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Shang J, Feng D, Liu H, Niu L, Li R, Li Y, Chen M, Li A, Liu Z, He Y, Gao X, Jian H, Wang C, Tang K, Bao M, Wang J, Yang S, Yan H, Ning G. Evolution of the biosynthetic pathways of terpene scent compounds in roses. Curr Biol 2024; 34:3550-3563.e8. [PMID: 39043188 DOI: 10.1016/j.cub.2024.06.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/28/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024]
Abstract
It is unknown why roses are terpene-rich, what the terpene biosynthetic pathways in roses are, and why only a few rose species produce the major components of rose essential oil. Here, we assembled two high-quality chromosome-level genomes for Rosa rugosa and Rosa multiflora. We also re-sequenced 132 individuals from the F1 progeny of Rosa chinensis and Rosa wichuraiana and 36 of their related species. Comparative genomics revealed that expansions of the 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) and terpene synthases (TPSs) gene families led to the enrichment of terpenes in rose scent components. We constructed a terpene biosynthesis network and discovered a TPS-independent citronellol biosynthetic pathway in roses through gene functional identification, genome-wide association studies (GWASs), and multi-omic analysis. Heterologous co-expression of rose citronellol biosynthetic genes in Nicotiana benthamiana led to citronellol production. Our genomic and metabolomic analyses suggested that the copy number of NUDX1-1a determines the citronellol content in different rose species. Our findings not only provide additional genome and gene resources and reveal the evolution of the terpene biosynthetic pathways but also present a nearly complete scenario for terpenoid metabolism that will facilitate the breeding of fragrant roses and the production of rose oil.
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Affiliation(s)
- Junzhong Shang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dedang Feng
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 671003, China
| | - Heng Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Lintao Niu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Runhui Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yajun Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengxi Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ao Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Yanhong He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 671003, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 671003, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 671003, China.
| | - Shuhua Yang
- Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 671003, China.
| | - Guogui Ning
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China.
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Wang Z, Zhang Q, Zhang H, Lu Y. Roles of alcohol dehydrogenase 1 in the biological activities of Candida albicans. Crit Rev Microbiol 2024:1-15. [PMID: 38916139 DOI: 10.1080/1040841x.2024.2371510] [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: 11/17/2023] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
Candida albicans stands as the foremost prevalent human commensal pathogen and a significant contributor to nosocomial fungal infections. In the metabolism of C. albicans, alcohol dehydrogenase 1 (Adh1) is one of the important enzymes that converts acetaldehyde produced by pyruvate decarboxylation into ethanol at the end of glycolysis. Leveraging the foundational processes of alcoholic fermentation, Adh1 plays an active role in multiple biological phenomena, including biofilm formation, interactions between different species, the development of drug resistance, and the potential initiation of gastrointestinal cancer. Additionally, Adh1 within C. albicans has demonstrated associations with regulating the cell cycle, stress responses, and various intracellular states. Furthermore, Adh1 is extracellularly localized on the cell wall surface, where it plays roles in processes such as tissue invasion and host immune responses. Drawing from an analysis of ADH1 gene structure, expression patterns, and fundamental functions, this review elucidates the intricate connections between Adh1 and various biological processes within C. albicans, underscoring its potential implications for the prevention, diagnosis, and treatment of candidiasis.
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Affiliation(s)
- Ziqi Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qi Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Haoying Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Lu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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3
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Lapish CC. Understanding How Acute Alcohol Impacts Neural Encoding in the Rodent Brain. Curr Top Behav Neurosci 2024. [PMID: 38858298 DOI: 10.1007/7854_2024_479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Alcohol impacts neural circuitry throughout the brain and has wide-ranging effects on the biophysical properties of neurons in these circuits. Articulating how these wide-ranging effects might eventually result in altered computational properties has the potential to provide a tractable working model of how alcohol alters neural encoding. This chapter reviews what is currently known about how acute alcohol influences neural activity in cortical, hippocampal, and dopaminergic circuits as these have been the primary focus of understanding how alcohol alters neural computation. While other neural systems have been the focus of exhaustive work on this topic, these brain regions are the ones where in vivo neural recordings are available, thus optimally suited to make the link between changes in neural activity and behavior. Rodent models have been key in developing an understanding of how alcohol impacts the function of these circuits, and this chapter therefore focuses on work from mice and rats. While progress has been made, it is critical to understand the challenges and caveats associated with experimental procedures, especially when performed in vivo, which are designed to answer this question and if/how to translate these data to humans. The hypothesis is discussed that alcohol impairs the ability of neural circuits to acquire states of neural activity that are transiently elevated and characterized by increased complexity. It is hypothesized that these changes are distinct from the traditional view of alcohol being a depressant of neural activity in the forebrain.
