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Conrado AC, Lemes Jorge G, Rao RSP, Xu C, Xu D, Li-Beisson Y, Thelen JJ. Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230353. [PMID: 39343023 PMCID: PMC11449227 DOI: 10.1098/rstb.2023.0353] [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: 01/11/2024] [Revised: 07/22/2024] [Accepted: 09/02/2024] [Indexed: 10/01/2024] Open
Abstract
The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in Arabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein-protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in Arabidopsis thaliana and Chlamydomonas reinhardtii unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in Arabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Ana Caroline Conrado
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Gabriel Lemes Jorge
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - R. S. P. Rao
- Center for Bioinformatics, NITTE University Centre, Mangaluru575018, India
| | - Chunhui Xu
- Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille,Aix Marseille Univ, CEA Cadarache, Saint Paul-Lez-Durance13108, France
| | - Jay J. Thelen
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
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Zhou F, Zhang Y, Zhu Y, Zhou Q, Shi Y, Hu Q. Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase. SCIENCE ADVANCES 2024; 10:eado4880. [PMID: 39383219 PMCID: PMC11463273 DOI: 10.1126/sciadv.ado4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
Abstract
Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs.
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Affiliation(s)
- Fayang Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Yuanyuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yuyao Zhu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Qiang Zhou
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yigong Shi
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Qi Hu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
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Li T, Zhu F, Dai L, Hogstrand C, Li B, Yue X, Wang J, Yu L, Li D. Effects of 2-ethylhexyl diphenyl phosphate (EHDPP) on glycolipid metabolism in male adult zebrafish revealed by targeted lipidomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174248. [PMID: 38936724 DOI: 10.1016/j.scitotenv.2024.174248] [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: 05/08/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
The present study aims to evaluate the effects of 2-ethylhexyldiphenyl phosphate (EHDPP) on glycolipid metabolism in vivo. Adult male zebrafish were exposed to various concentrations (0, 1, 10, 100 and 250 μg/L) of EHDPP for 28 days, and changes in lipid and glucose levels were measured. Results indicated significant liver damages in the 100 and 250 μg/L EHDPP groups, which both exhibited significant decreases in hepatic somatic index (HSI), elevated activities of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in serum and liver, as well as hepatocyte vacuolation and nuclear pyknosis. Exposure to 100 and 250 μg/L EHDPP led to significant reductions in serum and liver cholesterol (TC), triglycerides (TGs), and lipid droplet deposition, indicating a significant inhibition of EHDPP on hepatic lipid accumulation. Lipidomic analyses manifested that 250 μg/L EHDPP reduced the levels of 103 lipid metabolites which belong to glycerides (TGs, diglycerides, and monoglycerides), fatty acyles (fatty acids), sterol lipids (cholesterol, bile acids), sphingolipids, and glycerophospholipids, and downregulated genes involved in de novo synthesis of fatty acids (fas, acc, srebp1, and dagt2), while upregulated genes involved in fatty acid β-oxidation (pparα and cpt1). KEGG analyses revealed that EHDPP significantly disrupted glycerolipid metabolism, steroid biosynthesis and fatty acid biosynthesis pathways. Collectively, the results showed that EHDPP induced lipid reduction in zebrafish liver, possibly through inhibiting lipid synthesis and disrupting glycerolipid metabolism. Our findings provide a theoretical basis for evaluating the ecological hazards and health effects of EHDPP on glycolipid metabolism.
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Affiliation(s)
- Tao Li
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengyue Zhu
- National Agricultural Science Observing and Experimental Station of Chongqing, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430073, China
| | - Lili Dai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430073, China
| | - Christer Hogstrand
- King's College London, Franklin-Wilkins Building, 150 Stamford St., London SE1 9NH, United Kingdom
| | - Boqun Li
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xikai Yue
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianghua Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Liqin Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China; Engineering Research Center of Green development for Conventional Aquatic, Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China.
| | - Dapeng Li
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, China; Engineering Research Center of Green development for Conventional Aquatic, Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
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Scutt JN, Willetts NJ, Fernandes Campos B, Oliver S, Hennessy A, Joyce PM, Hutchings SJ, le Goupil G, Linares Colombo W, Kaundun SS. Metproxybicyclone, a Novel Carbocyclic Aryl-dione Acetyl-CoA Carboxylase-Inhibiting Herbicide for the Management of Sensitive and Resistant Grass Weeds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21380-21392. [PMID: 39311764 DOI: 10.1021/acs.jafc.4c02729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Postemergence control of grass weeds has become problematic due to the evolution of resistance to 5-enolpyruvylshikimate-3-phosphate synthase, acetyl-CoA carboxylase (ACCase), and acetolactate synthase-inhibiting herbicides. Herein we describe the invention and synthesis journey toward metproxybicyclone, the first commercial carbocyclic aryl-dione ACCase-inhibiting herbicide for the cost-effective management of grass weeds in dicotyledonous crops and in preplant burndown applications. Glasshouse and field experiments have shown that metproxybicyclone is safe for use on soybean, cotton, and sugar beet, among other crops. It is effective on a variety of key grass weeds including Eleusine indica, Digitaria insularis, Sorghum halepense, and Echinochloa crus-galli. Importantly, metproxybicyclone was more efficacious at killing resistant grass weed populations than current ACCase herbicides. Metproxybicyclone controlled the main ACCase target-site and nontarget site resistant mechanisms in characterized Lolium multiflorum and E. indica populations under glasshouse conditions. Excellent control of a broad resistance-causing D2078G target-site mutant E. indica population was also observed under field conditions.
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Affiliation(s)
- James Nicholas Scutt
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Nigel James Willetts
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Breno Fernandes Campos
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Sophie Oliver
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Alan Hennessy
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Philip Matthew Joyce
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Sarah-Jane Hutchings
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Gael le Goupil
- Syngenta Crop Protection AG, Rosentalstrasse 67, CH-4058 Basel, Switzerland
| | - Wendy Linares Colombo
- Syngenta Protecao de Cultivos Ltda, Av. Nacoes Unidas 17.007, Torre Sigma-13° andar, Sao Paulo, Sao Paulo 04730-300, Brazil
| | - Shiv Shankhar Kaundun
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
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Kirk A, Davidson E, Stavrinides J. The expanding antimicrobial diversity of the genus Pantoea. Microbiol Res 2024; 289:127923. [PMID: 39368256 DOI: 10.1016/j.micres.2024.127923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/07/2024] [Accepted: 09/26/2024] [Indexed: 10/07/2024]
Abstract
With the rise of antimicrobial resistance, there is high demand for novel antimicrobials to combat multi-drug resistant pathogens. The bacterial genus Pantoea produces a diversity of antimicrobial natural products effective against a wide range of bacterial and fungal targets. These antimicrobials are synthesized by specialized biosynthetic gene clusters that have unique distributions across Pantoea as well as several other genera outside of the Erwiniaceae. Phylogenetic and genomic evidence shows that these clusters can mobilize within and between species and potentially between genera. Pantoea antimicrobials belong to unique structural classes with diverse mechanisms of action, but despite their potential in antagonizing a wide variety of plant, human, and animal pathogens, little is known about many of these metabolites and how they function. This review will explore the known antimicrobials produced by Pantoea: agglomerins, andrimid, D-alanylgriseoluteic acid, dapdiamide, herbicolins, pantocins, and the various Pantoea Natural Products (PNPs). It will include information on the structure of each compound, their genetic basis, biosynthesis, mechanism of action, spectrum of activity, and distribution, highlighting the significance of Pantoea antimicrobials as potential therapeutics and for applications in biocontrol.
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Affiliation(s)
- Ashlyn Kirk
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada
| | - Emma Davidson
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada.
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Wang D, Bu F, Yang G, Brenke H, Liu B. Structure of the endogenous insect acetyl-coA carboxylase carboxyltransferase domain. J Biol Chem 2024; 300:107800. [PMID: 39305960 DOI: 10.1016/j.jbc.2024.107800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/02/2024] [Accepted: 09/13/2024] [Indexed: 10/14/2024] Open
Abstract
Acetyl-coenzyme A carboxylases (ACCs) are pivotal in fatty acid metabolism, converting acetyl-CoA to malonyl-CoA. While ACCs in humans, plants, and microbes have been extensively studied, insect ACCs, crucial for lipid biosynthesis and physiological processes, remain relatively unexplored. Unlike mammals, which have ACC1 and ACC2 in different tissues, insects possess a single ACC gene, underscoring its unique role in their metabolism. Noctuid moths, such as Trichoplusia ni, are major agricultural pests causing significant crop damage and economic loss. Their resistance to both biological and synthetic insecticides complicates pest control. Recent research has introduced cyclic ketoenols as novel insecticides targeting ACCs, yet structural information to guide their design is limited. Here, we present a 3.12 Å cryo-EM structure of the carboxyltransferase (CT) domain of T. ni ACC, offering the first detailed structural insights into insect ACCs. Our structural comparisons with ACC CT domains from other species and analyses of drug-binding sites can guide future drug modification and design. Notably, unique interactions between the CT and the central domain in T. ni ACC provide new directions for studying the ACC holoenzyme. These findings contribute valuable information for pest control and a basic biological understanding of lipid biosynthesis.
