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Jørgensen ME, Houston K, Jørgensen HJL, Thomsen HC, Tekaat L, Krogh CT, Mellor SB, Braune KB, Damm ML, Pedas PR, Voss C, Rasmussen MW, Nielsen K, Skadhauge B, Motawia MS, Møller BL, Dockter C, Sørensen M. Disentangling hydroxynitrile glucoside biosynthesis in a barley (Hordeum vulgare) metabolon provides access to elite malting barleys for ethyl carbamate-free whisky production. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:364-382. [PMID: 38652034 DOI: 10.1111/tpj.16768] [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: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
Barley produces several specialized metabolites, including five α-, β-, and γ-hydroxynitrile glucosides (HNGs). In malting barley, presence of the α-HNG epiheterodendrin gives rise to undesired formation of ethyl carbamate in the beverage production, especially after distilling. Metabolite-GWAS identified QTLs and underlying gene candidates possibly involved in the control of the relative and absolute content of HNGs, including an undescribed MATE transporter. By screening 325 genetically diverse barley accessions, we discovered three H. vulgare ssp. spontaneum (wild barley) lines with drastic changes in the relative ratios of the five HNGs. Knock-out (KO)-lines, isolated from the barley FIND-IT resource and each lacking one of the functional HNG biosynthetic genes (CYP79A12, CYP71C103, CYP71C113, CYP71U5, UGT85F22 and UGT85F23) showed unprecedented changes in HNG ratios enabling assignment of specific and mutually dependent catalytic functions to the biosynthetic enzymes involved. The highly similar relative ratios between the five HNGs found across wild and domesticated barley accessions indicate assembly of the HNG biosynthetic enzymes in a metabolon, the functional output of which was reconfigured in the absence of a single protein component. The absence or altered ratios of the five HNGs in the KO-lines did not change susceptibility to the fungal phytopathogen Pyrenophora teres causing net blotch. The study provides a deeper understanding of the organization of HNG biosynthesis in barley and identifies a novel, single gene HNG-0 line in an elite spring barley background for direct use in breeding of malting barley, eliminating HNGs as a source of ethyl carbamate formation in whisky production.
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Affiliation(s)
- Morten E Jørgensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Kelly Houston
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, Scotland
| | - Hans Jørgen L Jørgensen
- Section for Plant and Soil Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Hanne C Thomsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Linda Tekaat
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Camilla Timmermann Krogh
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Silas B Mellor
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | | | - Mette L Damm
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mohammed S Motawia
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799, Copenhagen V, Denmark
| | - Mette Sørensen
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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3
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Wen J, Zhang J, Zhang H, Zhang N, Lei R, Deng Y, Cheng Q, Li H, Luo P. Large-scale genome-wide association studies reveal the genetic causal etiology between air pollutants and autoimmune diseases. J Transl Med 2024; 22:392. [PMID: 38685026 PMCID: PMC11057084 DOI: 10.1186/s12967-024-04928-y] [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: 08/14/2023] [Accepted: 01/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Epidemiological evidence links a close correlation between long-term exposure to air pollutants and autoimmune diseases, while the causality remained unknown. METHODS Two-sample Mendelian randomization (TSMR) was used to investigate the role of PM10, PM2.5, NO2, and NOX (N = 423,796-456,380) in 15 autoimmune diseases (N = 14,890-314,995) using data from large European GWASs including UKB, FINNGEN, IMSGC, and IPSCSG. Multivariable Mendelian randomization (MVMR) was conducted to investigate the direct effect of each air pollutant and the mediating role of common factors, including body mass index (BMI), alcohol consumption, smoking status, and household income. Transcriptome-wide association studies (TWAS), two-step MR, and colocalization analyses were performed to explore underlying mechanisms between air pollution and autoimmune diseases. RESULTS In TSMR, after correction of multiple testing, hypothyroidism was causally associated with higher exposure to NO2 [odds ratio (OR): 1.37, p = 9.08 × 10-4] and NOX [OR: 1.34, p = 2.86 × 10-3], ulcerative colitis (UC) was causally associated with higher exposure to NOX [OR: 2.24, p = 1.23 × 10-2] and PM2.5 [OR: 2.60, p = 5.96 × 10-3], rheumatoid arthritis was causally associated with higher exposure to NOX [OR: 1.72, p = 1.50 × 10-2], systemic lupus erythematosus was causally associated with higher exposure to NOX [OR: 4.92, p = 6.89 × 10-3], celiac disease was causally associated with lower exposure to NOX [OR: 0.14, p = 6.74 × 10-4] and PM2.5 [OR: 0.17, p = 3.18 × 10-3]. The risky effects of PM2.5 on UC remained significant in MVMR analyses after adjusting for other air pollutants. MVMR revealed several common mediators between air pollutants and autoimmune diseases. Transcriptional analysis identified specific gene transcripts and pathways interconnecting air pollutants and autoimmune diseases. Two-step MR revealed that POR, HSPA1B, and BRD2 might mediate from air pollutants to autoimmune diseases. POR pQTL (rs59882870, PPH4=1.00) strongly colocalized with autoimmune diseases. CONCLUSION This research underscores the necessity of rigorous air pollutant surveillance within public health studies to curb the prevalence of autoimmune diseases.
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Affiliation(s)
- Jie Wen
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingwei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruoyan Lei
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yujia Deng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- First Clinical Department, Changsha Medical University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - He Li
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Roy P, Maturano J, Hasdemir H, Lopez A, Xu F, Hellman J, Tajkhorshid E, Sarlah D, Das A. Elucidating the Mechanism of Metabolism of Cannabichromene by Human Cytochrome P450s. JOURNAL OF NATURAL PRODUCTS 2024; 87:639-651. [PMID: 38477310 PMCID: PMC11061835 DOI: 10.1021/acs.jnatprod.3c00336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
Cannabichromene (CBC) is a nonpsychoactive phytocannabinoid well-known for its wide-ranging health advantages. However, there is limited knowledge regarding its human metabolism following CBC consumption. This research aimed to explore the metabolic pathways of CBC by various human liver cytochrome P450 (CYP) enzymes and support the outcomes using in vivo data from mice. The results unveiled two principal CBC metabolites generated by CYPs: 8'-hydroxy-CBC and 6',7'-epoxy-CBC, along with a minor quantity of 1″-hydroxy-CBC. Notably, among the examined CYPs, CYP2C9 demonstrated the highest efficiency in producing these metabolites. Moreover, through a molecular dynamics simulation spanning 1 μs, it was observed that CBC attains stability at the active site of CYP2J2 by forming hydrogen bonds with I487 and N379, facilitated by water molecules, which specifically promotes the hydroxy metabolite's formation. Additionally, the presence of cytochrome P450 reductase (CPR) amplified CBC's binding affinity to CYPs, particularly with CYP2C8 and CYP3A4. Furthermore, the metabolites derived from CBC reduced cytokine levels, such as IL6 and NO, by approximately 50% in microglia cells. This investigation offers valuable insights into the biotransformation of CBC, underscoring the physiological importance and the potential significance of these metabolites.