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Affiliation(s)
- Christopher C Lapish
- Department of Anatomy, Cell Biology, and Physiology, Stark Neuroscience Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
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Ghatak A, Shanbhag AP, Datta S. Reducing the vicissitudes of heterologous prochiral substrate catalysis by alcohol dehydrogenases through machine learning algorithms. Biochem Biophys Res Commun 2024; 691:149298. [PMID: 38011820 DOI: 10.1016/j.bbrc.2023.149298] [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: 08/24/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
Alcohol dehydrogenases (ADHs) are popular catalysts for synthesizing chiral synthons a vital step for active pharmaceutical intermediate (API) production. They are grouped into three superfamilies namely, medium-chain (MDRs), short-chain dehydrogenase/reductases (SDRs), and iron-containing alcohol dehydrogenases. The former two are used extensively for producing various chiral synthons. Many studies screen multiple enzymes or engineer a specific enzyme for catalyzing a substrate of interest. These processes are resource-intensive and intricate. The current study attempts to decipher the ability to match different ADHs with their ideal substrates using machine learning algorithms. We explore the catalysis of 284 antibacterial ketone intermediates, against MDRs and SDRs to demonstrate a unique pattern of activity. To facilitate machine learning we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques viz. Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Moreover, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, thereby refining and demarcating diverse compound classes. As such, this classification is useful for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening or engineering in identifying the optimal enzyme for specific substrate.
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Affiliation(s)
- Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India; Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
| | - Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India.
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
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Liu M, Niu Q, Wang Z, Qi H, Liang X, Gai Y, Wang B, Yin S. Comparative physiological and transcriptome analysis provide insights into the inhibitory effect of 6-pentyl-2H-pyran-2-one on Clarireedia jacksonii. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 193:105456. [PMID: 37248022 DOI: 10.1016/j.pestbp.2023.105456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023]
Abstract
Clarireedia spp. is a destructive phytopathogenic fungus that causes turf dollar spot of bent-grass, leading to widespread lawn death. In this study, we explored the antifungal capability of 6-pentyl-2H-pyran-2-one (6PP), a natural metabolite volatilized by microorganisms, which plays an important role in the biological control of turfgrass dollar spot. However, the mechanisms by which 6PP inhibits Clarireedia jacksonii remain unknown. In the present study, C. jacksonii mycelial growth was inhibited by the 6PP treatment and the 6PP treatment damaged cell membrane integrity, causing an increase in relative conduc-tivity. Furthermore, physiological and biochemistry assay showed that 6PP treatment can enhance reactive oxygen species (ROS) levels, malondialdehyde (MDA) content obviously increased with 6PP exposure, increased alchohol dehydrogenase (ADH) and depleted acetalde-hyde dehydrogenase (ALDH), and activated the activities of many antioxidant enzymes in C. jacksonii. Gen Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that some genes in C. jacksonii after 6PP treatment related to integrity of the cell wall and membrane, and oxidative stress were significantly downregulated. It is worth mentioning that the fatty acid degradation pathway is significantly upregulated, with an increase in ATP content and ATP synthase activity, which may promote fungal cell apoptosis. Moreover, we found that the expression of ABC transporters, and glutathione metabolism encoding genes were increased to respond to external stimuli. Taken together, these findings revealed the potential antifungal mechanism of 6PP against Clarireedia spp., which also provides a theoretical basis for the commercial utilization of 6PP as a green pesticide in the future.