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Affiliation(s)
- Dong Wang
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Fan Bu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Ge Yang
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Hannah Brenke
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; Department of Biology, Gustavus Adolphus College, Saint Peter, Minnesota, USA
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA.
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7
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Benselama W, Benchouk W. In silico design based on quantum chemical, molecular docking studies and ADMET predictions of ciprofloxacin derivatives as novel potential antibacterial and antimycrobacterium agents. J Biomol Struct Dyn 2024; 42:7650-7666. [PMID: 37551116 DOI: 10.1080/07391102.2023.2240906] [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: 02/23/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. In this paper, we report the prediction of new ciprofloxacin derivatives by quantum chemical, molecular docking studies and pharmacokinetic properties. Theoretical studies were performed by geometry optimization computation using B3LYP level at 6-311 G (d,p) basis set. The absorption, distribution, metabolism, excretion and toxicity (ADMET) parameters were predicted and the result show that all compounds have a great ADMET profile. To study the antibacterial, anti-Mycobacterium tuberculosis activities, ciprofloxacin and its derivatives were interacted with the proteins: Thymidylate Kinase (PDB: 4QGG), Biotin carboxylase (PDB: 3JZF) and β-lactamase BlaC (PDB: 3N7W). The results of the docking studies indicate that one pharmacophore designed presents a great inhibition behavior against gram-positive organism (4QGG) and significant interactions observed between the compound and ARG48, GLN101, ARG105 and GLU37 residues of 4QGG. Also, another derivative designed present the best inhibition against gram-negative organism (3JZF) several interactions were noticed between the compound and GLY165, ILE287, LEU278, HIS236, HIS209, MET169 and LYS159 residues of (3JZF). As well as, one designed candidate is good inhibitors for β-lactamase (3N7W) multiple no bonded interactions were observed between the compound and SER84, ILE117, ASN186, LYS87, ARG187, ASN186 and THR251 residues of(3N7W). Molecular dynamics (MD) simulation study was also performed for 100 ns to confirm the stability behaviour of the main protein and inhibitor complexes. The MD simulation study validated the stability of three compounds in the protein binding pocket as potent binders. Natural bonding orbital analysis, reactivity indices and molecular electrostatic potential were carried out. The research finding of this study can be helpful to design a new potent antibacterial, antimycrobacterium candidate's drugs that will serve as the basis for future in vitro and in vivo research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wafa Benselama
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
| | - Wafaa Benchouk
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
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Ning X, Li F, Wei X, Zhu Z, You C. A Light-Powered In Vitro Synthetic Enzymatic Biosystem for the Synthesis of 3-Hydroxypropionic Acid via CO 2 Fixation. ACS Synth Biol 2024; 13:2611-2620. [PMID: 39092606 DOI: 10.1021/acssynbio.4c00447] [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] [Indexed: 08/04/2024]
Abstract
3-Hydroxypropionic acid (3-HP) is a highly sought-after platform chemical serving as a precursor to a variety of high value-added chemical products. In this study, we designed and constructed a novel light-powered in vitro synthetic enzymatic biosystem comprising acetyl-CoA ligase, acetyl-CoA carboxylase, malonyl-CoA reductase, and phosphotransferase to efficiently produce 3-HP through CO2 fixation from acetate, a cost-effective and readily available substrate. The system employed natural thylakoid membranes (TMs) for the regeneration of adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. Comprehensive investigations were conducted on the effects of buffer solutions, substrate concentrations, enzyme loading levels, and TMs loading levels to optimize the yield of 3-HP. Following optimization, a production of 0.46 mM 3-HP was achieved within 6 h from an initial 0.5 mM acetate, with a yield nearing 92%. This work underscores the simplicity of 3-HP production via an in vitro biomanufacturing platform and highlights the potential for incorporating TMs as a sustainable and environmentally friendly approach in biomanufacturing processes.
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Affiliation(s)
- Xiao Ning
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Fei Li
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xinlei Wei
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zhiguang Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chun You
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Anandan V, Bao L, Zhu Z, Bradley J, Assi VF, Chavda H, Kitten T, Xu P. A novel infective endocarditis virulence factor related to multiple functions for bacterial survival in blood was discovered in Streptococcus sanguinis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601854. [PMID: 39005390 PMCID: PMC11244957 DOI: 10.1101/2024.07.03.601854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
We identified the role of a conserved hypothetical protein (SSA_0451) in S. sanguinis that is involved in the virulence of infective endocarditis. An in vitro whole blood killing assay and rabbit endocarditis model studies revealed that the SSA_0451 mutant (ΔSSA_0451) was significantly less virulent than the wild-type (SK36) and its complementation mutant (ΔSSA_0451C). The mechanism underlying the SSA_0451 mutant's reduced virulence in infective endocarditis was evidentially linked to oxidative stress and environmental stress. The genes related to the survival of S. sanguinis in an oxidative stress environment were downregulated in ΔSSA_0451, which affected its survival in blood. Our findings suggest that SSA_0451 is a novel IE virulence factor and a new target for drug discovery against IE.
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Affiliation(s)
- Vysakh Anandan
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Liang Bao
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Zan Zhu
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Jennifer Bradley
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Valery-Francine Assi
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Henna Chavda
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Todd Kitten
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
| | - Ping Xu
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
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Zhang Z, Lv Y, Sun Q, Yao X, Yan H. Comparative Phenotypic and Transcriptomic Analyses Provide Novel Insights into the Molecular Mechanism of Seed Germination in Response to Low Temperature Stress in Alfalfa. Int J Mol Sci 2024; 25:7244. [PMID: 39000350 PMCID: PMC11241472 DOI: 10.3390/ijms25137244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Low temperature is the most common abiotic factor that usually occurs during the seed germination of alfalfa (Medicago sativa L.). However, the potential regulatory mechanisms involved in alfalfa seed germination under low temperature stress are still ambiguous. Therefore, to determine the relevant key genes and pathways, the phenotypic and transcriptomic analyses of low-temperature sensitive (Instict) and low-temperature tolerant (Sardi10) alfalfa were conducted at 6 and 15 h of seed germination under normal (20 °C) and low (10 °C) temperature conditions. Germination phenotypic results showed that Sardi10 had the strongest germination ability under low temperatures, which was manifested by the higher germination-related indicators. Further transcriptome analysis indicated that differentially expressed genes were mainly enriched in galactose metabolism and carbon metabolism pathways, which were the most commonly enriched in two alfalfa genotypes. Additionally, fatty acid metabolism and glutathione metabolism pathways were preferably enriched in Sardi10 alfalfa. The Weighted Gene Co-Expression Network Analysis (WGCNA) suggested that genes were closely related to galactose metabolism, fatty acid metabolism, and glutathione metabolism in Sardi10 alfalfa at the module with the highest correlation (6 h of germination under low temperature). Finally, qRT-PCR analysis further validated the related genes involved in the above pathways, which might play crucial roles in regulating seed germination of alfalfa under low temperature conditions. These findings provide new insights into the molecular mechanisms of seed germination underlying the low temperature stress in alfalfa.
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Affiliation(s)
- Zhao Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Yanzhen Lv
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Qingying Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Xingjie Yao
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
| | - Huifang Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Z.Z.); (Y.L.); (Q.S.); (X.Y.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao 266109, China
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Wang M, Zheng J, Sun S, Wu Z, Shao Y, Xiang J, Yin C, Sedjoah RCAA, Xin Z. An Integrated Pipeline and Overexpression of a Novel Efflux Transporter, YoeA, Significantly Increases Plipastatin Production in Bacillus subtilis. Foods 2024; 13:1785. [PMID: 38891014 PMCID: PMC11171584 DOI: 10.3390/foods13111785] [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: 04/11/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
Plipastatin, an antimicrobial peptide produced by Bacillus subtilis, exhibits remarkable antimicrobial activity against a diverse range of pathogenic bacteria and fungi. However, the practical application of plipastatin has been significantly hampered by its low yield in wild Bacillus species. Here, the native promoters of both the plipastatin operon and the sfp gene in the mono-producing strain M-24 were replaced by the constitutive promoter P43, resulting in plipastatin titers being increased by 27% (607 mg/mL) and 50% (717 mg/mL), respectively. Overexpression of long chain fatty acid coenzyme A ligase (LCFA) increased the yield of plipastatin by 105% (980 mg/mL). A new efflux transporter, YoeA, was identified as a MATE (multidrug and toxic compound extrusion) family member, overexpression of yoeA enhanced plipastatin production to 1233 mg/mL, an increase of 157%, and knockout of yoeA decreased plipastatin production by 70%; in contrast, overexpression or knockout of yoeA in mono-producing surfactin and iturin engineered strains only slightly affected their production, demonstrating that YoeA acts as the major exporter for plipastatin. Co-overexpression of lcfA and yoeA improved plipastatin production to 1890 mg/mL, which was further elevated to 2060 mg/mL after abrB gene deletion. Lastly, the use of optimized culture medium achieved 2514 mg/mL plipastatin production, which was 5.26-fold higher than that of the initial strain. These results suggest that multiple strain engineering is an effective strategy for increasing lipopeptide production, and identification of the novel transport efflux protein YoeA provides new insights into the regulation and industrial application of plipastatin.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.W.); (J.Z.); (S.S.); (Z.W.); (Y.S.); (J.X.); (C.Y.); (R.C.A.A.S.)