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Affiliation(s)
- Pritam Roy
- School
of Chemistry and Biochemistry, College of Sciences, and Parker H.
Petit Institute for Bioengineering and Biosciences (IBB), Georgia Institute of Technology (GaTech), Atlanta, Georgia 30332, United States
| | - Jonathan Maturano
- Roger
Adams Laboratory, Department of Chemistry, Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Hale Hasdemir
- Theoretical
and Computational Biophysics Group, NIH Center for Macromolecular
Modeling and Visualization, Beckman Institute for Advanced Science
and Technology, Department of Biochemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Angel Lopez
- School
of Chemistry and Biochemistry, College of Sciences, and Parker H.
Petit Institute for Bioengineering and Biosciences (IBB), Georgia Institute of Technology (GaTech), Atlanta, Georgia 30332, United States
| | - Fengyun Xu
- Judith
Hellman Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143, United States
| | - Judith Hellman
- Department
of Anesthesia and Perioperative Care, University
of California, San Francisco, California 94143, United States
| | - Emad Tajkhorshid
- Theoretical
and Computational Biophysics Group, NIH Center for Macromolecular
Modeling and Visualization, Beckman Institute for Advanced Science
and Technology, Department of Biochemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - David Sarlah
- Roger
Adams Laboratory, Department of Chemistry, Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Aditi Das
- School
of Chemistry and Biochemistry, College of Sciences, and Parker H.
Petit Institute for Bioengineering and Biosciences (IBB), Georgia Institute of Technology (GaTech), Atlanta, Georgia 30332, United States
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5
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Hatzakis N, Kaestel-Hansen J, de Sautu M, Saminathan A, Scanavachi G, Correia R, Nielsen AJ, Bleshoey S, Boomsma W, Kirchhausen T. Deep learning assisted single particle tracking for automated correlation between diffusion and function. RESEARCH SQUARE 2024:rs.3.rs-3716053. [PMID: 38352328 PMCID: PMC10862944 DOI: 10.21203/rs.3.rs-3716053/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone illustrates that besides structure, motion encodes function at the molecular and subcellular level.
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6
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Martinez SE, Pandey AV, Perez Jimenez TE, Zhu Z, Court MH. Pharmacogenomics of poor drug metabolism in greyhounds: Canine P450 oxidoreductase genetic variation, breed heterogeneity, and functional characterization. PLoS One 2024; 19:e0297191. [PMID: 38300925 PMCID: PMC10833530 DOI: 10.1371/journal.pone.0297191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/31/2023] [Indexed: 02/03/2024] Open
Abstract
Greyhounds metabolize cytochrome P450 (CYP) 2B11 substrates more slowly than other dog breeds. However, CYP2B11 gene variants associated with decreased CYP2B11 expression do not fully explain reduced CYP2B11 activity in this breed. P450 oxidoreductase (POR) is an essential redox partner for all CYPs. POR protein variants can enhance or repress CYP enzyme function in a CYP isoform and substrate dependent manner. The study objectives were to identify POR protein variants in greyhounds and determine their effect on coexpressed CYP2B11 and CYP2D15 enzyme function. Gene sequencing identified two missense variants (Glu315Gln and Asp570Glu) forming four alleles, POR-H1 (reference), POR-H2 (570Glu), POR-H3 (315Gln, 570Glu) and POR-H4 (315Gln). Out of 68 dog breeds surveyed, POR-H2 was widely distributed across multiple breeds, while POR-H3 was largely restricted to greyhounds and Scottish deerhounds (35% allele frequencies), and POR-H4 was rare. Three-dimensional protein structure modelling indicated significant effects of Glu315Gln (but not Asp570Glu) on protein flexibility through loss of a salt bridge between Glu315 and Arg519. Recombinant POR-H1 (reference) and each POR variant (H2-H4) were expressed alone or with CYP2B11 or CYP2D15 in insect cells. No substantial effects on POR protein expression or enzyme activity (cytochrome c reduction) were observed for any POR variant (versus POR-H1) when expressed alone or with CYP2B11 or CYP2D15. Furthermore, there were no effects on CYP2B11 or CYP2D15 protein expression, or on CYP2D15 enzyme kinetics by any POR variant (versus POR-H1). However, Vmax values for 7-benzyloxyresorufin, propofol and bupropion oxidation by CYP2B11 were significantly reduced by coexpression with POR-H3 (by 34-37%) and POR-H4 (by 65-72%) compared with POR-H1. Km values were unaffected. Our results indicate that the Glu315Gln mutation (common to POR-H3 and POR-H4) reduces CYP2B11 enzyme function without affecting at least one other major canine hepatic P450 (CYP2D15). Additional in vivo studies are warranted to confirm these findings.
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Affiliation(s)
- Stephanie E. Martinez
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Amit V. Pandey
- Pediatric Endocrinology, Diabetology, and Metabolism, Department of Biomedical Research, University Children’s Hospital Bern, Switzerland and Translational Hormone Research Program, University of Bern, Bern, Switzerland
| | - Tania E. Perez Jimenez
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Zhaohui Zhu
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Michael H. Court
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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Kæstel-Hansen J, de Sautu M, Saminathan A, Scanavachi G, Da Cunha Correia RFB, Nielsen AJ, Bleshøy SV, Boomsma W, Kirchhausen T, Hatzakis NS. Deep learning assisted single particle tracking for automated correlation between diffusion and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567393. [PMID: 38014323 PMCID: PMC10680793 DOI: 10.1101/2023.11.16.567393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone indicates that besides structure, motion encodes function at the molecular and subcellular level.