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Affiliation(s)
- Man Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Qichen Niu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Ziyue Wang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Hongyin Qi
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Xingxing Liang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Baisen Wang
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Shuxia Yin
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
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6
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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7
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Kravitz SN, Ferris E, Love MI, Thomas A, Quinlan AR, Gregg C. Random allelic expression in the adult human body. Cell Rep 2023; 42:111945. [PMID: 36640362 PMCID: PMC10484211 DOI: 10.1016/j.celrep.2022.111945] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Genes are typically assumed to express both parental alleles similarly, yet cell lines show random allelic expression (RAE) for many autosomal genes that could shape genetic effects. Thus, understanding RAE in human tissues could improve our understanding of phenotypic variation. Here, we develop a methodology to perform genome-wide profiling of RAE and biallelic expression in GTEx datasets for 832 people and 54 tissues. We report 2,762 autosomal genes with some RAE properties similar to randomly inactivated X-linked genes. We found that RAE is associated with rapidly evolving regions in the human genome, adaptive signaling processes, and genes linked to age-related diseases such as neurodegeneration and cancer. We define putative mechanistic subtypes of RAE distinguished by gene overlaps on sense and antisense DNA strands, aggregation in clusters near telomeres, and increased regulatory complexity and inputs compared with biallelic genes. We provide foundations to study RAE in human phenotypes, evolution, and disease.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Elliott Ferris
- Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alun Thomas
- Department of Internal Medicine, Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA.
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Dragun Z, Ivanković D, Krasnići N, Kiralj Z, Cvitanović M, Karamatić I, Valić D, Barac F, Filipović Marijić V, Mijošek T, Gjurčević E, Matanović K, Kužir S. Metal-binding biomolecules in the liver of northern pike (Esox lucius Linnaeus, 1758): The first data for the family Esocidae. Comp Biochem Physiol C Toxicol Pharmacol 2022; 257:109327. [PMID: 35276358 DOI: 10.1016/j.cbpc.2022.109327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/26/2022] [Accepted: 03/06/2022] [Indexed: 11/28/2022]
Abstract
Metal-handling strategies of various fish species are known to vary significantly in association with their intracellular metal behaviour. Thus, to better understand the possible consequences of increased metal exposure in fish it is important to perform comparative studies on metal-binding biomolecules in organs of different species. This study was the first of this kind on a liver of an esocid fish (northern pike, Esox lucius), and the gathered information were compared to fish belonging to three other families, Leuciscidae, Cyprinidae and Salmonidae. Distributions of ten elements among cytosolic biomolecules of different molecular masses were studied by size exclusion HPLC combined offline with high resolution ICP-MS. The results indicated predominant association of Co, Fe and Mo to high molecular mass biomolecules (>100 kDa), of Zn and Bi to both high and medium molecular mass biomolecules (>30 kDa), of Mn and Se to medium molecular mass biomolecules (30-100 kDa), and Ag, Cd and Cu to low molecular mass biomolecules (10-30 kDa), presumably metallothioneins. Evident binding to metallothioneins was also detected for Zn and Bi. For several metals, distinct differences were observed when cytosolic metal distributions of northern pike were compared to leuciscids, salmonids and cyprinids. More pronounced Zn binding to metallothioneins was recorded in leuciscids and cyprinids than both esocids and salmonids, whereas cytosolic Mn and Se distributions clearly differed between all studied fish families. Accordingly, in assessment of metal pollution it is vital to consider the exposed species, which requires prior comprehensive comparative research on numerous aquatic organisms.
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Affiliation(s)
- Zrinka Dragun
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia.
| | - Dušica Ivanković
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia.
| | - Nesrete Krasnići
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Zoran Kiralj
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Marita Cvitanović
- Faculty of Science, Department of Biology, University of Zagreb, Rooseveltov trg 6, Zagreb, Croatia
| | - Ivana Karamatić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Damir Valić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Fran Barac
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Vlatka Filipović Marijić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Tatjana Mijošek
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, Zagreb, Croatia
| | - Emil Gjurčević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Krešimir Matanović
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Snježana Kužir
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
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9
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McDonald AG, Tipton KF. Enzyme Nomenclature and Classification: the State of the Art. FEBS J 2021; 290:2214-2231. [PMID: 34773359 DOI: 10.1111/febs.16274] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/14/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
The IUBMB Enzyme classification system, available at the IUBMB ExplorEnz website, uses a four component number (the EC number) that identifies an enzyme in terms of reaction catalysed. There were originally six recognised groups of enzymes: Oxidoreductases (EC 1), Transferases (EC 2), Hydrolases, Lyases (EC 4), Isomerases (EC 5) and Ligases (EC 6). Of these the lyases, which are defined as "enzymes that cleave C-C, C-O, C-N and other bonds by means other than by hydrolysis or oxidation" present particular recognition and classification problems. Recently a new class, the Translocases (EC 7) has been added, which incorporates enzymes that catalyse the movement of ions or molecules across membranes or their separation within membranes. A new subclass of the isomerases has also been included for those enzymes that alter the conformations of proteins and nucleic acids. Newly reported enzymes are being regularly added to the list after validation and where new information affects the classification of an existing entry, a new EC number is created, but the old one is not re-used.
