richard Niese
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- BioHealth, Field of Excellence, University of Graz, 8010, Graz, Austria
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17
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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18
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Keyl A, Herrfurth C, Pandey G, Kim RJ, Helwig L, Haslam TM, de Vries S, de Vries J, Gutsche N, Zachgo S, Suh MC, Kunst L, Feussner I. Divergent evolution of the alcohol-forming pathway of wax biosynthesis among bryophytes. THE NEW PHYTOLOGIST 2024. [PMID: 38501480 DOI: 10.1111/nph.19687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
The plant cuticle is a hydrophobic barrier, which seals the epidermal surface of most aboveground organs. While the cuticle biosynthesis of angiosperms has been intensively studied, knowledge about its existence and composition in nonvascular plants is scarce. Here, we identified and characterized homologs of Arabidopsis thaliana fatty acyl-CoA reductase (FAR) ECERIFERUM 4 (AtCER4) and bifunctional wax ester synthase/acyl-CoA:diacylglycerol acyltransferase 1 (AtWSD1) in the liverwort Marchantia polymorpha (MpFAR2 and MpWSD1) and the moss Physcomitrium patens (PpFAR2A, PpFAR2B, and PpWSD1). Although bryophyte harbor similar compound classes as described for angiosperm cuticles, their biosynthesis may not be fully conserved between the bryophytes M. polymorpha and P. patens or between these bryophytes and angiosperms. While PpFAR2A and PpFAR2B contribute to the production of primary alcohols in P. patens, loss of MpFAR2 function does not affect the wax profile of M. polymorpha. By contrast, MpWSD1 acts as the major wax ester-producing enzyme in M. polymorpha, whereas mutations of PpWSD1 do not affect the wax ester levels of P. patens. Our results suggest that the biosynthetic enzymes involved in primary alcohol and wax ester formation in land plants have either evolved multiple times independently or undergone pronounced radiation followed by the formation of lineage-specific toolkits.
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Affiliation(s)
- Alisa Keyl
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, University of Goettingen, Goettingen, 37077, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, University of Goettingen, Goettingen, 37077, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, 37077, Germany
| | - Garima Pandey
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Ryeo Jin Kim
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Lina Helwig
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, University of Goettingen, Goettingen, 37077, Germany
| | - Tegan M Haslam
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, University of Goettingen, Goettingen, 37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, 37077, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, 37077, Germany
- Department of Applied Informatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, 37077, Germany
| | - Nora Gutsche
- Division of Botany, Osnabrueck University, Osnabrueck, 49076, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrueck University, Osnabrueck, 49076, Germany
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Ljerka Kunst
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, University of Goettingen, Goettingen, 37077, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, 37077, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, 37077, Germany
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19
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Li L, Zhong W, Liu H, Espinosa-Artiles P, Xu YM, Wang C, Robles JMV, Paz TA, Inácio MC, Chen F, Xu Y, Gunatilaka AAL, Molnár I. Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi. J Am Chem Soc 2024; 146:6189-6198. [PMID: 38386630 PMCID: PMC11106036 DOI: 10.1021/jacs.3c14066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Polyketides with the isochroman-3-one pharmacophore are rare among fungal natural products as their biosynthesis requires an unorthodox S-type aromatic ring cyclization. Genome mining uncovered a conserved gene cluster in select leotiomycetous fungi that encodes the biosynthesis of cytosporones, including isochroman-3-one congeners. Combinatorial biosynthesis in total biosynthetic and biocatalytic formats in Saccharomyces cerevisiae and in vitro reconstitution of key reactions with purified enzymes revealed how cytosporone structural and bioactivity diversity is generated. The S-type acyl dihydroxyphenylacetic acid (ADA) core of cytosporones is assembled by a collaborating polyketide synthase pair. Thioesterase domain-catalyzed transesterification releases ADA esters, some of which are known Nur77 modulators. Alternatively, hydrolytic release allows C6 hydroxylation by a flavin-dependent monooxygenase, yielding a trihydroxybenzene moiety. Reduction of the C9 carbonyl by a short chain dehydrogenase/reductase initiates isochroman-3-one formation, affording cytosporones with cytotoxic and antimicrobial activity. Enoyl di- or trihydroxyphenylacetic acids are generated as shunt products, while isocroman-3,4-diones are formed by autoxidation. The cytosporone pathway offers novel polyketide biosynthetic enzymes for combinatorial synthetic biology to advance the production of "unnatural" natural products for drug discovery.
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Affiliation(s)
- Li Li
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- College of Life Science, Yangtze University, Jingzhou 434025, P. R. China
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Hang Liu
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Patricia Espinosa-Artiles
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Ya-ming Xu
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Chen Wang
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jose Manuel Verdugo Robles
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Tiago Antunes Paz
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Marielle Cascaes Inácio
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Fusheng Chen
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, P. R. China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- VTT Technical Research Center of Finland Ltd., Espoo 02150, Finland
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20
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Liu H, Liang S, Zhu M, Shi W, Xu C, Wei W, Zhan R, Ma D. A fused hybrid enzyme of 8-hydroxygeraniol oxidoreductase (8HGO) from Gardenia jasminoides and iridoid synthase (ISY) from Catharanthus roseus significantly enhances nepetalactol and iridoid production. PLANTA 2024; 259:62. [PMID: 38319463 DOI: 10.1007/s00425-023-04287-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/12/2023] [Indexed: 02/07/2024]
Abstract
MAIN CONCLUSION The operation of 8HGO-ISY fusion enzymes can increase nepetalactol flux to iridoid biosynthesis, and the Gj8HGO-CrISY expression in Gardenia jasminoides indicates that seco-iridoids and closed-ring iridoids share a nepetalactol pool. Nepetalactol is a common precursor of (seco)iridoids and their derivatives, which are a group of noncanonical monoterpenes. Functional characterization of an 8HGO (8-hydroxygeraniol oxidoreductase) from Catharanthus roseus, a seco-iridoids producing plant, has been reported; however, the 8HGO from G. jasminoides with plenty of closed-ring iridoids remains uninvestigated. In this work, a Gj8HGO was cloned and biochemically characterized. In addition, the relatively low production of nepetalactol in plants and engineered microbial host is likely to be attributed to the fact that Cr8HGO and CrISY (iridoid synthase) are substrate-promiscuous enzymes catalyzing unexpected substrates to the undesired products. Herein, a bifunctional enzyme consisting of an 8HGO fused to an ISY was designed for the proximity to the substrate and recycling of NADP+ and NADPH cofactor to reduce the undesired intermediate in the synthesis of nepetalactol. Of four fusion enzymes (i.e., Gj8HGO-GjISY, Gj8HGO-GjISY2, Gj8HGO-GjISY4, and Gj8HGO-CrISY), interestingly, only the last one can enable cascade reaction to form cis-trans-nepetalactol. Furthermore, we establish a reliable Agrobacterium-mediated transformation system. The expression of Gj8HGO-CrISY in G. jasminoides led to a significant enhancement of nepetalactol production, about 19-fold higher than that in wild-type plants, which further resulted in the twofold to fivefold increase of total iridoids and representative iridoid such as geniposide, indicating that seco-iridoids in C. roseus and closed-ring iridoids in G. jasminoides share a nepetalactol pool. All results suggest that 8HGO and ISY can be manipulated to maximize metabolic flux for nepetalactol and iridoid production.