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Affiliation(s)
- Jacob Kæstel-Hansen
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | - Marilina de Sautu
- Biological Chemistry and Molecular Pharmaceutics Harvard Medical School
- Laboratory of Molecular Medicine Boston Children's Hospital
| | - Anand Saminathan
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Gustavo Scanavachi
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Ricardo F Bango Da Cunha Correia
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Annette Juma Nielsen
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | - Sara Vogt Bleshøy
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | | | - Tom Kirchhausen
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Nikos S Hatzakis
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
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Zhang Y, Pan X, Shi T, Gu Z, Yang Z, Liu M, Xu Y, Yang Y, Ren L, Song X, Lin H, Deng K. P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes. J Adv Res 2023:S2090-1232(23)00316-8. [PMID: 37871773 DOI: 10.1016/j.jare.2023.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/03/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
INTRODUCTION Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2%) have undergone functional characterization. OBJECTIVES To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s. METHODS All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage. RESULTS The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/. CONCLUSIONS We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.
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Affiliation(s)
- Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianyu Shi
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhifeng Gu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhaochang Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Minghao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Kejun Deng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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9
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Iversen JF, Bohr SSR, Pinholt HD, Moses ME, Iversen L, Christensen SM, Hatzakis NS, Zhang M. Single-Particle Tracking of Thermomyces lanuginosus Lipase Reveals How Mutations in the Lid Region Remodel Its Diffusion. Biomolecules 2023; 13:biom13040631. [PMID: 37189378 DOI: 10.3390/biom13040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The function of most lipases is controlled by the lid, which undergoes conformational changes at a water–lipid interface to expose the active site, thus activating catalysis. Understanding how lid mutations affect lipases’ function is important for designing improved variants. Lipases’ function has been found to correlate with their diffusion on the substrate surface. Here, we used single-particle tracking (SPT), a powerful tool for deciphering enzymes’ diffusional behavior, to study Thermomyces lanuginosus lipase (TLL) variants with different lid structures in a laundry-like application condition. Thousands of parallelized recorded trajectories and hidden Markov modeling (HMM) analysis allowed us to extract three interconverting diffusional states and quantify their abundance, microscopic transition rates, and the energy barriers for sampling them. Combining those findings with ensemble measurements, we determined that the overall activity variation in the application condition is dependent on surface binding and lipase mobility when bound. Specifically, the L4 variant with a TLL-like lid and wild-type (WT) TLL displayed similar ensemble activity, but WT bound stronger to the surface than L4, while L4 had a higher diffusion coefficient and thus activity when bound to the surface. These mechanistic elements can only be de-convoluted by our combined assays. Our findings offer fresh perspectives on the development of the next iteration of enzyme-based detergent.
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Affiliation(s)
- Josephine F. Iversen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Søren S.-R. Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Henrik D. Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | - Nikos S. Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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10
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Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies. Commun Biol 2023; 6:178. [PMID: 36792809 PMCID: PMC9932072 DOI: 10.1038/s42003-022-04386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 02/17/2023] Open
Abstract
Insulin formulations with diverse oligomerization states are the hallmark of interventions for the treatment of diabetes. Here using single-molecule recordings we firstly reveal that insulin oligomerization can operate via monomeric additions and secondly quantify the existence, abundance and kinetic characterization of diverse insulin assembly and disassembly pathways involving addition of monomeric, dimeric or tetrameric insulin species. We propose and experimentally validate a model where the insulin self-assembly pathway is rerouted, favoring monomeric or oligomeric assembly, by solution concentration, additives and formulations. Combining our practically complete kinetic characterization with rate simulations, we calculate the abundance of each oligomeric species from nM to mM offering mechanistic insights and the relative abundance of all oligomeric forms at concentrations relevant both for secreted and administrated insulin. These reveal a high abundance of all oligomers and a significant fraction of hexamer resulting in practically halved bioavailable monomer concentration. In addition to providing fundamental new insights, the results and toolbox presented here can be universally applied, contributing to the development of optimal insulin formulations and the deciphering of oligomerization mechanisms for additional proteins.
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11
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Sakuma M, Honda S, Ueno H, Tabata KV, Miyazaki K, Tokuriki N, Noji H. Genetic Perturbation Alters Functional Substates in Alkaline Phosphatase. J Am Chem Soc 2023; 145:2806-2814. [PMID: 36706363 PMCID: PMC9912328 DOI: 10.1021/jacs.2c06693] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Enzymes inherently exhibit molecule-to-molecule heterogeneity in their conformational and functional states, which is considered to be a key to the evolution of new functions. Single-molecule enzyme assays enable us to directly observe such multiple functional states or functional substates. Here, we quantitatively analyzed functional substates in the wild-type and 69 single-point mutants of Escherichia coli alkaline phosphatase by employing a high-throughput single-molecule assay with a femtoliter reactor array device. Interestingly, many mutant enzymes exhibited significantly heterogeneous functional substates with various types, while the wild-type enzyme showed a highly homogeneous substate. We identified a correlation between the degree of functional substates and the level of improvement in promiscuous activities. Our work provides much comprehensive evidence that the functional substates can be easily altered by mutations, and the evolution toward a new catalytic activity may involve the modulation of the functional substates.
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Affiliation(s)
- Morito Sakuma
- Department
of Applied Chemistry, The University of
Tokyo, Tokyo113-8656, Japan,Michael
Smith Laboratories, The University of British
Columbia, British
ColumbiaV6T1Z4, Canada
| | - Shingo Honda
- Department
of Applied Chemistry, The University of
Tokyo, Tokyo113-8656, Japan
| | - Hiroshi Ueno
- Department
of Applied Chemistry, The University of
Tokyo, Tokyo113-8656, Japan
| | - Kazuhito V. Tabata
- Department
of Applied Chemistry, The University of
Tokyo, Tokyo113-8656, Japan
| | - Kentaro Miyazaki
- International
Center for Biotechnology, Osaka University, Suita565-0871, Japan
| | - Nobuhiko Tokuriki
- Michael
Smith Laboratories, The University of British
Columbia, British
ColumbiaV6T1Z4, Canada,
| | - Hiroyuki Noji
- Department
of Applied Chemistry, The University of
Tokyo, Tokyo113-8656, Japan,
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12
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Le Guilcher C, Merlen G, Dellaquila A, Labour MN, Aid R, Tordjmann T, Letourneur D, Simon-Yarza T. Engineered human liver based on pullulan-dextran hydrogel promotes mice survival after liver failure. Mater Today Bio 2023; 19:100554. [PMID: 36756209 PMCID: PMC9900439 DOI: 10.1016/j.mtbio.2023.100554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Liver tissue engineering approaches aim to support drug testing, assistance devices, or transplantation. However, their suitability for clinical application remains unsatisfactory. Herein, we demonstrate the beneficial and biocompatible use of porous pullulan-dextran hydrogel for the self-assembly of hepatocytes and biliary-like cells into functional 3D microtissues. Using HepaRG cells, we obtained 21 days maintenance of engineered liver polarity, functional detoxification and excretion systems, as well as glycogen storage in hydrogel. Implantation on two liver lobes in mice of hydrogels containing 3800 HepaRG 3D structures of 100 μm in diameter, indicated successful engraftment and no signs of liver toxicity after one month. Finally, after acetaminophen-induced liver failure, when mice were transplanted with engineered livers on left lobe and peritoneal cavity, the survival rate at 7 days significantly increased by 31.8% compared with mice without cell therapy. These findings support the clinical potential of pullulan-dextran hydrogel for liver failure management.