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12
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Zhou Z, Jiang Q, Qiu Z, Hou X, Yang X, Yang Y, Hao T, Guo D, Wang J, Li Y, Liu Q, Ling X, Zhang B. Differential Resistance to Acetyl-CoA Carboxylase Inhibitors in Rice: Insights from Two Distinct Target-Site Mutations. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12029-12044. [PMID: 38752706 DOI: 10.1021/acs.jafc.4c01889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Weeds present a significant challenge to agricultural productivity, and acetyl-CoA carboxylase (ACCase)-inhibiting herbicides have proven to be effective in managing weed populations in rice fields. To develop ACCase-inhibiting herbicide-resistant rice, we generated mutants of rice ACCase (OsACC) featuring Ile-1792-Leu or Gly-2107-Ser substitutions through ethyl methyl sulfonate (EMS) mutagenesis. The Ile-1792-Leu mutant displayed cross-resistance to aryloxyphenoxypropionate (APP) and phenylpyrazoline (DEN) herbicides, whereas the Gly-2107-Ser mutants primarily exhibited cross-resistance to APP herbicides with diminished resistance to the DEN herbicide. In vitro assays of the OsACC activity revealed an increase in resistance to haloxyfop and quizalofop, ranging from 4.84- to 29-fold in the mutants compared to that in wild-type. Structural modeling revealed that both mutations likely reduce the binding affinity between OsACC and ACCase inhibitors, thereby imparting resistance. This study offers insights into two target-site mutations, contributing to the breeding of herbicide-resistant rice and presenting alternative weed management strategies in rice cultivation.
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Affiliation(s)
- Zhenzhen Zhou
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Qun Jiang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya Hainan 572025, China
| | - Zeyu Qiu
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Xiaodong Hou
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Xia Yang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Yuwen Yang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Tingting Hao
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Dongshu Guo
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Jinyan Wang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Yongfeng Li
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Qing Liu
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
- College of Agriculture, Yangzhou University, Yangzhou Jiangsu 225009, China
| | - Xitie Ling
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing Jiangsu 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing Jiangsu 210014, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya Hainan 572025, China
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13
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Xu X, de Sousa AS, Boram TJ, Jiang W, Lohman JR. Active E. coli heteromeric acetyl-CoA carboxylase forms polymorphic helical tubular filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596234. [PMID: 38854064 PMCID: PMC11160672 DOI: 10.1101/2024.05.28.596234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Escherichia coli heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional regulation. The E. coli ACC represents almost all ACCs from pathogenic bacteria making it a key antibiotic development target to fight growing antibiotic resistance. Furthermore, it is a model for cyanobacterial and plant plastid ACCs as biofuel engineering targets. Here we report the catalytic E. coli ACC complex surprisingly forms tubes rather than dispersed particles. The cryo-EM structure reveals key protein-protein interactions underpinning efficient catalysis and how transcriptional regulatory roles are masked during catalysis. Discovering the protein-protein interaction interfaces that facilitate catalysis, allosteric and transcriptional regulation provides new routes to engineering catalytic activity and new targets for drug discovery.
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Affiliation(s)
- Xueyong Xu
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Amanda Silva de Sousa
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Trevor J. Boram
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Jeremy R. Lohman
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
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14
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Sun HZ, Li Q, Shang W, Qiao B, Xu QM, Cheng JS. Combinatorial metabolic engineering of Bacillus subtilis for de novo production of polymyxin B. Metab Eng 2024; 83:123-136. [PMID: 38582143 DOI: 10.1016/j.ymben.2024.04.001] [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: 12/23/2023] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Polymyxin is a lipopeptide antibiotic that is effective against multidrug-resistant Gram-negative bacteria. However, its clinical development is limited due to low titer and the presence of homologs. To address this, the polymyxin gene cluster was integrated into Bacillus subtilis, and sfp from Paenibacillus polymyxa was expressed heterologously, enabling recombinant B. subtilis to synthesize polymyxin B. Regulating NRPS domain inhibited formation of polymyxin B2 and B3. The production of polymyxin B increased to 329.7 mg/L by replacing the native promoters of pmxA, pmxB, and pmxE with PfusA, C2up, and PfusA, respectively. Further enhancement in this production, up to 616.1 mg/L, was achieved by improving the synthesis ability of 6-methyloctanoic acid compared to the original strain expressing polymyxin heterologously. Additionally, incorporating an anikasin-derived domain into the hybrid nonribosomal peptide synthase of polymyxin increased the B1 ratio in polymyxin B from 57.5% to 62.2%. Through optimization of peptone supply in the fermentation medium and fermentation in a 5.0-L bioreactor, the final polymyxin B titer reached 962.1 mg/L, with a yield of 19.24 mg/g maltodextrin and a productivity of 10.02 mg/(L·h). This study demonstrates a successful approach for enhancing polymyxin B production and increasing the B1 ratio through combinatorial metabolic engineering.
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Affiliation(s)
- Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qing Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Wei Shang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, China.
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
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15
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Liao W, Guo R, Qian K, Shi W, Whelan J, Shou H. The acyl-acyl carrier protein thioesterases GmFATA1 and GmFATA2 are essential for fatty acid accumulation and growth in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:823-838. [PMID: 38224529 DOI: 10.1111/tpj.16638] [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: 03/10/2023] [Revised: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Acyl-acyl carrier protein (ACP) thioesterases (FAT) hydrolyze acyl-ACP complexes to release FA in plastids, which ultimately affects FA biosynthesis and profiles. Soybean GmFATA1 and GmFATA2 are homoeologous genes encoding oleoyl-ACP thioesterases whose role in seed oil accumulation and plant growth has not been defined. Using CRISPR/Cas9 gene editing mutation of Gmfata1 or 2 led to reduced leaf FA content and growth defect at the early seedling stage. In contrast, no homozygous double mutants were obtained. Combined this indicates that GmFATA1 and GmFATA2 display overlapping, but not complete functional redundancy. Combined transcriptomic and lipidomic analysis revealed a large number of genes involved in FA synthesis and FA chain elongation are expressed at reduced level in the Gmfata1 mutant, accompanied by a lower triacylglycerol abundance at the early seedling stage. Further analysis showed that the Gmfata1 or 2 mutants had increased composition of the beneficial FA, oleic acid. The growth defect of Gmfata1 could be at least partially attributed to reduced acetyl-CoA carboxylase activity, reduced abundance of five unsaturated monogalactosyldiacylglycerol lipids, and altered chloroplast morphology. On the other hand, overexpression of GmFATA in soybean led to significant increases in leaf FA content by 5.7%, vegetative growth, and seed yield by 26.9%, and seed FA content by 23.2%. Thus, overexpression of GmFATA is an effective strategy to enhance soybean oil content and yield.
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Affiliation(s)
- Wenying Liao
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
| | - Runze Guo
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
| | - Kun Qian
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
| | - Wanxuan Shi
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
| | - James Whelan
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, China
| | - Huixia Shou
- State Key Lab of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, China
- Hainan Institute, Zhejiang University, Sanya, Hainan, 572025, China
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16
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Soskic MB, Zakic T, Korac A, Korac B, Jankovic A. Metabolic remodeling of visceral and subcutaneous white adipose tissue during reacclimation of rats after cold. Appl Physiol Nutr Metab 2024; 49:649-658. [PMID: 38241659 DOI: 10.1139/apnm-2023-0448] [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] [Indexed: 01/21/2024]
Abstract
Deciphering lipid metabolism in white adipose tissue (WAT) depots during weight gain is important to understand the heterogeneity of WAT and its roles in obesity. Here, we examined the expression of key enzymes of lipid metabolism and changes in the morphology of representative visceral (epididymal) and subcutaneous (inguinal) WAT (eWAT and iWAT, respectively)-in adult male rats acclimated to cold (4 ± 1 °C) for 45 days and reacclimated to room temperature (RT, 22 ± 1 °C) for 1, 3, 7, 12, 21, or 45 days. The relative mass of both depots decreased to a similar extent after cold acclimation. However, fatty acid synthase (FAS), glucose-6-phosphate dehydrogenase (G6PDH), and medium-chain acyl-CoA dehydrogenase (ACADM) protein level increased only in eWAT, whereas adipose triglyceride lipase (ATGL) expression increased only in iWAT. During reacclimation, the relative mass of eWAT reached control values on day 12 and that of iWAT on day 45 of reacclimation. The faster recovery of eWAT mass is associated with higher expression of FAS, acetyl-CoA carboxylase (ACC), G6PDH, and ACADM during reacclimation and a delayed increase in ATGL. The absence of an increase in proliferating cell nuclear antigen suggests that the observed depot-specific mass increase is predominantly due to metabolic adjustments. In summary, this study shows a differential rate of visceral and subcutaneous adipose tissue weight regain during post-cold reacclimation of rats at RT. Faster recovery of the visceral WAT as compared to subcutaneous WAT during reacclimation at RT could be attributed to observed differences in the expression patterns of lipid metabolic enzymes.