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Affiliation(s)
- Hui Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Shuangcheng Liang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Meixian Zhu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Wenjing Shi
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chong Xu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Wuke Wei
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Dongming Ma
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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21
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Kato R, Takenaka Y, Ohno Y, Kihara A. Catalytic mechanism of trans-2-enoyl-CoA reductases in the fatty acid elongation cycle and its cooperative action with fatty acid elongases. J Biol Chem 2024; 300:105656. [PMID: 38224948 PMCID: PMC10864336 DOI: 10.1016/j.jbc.2024.105656] [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: 09/24/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
The fatty acid (FA) elongation cycle produces very-long-chain FAs with ≥C21, which have unique physiological functions. Trans-2-enoyl-CoA reductases (yeast, Tsc13; mammals, TECR) catalyze the reduction reactions in the fourth step of the FA elongation cycle and in the sphingosine degradation pathway. However, their catalytic residues and coordinated action in the FA elongation cycle complex are unknown. To reveal these, we generated and analyzed Ala-substituted mutants of 15 residues of Tsc13. An in vitro FA elongation assay showed that nine of these mutants were less active than WT protein, with E91A and Y256A being the least active. Growth complementation analysis, measurement of ceramide levels, and deuterium-sphingosine labeling revealed that the function of the E91A mutant was substantially impaired in vivo. In addition, we found that the activity of FA elongases, which catalyze the first step of the FA elongation cycle, were reduced in the absence of Tsc13. Similar results were observed in Tsc13 E91A-expressing cells, which is attributable to reduced interaction between the Tsc13 E91A mutant and the FA elongases Elo2/Elo3. Finally, we found that E94A and Y248A mutants of human TECR, which correspond to E91A and Y256A mutants of Tsc13, showed reduced and almost no activity, respectively. Based on these results and the predicted three-dimensional structure of Tsc13, we speculate that Tyr256/Tyr248 of Tsc13/TECR is the catalytic residue that supplies a proton to trans-2-enoyl-CoAs. Our findings provide a clue concerning the catalytic mechanism of Tsc13/TECR and the coordinated action in the FA elongation cycle complex.
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Affiliation(s)
- Ryoya Kato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yuka Takenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yusuke Ohno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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22
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Cavuzic MT, Waldrop GL. Kinetic characterization of the N-terminal domain of Malonyl-CoA reductase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140986. [PMID: 38122963 DOI: 10.1016/j.bbapap.2023.140986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Climate change is driving a search for environmentally safe methods to produce chemicals used in ordinary life. One such molecule is 3-hydroxypropionic acid, which is a platform industrial chemical used as a precursor for a variety of other chemical end products. The biosynthesis of 3-hydroxypropionic acid can be achieved in recombinant microorganisms via malonyl-CoA reductase in two separate reactions. The reduction of malonyl-CoA by NADPH to form malonic semialdehyde is catalyzed in the C-terminal domain of malonyl-CoA reductase, while the subsequent reduction of malonic semialdehyde to 3-hydroxypropionic acid is accomplished in the N-terminal domain of the enzyme. A new assay for the reverse reaction of the N-terminal domain of malonyl-CoA reductase from Chloroflexus aurantiacus activity has been developed. This assay was used to determine the kinetic mechanism and for isotope effect studies. Kinetic characterization using initial velocity patterns revealed random binding of the substrates NADP+ and 3-hydroxypropionic acid. Isotope effects showed substrates react to give products faster than they dissociate and that the products of the reverse reaction, NADPH and malonic semialdehyde, have a low affinity for the enzyme. Multiple isotope effects suggest proton and hydride transfer occur in a concerted fashion. This detailed kinetic characterization of the reaction catalyzed by the N-terminal domain of malonyl-CoA reductase could aid in engineering of the enzyme to make the biosynthesis of 3-hydroxypropionic acid commercially competitive with its production from fossil fuels.
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Affiliation(s)
- Mirela Tkalcic Cavuzic
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Grover L Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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23
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Heinemann H, Zhang H, Cox RJ. Reductive Release from a Hybrid PKS-NRPS during the Biosynthesis of Pyrichalasin H. Chemistry 2024; 30:e202302590. [PMID: 37926691 DOI: 10.1002/chem.202302590] [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: 09/08/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Three central steps during the biosynthesis of cytochalasan precursors, including reductive release, Knoevenagel cyclisation and Diels Alder cyclisation are not yet understood at a detailed molecular level. In this work we investigated the reductive release step catalysed by a hybrid polyketide synthase non-ribosomal peptide synthetase (PKS-NRPS) from the pyrichalasin H pathway. Synthetic thiolesters were used as substrate mimics for in vitro studies with the isolated reduction (R) and holo-thiolation (T) domains of the PKS-NRPS hybrid PyiS. These assays demonstrate that the PyiS R-domain mainly catalyses an NADPH-dependent reductive release of an aldehyde intermediate that quickly undergoes spontaneous Knoevenagel cyclisation. The R-domain can only process substrates that are covalently bound to the phosphopantetheine thiol of the upstream T-domain, but it shows little selectivity for the polyketide.
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Affiliation(s)
- Henrike Heinemann
- Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Haili Zhang
- Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
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24
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Qian L, Mohanty P, Jayaraman A, Mittal J, Zhu X. Specific residues and conformational plasticity define the substrate specificity of short-chain dehydrogenases/reductases. J Biol Chem 2024; 300:105596. [PMID: 38145745 PMCID: PMC10827548 DOI: 10.1016/j.jbc.2023.105596] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023] Open
Abstract
Short-chain dehydrogenases/reductases (SDRs) are one of the most prevalent enzyme families distributed among the sequenced microorganisms. Despite the presence of a conserved catalytic tetrad and high structural similarity, these enzymes exhibit different substrate specificities. The insufficient knowledge regarding the amino acids underlying substrate specificity hinders the understanding of the SDRs' roles in diverse and significant biological processes. Here, we performed bioinformatic analysis, molecular modeling, and mutagenesis studies to identify the key residues that regulate the substrate specificities of two homologous microbial SDRs (i.e., DesE and KduD). Further, we investigated the impact of altering the physicochemical properties of these amino acids on enzyme activity. Interestingly, molecular dynamics simulations also suggest a critical role of enzyme conformational flexibility in substrate recognition and catalysis. Overall, our findings improve the understanding of microbial SDR substrate specificity and shed light on future rational design of more efficient and effective biocatalysts.
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Affiliation(s)
- Liangyu Qian
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Department of Biomedical Engineering, Texas A&M University, College Station, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Department of Chemistry, Texas A&M University, College Station, USA; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, USA
| | - Xuejun Zhu
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, USA.