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Affiliation(s)
- Camille Le Guilcher
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France,Corresponding author.
| | - Grégory Merlen
- Université Paris-Saclay, INSERM U1193, F- 94800 Villejuif, France
| | - Alessandra Dellaquila
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France
| | - Marie-Noëlle Labour
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France,ICGM, Université de Montpellier, CNRS, ENSCM, F- 34293 Montpellier, France,École Pratique des Hautes Études, Université Paris Sciences et Lettres, F-75014 Paris, France
| | - Rachida Aid
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France
| | | | - Didier Letourneur
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France,Corresponding author.
| | - Teresa Simon-Yarza
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, LVTS, U1148, F-75018 Paris, France,Corresponding author.
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13
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Mellor SB, Behrendorff JBYH, Ipsen JØ, Crocoll C, Laursen T, Gillam EMJ, Pribil M. Exploiting photosynthesis-driven P450 activity to produce indican in tobacco chloroplasts. FRONTIERS IN PLANT SCIENCE 2023; 13:1049177. [PMID: 36743583 PMCID: PMC9890960 DOI: 10.3389/fpls.2022.1049177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 05/28/2023]
Abstract
Photosynthetic organelles offer attractive features for engineering small molecule bioproduction by their ability to convert solar energy into chemical energy required for metabolism. The possibility to couple biochemical production directly to photosynthetic assimilation as a source of energy and substrates has intrigued metabolic engineers. Specifically, the chemical diversity found in plants often relies on cytochrome P450-mediated hydroxylations that depend on reductant supply for catalysis and which often lead to metabolic bottlenecks for heterologous production of complex molecules. By directing P450 enzymes to plant chloroplasts one can elegantly deal with such redox prerequisites. In this study, we explore the capacity of the plant photosynthetic machinery to drive P450-dependent formation of the indigo precursor indoxyl-β-D-glucoside (indican) by targeting an engineered indican biosynthetic pathway to tobacco (Nicotiana benthamiana) chloroplasts. We show that both native and engineered variants belonging to the human CYP2 family are catalytically active in chloroplasts when driven by photosynthetic reducing power and optimize construct designs to improve productivity. However, while increasing supply of tryptophan leads to an increase in indole accumulation, it does not improve indican productivity, suggesting that P450 activity limits overall productivity. Co-expression of different redox partners also does not improve productivity, indicating that supply of reducing power is not a bottleneck. Finally, in vitro kinetic measurements showed that the different redox partners were efficiently reduced by photosystem I but plant ferredoxin provided the highest light-dependent P450 activity. This study demonstrates the inherent ability of photosynthesis to support P450-dependent metabolic pathways. Plants and photosynthetic microbes are therefore uniquely suited for engineering P450-dependent metabolic pathways regardless of enzyme origin. Our findings have implications for metabolic engineering in photosynthetic hosts for production of high-value chemicals or drug metabolites for pharmacological studies.
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Affiliation(s)
- Silas B. Mellor
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - James B. Y. H. Behrendorff
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johan Ø. Ipsen
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Tomas Laursen
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Mathias Pribil
- Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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14
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Lopez M, Malacarne PF, Ramanujam DP, Warwick T, Müller N, Hu J, Dewenter M, Weigert A, Günther S, Gilsbach R, Engelhardt S, Brandes RP, Rezende F. Endothelial deletion of the cytochrome P450 reductase leads to cardiac remodelling. Front Physiol 2022; 13:1056369. [DOI: 10.3389/fphys.2022.1056369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Abstract
The cytochrome P450 reductase (POR) transfers electrons to all microsomal cytochrome P450 enzymes (CYP450) thereby driving their activity. In the vascular system, the POR/CYP450 system has been linked to the production of epoxyeicosatrienoic acids (EETs) but also to the generation of reactive oxygen species. In cardiac myocytes (CMs), EETs have been shown to modulate the cardiac function and have cardioprotective effects. The functional importance of the endothelial POR/CYP450 system in the heart is unclear and was studied here using endothelial cell-specific, inducible knockout mice of POR (ecPOR−/−). RNA sequencing of murine cardiac cells revealed a cell type-specific expression of different CYP450 homologues. Cardiac endothelial cells mainly expressed members of the CYP2 family which produces EETs, and of the CYP4 family that generates omega fatty acids. Tamoxifen-induced endothelial deletion of POR in mice led to cardiac remodelling under basal conditions, as shown by an increase in heart weight to body weight ratio and an increased CM area as compared to control animals. Endothelial deletion of POR was associated with a significant increase in endothelial genes linked to protein synthesis with no changes in genes of the oxidative stress response. CM of ecPOR−/− mice exhibited attenuated expression of genes linked to mitochondrial function and an increase in genes related to cardiac myocyte contractility. In a model of pressure overload (transverse aortic constriction, TAC with O-rings), ecPOR−/− mice exhibited an accelerated reduction in cardiac output (CO) and stroke volume (SV) as compared to control mice. These results suggest that loss of endothelial POR along with a reduction in EETs leads to an increase in vascular stiffness and loss in cardioprotection, resulting in cardiac remodelling.