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Affiliation(s)
- Andrew G McDonald
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Keith F Tipton
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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Ribeaucourt D, Bissaro B, Lambert F, Lafond M, Berrin JG. Biocatalytic oxidation of fatty alcohols into aldehydes for the flavors and fragrances industry. Biotechnol Adv 2021; 56:107787. [PMID: 34147589 DOI: 10.1016/j.biotechadv.2021.107787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023]
Abstract
From Egyptian mummies to the Chanel n°5 perfume, fatty aldehydes have long been used and keep impacting our senses in a wide range of foods, beverages and perfumes. Natural sources of fatty aldehydes are threatened by qualitative and quantitative variability while traditional chemical routes are insufficient to answer the society shift toward more sustainable and natural products. The production of fatty aldehydes using biotechnologies is therefore the most promising alternative for the flavors and fragrances industry. In this review, after drawing the portrait of the origin and characteristics of fragrant fatty aldehydes, we present the three main classes of enzymes that catalyze the reaction of fatty alcohols oxidation into aldehydes, namely alcohol dehydrogenases, flavin-dependent alcohol oxidases and copper radical alcohol oxidases. The constraints, challenges and opportunities to implement these oxidative enzymes in the flavors and fragrances industry are then discussed. By setting the scene on the biocatalytic production of fatty aldehydes, and providing a critical assessment of its potential, we expect this review to contribute to the development of biotechnology-based solutions in the flavors and fragrances industry.
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Affiliation(s)
- David Ribeaucourt
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France; Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Fanny Lambert
- V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France
| | - Mickael Lafond
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France.
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12
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Dragun Z, Krasnići N, Ivanković D, Filipović Marijić V, Mijošek T, Redžović Z, Erk M. Comparison of intracellular trace element distributions in the liver and gills of the invasive freshwater fish species, Prussian carp (Carassius gibelio Bloch, 1782). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 730:138923. [PMID: 32388370 DOI: 10.1016/j.scitotenv.2020.138923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Prussian carp (Carassius gibelio) is an invasive freshwater fish known for its high tolerance to aquatic pollution. Our aim was to try to clarify its tolerance to increased exposure to metals/nonmetals, by determining their cytosolic distributions among peptides/proteins of different molecular masses (MM), which form a part of the fish protective mechanisms. The applied approach consisted of fractionation of gill and hepatic cytosols of Prussian carp from the Croatian river Ilova by size-exclusion high performance liquid chromatography, whereas Cd, Cu, Zn, Fe, Mo, and Se analyses were done by high resolution inductively coupled plasma mass spectrometry. The results indicated high detoxification of Cd by its binding to metallothioneins (MTs) in both fish organs. In addition, binding to MTs was observed for Cu in both organs and for Zn in the liver, whereas clear Zn binding to MTs in the gills was not recorded. Zinc in the gills was predominantly bound to proteins of higher MM (50-250 kDa) and to biomolecules of MM below 2 kDa. Predominant Fe binding to proteins of MM of ~400 kDa (presumably storage protein ferritin) was observed in the liver, whereas in the gills Fe was mainly associated to proteins of MM of ~15-65 kDa (presumably hemoglobin oligomers). Maximum Mo and Se elutions in the liver were noted at 235 kDa and 141 kDa, respectively, and in the gills below 10 kDa. The striking difference was observed between two organs of Prussian carp, with predominant metal/nonmetal binding to high MM proteins (e.g., enzymes, storage proteins) in the liver, and to very low MM biomolecules (<10 kDa) in the gills (e.g., antioxidants, metallochaperones, nonprotein cofactors). Such metal/nonmetal distributions within the gills, as the first site of defense, as well as association of several metals to MTs, indicated highly developed defense mechanisms in some organs of Prussian carp.