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Affiliation(s)
- Marta Budnar Soskic
- Department of Physiology, Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Tamara Zakic
- Department of Physiology, Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Aleksandra Korac
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Bato Korac
- Department of Physiology, Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Aleksandra Jankovic
- Department of Physiology, Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
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17
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Pan H, Wei L, Zhao H, Xiao Y, Li Z, Ding H. Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4834-4848. [PMID: 38401001 DOI: 10.1021/acs.jafc.3c06411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.
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Affiliation(s)
- Hang Pan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Hao Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang 550004, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
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18
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Sears A, Hentz F, de Souza J, Wenner B, Ward RE, Batistel F. Supply of palmitic, stearic, and oleic acid changes rumen fiber digestibility and microbial composition. J Dairy Sci 2024; 107:902-916. [PMID: 37776997 DOI: 10.3168/jds.2023-23568] [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: 04/03/2023] [Accepted: 09/10/2023] [Indexed: 10/02/2023]
Abstract
The concept that fat supplementation impairs total-tract fiber digestibility in ruminants has been widely accepted over the past decades. Nevertheless, the recent interest in the dietary fatty acid profile to dairy cows enlightened the possible beneficial effect of specific fatty acids (e.g., palmitic, stearic, and oleic acids) on total-tract fiber digestibility. Because palmitic, stearic, and oleic acids are the main fatty acids present in ruminal bacterial cells, we hypothesize that the dietary supply of these fatty acids will favor their incorporation into the bacterial cell membranes, which will support the growth and enrichment of fiber-digesting bacteria in the rumen. Our objective in this experiment was to investigate how dietary supply of palmitic, stearic, and oleic acid affect fiber digestion, bacterial membrane fatty acid profile, microbial growth, and composition of the rumen bacterial community. Diets were randomly assigned to 8 single-flow continuous culture fermenters arranged in a replicated 4 × 4 Latin square with four 11-d experimental periods. Treatments were (1) a control basal diet without supplemental fatty acids (CON); (2) the control diet plus palmitic acid (PA); (3) the control diet plus stearic acid (SA); and (4) the control diet plus oleic acid (OA). All fatty acid treatments were included in the diet at 1.5% of the diet (dry matter [DM] basis). The basal diet contained 50% orchardgrass hay and 50% concentrate (DM basis) and was supplied at a rate of 60 g of DM/d in 2 equal daily offers (0800 and 1600 h). Data were analyzed using a mixed model considering treatments as fixed effect and period and fermenter as random effects. Our results indicate that PA increased in vitro fiber digestibility by 6 percentage units compared with the CON, while SA had no effect and OA decreased fiber digestibility by 8 percentage units. Oleic acid decreased protein expression of the enzymes acetyl-CoA carboxylase compared with CON and PA, while fatty acid synthase was reduced by PA, SA, and OA. We observed that PA, but not SA or OA, altered the bacterial community composition by enhancing bacterial groups responsible for fiber digestion. Although the dietary fatty acids did not affect the total lipid content and the phospholipid fraction in the bacterial cell, PA increased the flow of anteiso C13:0 and anteiso C15:0 in the phospholipidic membrane compared to the other treatments. In addition, OA increased the flow of C18:1 cis-9 and decreased C18:2 cis-9,cis-12 in the bacterial phospholipidic membranes compared to the other treatments. Palmitic acid tended to increase bacterial growth compared to other treatments, whereas SA and OA did not affect bacterial growth compared with CON. To our knowledge, this is the first research providing evidence that palmitic acid supports ruminal fiber digestion through shifts in bacterial fatty acid metabolism that result in changes in growth and abundance of fiber-degrading bacteria in the microbial community.
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Affiliation(s)
- Austin Sears
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 53706
| | - Fernanda Hentz
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | | | - Benjamin Wenner
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210
| | - Robert E Ward
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT 43210
| | - Fernanda Batistel
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611.
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19
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Chugh S, Tiwari P, Suri C, Gupta SK, Singh P, Bouzeyen R, Kidwai S, Srivastava M, Rameshwaram NR, Kumar Y, Asthana S, Singh R. Polyphosphate kinase-1 regulates bacterial and host metabolic pathways involved in pathogenesis of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2024; 121:e2309664121. [PMID: 38170746 PMCID: PMC10786269 DOI: 10.1073/pnas.2309664121] [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: 06/18/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Inorganic polyphosphate (polyP) is primarily synthesized by Polyphosphate Kinase-1 (PPK-1) and regulates numerous cellular processes, including energy metabolism, stress adaptation, drug tolerance, and microbial pathogenesis. Here, we report that polyP interacts with acyl CoA carboxylases, enzymes involved in lipid biosynthesis in Mycobacterium tuberculosis. We show that deletion of ppk-1 in M. tuberculosis results in transcriptional and metabolic reprogramming. In comparison to the parental strain, the Δppk-1 mutant strain had reduced levels of virulence-associated lipids such as PDIMs and TDM. We also observed that polyP deficiency in M. tuberculosis is associated with enhanced phagosome-lysosome fusion in infected macrophages and attenuated growth in mice. Host RNA-seq analysis revealed decreased levels of transcripts encoding for proteins involved in either type I interferon signaling or formation of foamy macrophages in the lungs of Δppk-1 mutant-infected mice relative to parental strain-infected animals. Using target-based screening and molecular docking, we have identified raloxifene hydrochloride as a broad-spectrum PPK-1 inhibitor. We show that raloxifene hydrochloride significantly enhanced the activity of isoniazid, bedaquiline, and pretomanid against M. tuberculosis in macrophages. Additionally, raloxifene inhibited the growth of M. tuberculosis in mice. This is an in-depth study that provides mechanistic insights into the regulation of mycobacterial pathogenesis by polyP deficiency.
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Affiliation(s)
- Saurabh Chugh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Prabhakar Tiwari
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Charu Suri
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Padam Singh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Rania Bouzeyen
- Institut Pasteur de Tunis, Laboratory of Transmission, Control and Immunobiology of Infections, LRII IPT02, Tunis1002, Tunisia
| | - Saqib Kidwai
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Nagender Rao Rameshwaram
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad121001, India
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20
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Jiao R, Jiang W, Xu K, Luo Q, Wang L, Zhao C. Lipid metabolism analysis in esophageal cancer and associated drug discovery. J Pharm Anal 2024; 14:1-15. [PMID: 38352954 PMCID: PMC10859535 DOI: 10.1016/j.jpha.2023.08.019] [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: 04/03/2023] [Revised: 07/27/2023] [Accepted: 08/29/2023] [Indexed: 02/16/2024] Open
Abstract
Esophageal cancer is an upper gastrointestinal malignancy with a bleak prognosis. It is still being explored in depth due to its complex molecular mechanisms of occurrence and development. Lipids play a crucial role in cells by participating in energy supply, biofilm formation, and signal transduction processes, and lipid metabolic reprogramming also constitutes a significant characteristic of malignant tumors. More and more studies have found esophageal cancer has obvious lipid metabolism abnormalities throughout its beginning, progress, and treatment resistance. The inhibition of tumor growth and the enhancement of antitumor therapy efficacy can be achieved through the regulation of lipid metabolism. Therefore, we reviewed and analyzed the research results and latest findings for lipid metabolism and associated analysis techniques in esophageal cancer, and comprehensively proved the value of lipid metabolic reprogramming in the evolution and treatment resistance of esophageal cancer, as well as its significance in exploring potential therapeutic targets and biomarkers.
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Affiliation(s)
- Ruidi Jiao
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518000, China
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China
| | - Wei Jiang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, China
| | - Kunpeng Xu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, China
| | - Qian Luo
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luhua Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China
| | - Chao Zhao
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518000, China
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21
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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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22
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Li S, Chiu TY, Jin X, Cao D, Xu M, Zhu M, Zhou Q, Liu C, Zong Y, Wang S, Yu K, Zhang F, Bai M, Liu G, Liang Y, Zhang C, Simonsen HT, Zhao J, Liu B, Zhao S. Integrating genomic and multiomic data for Angelica sinensis provides insights into the evolution and biosynthesis of pharmaceutically bioactive compounds. Commun Biol 2023; 6:1198. [PMID: 38001348 PMCID: PMC10674023 DOI: 10.1038/s42003-023-05569-5] [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: 05/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Angelica sinensis roots (Angelica roots) are rich in many bioactive compounds, including phthalides, coumarins, lignans, and terpenoids. However, the molecular bases for their biosynthesis are still poorly understood. Here, an improved chromosome-scale genome for A. sinensis var. Qinggui1 is reported, with a size of 2.16 Gb, contig N50 of 4.96 Mb and scaffold N50 of 198.27 Mb, covering 99.8% of the estimated genome. Additionally, by integrating genome sequencing, metabolomic profiling, and transcriptome analysis of normally growing and early-flowering Angelica roots that exhibit dramatically different metabolite profiles, the pathways and critical metabolic genes for the biosynthesis of these major bioactive components in Angelica roots have been deciphered. Multiomic analyses have also revealed the evolution and regulation of key metabolic genes for the biosynthesis of pharmaceutically bioactive components; in particular, TPSs for terpenoid volatiles, ACCs for malonyl CoA, PKSs for phthalide, and PTs for coumarin biosynthesis were expanded in the A. sinensis genome. These findings provide new insights into the biosynthesis of pharmaceutically important compounds in Angelica roots for exploration of synthetic biology and genetic improvement of herbal quality.