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25
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Wang YX, Cai XY, Liu JM, Han YT, Sui SY, Chen DW, Xie KB, Chen RD, Dai JG. Exploring the catalytic diversity of two short-chain dehydrogenases/reductases from Stachybotrys chartarum. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:102-111. [PMID: 38126332 DOI: 10.1080/10286020.2023.2288291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Short-chain dehydrogenase/reductases (SDRs) belong to the NAD(P)(H)-dependent oxidoreductase superfamily, which have various functions of catalyzing oxidation/reduction reactions and have been generally used as powerful biocatalysts in the production of pharmaceuticals. In this study, ScSDR1 and ScSDR2, two new SDRs have been identified and characterized from Stachybotrys chartarum 3.5365. Substrate scope investigation revealed that both of the enzymes possessed the ability to oxidize β-OH to ketone specifically, and exhibited substrate promiscuity and high stereo-selectivity for efficiently catalyzing the structurally different prochiral ketones to chiral alcohols. These findings not only suggest that ScSDR1 and ScSDR2 might be potent synthetic tools in drug research and development, but also provide good examples for further engineered enzymes with higher efficiency and stereo-selectivity.
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Affiliation(s)
- Yu-Xin Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xin-Yu Cai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ji-Mei Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yao-Tian Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song-Yang Sui
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Da-Wei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ke-Bo Xie
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ri-Dao Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jun-Gui Dai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs; NHC Key Laboratory of Biosynthesis of Natural Products, and Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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26
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Hu X, Liu W, Yan Y, Deng H, Cai Y. Tropinone reductase: A comprehensive review on its role as the key enzyme in tropane alkaloids biosynthesis. Int J Biol Macromol 2023; 253:127377. [PMID: 37839598 DOI: 10.1016/j.ijbiomac.2023.127377] [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: 07/09/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
TAs, including hyoscyamine and scopolamine, were used to treat neuromuscular disorders ranging from nerve agent poisoning to Parkinson's disease. Tropinone reductase I (TR-I; EC 1.1.1.206) catalyzed the conversion of tropinone into tropine in the biosynthesis of TAs, directing the metabolic flow towards hyoscyamine and scopolamine. Tropinone reductase II (TR-II; EC 1.1.1.236) was responsible for the conversion of tropinone into pseudotropine, diverting the metabolic flux towards calystegine A3. The regulation of metabolite flow through both branches of the TAs pathway seemed to be influenced by the enzymatic activity of both enzymes and their accessibility to the precursor tropinone. The significant interest in the utilization of metabolic engineering for the efficient production of TAs has highlighted the importance of TRs as crucial enzymes that govern both the direction of metabolic flow and the yield of products. This review discussed recent advances for the TRs sources, properties, protein structure and biocatalytic mechanisms, and a detailed overview of its crucial role in the metabolism and synthesis of TAs was summarized. Furthermore, we conducted a detailed investigation into the evolutionary origins of these two TRs. A prospective analysis of potential challenges and applications of TRs was presented.
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Affiliation(s)
- Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Wenjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yi Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huaxiang Deng
- Center for Synthetic Biochemistry, Institute of Synthetic Biology, Institutes of Advanced Technologies, Shenzhen, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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27
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Kaur A, Pickles IB, Sharma M, Madeido Soler N, Scott NE, Pidot SJ, Goddard-Borger ED, Davies GJ, Williams SJ. Widespread Family of NAD +-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. J Am Chem Soc 2023; 145:28216-28223. [PMID: 38100472 PMCID: PMC10755693 DOI: 10.1021/jacs.3c11126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+ as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+ provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.
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Affiliation(s)
- Arashdeep Kaur
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Isabelle B. Pickles
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Niccolay Madeido Soler
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nichollas E. Scott
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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28
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Walker MA, Chen H, Yadav A, Ritterhoff J, Villet O, McMillen T, Wang Y, Purcell H, Djukovic D, Raftery D, Isoherranen N, Tian R. Raising NAD + Level Stimulates Short-Chain Dehydrogenase/Reductase Proteins to Alleviate Heart Failure Independent of Mitochondrial Protein Deacetylation. Circulation 2023; 148:2038-2057. [PMID: 37965787 PMCID: PMC10842390 DOI: 10.1161/circulationaha.123.066039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Strategies to increase cellular NAD+ (oxidized nicotinamide adenine dinucleotide) level have prevented cardiac dysfunction in multiple models of heart failure, but molecular mechanisms remain unclear. Little is known about the benefits of NAD+-based therapies in failing hearts after the symptoms of heart failure have appeared. Most pretreatment regimens suggested mechanisms involving activation of sirtuin, especially Sirt3 (sirtuin 3), and mitochondrial protein acetylation. METHODS We induced cardiac dysfunction by pressure overload in SIRT3-deficient (knockout) mice and compared their response with nicotinamide riboside chloride treatment with wild-type mice. To model a therapeutic approach, we initiated the treatment in mice with established cardiac dysfunction. RESULTS We found nicotinamide riboside chloride improved mitochondrial function and blunted heart failure progression. Similar benefits were observed in wild-type and knockout mice. Boosting NAD+ level improved the function of NAD(H) redox-sensitive SDR (short-chain dehydrogenase/reductase) family proteins. Upregulation of Mrpp2 (mitochondrial ribonuclease P protein 2), a multifunctional SDR protein and a subunit of mitochondrial ribonuclease P, improves mitochondrial DNA transcripts processing and electron transport chain function. Activation of SDRs in the retinol metabolism pathway stimulates RXRα (retinoid X receptor α)/PPARα (proliferator-activated receptor α) signaling and restores mitochondrial oxidative metabolism. Downregulation of Mrpp2 and impaired mitochondrial ribonuclease P were found in human failing hearts, suggesting a shared mechanism of defective mitochondrial biogenesis in mouse and human heart failure. CONCLUSIONS These findings identify SDR proteins as important regulators of mitochondrial function and molecular targets of NAD+-based therapy. Furthermore, the benefit is observed regardless of Sirt3-mediated mitochondrial protein deacetylation, a widely held mechanism for NAD+-based therapy for heart failure. The data also show that NAD+-based therapy can be useful in pre-existing heart failure.