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15
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Mortensen JS, Bohr SSR, Harloff-Helleberg S, Hatzakis NS, Saaby L, Nielsen HM. Physical and barrier changes in gastrointestinal mucus induced by the permeation enhancer sodium 8-[(2-hydroxybenzoyl)amino]octanoate (SNAC). J Control Release 2022; 352:163-178. [PMID: 36314534 DOI: 10.1016/j.jconrel.2022.09.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Drug delivery systems (DDS) for oral delivery of peptide drugs contain excipients that facilitate and enhance absorption. However, little knowledge exists on how DDS excipients such as permeation enhancers interact with the gastrointestinal mucus barrier. This study aimed to investigate interactions of the permeation enhancer sodium 8-[(2-hydroxybenzoyl)amino]octanoate (SNAC) with ex vivo porcine intestinal mucus (PIM), ex vivo porcine gastric mucus (PGM), as well as with in vitro biosimilar mucus (BM) by profiling their physical and barrier properties upon exposure to SNAC. Bulk mucus permeability studies using the peptides cyclosporine A and vancomycin, ovalbumin as a model protein, as well as fluorescein-isothiocyanate dextrans (FDs) of different molecular weights and different surface charges were conducted in parallel to mucus retention force studies using a texture analyzer, rheological studies, cryo-scanning electron microscopy (cryo-SEM), and single particle tracking of fluorescence-labelled nanoparticles to investigate the effects of the SNAC-mucus interaction. The exposure of SNAC to PIM increased the mucus retention force, storage modulus, viscosity, increased nanoparticle confinement within PIM as well as decreased the permeation of cyclosporine A and ovalbumin through PIM. Surprisingly, the viscosity of PGM and the permeation of cyclosporine A and ovalbumin through PGM was unaffected by the presence of SNAC, thus the effect of SNAC depended on the regional site that mucus was collected from. In the absence of SNAC, the permeation of different molecular weight and differently charged FDs through PIM was comparable to that through BM. However, while bulk permeation of neither of the FDs through PIM was affected by SNAC, the presence of SNAC decreased the permeation of FD4 and increased the permeation of FD150 kDa through BM. Additionally, and in contrast to observations in PIM, nanoparticle confinement within BM remained unaffected by the presence of SNAC. In conclusion, the present study showed that SNAC altered the physical and barrier properties of PIM, but not of PGM. The effects of SNAC in PIM were not observed in the BM in vitro model. Altogether, the study highlights the need for further understanding how permeation enhancers influence the mucus barrier and illustrates that the selected mucus model for such studies should be chosen with care.
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Affiliation(s)
- J S Mortensen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - S S-R Bohr
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; Department of Chemistry, Nano-Science Center, Faculty of Science, University of Copenhagen, Bülowsvej 17, DK-1870 Frederiksberg, Denmark
| | - S Harloff-Helleberg
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - N S Hatzakis
- Department of Chemistry, Nano-Science Center, Faculty of Science, University of Copenhagen, Bülowsvej 17, DK-1870 Frederiksberg, Denmark; Novo Nordisk Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - L Saaby
- CNS Drug Delivery and Barrier Modelling, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; Bioneer A/S, Kogle Alle 2, DK-2970 Hørsholm, Denmark
| | - H M Nielsen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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16
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Enzymology on an Electrode and in a Nanopore: Analysis Algorithms, Enzyme Kinetics, and Perspectives. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-022-01037-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Loss of Protein Stability and Function Caused by P228L Variation in NADPH-Cytochrome P450 Reductase Linked to Lower Testosterone Levels. Int J Mol Sci 2022; 23:ijms231710141. [PMID: 36077536 PMCID: PMC9456303 DOI: 10.3390/ijms231710141] [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: 08/16/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 oxidoreductase (POR) is the redox partner of steroid and drug-metabolising cytochromes P450 located in the endoplasmic reticulum. Mutations in POR cause a broad range of metabolic disorders. The POR variant rs17853284 (P228L), identified by genome sequencing, has been linked to lower testosterone levels and reduced P450 activities. We expressed the POR wild type and the P228L variant in bacteria, purified the proteins, and performed protein stability and catalytic functional studies. Variant P228L affected the stability of the protein as evidenced by lower unfolding temperatures and higher sensitivity to urea denaturation. A significant decline in the rate of electron transfer to cytochrome c and thiazolyl blue tetrazolium (MTT) was observed with POR P228L, while activities of CYP3A4 were reduced by 25% and activities of CYP3A5 and CYP2C9 were reduced by more than 40% compared with WT POR. The 17,20 lyase activity of CYP17A1, responsible for the production of the main androgen precursor dehydroepiandrosterone, was reduced to 27% of WT in the presence of the P228L variant of POR. Based on in silico and in vitro studies, we predict that the change of proline to leucine may change the rigidity of the protein, causing conformational changes in POR, leading to altered electron transfer to redox partners. A single amino acid change can affect protein stability and cause a severe reduction in POR activity. Molecular characterisation of individual POR mutations is crucial for a better understanding of the impact on different redox partners of POR.
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18
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Direct observation of heterogeneous formation of amyloid spherulites in real-time by super-resolution microscopy. Commun Biol 2022; 5:850. [PMID: 35987792 PMCID: PMC9392779 DOI: 10.1038/s42003-022-03810-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Protein misfolding in the form of fibrils or spherulites is involved in a spectrum of pathological abnormalities. Our current understanding of protein aggregation mechanisms has primarily relied on the use of spectrometric methods to determine the average growth rates and diffraction-limited microscopes with low temporal resolution to observe the large-scale morphologies of intermediates. We developed a REal-time kinetics via binding and Photobleaching LOcalization Microscopy (REPLOM) super-resolution method to directly observe and quantify the existence and abundance of diverse aggregate morphologies of human insulin, below the diffraction limit and extract their heterogeneous growth kinetics. Our results revealed that even the growth of microscopically identical aggregates, e.g., amyloid spherulites, may follow distinct pathways. Specifically, spherulites do not exclusively grow isotropically but, surprisingly, may also grow anisotropically, following similar pathways as reported for minerals and polymers. Combining our technique with machine learning approaches, we associated growth rates to specific morphological transitions and provided energy barriers and the energy landscape at the level of single aggregate morphology. Our unifying framework for the detection and analysis of spherulite growth can be extended to other self-assembled systems characterized by a high degree of heterogeneity, disentangling the broad spectrum of diverse morphologies at the single-molecule level. Real-time super-resolution microscopy analysis reveals the growth kinetics, morphology, and abundance of human insulin amyloid spherulites with different growth pathways.