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Affiliation(s)
- Shiming Li
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Tsan-Yu Chiu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Dong Cao
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Meng Xu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Mingzhi Zhu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Qi Zhou
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Chun Liu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Yuan Zong
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Shujie Wang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Feng Zhang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Mingzhou Bai
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
- Department of Biotechnology and Biomedicine, The Technical University of Denmark, 2800, Kongens, Lyngby, Denmark
| | - Guangrui Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Yunlong Liang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Chi Zhang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Henrik Toft Simonsen
- Department of Biotechnology and Biomedicine, The Technical University of Denmark, 2800, Kongens, Lyngby, Denmark
- Laboratory of Plant Biotechnology, Université Jean Monnet, 23 Rue du Dr Michelon, 42000, Saint-Etienne, France
| | - Jian Zhao
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, Hunan, China.
| | - Baolong Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China.
| | - Shancen Zhao
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.
- Beijing Life Science Academy, 102200, Beijing, China.
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23
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Zhao L, Ge T, Cheng T, Wang Q, Cui M, Yuan H, Zhao L. Fine-tuning gene expression of regulator AdmX for improved biosynthesis of andrimid in Erwinia persicina BST187. Appl Microbiol Biotechnol 2023; 107:6775-6788. [PMID: 37715803 DOI: 10.1007/s00253-023-12770-3] [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: 05/09/2023] [Revised: 08/17/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023]
Abstract
Andrimid is a potent antibiotic that inhibits acetyl-CoA carboxylase. However, its low biological yield and complex chemical synthesis have hindered its large-scale application. In this study, we found that the LysR-type transcriptional activator AdmX controls andrimid yield by adjusting its expression level in the andrimid-producing bacterium Erwinia persicina strain BST187. Our results showed that gradually increasing of admX transcriptional levels significantly improved andrimid yield, while the yield declined when admX was overexpressed excessively. To further estimate the effect of AdmX on andrimid promotion, we fitted and developed a model which was y = -0.5576x2 + 61.945x + 800.63 (R2 = 0.9591), where x represents the admX transcriptional level and y represents andrimid yield. Andrimid yield of admX overexpression strain BST187ΔadmX/pET28a-Pgap-1::admX was greatly improved by 260%, which was reported for the first time that andrimid yield could be promoted by genetic engineering. Thus, this study provides important insights that the biosynthesis of andrimid would be improved by bioengineering and sheds lights on the potential application of andrimid in both biomedicine and bioagricultural manipulation with its large-scale production in the future. KEY POINTS: • Andrimid production can be greatly promoted by genetic engineering on non-model chassis. • The relationship between AdmX abundance and andrimid yield in Erwinia persicina strain BST187 might be parabolic. • Erwinia persicina BST187 combined with chassis modification enable the promising applications in andrimid industrialization.
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Affiliation(s)
- Lunqiang Zhao
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tongling Ge
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Tingfeng Cheng
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Qing Wang
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Meijie Cui
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Hongli Yuan
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lei Zhao
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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24
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Du J, Shao J, Li S, Zhu T, Song H, Lei C, Zhang M, Cen Y. Integrated transcriptomic and proteomic analyses reveal the mechanism of easy acceptance of artificial pelleted diets during food habit domestication in Largemouth bass (Micropterus salmoides). Sci Rep 2023; 13:18461. [PMID: 37891233 PMCID: PMC10611700 DOI: 10.1038/s41598-023-45645-8] [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: 06/30/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
Acceptance of artificial pelleted diets contributes to increasing the cultured areas and output of carnivorous fish. However, the mechanism of acceptance of artificial pelleted diets remains largely unknown. In this study, the easy acceptance of artificial pelleted diets (EAD) group and the not easy acceptance of artificial pelleted diets (NAD) group of Largemouth bass (Micropterus salmoides) were divided based on the ratios of stomach weight/body weight (SB) after 0.5 h feeding, which was bigger than 18% in the EAD group and ranged from 8 to 12% in the NAD group. Through transcriptome and proteome sequencing, a total of 2463 differentially expressed genes (DEGs) and 230 differentially expressed proteins (DEPs) were identified, respectively. Integrated analyses of transcriptome and proteome data revealed that 152 DEPs were matched with the corresponding DEGs (named co-DEGs-DEPs), and 54 co-DEGs-DEPs were enriched in 16 KEGG pathways, including the metabolic pathways, steroid biosynthesis, fatty acid biosynthesis, etc. Furthermore, 3 terpenoid backbone biosynthesis-related genes (Hmgcr, Hmgcs, and Fdps) in metabolic pathways, 10 steroid biosynthesis-related genes (Fdft1, Sqle, Lss, Cyp51a1, Tm7sf2, Nsdhl, Hsd17b7, Dhcr24, Sc5d, and Dhcr7), and 3 fatty acid biosynthesis-related genes (Acaca, Fasn, and Ascl) were all up-regulated in the EAD group, suggesting that the lipid metabolism pathway and steroid biosynthesis pathway play important roles in early food habit domestication in Largemouth bass. In addition, the detection results of randomly selected 15 DEGs and 15 DEPs indicated that both transcriptome and proteome results in the study were reliable. Our study provides useful information for further research on the mechanisms of food habit domestication in fish.
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Affiliation(s)
- Jinxing Du
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Jiaqi Shao
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Shengjie Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China.
| | - Tao Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Caixia Lei
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Meng Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Yingkun Cen
- Jiyurunda Fishery Technology Co., Ltd, Foshan, 528203, China
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25
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Torrecilhas JA, Pereira GL, Vito ES, Fiorentini G, Ramirez-Zamudio GD, Fonseca LS, Torres RDNS, Simioni TA, Duarte JM, Machado Neto OR, Curi RA, Chardulo LAL, Baldassini WA, Berchielli TT. Changes in the Lipid Metabolism of the Longissimus thoracis Muscle in Bulls When Using Different Feeding Strategies during the Growing and Finishing Phases. Metabolites 2023; 13:1042. [PMID: 37887367 PMCID: PMC10608670 DOI: 10.3390/metabo13101042] [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: 08/14/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
The objective was to evaluate the supplementation strategy's effect on beef cattle during the growing phase and two systems during the finishing phase. One hundred and twenty young bulls were randomly divided in a 2 × 2 factorial design to receive either mineral (ad libitum) or protein + energy (3 g/kg body weight (BW)/day) during the growing phase and pasture plus concentrate supplementation (20 g/kg BW/day) or feedlot (25:75% corn silage:concentrate) during the finishing phase. Feedlot-fed bulls had meat (Longissimus thoracis-LT) with a higher content of lipids and saturated and monounsaturated fatty acids and a greater upregulation of stearoyl-CoA desaturase and sterol regulatory element-binding protein-1c than animals that fed on pasture (p < 0.05). On the other hand, pasture-fed bulls had meat with a higher content of α-linoleic acid, linolenic acid, and n6 and a greater n6:n3 ratio compared to the feedlot-fed group (p < 0.05). In addition, meat from pasture-fed bulls during the finishing phase had 17.6% more isocitrate dehydrogenase enzyme concentration than the feedlot group (p = 0.02). Mineral-fed and pasture-finished bulls showed down-regulation of peroxisome proliferator-activated receptor gamma (p < 0.05), while the bulls fed protein + energy and finished in the feedlot had higher carnitine palmitoyltransferase 2 expression (p ≤ 0.013). In conclusion, mineral or protein + energy supplementation in the growing does not affect the fatty acid composition of intramuscular fat of LT muscle. In the finishing phase, feeding bulls in the feedlot upregulates the lipogenic genes and consequently improves the intramuscular fat content in the meat.
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Affiliation(s)
- Juliana Akamine Torrecilhas
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Guilherme Luis Pereira
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Elias San Vito
- Confina Beef Cattle Consulting, Sinop 78555-603, MT, Brazil;
| | - Giovani Fiorentini
- Department of Animal Science, Federal University of Pelotas (UFPEL), Pelotas 96160-000, RS, Brazil;
| | - Germán Darío Ramirez-Zamudio
- College of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil;
| | - Larissa Simielli Fonseca
- School of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (L.S.F.); (T.A.S.); (J.M.D.); (T.T.B.)
| | - Rodrigo de Nazaré Santos Torres
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Tiago Adriano Simioni
- School of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (L.S.F.); (T.A.S.); (J.M.D.); (T.T.B.)
| | - Juliana Messana Duarte
- School of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (L.S.F.); (T.A.S.); (J.M.D.); (T.T.B.)
| | - Otavio Rodrigues Machado Neto
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Rogério Abdallah Curi
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Luis Artur Loyola Chardulo
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Welder Angelo Baldassini
- School of Veterinary e Animal Science (FMVZ), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (J.A.T.); (R.d.N.S.T.); (O.R.M.N.); (R.A.C.); (L.A.L.C.); (W.A.B.)
| | - Telma Teresinha Berchielli
- School of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil; (L.S.F.); (T.A.S.); (J.M.D.); (T.T.B.)