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Affiliation(s)
- Matthew A. Walker
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Hongye Chen
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Aprajita Yadav
- Department of Pharmaceutics, School of Pharmacy, University
of Washington, Seattle, WA 98195
| | - Julia Ritterhoff
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Outi Villet
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Tim McMillen
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Yuliang Wang
- Department of Computer Science & Engineering,
University of Washington, Seattle, WA 98195
| | - Hayley Purcell
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Danijel Djukovic
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Daniel Raftery
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University
of Washington, Seattle, WA 98195
| | - Rong Tian
- Mitochondria and Metabolism Center, Department of
Anesthesiology & Pain Medicine, University of Washington, Seattle, WA
98109
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Sharma G, Zee PC, Zea L, Curtis PD. Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight. BMC Genomics 2023; 24:782. [PMID: 38102595 PMCID: PMC10725011 DOI: 10.1186/s12864-023-09799-z] [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: 08/11/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
In microgravity, bacteria undergo intriguing physiological adaptations. There have been few attempts to assess global bacterial physiological responses to microgravity, with most studies only focusing on a handful of individual systems. This study assessed the fitness of each gene in the genome of the aromatic compound-degrading Alphaproteobacterium Novosphingobium aromaticavorans during growth in spaceflight. This was accomplished using Comparative TnSeq, which involves culturing the same saturating transposon mutagenized library under two different conditions. To assess gene fitness, a novel comparative TnSeq analytical tool was developed, named TnDivA, that is particularly useful in leveraging biological replicates. In this approach, transposon diversity is represented numerically using a modified Shannon diversity index, which was then converted into effective transposon density. This transformation accounts for variability in read distribution between samples, such as cases where reads were dominated by only a few transposon inserts. Effective density values were analyzed using multiple statistical methods, including log2-fold change, least-squares regression analysis, and Welch's t-test. The results obtained across applied statistical methods show a difference in the number of significant genes identified. However, the functional categories of genes important to growth in microgravity showed similar patterns. Lipid metabolism and transport, energy production, transcription, translation, and secondary metabolite biosynthesis and transport were shown to have high fitness during spaceflight. This suggests that core metabolic processes, including lipid and secondary metabolism, play an important role adapting to stress and promoting growth in microgravity.
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Affiliation(s)
- Gayatri Sharma
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA
| | - Peter C Zee
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA
| | - Luis Zea
- Aerospace Engineering Sciences, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, 402 Shoemaker Hall, University, MS, 38677, USA.
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30
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Liu Y, Luo S, Yang Z, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A, Zhu D. Capsular polysaccharide determines the serotyping of Riemerella anatipestifer. Microbiol Spectr 2023; 11:e0180423. [PMID: 37823636 PMCID: PMC10714938 DOI: 10.1128/spectrum.01804-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Riemerella anatipestifer (R. anatipestifer) is one of the most important veterinary pathogens with at least 21 serotypes. However, the exact polysaccharide(s) that determine R. anatipestifer serotype is still unknown. This study has provided a preliminary exploration of the relationship between capsular polysaccharides and serotyping in R. anatipestifer and suggests possible directions for further investigation of the genetic basis of serotypes in this bacterium.
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Affiliation(s)
- Yanling Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Shuxin Luo
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
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Bhargavi G, Mallakuntla MK, Kale D, Tiwari S. Rv0687 a Putative Short-Chain Dehydrogenase is indispensable for pathogenesis of Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571312. [PMID: 38168250 PMCID: PMC10760034 DOI: 10.1101/2023.12.12.571312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mycobacterium tuberculosis (Mtb), a successful human pathogen, resides in host sentinel cells and combats the stressful intracellular environment induced by reactive oxygen and nitrogen species during infection. Mtb employs several evasion mechanisms in the face of the host as a survival strategy, including detoxifying enzymes as short-chain dehydrogenases/ reductases (SDRs) to withstand host-generated insults. In this study, using specialized transduction we have generated a Rv0687 deletion mutant and its complemented strain and investigated the functional role of Rv0687, a member of SDRs family genes in Mtb pathogenesis. Wildtype (WT) and mutant Mtb strain lacking Rv0687 (RvΔ0687) were tested for in-vitro stress response and in-vivo survival in macrophages and mice models of infection. The study demonstrates that Rv0687 is crucial for sustaining bacterial growth in nutrition-limited conditions. The deletion of Rv0687 elevated the sensitivity of Mtb to oxidative and nitrosative stress-inducing agents. Furthermore, the lack of Rv0687 compromised the survival of Mtb in primary bone marrow macrophages and led to an increase in the levels of the secreted proinflammatory cytokines TNF-α, and MIP-1α. Interestingly, the growth of WT and RvΔ0687 was similar in the lungs of infected immunocompromised mice however, a significant reduction in RvΔ0687 growth was observed in the spleen of immunocompromised Rag -/- mice at 4 weeks post-infection. Moreover Rag -/- mice infected with RvΔ0687 survived longer compared to WT Mtb strain. Additionally, we observed significant reduction in bacterial burden in spleens and lungs of immunocompetent C57BL/6 mice infected with RvΔ0687 compared to complemented and WT Mtb strains. Collectively, this study reveals that Rv0687 plays a role in Mtb pathogenesis.
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Vogel U, Da Costa M, Alvarez Quispe C, Stragier R, Joosten HJ, Beerens K, Desmet T. The Conversion of UDP-Glc to UDP-Man: In Silico and Biochemical Exploration To Improve the Catalytic Efficiency of CDP-Tyvelose C2-Epimerases. Chembiochem 2023; 24:e202300549. [PMID: 37728070 DOI: 10.1002/cbic.202300549] [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: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
A promiscuous CDP-tyvelose 2-epimerase (TyvE) from Thermodesulfatator atlanticus (TaTyvE) belonging to the nucleotide sugar active short-chain dehydrogenase/reductase superfamily (NS-SDRs) was recently discovered. TaTyvE performs the slow conversion of NDP-glucose (NDP-Glc) to NDP-mannose (NDP-Man). Here, we present the sequence fingerprints that are indicative of the conversion of UDP-Glc to UDP-Man in TyvE-like enzymes based on the heptagonal box motifs. Our data-mining approach led to the identification of 11 additional TyvE-like enzymes for the conversion of UDP-Glc to UDP-Man. We characterized the top two wild-type candidates, which show a 15- and 20-fold improved catalytic efficiency, respectively, on UDP-Glc compared to TaTyvE. In addition, we present a quadruple variant of one of the identified enzymes with a 70-fold improved catalytic efficiency on UDP-Glc compared to TaTyvE. These findings could help the design of new nucleotide production pathways starting from a cheap sugar substrate like glucose or sucrose.
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Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Carlos Alvarez Quispe
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Robin Stragier
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511 AA, Nijmegen, The Netherlands
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
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33
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Mao Z, Fleming JR, Mayans O, Frey J, Schleheck D, Schink B, Müller N. AMP-dependent phosphite dehydrogenase, a phosphorylating enzyme in dissimilatory phosphite oxidation. Proc Natl Acad Sci U S A 2023; 120:e2309743120. [PMID: 37922328 PMCID: PMC10636320 DOI: 10.1073/pnas.2309743120] [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: 06/14/2023] [Accepted: 09/20/2023] [Indexed: 11/05/2023] Open
Abstract
Oxidation of phosphite (HPO32-) to phosphate (HPO42-) releases electrons at a very low redox potential (E0'= -690 mV) which renders phosphite an excellent electron donor for microbial energy metabolism. To date, two pure cultures of strictly anaerobic bacteria have been isolated that run their energy metabolism on the basis of phosphite oxidation, the Gram-negative Desulfotignum phosphitoxidans (DSM 13687) and the Gram-positive Phosphitispora fastidiosa (DSM 112739). Here, we describe the key enzyme for dissimilatory phosphite oxidation in these bacteria. The enzyme catalyzed phosphite oxidation in the presence of adenosine monophosphate (AMP) to form adenosine diphosphate (ADP), with concomitant reduction of oxidized nicotinamide adenine dinucleotide (NAD+) to reduced nicotinamide adenine dinucleotide (NADH). The enzyme of P. fastidiosa was heterologously expressed in Escherichia coli. It has a molecular mass of 35.2 kDa and a high affinity for phosphite and NAD+. Its activity was enhanced more than 100-fold by addition of ADP-consuming adenylate kinase (myokinase) to a maximal activity between 30 and 80 mU x mg protein-1. A similar NAD-dependent enzyme oxidizing phosphite to phosphate with concomitant phosphorylation of AMP to ADP is found in D. phosphitoxidans, but this enzyme could not be heterologously expressed. Based on sequence analysis, these phosphite-oxidizing enzymes are related to nucleotide-diphosphate-sugar epimerases and indeed represent AMP-dependent phosphite dehydrogenases (ApdA). A reaction mechanism is proposed for this unusual type of substrate-level phosphorylation reaction.