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Affiliation(s)
- Zrinka Dragun
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia.
| | - Nesrete Krasnići
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
| | - Dušica Ivanković
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
| | - Vlatka Filipović Marijić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
| | - Tatjana Mijošek
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
| | - Zuzana Redžović
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
| | - Marijana Erk
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička c. 54, 10002 Zagreb, Croatia
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Liu C, Jiang X, Liu G, Wassie T, Girmay S. An Ancient Mutation in the TPH1 Gene is Consistent with the Changes in Mammalian Reproductive Rhythm. Int J Mol Sci 2019; 20:ijms20236065. [PMID: 31810154 PMCID: PMC6928614 DOI: 10.3390/ijms20236065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022] Open
Abstract
The reproductive rhythm undergoes several changes during the evolution of mammals to adapt to local environmental changes. Although the critical roles of melatonin (MLT) in the formation of reproductive rhythm have been well established, the genetic basis for the changes of reproductive rhythm remains uncertain. Here, we constructed the phylogenetic trees of 13 melatonin synthesis, metabolism and receptor genes, estimated their divergence times, and calculated their selection pressures. Then, we evaluated the effect of positively selected and functionally related mutations on protein activity. Our results showed that there were significant positive selection sites in the three major genes, including tryptophan hydroxylase 1 (TPH1), tryptophan hydroxylase 2 (TPH2) and indoleamine-2,3-dioxygenase 1 (IDO1) that are involved in melatonin synthesis, metabolism and function. At the protein level, amino acids at the 442nd site of TPH1 protein and the 194th, 286th, 315th and 404th sites of IDO1 protein were under positive selection, and the variants of the amino acid in these sites might lead to the changes in protein function. Remarkably, the 442nd site of these positive selection sites is in the tetramerization domain of TPH1 protein, and it is proline or leucine. At this site, 89.5% of the amino acid of non-seasonal reproducing mammals was proline, while that of 88.9% of seasonal reproducing mammals was leucine. This variation of the amino acid was derived from the T/C polymorphism at the 1325th site of the TPH1 gene coding sequence, which significantly altered the TPH1 activity (p < 0.01). Interestingly, the predicted age of the allele C in the mammalian genome appeared about 126.6 million years ago, and allele T appeared about 212.6 million years ago, indicating that the evolution of the TPH1 gene was affected by the two mammalian split events and the K-T extinction event. In conclusion, the T/C polymorphism at the 1325th site in the TPH1 gene coding sequence altered TPH1 activity, suggesting that this polymorphism is consistent with the reproductive rhythm of mammals.
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Affiliation(s)
- Chenhui Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.L.); (X.J.); (T.W.); (S.G.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan 430070, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.L.); (X.J.); (T.W.); (S.G.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan 430070, China
| | - Guiqiong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan 430070, China
- Correspondence: ; Tel./Fax: +86-27-87585120
| | - Teketay Wassie
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.L.); (X.J.); (T.W.); (S.G.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan 430070, China
| | - Shishay Girmay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.L.); (X.J.); (T.W.); (S.G.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan 430070, China
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14
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Caruana NJ, Strugnell JM, Faou P, Finn J, Cooke IR. Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). J Proteome Res 2019; 18:890-899. [PMID: 30628786 DOI: 10.1021/acs.jproteome.8b00569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic bobtail squid distributed along the Southern Indo-Pacific coast of Australia. Like other sepiadariid squids, it is known to secrete large volumes of viscous slime when stressed. In order to identify key proteins involved in the function of sepiadariid slimes, we compared the slime proteome of Sepioloidea lineolata with that of a closely related species, Sepiadarium austrinum. Of the 550 protein groups identified in Sepioloidea lineolata slime, 321 had orthologs in Sepiadarium austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of abundant proteins, and several of these were short secreted proteins with no homologues outside the class Cephalopoda. No mucins were identified within either species' slime, suggesting that it is structurally distinct from mucin polymer-based gels found in many vertebrate and echinoderm secretions. The extent of N-glycosylation in the slime of Sepioloidea lineolata was also studied via glycan cleavage with Peptide: N-glycosidase F (PNGase-F). Although very few (four) proteins showed strong evidence of N-glycosylation, we found that treatment with PNGase-F led to a slight increase in peptide identification rates compared with controls.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture , James Cook University , Townsville , QLD 4811 , Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Julian Finn
- Sciences , Museums Victoria , Carlton , VIC 3053 , Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia.,Department of Molecular and Cell Biology , James Cook University , Townsville , QLD 4811 , Australia
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