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26
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Cheng T, Ge T, Zhao L, Hou Y, Xia J, Zhao L. Improved production of andrimid in Erwinia persicina BST187 strain by fermentation optimization. BMC Microbiol 2023; 23:268. [PMID: 37749510 PMCID: PMC10519088 DOI: 10.1186/s12866-023-02946-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/14/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Andrimid is reported to be a novel kind of polyketide-nonribosomal peptide hybrid product (PK-NRPs) that inhibits fatty acid biosynthesis in bacteria. Considering its great potential in biomedicine and biofarming, intensive studies have been conducted to increase the production of andrimid to overcome the excessive costs of chemosynthesis. In screening for species with broad-spectrum antibacterial activity, we detected andrimid in the fermentation products of Erwinia persicina BST187. To increase andrimid production, the BST187 fermentation medium formulation and fermentation conditions were optimized by using systematic design of experiments (One-Factor-At-A-Time, Plackett-Burman design, Response Surface Methodology). RESULTS The results indicate that the actual andrimid production reached 140.3 ± 1.28 mg/L under the optimized conditions (trisodium citrate dihydrate-30 g/L, beef extract-17.1 g/L, MgCl2·6H2O-100 mM, inoculation amount-1%, initial pH-7.0, fermentation time-36 h, temperature-19.7℃), which is 20-fold greater than the initial condition without optimization (7.00 ± 0.40 mg/L), consistent with the improved antibacterial effect of the fermentation supernatant. CONCLUSIONS The present study provides valuable information for improving andrimid production via optimization of the fermentation process, which will be of great value in the future industrialization of andrimid production.
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Affiliation(s)
- Tingfeng Cheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tongling Ge
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Lunqiang Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuyong Hou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jianye Xia
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Lei Zhao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
- College of Biological Sciences, China Agricultural University, Beijing, China.
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27
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Mao M, Deng Y, Wang L, Zhao G, Qi R, Gong H, Shen T, Xu Y, Liu D, Chen B. Chronic unpredictable mild stress promotes atherosclerosis via adipose tissue dysfunction in ApoE -/- mice. PeerJ 2023; 11:e16029. [PMID: 37692113 PMCID: PMC10484201 DOI: 10.7717/peerj.16029] [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: 02/08/2023] [Accepted: 08/13/2023] [Indexed: 09/12/2023] Open
Abstract
Background Chronic unpredictable mild stress (CUMS) has been shown to exacerbate atherosclerosis, but the underlying mechanism remains unknown. Adipose tissue is an energy storage organ and the largest endocrine organ in the human body, playing a key role in the development of cardiovascular disease. In this research, it was hypothesized that CUMS may exacerbate the development of atherosclerosis by inducing the hypertrophy and dysfunction of white adipocytes. Methods The CUMS-induced atherosclerosis model was developed in Western diet-fed apolipoprotein E (ApoE)-/- mice. White adipose tissue (WAT), serum, aortic root, and the brachiocephalic trunk were collected and tested after 12 weeks of CUMS development. The mouse model of CUMS was evaluated for depression-like behavior using the open field test (OFT) and the elevated plus maze (EPM) test. Enzyme-linked immunosorbent assay (ELISA) was conducted to detect serum noradrenaline and urine adrenaline protein levels. Serological assays were used to detect serum low-density lipoprotein (LDL), high-density lipoprotein (HDL), total cholesterol (TC), and free fatty acid (FFA) concentrations. Hematoxylin and eosin (H&E) staining and oil red O were used to detect atherosclerotic plaque area, lipid deposition, and adipocyte size. The mRNA levels of genes related to aberrant adipose tissue function were determined using real-time PCR. Immunofluorescence assay and western blotting were conducted to examine the expression of proteins in the adipose tissue samples. Results CUMS aggravated vascular atherosclerotic lesions in ApoE-/- mice. It decreased body weight while increasing the percentage of WAT. The serological results indicated that the concentration of HDL decreased in CUMS mice. Notably, adipocyte hypertrophy increased, whereas the mRNA levels of Pparg and its target genes (Slc2a4 (encodes for GLUT4), Adipoq, and Plin1) decreased. Further investigation revealed that CUMS increased subcutaneous inguinal WAT (iWAT) lipid synthesis and adipocyte inflammation while decreasing lipid hydrolysis and the expression of HDL-associated protein ApoA-I. Moreover, CUMS aggravated insulin resistance in mice and inhibited the insulin pathway in iWAT. Conclusions These findings indicated that CUMS induces adipose tissue dysfunction via a mechanism that leads to dyslipidemia, increased inflammation, and insulin resistance in the body, thereby exacerbating atherosclerosis. Notably, CUMS that is involved in decreasing the expression of HDL-associated proteins in adipose tissue may be a crucial link between adipose hypertrophy and advanced atherosclerosis. This study reveals a novel mechanism via which CUMS exacerbates atherosclerosis from the novel perspective of abnormal adipose function and identifies a novel potential therapeutic target for this disease.
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Affiliation(s)
- Min Mao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Yalan Deng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Li Wang
- Department of Neurology, Beijing Hospital, Beijing, China
| | - Gexin Zhao
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, United States of America
| | - Ruomei Qi
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Huan Gong
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Tao Shen
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Yitian Xu
- Beijing Union University, Beijing, China
| | - Deping Liu
- Department of Cardiology, Beijing Hospital, Beijing, China
| | - Beidong Chen
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
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28
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Li L, Tian Z, Chen J, Tan Z, Zhang Y, Zhao H, Wu X, Yao X, Wen W, Chen W, Guo L. Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis. Genome Biol 2023; 24:141. [PMID: 37337206 DOI: 10.1186/s13059-023-02984-z] [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: 12/10/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. RESULTS Using a widely targeted metabolomics analysis in a natural population of 388 B. napus inbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus. CONCLUSIONS This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops.
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Affiliation(s)
- Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaowei Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Liu X, Zhang Y, Du X, Luo X, Tan W, Guan X, Zhang L. Effect of yhfS gene on Bt LLP29 antioxidant and UV ray resistance. PEST MANAGEMENT SCIENCE 2023; 79:2087-2097. [PMID: 36715224 DOI: 10.1002/ps.7385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) is a widely used microbial insecticide. However, its persistence is limited because of ultraviolet (UV) rays or other environmental factors. The yhfS gene, which encodes acetyl-CoA acyltransferase, plays an important role in lipid transport and metabolism in many organisms. To explore whether it is related to the stress resistance of Bt LLP29, the yhfS gene knockout strain LLP29 Δ-yhfS and the complementary strain LLP29 R-yhfS were generated successfully by homologous recombination technology, and the related phenotypic changes were compared in this study. RESULTS Gene yhfS was found to be functional in response to UV radiation in Bt by comparing the survival rates of Bt LLP29 harboring yhfS or not under UV light. Enzyme activity assays of key enzymes showed the the Embden-Meyerhof-Parnas pathway was enhanced yet the tricarboxylic acid cycle as well as butanoate synthesis were repressed when the gene was deleted. At the same time, the amino acid content was decreased, but reduced nicotinamide adenine dinucleotide (NADH) and reactive oxygen species (ROS) content were increased. Most noteworthy, antioxidase (such as superoxide dismutase and peroxidase) activities and contents of some potent antioxidants (such as pyruvate, carotenoids and NADPH) were lower in LLP29 Δ-yhfS than in LLP29. CONCLUSION These tests revealed that the loss of the yhfS gene led to metabolic disorders and reduction of the antioxidant ability of Bt. Higher ROS level and lower anti-oxidative capacity might be responsible for the reduced UV resistance when the gene was deleted. These results not only greatly enrich understanding of the mechanism of Bt UV resistance, but also provide an important theoretical basis for Bt application. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xihua Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, China
| | - Yile Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingyu Luo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Center for Disease Control and Prevention of Eastern Command, Nanjing, Jiangsu, China
| | - Xiong Guan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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31
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Liang M, Zhang X, Dong Q, Li H, Guo S, Luan H, Jia P, Yang M, Qi G. Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut ( Juglans regia L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:538. [PMID: 36771622 PMCID: PMC9921657 DOI: 10.3390/plants12030538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut.