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Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jennifer R. Fleming
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance78457, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance78457, Germany
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McGary LC, Regan GL, Bearne SL. Reactive architecture profiling with a methyl acyl phosphate electrophile. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140945. [PMID: 37536394 DOI: 10.1016/j.bbapap.2023.140945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Activity-based protein profiling has facilitated the study of the activity of enzymes in proteomes, inhibitor development, and identification of enzymes that share mechanistic and active-site architectural features. Since methyl acyl phosphate monoesters act as electrostatically selective anionic electrophiles for the covalent modification of nucleophiles that reside adjacent to cationic sites in proteins, we synthesized methyl hex-5-ynoyl phosphate (MHP) to broadly target such protein architectures. After treating the soluble proteome of Paucimonas lemoignei with MHP, biotinylating the resulting acylated proteins using click chemistry, enriching the protein adducts using streptavidin, and analyzing the proteins by LC-MS/MS, a set of 240 enzymes and 132 non-enzyme proteins were identified for a wide spectrum of biological processes and from all 7 enzyme classes. Among those enzymes identified, β-hydroxybutyrate dehydrogenase (PlHBDH) and CTP synthase (E. coli orthologue, EcCTPS) were purified as recombinant enzymes and their rates of inactivation and sites of modification by MHP and methyl acetyl phosphate (MAP) were characterized. MHP reacted more slowly with these proteins than MAP but exhibited greater specificity, despite its lack of multiple binding determinants. Generally, MAP modified more surface residues than MHP. MHP specifically modified Ser 146, Lys 156, and Lys 163 at the active site of PlHBDH. MHP and MAP modified numerous residues of EcCTPS with CTP furnishing the greatest level of protection against MHP- and MAP-dependent modification and inactivation, respectively, followed by ATP and glutamine. Overall, MHP served as an effective probe to identify proteins that are potentially amenable to inhibition by methyl acyl phosphates.
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Affiliation(s)
- Laura C McGary
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Gemma L Regan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Kono H, Hara S, Furuta T, Ichinose H. Binding profile of quinonoid-dihydrobiopterin to quinonoid-dihydropteridine reductase examined by in silico and in vitro analyses. J Biochem 2023; 174:441-450. [PMID: 37540845 DOI: 10.1093/jb/mvad062] [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: 06/08/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023] Open
Abstract
Quinonoid dihydropteridine reductase (QDPR) catalyses the reduction of quinonoid-form dihydrobiopterin (qBH2) to tetrahydrobiopterin (BH4). BH4 metabolism is a drug target for neglected tropical disorders because trypanosomatid protozoans, including Leishmania and Trypanosoma, require exogenous sources of biopterin for growth. Although QDPR is a key enzyme for maintaining intracellular BH4 levels, the precise catalytic properties and reaction mechanisms of QDPR are poorly understood due to the instability of quinonoid-form substrates. In this study, we analysed the binding profile of qBH2 to human QDPR in combination with in silico and in vitro methods. First, we performed docking simulation of qBH2 to QDPR to obtain possible binding modes of qBH2 at the active site of QDPR. Then, among them, we determined the most plausible binding mode using molecular dynamics simulations revealing its atomic-level interactions and confirmed it with the in vitro assay of mutant enzymes. Moreover, it was found that not only qBH2 but also quinonoid-form dihydrofolate (qDHF) could be potential physiological substrates for QDPR, suggesting that QDPR may be a bifunctional enzyme. These findings in this study provide important insights into biopterin and folate metabolism and would be useful for developing drugs for neglected tropical diseases.
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Key Words
- molecular dynamics
- pteridine reductase
- quinonoid-dihydropteridine reductase
- tetrahydrobiopterinAbbreviations:
AAAH, aromatic aminoacid hydroxylase;
BH2, dihydrobiopterin; BH4, tetrahydrobiopterin; DHFR, dihydrofolate reductase; NADH, nicotinamide adenine dinucleotide; NAM, nicotinamide; MD, molecular dynamics; PT, pterin; PTR1, pteridine reductase 1; qBH2; quinonoid dihydrobiopterin; qDHF, quinonoid dihydrofolate; QDPR, quinonoid dihydropteridine reductase; SDR, short-chain dehydrogenase/reductase; THF, tetrahydrofolate
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Affiliation(s)
- Haruka Kono
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B7, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Hara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B7, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B7, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroshi Ichinose
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B7, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Rajput A, Manna T, Husain SM. Anthrol reductases: discovery, role in biosynthesis and applications in natural product syntheses. Nat Prod Rep 2023; 40:1672-1686. [PMID: 37475701 DOI: 10.1039/d3np00027c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Covering: up to 2023Short-chain dehydrogenase/reductases (SDR) are known to catalyze the regio- and stereoselective reduction of a variety of substrate types. Investigations of the deoxygenation of emodin to chrysophanol has led to the discovery of the anthrol reductase activity of an SDR, MdpC involved in monodictyphenone biosynthesis of Aspergillus nidulans and provided access to (R)-dihydroanthracenone, a putative biosynthetic intermediate. This facilitated the identification of several MdpC-related enzymes involved in the biosynthesis of aflatoxins B1, cladofulvin, neosartorin, agnestins and bisanthraquinones. Because of their ability to catalyze the reduction of hydroanthraquinone (anthrols) using NADPH, they were named anthrol reductases. This review provides a comprehensive summary of all the anthrol reductases that have been identified and characterized in the last decade along with their role in the biosynthesis of natural products. In addition, the applications of these enzymes towards the chemoenzymatic synthesis of flavoskyrins, modified bisanthraquinones, 3-deoxy anthraquinones, chiral cycloketones and β-halohydrins have been discussed.
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Affiliation(s)
- Anshul Rajput
- Department of Biological and Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India.
| | - Tanaya Manna
- Department of Biological and Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India.
| | - Syed Masood Husain
- Department of Biological and Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India.