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19
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Semple SJ, Staerk D, Buirchell BJ, Fowler RM, Gericke O, Kjaerulff L, Zhao Y, Pedersen HA, Petersen MJ, Rasmussen LF, Bredahl EK, Pedersen GB, McNair LM, Ndi CP, Hansen NL, Heskes AM, Bayly MJ, Loland CJ, Heinz N, Møller BL. Biodiscoveries within the Australian plant genus Eremophila based on international and interdisciplinary collaboration: results and perspectives on outstanding ethical dilemmas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:936-953. [PMID: 35696314 PMCID: PMC9543726 DOI: 10.1111/tpj.15866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
In a cross-continental research initiative, including researchers working in Australia and Denmark, and based on joint external funding by a 3-year grant from the Novo Nordisk Foundation, we have used DNA sequencing, extensive chemical profiling and molecular networking analyses across the entire Eremophila genus to provide new knowledge on the presence of natural products and their bioactivities using polypharmocological screens. Sesquiterpenoids, diterpenoids and dimers of branched-chain fatty acids with previously unknown chemical structures were identified. The collection of plant material from the Eremophila genus was carried out according to a 'bioprospecting agreement' with the Government of Western Australia. We recognize that several Eremophila species hold immense cultural significance to Australia's First Peoples. In spite of our best intentions to ensure that new knowledge gained about the genus Eremophila and any potential future benefits are shared in an equitable manner, in accordance with the Nagoya Protocol, we encounter serious dilemmas and potential conflicts in making benefit sharing with Australia's First Peoples a reality.
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Affiliation(s)
- Susan J. Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health SciencesUniversity of South AustraliaAdelaide5000Australia
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | | | - Rachael M. Fowler
- School of BioSciencesThe University of MelbourneParkvilleVictoria3010Australia
| | - Oliver Gericke
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
- Present address:
Carlsberg Research LaboratoryJ.C. Jacobsens Gade 4DK‐1799CopenhagenValbyDenmark.
| | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Yong Zhao
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Hans Albert Pedersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Malene J. Petersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Line Fentz Rasmussen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Emilie Kold Bredahl
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Gustav Blichfeldt Pedersen
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
| | - Laura Mikél McNair
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Chi P. Ndi
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health SciencesUniversity of South AustraliaAdelaide5000Australia
| | - Nikolaj Lervad Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
| | - Allison M. Heskes
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
| | - Michael J. Bayly
- School of BioSciencesThe University of MelbourneParkvilleVictoria3010Australia
| | - Claus J. Loland
- Department of Neuroscience, Faculty of Health and Medical SciencesUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Nanna Heinz
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871Frederiksberg CDenmark
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20
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Brucato N, André M, Hudjashov G, Mondal M, Cox MP, Leavesley M, Ricaut FX. Chronology of natural selection in Oceanian genomes. iScience 2022; 25:104583. [PMID: 35880026 PMCID: PMC9308150 DOI: 10.1016/j.isci.2022.104583] [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: 03/15/2022] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul. 239 human genomes from both sides of the Wallacean ecogeographical barriers Signals of selection are dated between -54,000 to -52,000 in modern Oceanian genomes Genes related to immunity and diet were under strong selection Denisovan introgressions participated to the genetic adaptations present in Oceanians
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Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
| | - Mathilde André
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France.,Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Georgi Hudjashov
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, 51010 Tartumaa, Estonia
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, National Capital District 134, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, QLD 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 cedex 9 Toulouse, France
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21
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Sørensen M, Andersen-Ranberg J, Hankamer B, Møller BL. Circular biomanufacturing through harvesting solar energy and CO 2. TRENDS IN PLANT SCIENCE 2022; 27:655-673. [PMID: 35396170 DOI: 10.1016/j.tplants.2022.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Using synthetic biology, it is now time to expand the biosynthetic repertoire of plants and microalgae by utilizing the chloroplast to augment the production of desired high-value compounds and of oil-, carbohydrate-, or protein-enriched biomass based on direct harvesting of solar energy and the consumption of CO2. Multistream product lines based on separate commercialization of the isolated high-value compounds and of the improved bulk products increase the economic potential of the light-driven production system and accelerate commercial scale up. Here we outline the scientific basis for the establishment of such green circular biomanufacturing systems and highlight recent results that make this a realistic option based on cross-disciplinary basic and applied research to advance long-term solutions.
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Affiliation(s)
- Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ben Hankamer
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Overmans S, Lauersen KJ. Biocompatible fluorocarbon liquid underlays for in situ extraction of isoprenoids from microbial cultures. RSC Adv 2022; 12:16632-16639. [PMID: 35754885 PMCID: PMC9169902 DOI: 10.1039/d2ra01112c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/29/2022] [Indexed: 01/19/2023] Open
Abstract
Microbial production of heterologous metabolites is now a mature technology in many host organisms, opening new avenues for green production processes of specialty chemicals. At lab scale, petroleum-based hydrophobic bio-compatible solvents like dodecane can be used as a second phase on top of microbial cultures to act as a physical sink for heterologous hydrocarbon products like isoprenoids. However, this approach has significant drawbacks at scale due to the difficulty of handling solvents and their potential contamination with unwanted byproducts of their manufacture. We discovered that synthetic perfluorocarbon liquids (FCs), commonly used for heat transfer, can also act as physical sinks for microbially produced isoprenoid compounds. FCs are stable, inert, and are amenable to direct liquid-liquid extraction with alcohols for rapid product isolation. These liquids are more dense than water and form a lower phase to microbial cultures rather than an upper phase as with other solvents. Their ability to form an under-layer or 'underlay' also enables the cultivation of microbes directly at the FC-culture medium interface via gravity settling, which could open their application for filamentous or mat-forming organisms. We present comparisons of the isoprenoid extraction potential of three commercial FCs: FC-3283, FC-40, and FC-770 with engineered green microalga cultures producing patchoulol, taxadiene, casbene, or 13R(+) manoyl oxide. We demonstrate that FCs are promising alternatives to traditional solvents and open new avenues in bio-process design for microbial heterologous metabolite milking.