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Affiliation(s)
- Manman Liang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Xuemei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Qinglong Dong
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Han Li
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Suping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Haoan Luan
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
| | - Minsheng Yang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
| | - Guohui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071001, China
- Technology Innovation Center of Hebei Province, Xingtai 054000, China
- Institute of Walnut Industry Technology of Hebei Province (Xingtai), Lincheng 054300, China
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32
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Shan L, Tyagi A, Chen X, Yan P, Oh DH. Potential anti-obesity effect of fermented adzuki beans and their untargeted metabolomics using UHPLC-QTOF-MS. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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33
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Gao GR, Hou ZJ, Ding MZ, Bai S, Wei SY, Qiao B, Xu QM, Cheng JS, Yuan YJ. Improved Production of Fengycin in Bacillus subtilis by Integrated Strain Engineering Strategy. ACS Synth Biol 2022; 11:4065-4076. [PMID: 36379006 DOI: 10.1021/acssynbio.2c00380] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fengycin is a lipopeptide with broad-spectrum antifungal activity. However, its low yield limits its commercial application. Therefore, we iteratively edited multiple target genes associated with fengycin synthesis by combinatorial metabolic engineering. The ability of Bacillus subtilis 168 to manufacture lipopeptides was restored, and the fengycin titer was 1.81 mg/L. Fengycin production was further increased to 174.63 mg/L after knocking out pathways associated with surfactin and bacillaene synthesis and replacing the native promoter (PppsA) with the Pveg promoter. Subsequently, fengycin levels were elevated to 258.52 mg/L by upregulating the expression of relevant genes involved in the fatty acid pathway. After blocking spore and biofilm formation, fengycin production reached 302.51 mg/L. Finally, fengycin production was increased to approximately 885.37 mg/L after adding threonine in the optimized culture medium, which was 488-fold higher compared with that of the initial strain. Integrated strain engineering provides a strategy to construct a system for improving fengycin production.
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Affiliation(s)
- Geng-Rong Gao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Zheng-Jie Hou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Ming-Zhu Ding
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Si-Yu Wei
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, PR China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.,Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
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34
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Liu X, Tian W, Wang L, Zhang L, Liang J, Wang L. Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig. Foods 2022; 11:3654. [PMID: 36429246 PMCID: PMC9689697 DOI: 10.3390/foods11223654] [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: 09/16/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.
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Affiliation(s)
- Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weilong Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Kumar L, Mohan L, Anand R, Joshi V, Chugh M, Bharadvaja N. A review on unit operations, challenges, opportunities, and strategies to improve algal based biodiesel and biorefinery. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.998289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Globally, the demand for energy is increasing with an emphasis on green fuels for a sustainable future. As the urge for alternative fuels is accelerating, microalgae have emerged as a promising source that can not only produce high lipid but many other platform chemicals. Moreover, it is a better alternative in comparison to conventional feedstock due to yearlong easy and mass cultivation, carbon fixation, and value-added products extraction. To date, numerous studies have been done to elucidate these organisms for large-scale fuel production. However, enhancing the lipid synthesis rate and reducing the production cost still remain a major bottleneck for its economic viability. Therefore, this study compiles information on algae-based biodiesel production with an emphasis on its unit operations from strain selection to biofuel production. Additionally, strategies to enhance lipid accumulation by incorporating genetic, and metabolic engineering and the use of leftover biomass for harnessing bio-products have been discussed. Besides, implementing a biorefinery for extracting oil followed by utilizing leftover biomass to generate value-added products such as nanoparticles, biofertilizers, biochar, and biopharmaceuticals has also been discussed.
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Abstract
Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
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Walsh BJC, Costa SS, Edmonds KA, Trinidad JC, Issoglio FM, Brito JA, Giedroc DP. Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis. Antioxidants (Basel) 2022; 11:1607. [PMID: 36009332 PMCID: PMC9405070 DOI: 10.3390/antiox11081607] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Hydrogen sulfide (H2S) is implicated as a cytoprotective agent that bacteria employ in response to host-induced stressors, such as oxidative stress and antibiotics. The physiological benefits often attributed to H2S, however, are likely a result of downstream, more oxidized forms of sulfur, collectively termed reactive sulfur species (RSS) and including the organic persulfide (RSSH). Here, we investigated the metabolic response of the commensal gut microorganism Enterococcus faecalis to exogenous Na2S as a proxy for H2S/RSS toxicity. We found that exogenous sulfide increases protein abundance for enzymes responsible for the biosynthesis of coenzyme A (CoA). Proteome S-sulfuration (persulfidation), a posttranslational modification implicated in H2S signal transduction, is also widespread in this organism and is significantly elevated by exogenous sulfide in CstR, the RSS sensor, coenzyme A persulfide (CoASSH) reductase (CoAPR) and enzymes associated with de novo fatty acid biosynthesis and acetyl-CoA synthesis. Exogenous sulfide significantly impacts the speciation of fatty acids as well as cellular concentrations of acetyl-CoA, suggesting that protein persulfidation may impact flux through these pathways. Indeed, CoASSH is an inhibitor of E. faecalis phosphotransacetylase (Pta), suggesting that an important metabolic consequence of increased levels of H2S/RSS may be over-persulfidation of this key metabolite, which, in turn, inhibits CoA and acyl-CoA-utilizing enzymes. Our 2.05 Å crystallographic structure of CoA-bound CoAPR provides new structural insights into CoASSH clearance in E. faecalis.
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Affiliation(s)
- Brenna J. C. Walsh
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Sofia Soares Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | | | | | - Federico M. Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET and Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - José A. Brito
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7003, USA
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38
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Dey S, Shahrear S, Afroj Zinnia M, Tajwar A, Islam ABMMK. Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity. Bioinform Biol Insights 2022; 16:11779322221115535. [PMID: 35958299 PMCID: PMC9358594 DOI: 10.1177/11779322221115535] [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: 04/01/2022] [Accepted: 06/11/2022] [Indexed: 11/25/2022] Open
Abstract
Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.
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Affiliation(s)
- Supantha Dey
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Ahnaf Tajwar
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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40
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Kitahara Y, Oldewurtel ER, Wilson S, Sun Y, Altabe S, de Mendoza D, Garner EC, van Teeffelen S. The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis. PNAS NEXUS 2022; 1:pgac134. [PMID: 36082236 PMCID: PMC9437589 DOI: 10.1093/pnasnexus/pgac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/21/2022] [Indexed: 01/29/2023]
Abstract
All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium Bacillus subtilis. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative Escherichia coli, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth, and biomass growth.
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Affiliation(s)
- Yuki Kitahara
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada,Université de Paris, Paris, France,Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Enno R Oldewurtel
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Silvia Altabe
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
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41
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Kaku M, Ishidaira M, Satoh S, Ozaki M, Kohari D, Chohnan S. Fatty Acid Production by Enhanced Malonyl-CoA Supply in Escherichia coli. Curr Microbiol 2022; 79:269. [PMID: 35881256 DOI: 10.1007/s00284-022-02969-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022]
Abstract
The expression of exogenous genes encoding acetyl-CoA carboxylase (Acc) and pantothenate kinase (CoaA) in Escherichia coli enable highly effective fatty acid production. Acc-only strains grown at 37 °C or 23 °C produced an approximately twofold increase in fatty acid content, and additional expression of CoaA achieved a further twofold accumulation. In the presence of pantothenate, which is the starting material for the CoA biosynthetic pathway, the size of the intracellular CoA pool at 23 °C was comparable to that at 30 °C during cultivation, and more than 500 mg/L of culture containing cellular fatty acids was produced, even at 23 °C. However, the highest yield of cellular fatty acids (1100 mg/L of culture) was produced in cells possessing the gene encoding type I bacterial fatty acid synthase (FasA) along with the acc and coaA, when the transformant was cultivated at 30 °C in M9 minimal salt medium without pantothenate or IPTG. This E. coli transformant contained 141 mg/L of oleic acid attributed to FasA under noninducible conditions. The increased fatty acid content was brought about by a greatly improved specific productivity of 289 mg/g of dry cell weight. Thus, the effectiveness of the foreign acc and coaA in fatty acid production was unambiguously confirmed at culture temperatures of 23 °C to 37 °C. Cofactor engineering in E. coli using the exogenous coaA and acc genes resulted in fatty acid production over 1 g/L of culture and could effectively function at 23 °C.
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Affiliation(s)
- Moena Kaku
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Mei Ishidaira
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Shusaku Satoh
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Miho Ozaki
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Daisuke Kohari
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Shigeru Chohnan
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan.
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42
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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43
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Winkelman DC, Nikolau BJ. The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca. Front Mol Biosci 2022; 9:896226. [PMID: 35720111 PMCID: PMC9198275 DOI: 10.3389/fmolb.2022.896226] [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: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The aerobic, thermophilic Actinobacterium, Thermobifida fusca has been proposed as an organism to be used for the efficient conversion of plant biomass to fatty acid-derived precursors of biofuels or biorenewable chemicals. Despite the potential of T. fusca to catabolize plant biomass, there is remarkably little data available concerning the natural ability of this organism to produce fatty acids. Therefore, we determined the fatty acids that T. fusca produces when it is grown on different carbon sources (i.e., glucose, cellobiose, cellulose and avicel) and at two different growth temperatures, namely at the optimal growth temperature of 50°C and at a suboptimal temperature of 37°C. These analyses establish that T. fusca produces a combination of linear and branched chain fatty acids (BCFAs), including iso-, anteiso-, and 10-methyl BCFAs that range between 14- and 18-carbons in length. Although different carbon sources and growth temperatures both quantitatively and qualitatively affect the fatty acid profiles produced by T. fusca, growth temperature is the greater modifier of these traits. Additionally, genome scanning enabled the identification of many of the fatty acid biosynthetic genes encoded by T. fusca.