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Sivasankar S, Premnath MA, Boppe A, Grobusch MP, Jeyaraj S. Screening of MMV pandemic response and pathogen box compounds against pan-drug-resistant Klebsiella pneumoniae to identify potent inhibitory compounds. New Microbes New Infect 2023; 55:101193. [PMID: 38046897 PMCID: PMC10690571 DOI: 10.1016/j.nmni.2023.101193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
Background The recent emergence of pan-drug-resistant (PDR) K. pneumoniae strains hinders the success rate of treatment procedures for patients. High mortality, extended duration of hospitalization with high costs is associated with such infections. Discovery and identification of new drugs are inevitable to combat PDR clinical pathogens. We aim to identify and evaluate new compounds in vitro against a PDR clinical K. pneumoniae isolate using compounds of Pathogen Box and Pandemic Response Box from Medicines for Malaria Venture (MMV). Methods The PDR strain was initially screened with the 601 compounds from both Boxes at 10 μM concentration. Formation of dormant cells against the drug activity was assessed using persister assay. MIC was determined for the drugs inhibiting PDR K. pneumoniae during initial screening. Results Five compounds were identified to inhibit the test strain. MMV1580854 (94.60 %), MMV1579788 (94.65 %), MMV1578574 (eravacycline; 93.13 %), MMV1578566 (epetraborole; 95.29 %) and MMV1578564 (96.32 %) were able to exhibit a higher percentage of growth inhibition. Persisters were found to be growing in a range from 104 to 107 CFU/ml. Minimum inhibitory concentrations (MIC) of all compounds were ≥ 2 μM except for MMV1579788, which had a MIC of ≥ 5 μM. Conclusion Five novel compounds were identified against the highly evolved pan-drug-resistant K. pneumoniae. Among the five, epetraborole andMMV1578564 were identified as highly potent based on the persister frequency and MICs. The pan-drug resistant clinical isolate used in this study was found to be acting differently from the reference or wild type strains against the test compounds in a previous study.
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Affiliation(s)
- Seshan Sivasankar
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
| | - Mari Abinaya Premnath
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
| | - Appalaraju Boppe
- Department of Microbiology, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Martin Peter Grobusch
- Centre de Recherches Médicales de Lambaréné CERMEL, Hospital Albert Schweitzer, BP 242, Lambaréné, Gabon
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
- Institut für Tropenmedizin, Eberhard Karls Universität Tübingen and German Center for Infection Research (DZIF), Tubingen, Germany
- Masanga Medical Research Unit, Masanga, Sierra Leone
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sankarganesh Jeyaraj
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
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Tian J, Boggs DG, Donnan PH, Barroso GT, Garcia AA, Dowling DP, Buss JA, Bridwell-Rabb J. The NADH recycling enzymes TsaC and TsaD regenerate reducing equivalents for Rieske oxygenase chemistry. J Biol Chem 2023; 299:105222. [PMID: 37673337 PMCID: PMC10579966 DOI: 10.1016/j.jbc.2023.105222] [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: 05/27/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023] Open
Abstract
Many microorganisms use both biological and nonbiological molecules as sources of carbon and energy. This resourcefulness means that some microorganisms have mechanisms to assimilate pollutants found in the environment. One such organism is Comamonas testosteroni, which metabolizes 4-methylbenzenesulfonate and 4-methylbenzoate using the TsaMBCD pathway. TsaM is a Rieske oxygenase, which in concert with the reductase TsaB consumes a molar equivalent of NADH. Following this step, the annotated short-chain dehydrogenase/reductase and aldehyde dehydrogenase enzymes TsaC and TsaD each regenerate a molar equivalent of NADH. This co-occurrence ameliorates the need for stoichiometric addition of reducing equivalents and thus represents an attractive strategy for integration of Rieske oxygenase chemistry into biocatalytic applications. Therefore, in this work, to overcome the lack of information regarding NADH recycling enzymes that function in partnership with Rieske non-heme iron oxygenases (Rieske oxygenases), we solved the X-ray crystal structure of TsaC to a resolution of 2.18 Å. Using this structure, a series of substrate analog and protein variant combination reactions, and differential scanning fluorimetry experiments, we identified active site features involved in binding NAD+ and controlling substrate specificity. Further in vitro enzyme cascade experiments demonstrated the efficient TsaC- and TsaD-mediated regeneration of NADH to support Rieske oxygenase chemistry. Finally, through in-depth bioinformatic analyses, we illustrate the widespread co-occurrence of Rieske oxygenases with TsaC-like enzymes. This work thus demonstrates the utility of these NADH recycling enzymes and identifies a library of short-chain dehydrogenase/reductase enzyme prospects that can be used in Rieske oxygenase pathways for in situ regeneration of NADH.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gage T Barroso
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Joshua A Buss
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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Kawakami R, Takami N, Hayashi J, Yoneda K, Ohmori T, Ohshima T, Sakuraba H. First crystal structure of an NADP +-dependent l-arginine dehydrogenase belonging to the μ-crystallin family. Int J Biol Macromol 2023; 249:126070. [PMID: 37524275 DOI: 10.1016/j.ijbiomac.2023.126070] [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: 04/28/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the μ-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP+ and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP+ was postulated. However, the residues recognizing the α-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the α-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.
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Affiliation(s)
- Ryushi Kawakami
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1, Minamijosanjima-cho, Tokushima 770-8513, Tokushima, Japan
| | - Naoki Takami
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Junji Hayashi
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1, Minamijosanjima-cho, Tokushima 770-8513, Tokushima, Japan
| | - Kazunari Yoneda
- Department of Food and Life Sciences, School of Agriculture, Tokai University, 871-12 Sugido, Mashiki-machi, Kamimashiki-gun, Kumamoto 861-2205, Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.
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Wang J, Deng Z, Liang J, Wang Z. Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming. Nat Prod Rep 2023; 40:1498-1520. [PMID: 37581222 DOI: 10.1039/d3np00015j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Time span of literature covered: up to mid-2023Iterative type I polyketide synthases (iPKSs) are outstanding natural chemists: megaenzymes that repeatedly utilize their catalytic domains to synthesize complex natural products with diverse bioactivities. Perhaps the most fascinating but least understood question about type I iPKSs is how they perform the iterative yet programmed reactions in which the usage of domain combinations varies during the synthetic cycle. The programmed patterns are fulfilled by multiple factors, and strongly influence the complexity of the resulting natural products. This article reviews selected reports on the structural enzymology of iPKSs, focusing on the individual domain structures followed by highlighting the representative programming activities that each domain may contribute.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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Lewis JA, Zhang B, Harza R, Palmer N, Sarath G, Sattler SE, Twigg P, Vermerris W, Kang C. Structural Similarities and Overlapping Activities among Dihydroflavonol 4-Reductase, Flavanone 4-Reductase, and Anthocyanidin Reductase Offer Metabolic Flexibility in the Flavonoid Pathway. Int J Mol Sci 2023; 24:13901. [PMID: 37762209 PMCID: PMC10531346 DOI: 10.3390/ijms241813901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Flavonoids are potent antioxidants that play a role in defense against pathogens, UV-radiation, and the detoxification of reactive oxygen species. Dihydroflavonol 4-reductase (DFR) and flavanone 4-reductase (FNR) reduce dihydroflavonols and flavanones, respectively, using NAD(P)H to produce flavan-(3)-4-(di)ols in flavonoid biosynthesis. Anthocyanidin reductase (ANR) reduces anthocyanidins to flavan-3-ols. In addition to their sequences, the 3D structures of recombinant DFR, FNR and ANR from sorghum and switchgrass showed a high level of similarity. The catalytic mechanism, substrate-specificity and key residues of three reductases were deduced from crystal structures, site-directed mutagenesis, molecular docking, kinetics, and thermodynamic ana-lyses. Although DFR displayed its highest activity against dihydroflavonols, it also showed activity against flavanones and anthocyanidins. It was inhibited by the flavonol quercetin and high concentrations of dihydroflavonols/flavonones. SbFNR1 and SbFNR2 did not show any activity against dihydroflavonols. However, SbFNR1 displayed activity against flavanones and ANR activity against two anthocyanidins, cyanidin and pelargonidin. Therefore, SbFNR1 and SbFNR2 could be specific ANR isozymes without delphinidin activity. Sorghum has high concentrations of 3-deoxyanthocyanidins in vivo, supporting the observed high activity of SbDFR against flavonols. Mining of expression data indicated substantial induction of these three reductase genes in both switchgrass and sorghum in response to biotic stress. Key signature sequences for proper DFR/ANR classification are proposed and could form the basis for future metabolic engineering of flavonoid metabolism.