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Affiliation(s)
- Sebastian Overmans
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
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23
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Human Cytochrome P450 2C9 and Its Polymorphic Modifications: Electroanalysis, Catalytic Properties, and Approaches to the Regulation of Enzymatic Activity. Processes (Basel) 2022. [DOI: 10.3390/pr10020383] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The electrochemical properties of cytochrome P450 2C9 (CYP2C9) and polymorphic modifications P450 2C9*2 (CYP2C9*2) and P450 2C9*3 (CYP2C9*3) were studied. To analyze the comparative electrochemical and electrocatalytic activity, the enzymes were immobilized on electrodes modified with a membrane-like synthetic surfactant (didodecyldimethylammonium bromide (DDAB)). An adequate choice of the type of modified electrode was confirmed by cyclic voltammetry of cytochromes P450 under anaerobic conditions, demonstrating well-defined peaks of reduction and oxidation of the heme iron. The midpoint potential, Emid, of cytochrome P450 2C9 is −0.318 ± 0.01 V, and Emid = −0.324 ± 0.01 V, and Emid = −0.318 ± 0.03 V for allelic variant 2C9*2 and allelic variant 2C9*3, respectively. In the presence of substrate diclofenac under aerobic conditions, cytochrome P450 2C9 and its polymorphic modifications P450 2C9*2 and P450 2C9*3 exhibit catalytic properties. Stimulation of the metabolism of diclofenac by cytochrome P450 2C9 in the presence of antioxidant medications mexidol and taurine was shown.
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24
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Kolb P, Kenakin T, Alexander SPH, Bermudez M, Bohn LM, Breinholt CS, Bouvier M, Hill SJ, Kostenis E, Martemyanov K, Neubig RR, Onaran HO, Rajagopal S, Roth BL, Selent J, Shukla AK, Sommer ME, Gloriam DE. Community Guidelines for GPCR Ligand Bias: IUPHAR Review XX. Br J Pharmacol 2022; 179:3651-3674. [PMID: 35106752 PMCID: PMC7612872 DOI: 10.1111/bph.15811] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 11/29/2022] Open
Abstract
G protein-coupled receptors modulate a plethora of physiological processes and mediate the effects of one-third of FDA-approved drugs. Depending on which ligand activates a receptor, it can engage different intracellular transducers. This 'biased signaling' paradigm requires that we now characterize physiological signaling not just by receptors but by ligand-receptor pairs. Ligands eliciting biased signaling may constitute better drugs with higher efficacy and fewer adverse effects. However, ligand bias is very complex, making reproducibility and description challenging. Here, we provide guidelines and terminology for any scientists to design and report ligand bias experiments. The guidelines will aid consistency and clarity, as the basic receptor research and drug discovery communities continue to advance our understanding and exploitation of ligand bias. Scientific insight, biosensors, and analytical methods are still evolving and should benefit from and contribute to the implementation of the guidelines, together improving translation from in vitro to disease-relevant in vivo models.
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Affiliation(s)
- Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, North, Carolina, USA
| | | | - Marcel Bermudez
- Department of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Laura M Bohn
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Christian S Breinholt
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Stephen J Hill
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Evi Kostenis
- Molecular, Cellular, and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Kirill Martemyanov
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Rick R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - H Ongun Onaran
- Molecular Biology and Technology Development Unit, Department of Pharmacology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Sudarshan Rajagopal
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine, North, Carolina, USA
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital Del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Martha E Sommer
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Current affiliation: ISAR Bioscience Institute, Munich-Planegg, Germany
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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25
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Ananda GKS, Norton SL, Blomstedt C, Furtado A, Møller BL, Gleadow R, Henry RJ. Transcript profiles of wild and domesticated sorghum under water-stressed conditions and the differential impact on dhurrin metabolism. PLANTA 2022; 255:51. [PMID: 35084593 PMCID: PMC8795013 DOI: 10.1007/s00425-022-03831-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Australian native species of sorghum contain negligible amounts of dhurrin in their leaves and the cyanogenesis process is regulated differently under water-stress in comparison to domesticated sorghum species. Cyanogenesis in forage sorghum is a major concern in agriculture as the leaves of domesticated sorghum are potentially toxic to livestock, especially at times of drought which induces increased production of the cyanogenic glucoside dhurrin. The wild sorghum species endemic to Australia have a negligible content of dhurrin in the above ground tissues and thus represent a potential resource for key agricultural traits like low toxicity. In this study we investigated the differential expression of cyanogenesis related genes in the leaf tissue of the domesticated species Sorghum bicolor and the Australian native wild species Sorghum macrospermum grown in glasshouse-controlled water-stress conditions using RNA-Seq analysis to analyse gene expression. The study identified genes, including those in the cyanogenesis pathway, that were differentially regulated in response to water-stress in domesticated and wild sorghum. In the domesticated sorghum, dhurrin content was significantly higher compared to that in the wild sorghum and increased with stress and decreased with age whereas in wild sorghum the dhurrin content remained negligible. The key genes in dhurrin biosynthesis, CYP79A1, CYP71E1 and UGT85B1, were shown to be highly expressed in S. bicolor. DHR and HNL encoding the dhurrinase and α-hydroxynitrilase catalysing bio-activation of dhurrin were also highly expressed in S. bicolor. Analysis of the differences in expression of cyanogenesis related genes between domesticated and wild sorghum species may allow the use of these genetic resources to produce more acyanogenic varieties in the future.
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Affiliation(s)
- Galaihalage K S Ananda
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Sally L Norton
- Australian Grains Genebank, Agriculture Victoria, Horsham, VIC, Australia
| | - Cecilia Blomstedt
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roslyn Gleadow
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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26
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Wróbel TM, Rogova O, Sharma K, Rojas Velazquez MN, Pandey AV, Jørgensen FS, Arendrup FS, Andersen KL, Björkling F. Synthesis and Structure–Activity Relationships of Novel Non-Steroidal CYP17A1 Inhibitors as Potential Prostate Cancer Agents. Biomolecules 2022; 12:biom12020165. [PMID: 35204665 PMCID: PMC8961587 DOI: 10.3390/biom12020165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/05/2023] Open
Abstract
Twenty new compounds, targeting CYP17A1, were synthesized, based on our previous work on a benzimidazole scaffold, and their biological activity evaluated. Inhibition of CYP17A1 is an important modality in the treatment of prostate cancer, which remains the most abundant cancer type in men. The biological assessment included CYP17A1 hydroxylase and lyase inhibition, CYP3A4 and P450 oxidoreductase (POR) inhibition, as well as antiproliferative activity in PC3 prostate cancer cells. The most potent compounds were selected for further analyses including in silico modeling. This combined effort resulted in a compound (comp 2, IC50 1.2 µM, in CYP17A1) with a potency comparable to abiraterone and selectivity towards the other targets tested. In addition, the data provided an understanding of the structure–activity relationship of this novel non-steroidal compound class.
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Affiliation(s)
- Tomasz M. Wróbel
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; (O.R.); (F.S.J.); (F.B.)