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Affiliation(s)
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology and the Center of Metabolic Biology, Iowa State University, Ames, IA, United States
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44
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Choi YJ, Zaikova K, Yeom SJ, Kim YS, Lee DW. Biogenesis and Lipase-Mediated Mobilization of Lipid Droplets in Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:1243. [PMID: 35567244 PMCID: PMC9105935 DOI: 10.3390/plants11091243] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Cytosolic lipid droplets (LDs) derived from the endoplasmic reticulum (ER) mainly contain neutral lipids, such as triacylglycerols (TAGs) and sterol esters, which are considered energy reserves. The metabolic pathways associated with LDs in eukaryotic species are involved in diverse cellular functions. TAG synthesis in plants is mediated by the sequential involvement of two subcellular organelles, i.e., plastids - plant-specific organelles, which serve as the site of lipid synthesis, and the ER. TAGs and sterol esters synthesized in the ER are sequestered to form LDs through the cooperative action of several proteins, such as SEIPINs, LD-associated proteins, LDAP-interacting proteins, and plant-specific proteins such as oleosins. The integrity and stability of LDs are highly dependent on oleosins, especially in the seeds, and oleosin degradation is critical for efficient mobilization of the TAGs of plant LDs. As the TAGs mobilize in LDs during germination and post-germinative growth, a plant-specific lipase-sugar-dependent 1 (SDP1)-plays a major role, through the inter-organellar communication between the ER and peroxisomes. In this review, we briefly recapitulate the different processes involved in the biogenesis and degradation of plant LDs, followed by a discussion of future perspectives in this field.
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Affiliation(s)
- Yun Ju Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (Y.J.C.); (K.Z.)
| | - Kseniia Zaikova
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (Y.J.C.); (K.Z.)
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Yeong-Su Kim
- Wild Plants Industrialization Research Division, Baekdudaegan National Arboretum, Bonghwa 36209, Korea
| | - Dong Wook Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (Y.J.C.); (K.Z.)
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
- Bio-Energy Research Center, Chonnam National University, Gwangju 61186, Korea
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45
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Cai B, Ma M, Zhang J, Kong S, Zhou Z, Li Z, Abdalla BA, Xu H, Zhang X, Lawal RA, Nie Q. Long noncoding RNA ZFP36L2-AS functions as a metabolic modulator to regulate muscle development. Cell Death Dis 2022; 13:389. [PMID: 35449125 PMCID: PMC9023450 DOI: 10.1038/s41419-022-04772-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 01/17/2023]
Abstract
Skeletal muscle is the largest metabolic organ in the body, and its metabolic flexibility is essential for maintaining systemic energy homeostasis. Metabolic inflexibility in muscles is a dominant cause of various metabolic disorders, impeding muscle development. In our previous study, we found lncRNA ZFP36L2-AS (for “ZFP36L2-antisense transcript”) is specifically enriched in skeletal muscle. Here, we report that ZFP36L2-AS is upregulated during myogenic differentiation, and highly expressed in breast and leg muscle. In vitro, ZFP36L2-AS inhibits myoblast proliferation but promotes myoblast differentiation. In vivo, ZFP36L2-AS facilitates intramuscular fat deposition, as well as activates fast-twitch muscle phenotype and induces muscle atrophy. Mechanistically, ZFP36L2-AS interacts with acetyl-CoA carboxylase alpha (ACACA) and pyruvate carboxylase (PC) to induce ACACA dephosphorylation and damaged PC protein stability, thus modulating muscle metabolism. Meanwhile, ZFP36L2-AS can activate ACACA to reduce acetyl-CoA content, which enhances the inhibition of PC activity. Our findings present a novel model about the regulation of lncRNA on muscle metabolism.
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Affiliation(s)
- Bolin Cai
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Manting Ma
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Jing Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Shaofen Kong
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Zhen Zhou
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Zhenhui Li
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Bahareldin Ali Abdalla
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Haiping Xu
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | | | - Qinghua Nie
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.
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C C, A V, B A, J L, G F, L FO, S M, T C. Nitrogen source as a modulator of the metabolic activity of Pedobacter lusitanus NL19: a transcriptomic approach. Appl Microbiol Biotechnol 2022; 106:1583-1597. [PMID: 35122154 DOI: 10.1007/s00253-022-11796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/02/2022]
Abstract
Secondary metabolites (SMs) are compounds with relevant biological activities. Their production under laboratory conditions, especially in broth, is still challenging. An example is the pedopeptins, which are nonribosomal peptides active against some bacteria listed by the WHO for which new antibiotics are urgently needed. Their biosynthesis is inhibited by high concentrations of peptone from casein (PC) in tryptic soy broth (TSB), and we applied a RNA-seq approach to identify Pedobacter lusitanus NL19 cellular pathways modulated by this condition. Results were validated by qPCR and revealed 261 differentially expressed genes (DEGs), 46.3% of them with a predicted biological function. Specifically, high concentration of PC significantly repressed the de novo biosynthesis of biotin (- 60X) and the production of nonribosomal peptide synthetases (NRPS) of pedopeptins (about - 14X), but no effect was observed on the expression of other NRPS. Transcription of a L-Dap synthesis operon that includes a protein with a σ70-like domain was also reduced (about - 7X). High concentrations of PC led to a significant overexpression of MFS and RND efflux pumps and a ferrous iron uptake system, suggesting the redirection of cell machinery to export compounds such as amino acids, sugars and metal divalent cations, alongside with a slight increase of iron import. KEY POINTS: • Higher concentrations of phosphate sources highly repress many operons • High concentrations of peptone from casein (PC) cause biotin's operon repression • High concentrations of PC downregulate the production of peptides of unknown function.
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Affiliation(s)
- Covas C
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Vaz A
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Almeida B
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Lourenço J
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Figueiredo G
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Franco O L
- S-Inova Biotech, Programa de Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Mendo S
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal.
| | - Caetano T
- CESAM and Department of Biology, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal.
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Abstract
Fatty acid (FA) biosynthesis plays a central role in the metabolism of living cells as building blocks of biological membranes, energy reserves of the cell, and precursors to second messenger molecules. In keeping with its central metabolic role, FA biosynthesis impacts several cellular functions and its misfunction is linked to disease, such as cancer, obesity, and non-alcoholic fatty liver disease. Cellular FA biosynthesis is conducted by fatty acid synthases (FAS). All FAS enzymes catalyze similar biosynthetic reactions, but the functional architectures adopted by these cellular catalysts can differ substantially. This variability in FAS structure amongst various organisms and the essential role played by FA biosynthetic pathways makes this metabolic route a valuable target for the development of antibiotics. Beyond cellular FA biosynthesis, the quest for renewable energy sources has piqued interest in FA biosynthetic pathway engineering to generate biofuels and fatty acid derived chemicals. For these applications, based on FA biosynthetic pathways, to succeed, detailed metabolic, functional and structural insights into FAS are required, along with an intimate knowledge into the regulation of FAS. In this review, we summarize our present knowledge about the functional, structural, and regulatory aspects of FAS.
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Affiliation(s)
- Aybeg N Günenc
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Benjamin Graf
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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48
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Craft MK, Waldrop GL. Mechanism of biotin carboxylase inhibition by ethyl 4-[[2-chloro-5-(phenylcarbamoyl)phenyl]sulphonylamino]benzoate. J Enzyme Inhib Med Chem 2021; 37:100-108. [PMID: 34894987 PMCID: PMC8667948 DOI: 10.1080/14756366.2021.1994558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The rise of antibacterial-resistant bacteria is a major problem in the United States of America and around the world. Millions of patients are infected with antimicrobial resistant bacteria each year. Novel antibacterial agents are needed to combat the growing and present crisis. Acetyl-CoA carboxylase (ACC), the multi-subunit complex which catalyses the first committed step in fatty acid synthesis, is a validated target for antibacterial agents. However, there are at present, no commercially available antibiotics that target ACC. Ethyl 4-[[2-chloro-5-(phenylcarbamoyl)phenyl]sulfonylamino]benzoate (SABA1) is a compound that has been shown to have antibacterial properties against Pseudomonas aeruginosa and Escherichia coli. SABA1 inhibits biotin carboxylase (BC), the enzyme that catalyses the first half reaction of ACC. SABA1 inhibits BC via an atypical mechanism. It binds in the biotin binding site in the presence of ADP. SABA1 represents a potentially new class of antibiotics that can be used to combat the antibacterial resistance crisis.
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Affiliation(s)
- Matthew K Craft
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Grover L Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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49
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Yuan Z, Ge L, Sun J, Zhang W, Wang S, Cao X, Sun W. Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PeerJ 2021; 9:e12454. [PMID: 34760406 PMCID: PMC8571958 DOI: 10.7717/peerj.12454] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023] Open
Abstract
Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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50
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Zhang J, Zheng M, Yan J, Deng Z, Zhu D, Qu X. A Permissive Medium Chain Acyl-CoA Carboxylase Enables the Efficient Biosynthesis of Extender Units for Engineering Polyketide Carbon Scaffolds. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jun Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayan Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Dongqing Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceuticeal Sciences, Wuhan University, 185 Donghu Rd., Wuhan 430071, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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