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Affiliation(s)
- Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Rishi Harza
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
| | - Nathan Palmer
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Gautam Sarath
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Scott E. Sattler
- Wheat, Sorghum, Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA; (N.P.); (G.S.); (S.E.S.)
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA;
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA;
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (B.Z.)
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Keeler AM, Petruzziello PE, Boger EG, D'Ambrosio HK, Derbyshire ER. Exploring the Chain Release Mechanism from an Atypical Apicomplexan Polyketide Synthase. Biochemistry 2023; 62:2677-2688. [PMID: 37556730 DOI: 10.1021/acs.biochem.3c00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Polyketide synthases (PKSs) are megaenzymes that form chemically diverse polyketides and are found within the genomes of nearly all classes of life. We recently discovered the type I PKS from the apicomplexan parasite Toxoplasma gondii, TgPKS2, which contains a unique putative chain release mechanism that includes ketosynthase (KS) and thioester reductase (TR) domains. Our bioinformatic analysis of the thioester reductase of TgPKS2, TgTR, suggests differences compared to other systems and hints at a possibly conserved release mechanism within the apicomplexan subclass Coccidia. To evaluate this release module, we first isolated TgTR and observed that it is capable of 4 electron (4e-) reduction of octanoyl-CoA to the primary alcohol, octanol, utilizing NADH. TgTR was also capable of generating octanol in the presence of octanal and NADH, but no reactions were observed when NADPH was supplied as a cofactor. To biochemically characterize the protein, we measured the catalytic efficiency of TgTR using a fluorescence assay and determined the TgTR binding affinity for cofactor and substrates using isothermal titration calorimetry (ITC). We additionally show that TgTR is capable of reducing an acyl carrier protein (ACP)-tethered substrate by liquid chromatography mass spectrometry and determine that TgTR binds to holo-TgACP4, its predicted cognate ACP, with a KD of 5.75 ± 0.77 μM. Finally, our transcriptional analysis shows that TgPKS2 is upregulated ∼4-fold in the parasite's cyst-forming bradyzoite stage compared to tachyzoites. Our study identifies features that distinguish TgPKS2 from well-characterized systems in bacteria and fungi and suggests it aids the T. gondii cyst stage.
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Affiliation(s)
- Aaron M Keeler
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Porter E Petruzziello
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth G Boger
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Hannah K D'Ambrosio
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
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Liu Y, Yamamoto T, Kohaya N, Yamamoto K, Okano K, Sumiyoshi T, Hasegawa Y, Lau PCK, Iwaki H. Cloning of two gene clusters involved in the catabolism of 2,4-dinitrophenol by Paraburkholderia sp. strain KU-46 and characterization of the initial DnpAB enzymes and a two-component monooxygenases DnpC1C2. J Biosci Bioeng 2023; 136:223-231. [PMID: 37344279 DOI: 10.1016/j.jbiosc.2023.05.013] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
Little is currently known about the metabolism of the industrial pollutant 2,4-dinitrophenol (DNP), particularly among gram-negative bacteria. In this study, we identified two non-contiguous genetic loci spanning 22 kb of Paraburkholderia (formerly Burkholderia) sp. strain KU-46. Additionally, we characterized four key initial genes (dnpA, dnpB, and dnpC1C2) responsible for DNP degradation, providing molecular and biochemical evidence for the degradation of DNP via the formation of 4-nitrophenol (NP), a pathway that is unique among DNP utilizing bacteria. Reverse transcription polymerase chain reaction (PCR) analysis indicated that dnpA, which encodes the initial hydride transferase, and dnpB which encodes a nitrite-eliminating enzyme, were induced by DNP and organized in an operon. Moreover, we purified DnpA and DnpB from recombinant Escherichia coli to demonstrate their effect on the transformation of DNP to NP through the formation of a hydride-Meisenheimer complex of DNP, designated as H--DNP. The function of DnpB appears new since all homologs of the DnpB sequences in the protein database are annotated as putative nitrate ABC transporter substrate-binding proteins. The gene cluster responsible for the degradation of DNP after NP formation was designated dnpC1C2DXFER, and DnpC1 and DnpC2 were functionally characterized as the FAD reductase and oxygenase components of the two-component DNP monooxygenase, respectively. By elucidating the hqdA1A2BCD gene cluster, we are now able to delineate the final degradation pathway of hydroquinone to β-ketoadipate before it enters the tricarboxylic acid cycle.
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Affiliation(s)
- Yaxuan Liu
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Nozomi Kohaya
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Kota Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Kenji Okano
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Takaaki Sumiyoshi
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Peter C K Lau
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan.
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Lin X, Huang L, Liang H, Hou C, Ling X, Chen Y, Yang P, Wu Q, Zhao H, Wu S, Zhan R, Ma D, Yang J. Genome-wide identification and functional characterization of borneol dehydrogenases in Wurfbainia villosa. PLANTA 2023; 258:69. [PMID: 37608037 DOI: 10.1007/s00425-023-04221-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
MAIN CONCLUSION Genome-wide screening of short-chain dehydrogenases/reductases (SDR) family reveals functional diversification of borneol dehydrogenase (BDH) in Wurfbainia villosa. Wurfbainia villosa is an important medicinal plant, the fruits of which accumulate abundant terpenoids, especially bornane-type including borneol and camphor. The borneol dehydrogenase (BDH) responsible for the conversion of borneol to camphor in W. villosa remains unknown. BDH is one member of short-chain dehydrogenases/reductases (SDR) family. Here, a total of 115 classical WvSDR genes were identified through genome-wide screening. These WvSDRs were unevenly distributed on different chromosomes. Seven candidate WvBDHs based on phylogenetic analysis and expression levels were selected for cloning. Of them, four BDHs can catalyze different configurations of borneol and other monoterpene alcohol substrates to generate the corresponding oxidized products. WvBDH1 and WvBDH2, preferred (+)-borneol to (-)-borneol, producing the predominant ( +)-camphor. WvBDH3 yielded approximate equivalent amount of (+)-camphor and (-)-camphor, in contrast, WvBDH4 generated exclusively (+)-camphor. The metabolic profiles of the seeds showed that the borneol and camphor present were in the dextrorotatory configuration. Enzyme kinetics and expression pattern in different tissues suggested WvBDH2 might be involved in the biosynthesis of camphor in W. villosa. All results will increase the understanding of functional diversity of BDHs.