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
- Correspondence: ; Tel.: +48-814487273
| | - Oksana Rogova
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; (O.R.); (F.S.J.); (F.B.)
| | - Katyayani Sharma
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (K.S.); (M.N.R.V.); (A.V.P.)
- Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
| | - Maria Natalia Rojas Velazquez
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (K.S.); (M.N.R.V.); (A.V.P.)
- Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
| | - Amit V. Pandey
- Division of Pediatric Endocrinology, Department of Pediatrics, University Children’s Hospital Bern, 3010 Bern, Switzerland; (K.S.); (M.N.R.V.); (A.V.P.)
- Department of Biomedical Research, University of Bern, 3010 Bern, Switzerland
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; (O.R.); (F.S.J.); (F.B.)
| | - Frederic S. Arendrup
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (F.S.A.); (K.L.A.)
| | - Kasper L. Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (F.S.A.); (K.L.A.)
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark; (O.R.); (F.S.J.); (F.B.)
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27
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Guengerich FP. Roles of cytochrome P450 enzymes in pharmacology and toxicology: Past, present, and future. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:1-47. [PMID: 35953152 PMCID: PMC9869358 DOI: 10.1016/bs.apha.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of the cytochrome P450 (P450) field has been remarkable in the areas of pharmacology and toxicology, particularly in drug development. Today it is possible to use the knowledge base and relatively straightforward assays to make intelligent predictions about drug disposition prior to human dosing. Much is known about the structures, regulation, chemistry of catalysis, and the substrate and inhibitor specificity of human P450s. Many aspects of drug-drug interactions and side effects can be understood in terms of P450s. This knowledge has also been useful in pharmacy practice, as well as in the pharmaceutical industry and medical practice. However, there are still basic and practical questions to address regarding P450s and their roles in pharmacology and toxicology. Another aspect is the discovery of drugs that inhibit P450 to treat diseases.
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28
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Zhang L, Wang Q. Harnessing P450 Enzyme for Biotechnology and Synthetic Biology. Chembiochem 2021; 23:e202100439. [PMID: 34542923 DOI: 10.1002/cbic.202100439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/18/2021] [Indexed: 12/29/2022]
Abstract
Cytochrome P450 enzymes (P450s, CYPs) catalyze the oxidative transformation of a wide range of organic substrates. Their functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The enzymes are promising for synthetic biology applications but limited by several drawbacks including low turnover rates, poor stability, the dependance of expensive cofactors and redox partners, and the narrow substrate scope. To conquer these obstacles, emerging strategies including substrate engineering, usage of decoy and decoy-based small molecules auxiliaries, designing of artificial enzyme cascades and the incorporation of materials have been explored based on the unique properties of P450s. These strategies can be applied to a wide range of P450s and can be combined with protein engineering to improve the enzymatic activities. This minireview will focus on some recent developments of these strategies which have been used to leverage P450 catalysis. Remaining challenges and future opportunities will also be discussed.
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Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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29
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Laursen T, Lam HYM, Sørensen KK, Tian P, Hansen CC, Groves JT, Jensen KJ, Christensen SM. Membrane anchoring facilitates colocalization of enzymes in plant cytochrome P450 redox systems. Commun Biol 2021; 4:1057. [PMID: 34504298 PMCID: PMC8429664 DOI: 10.1038/s42003-021-02604-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/25/2021] [Indexed: 01/03/2023] Open
Abstract
Plant metabolism depends on cascade reactions mediated by dynamic enzyme assemblies known as metabolons. In this context, the cytochrome P450 (P450) superfamily catalyze key reactions underpinning the unique diversity of bioactive compounds. In contrast to their soluble bacterial counterparts, eukaryotic P450s are anchored to the endoplasmic reticulum membrane and serve as metabolon nucleation sites. Hence, membrane anchoring appears to play a pivotal role in the evolution of complex biosynthetic pathways. Here, a model membrane assay enabled characterization of membrane anchor dynamics by single molecule microscopy. As a model system, we reconstituted the membrane anchor of cytochrome P450 oxidoreductase (POR), the ubiquitous electron donor to all microsomal P450s. The transmembrane segment in the membrane anchor of POR is relatively conserved, corroborating its functional importance. We observe dynamic colocalization of the POR anchors in our assay suggesting that membrane anchoring might promote intermolecular interactions and in this way impact assembly of metabolic multienzyme complexes.
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Affiliation(s)
- Tomas Laursen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA, USA
| | | | - Sune M Christensen
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Enzyme Research, Lyngby, Denmark.
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30
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Moses ME, Lund PM, Bohr SSR, Iversen JF, Kæstel-Hansen J, Kallenbach AS, Iversen L, Christensen SM, Hatzakis NS. Single-Molecule Study of Thermomyces lanuginosus Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33704-33712. [PMID: 34235926 DOI: 10.1021/acsami.1c08809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lipases comprise one of the major enzyme classes in biotechnology with applications within, e.g., baking, brewing, biocatalysis, and the detergent industry. Understanding the mechanisms of lipase function and regulation is therefore important to facilitate the optimization of their function by protein engineering. Advances in single-molecule studies in model systems have provided deep mechanistic insights on lipase function, such as the existence of functional states, their dependence on regulatory cues, and their correlation to activity. However, it is unclear how these observations translate to enzyme behavior in applied settings. Here, single-molecule tracking of individual Thermomyces lanuginosus lipase (TLL) enzymes in a detergency application system allowed real-time direct observation of spatiotemporal localization, and thus diffusional behavior, of TLL enzymes on a lard substrate. Parallelized imaging of thousands of individual enzymes allowed us to observe directly the existence and quantify the abundance and interconversion kinetics between three diffusional states that we recently provided evidence to correlate with function. We observe redistribution of the enzyme's diffusional pattern at the lipid-water interface as well as variations in binding efficiency in response to surfactants and calcium, demonstrating that detergency effectors can drive the sampling of lipase functional states. Our single-molecule results combined with ensemble activity assays and enzyme surface binding efficiency readouts allowed us to deconvolute how application conditions can significantly alter protein functional dynamics and/or surface binding, both of which underpin enzyme performance. We anticipate that our results will inspire further efforts to decipher and integrate the dynamic nature of lipases, and other enzymes, in the design of new biotechnological solutions.
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Affiliation(s)
- Matias E Moses
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Philip M Lund
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Josephine F Iversen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Lars Iversen
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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