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Affiliation(s)
- Xiaojing Lin
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Linxuan Huang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Huilin Liang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Chen Hou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510006, People's Republic of China
- Guangdong Academy of Forestry, Guangzhou, 510006, People's Republic of China
| | - Xuli Ling
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Yuanxia Chen
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Peng Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Qingwen Wu
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Haiying Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Sirong Wu
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Ruoting Zhan
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
| | - Dongming Ma
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
| | - Jinfen Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
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Arnold ND, Garbe D, Brück TB. Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp. Mar Drugs 2023; 21:448. [PMID: 37623729 PMCID: PMC10455584 DOI: 10.3390/md21080448] [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: 07/25/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
In nature, chitin, the most abundant marine biopolymer, does not accumulate due to the action of chitinolytic organisms, whose saccharification systems provide instructional blueprints for effective chitin conversion. Therefore, discovery and deconstruction of chitinolytic machineries and associated enzyme systems are essential for the advancement of biotechnological chitin valorization. Through combined investigation of the chitin-induced secretome with differential proteomic and transcriptomic analyses, a holistic system biology approach has been applied to unravel the chitin response mechanisms in the Gram-negative Jeongeupia wiesaeckerbachi. Hereby, the majority of the genome-encoded chitinolytic machinery, consisting of various glycoside hydrolases and a lytic polysaccharide monooxygenase, could be detected extracellularly. Intracellular proteomics revealed a distinct translation pattern with significant upregulation of glucosamine transport, metabolism, and chemotaxis-associated proteins. While the differential transcriptomic results suggested the overall recruitment of more genes during chitin metabolism compared to that of glucose, the detected protein-mRNA correlation was low. As one of the first studies of its kind, the involvement of over 350 unique enzymes and 570 unique genes in the catabolic chitin response of a Gram-negative bacterium could be identified through a three-way systems biology approach. Based on the cumulative data, a holistic model for the chitinolytic machinery of Jeongeupia spp. is proposed.
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Affiliation(s)
| | | | - Thomas B. Brück
- TUM School of Natural Sciences, Department of Chemistry, Technical University of Munich, Werner-Siemens Chair for Synthetic Biotechnology (WSSB), Lichtenbergstr. 4, 85748 Garching, Germany; (N.D.A.); (D.G.)
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Lee E, McLeod MJ, Redzic JS, Marcolin B, Thorne RE, Agarwal P, Eisenmesser EZ. Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle. Front Mol Biosci 2023; 10:1244587. [PMID: 37645217 PMCID: PMC10461185 DOI: 10.3389/fmolb.2023.1244587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that "clamps" the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Matthew J. McLeod
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Barbara Marcolin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Robert E. Thorne
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
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48
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Chen X, Sun S, Han X, Li C, Wang F, Nie B, Hou Z, Yang S, Ji J, Li G, Wang Y, Han X, Yue J, Li C, Li W, Zhang L, Yang D, Wang L. Multiomics comparison among populations of three plant sources of Amomi Fructus. HORTICULTURE RESEARCH 2023; 10:uhad128. [PMID: 37560015 PMCID: PMC10407604 DOI: 10.1093/hr/uhad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/11/2023] [Indexed: 08/11/2023]
Abstract
Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or varieties), including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX), or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region, Guangdong, to its current main production area, Yunnan, for >50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source species (or varieties) and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV. We also screened six candidate borneol dehydrogenases (BDHs) that potentially catalyzed borneol into camphor in WVV and functionally verified them. Highly expressed genes at the P2 stage of WVV, Wv05G1424 and Wv05G1438, were capable of catalyzing the formation of camphor from (+)-borneol, (-)-borneol and DL-isoborneol. Moreover, the BDH genes may experience independent evolution after acquiring the ancestral copies, and the following tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX, and WL are genetically differentiated, and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population (WVV-JH) than in its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, terpene synthesis (TPS) and BDH genes were selected among populations of multiple AF source species (or varieties) and between the top- and non-top-geoherb regions, which might explain the difference in metabolites between these populations. Our findings provide important guidance for the conservation, genetic improvement, and industrial development of the three source species (or varieties) and for identifying top-geoherbalism with molecular markers, and proper clinical application of AF.
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Affiliation(s)
- Xinlian Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Fengjiao Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Song Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Ge Li
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Yanqian Wang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Xiaoyu Han
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Jianjun Yue
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, 666100 Jinghong, China
| | - Cui Li
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, 530023 Nanning, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Lixia Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, 528200 Foshan, China
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Liu R, Wang L, Meng Y, Tian Y, Li F, Lu H. Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37467369 DOI: 10.1021/acs.jafc.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC50 reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.
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Affiliation(s)
- Ruiyuan Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Leng Wang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yue Meng
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yiyi Tian
- College of Science, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Science, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- College of Science, China Agricultural University, Beijing 100193, China
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50
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Gu T, Lu H, Liu H, Zhang G, Wang Y. Function discovery of a non-ribosomal peptide synthetase-like encoding gene in the nematode-trapping fungus Arthrobotrys oligospora. Front Microbiol 2023; 14:1210288. [PMID: 37520361 PMCID: PMC10373296 DOI: 10.3389/fmicb.2023.1210288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
In this study, the function of a non-ribosomal peptide synthetase-like (NRPS-like) encoding gene AOL_s00188g306 (g306) was investigated to reveal the association between NRPS and nematocidal activity in the nematode-trapping fungus Arthrobotrys oligospora. Sequence analysis indicated that the encoded product of g306 is an adenylation domain of non-ribosomal peptide synthetases and extended short-chain dehydrogenase/reductase domain-containing proteins, and displays a wide substrate spectrum. The Δg306 mutants were more sensitive to chemical stressors than the wild type. Disruption of g306 impeded the nematocidal efficiency of A. oligospora. Metabolomics analysis showed that secondary metabolite biosynthesis and lipid metabolism were altered in the mutants. The phenotypic changes in the mutants can be attributed to the down-regulation of various metabolites, including fatty acyls, prenol lipids, steroidsand steroid derivative, and amino acid derivatives, identified in the present study. This study investigated the association between the non-ribosomal polypeptide-encoding gene g306 and nematicidal activity in A. oligospora, providing a reference for resolving the predation mechanism of nematode-trapping fungus.
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Affiliation(s)
- Tiantian Gu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Hengqian Lu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Huiwen Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Guanghui Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
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