1
|
Chavez D, Amarquaye GN, Mejia-Santana A, Dyotima, Ryan K, Zeng L, Landeta C. Warfarin analogs target disulfide bond-forming enzymes and suggest a residue important for quinone and coumarin binding. J Biol Chem 2024; 300:107383. [PMID: 38762182 PMCID: PMC11208910 DOI: 10.1016/j.jbc.2024.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Disulfide bond formation has a central role in protein folding of both eukaryotes and prokaryotes. In bacteria, disulfide bonds are catalyzed by DsbA and DsbB/VKOR enzymes. First, DsbA, a periplasmic disulfide oxidoreductase, introduces disulfide bonds into substrate proteins. Then, the membrane enzyme, either DsbB or VKOR, regenerate DsbA's activity by the formation of de novo disulfide bonds which reduce quinone. We have previously performed a high-throughput chemical screen and identified a family of warfarin analogs that target either bacterial DsbB or VKOR. In this work, we expressed functional human VKORc1 in Escherichia coli and performed a structure-activity-relationship analysis to study drug selectivity between bacterial and mammalian enzymes. We found that human VKORc1 can function in E. coli by removing two positive residues, allowing the search for novel anticoagulants using bacteria. We also found one warfarin analog capable of inhibiting both bacterial DsbB and VKOR and a second one antagonized only the mammalian enzymes when expressed in E. coli. The difference in the warfarin structure suggests that substituents at positions three and six in the coumarin ring can provide selectivity between the bacterial and mammalian enzymes. Finally, we identified the two amino acid residues responsible for drug binding. One of these is also essential for de novo disulfide bond formation in both DsbB and VKOR enzymes. Our studies highlight a conserved role of this residue in de novo disulfide-generating enzymes and enable the design of novel anticoagulants or antibacterials using coumarin as a scaffold.
Collapse
Affiliation(s)
- Dariana Chavez
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | | | - Dyotima
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kayley Ryan
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Lifan Zeng
- Department of Biochemistry and Molecular Biology, Indiana University Chemical Genomics Core Facility, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Cristina Landeta
- Department of Biology, Indiana University, Bloomington, Indiana, USA.
| |
Collapse
|
2
|
Dirnberger B, Korona D, Popovic R, Deery MJ, Barber H, Russell S, Lilley KS. Enrichment of Membrane Proteins for Downstream Analysis Using Styrene Maleic Acid Lipid Particles (SMALPs) Extraction. Bio Protoc 2023; 13:e4728. [PMID: 37575399 PMCID: PMC10415199 DOI: 10.21769/bioprotoc.4728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/17/2023] [Accepted: 05/08/2023] [Indexed: 08/15/2023] Open
Abstract
Integral membrane proteins are an important class of cellular proteins. These take part in key cellular processes such as signaling transducing receptors to transporters, many operating within the plasma membrane. More than half of the FDA-approved protein-targeting drugs operate via interaction with proteins that contain at least one membrane-spanning region, yet the characterization and study of their native interactions with therapeutic agents remains a significant challenge. This challenge is due in part to such proteins often being present in small quantities within a cell. Effective solubilization of membrane proteins is also problematic, with the detergents typically employed in solubilizing membranes leading to a loss of functional activity and key interacting partners. In recent years, alternative methods to extract membrane proteins within their native lipid environment have been investigated, with the aim of producing functional nanodiscs, maintaining protein-protein and protein-lipid interactions. A promising approach involves extracting membrane proteins in the form of styrene maleic acid lipid particles (SMALPs) that allow the retention of their native conformation. This extraction method offers many advantages for further protein analysis and allows the study of the protein interactions with other molecules, such as drugs. Here, we describe a protocol for efficient SMALP extraction of functionally active membrane protein complexes within nanodiscs. We showcase the method on the isolation of a low copy number plasma membrane receptor complex, the nicotinic acetylcholine receptor (nAChR), from adult Drosophila melanogaster heads. We demonstrate that these nanodiscs can be used to study native receptor-ligand interactions. This protocol can be applied across many biological scenarios to extract the native conformations of low copy number integral membrane proteins.
Collapse
Affiliation(s)
- Benedict Dirnberger
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Rebeka Popovic
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Helen Barber
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
3
|
Pei H, Han Z, Wang Y, Xu C, Li Y, Fan Y, Li L, Tang B. Retraction of "Label-Free Isolation of Low-Adhesion Cells with Stem Properties for Cancer Stem Cell-Specific Drug Evaluation". Anal Chem 2023; 95:6191. [PMID: 36122350 DOI: 10.1021/acs.analchem.2c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
4
|
Li W. Distinct enzymatic strategies for de novo generation of disulfide bonds in membranes. Crit Rev Biochem Mol Biol 2023; 58:36-49. [PMID: 37098102 PMCID: PMC10460286 DOI: 10.1080/10409238.2023.2201404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Disulfide bond formation is a catalyzed reaction essential for the folding and stability of proteins in the secretory pathway. In prokaryotes, disulfide bonds are generated by DsbB or VKOR homologs that couple the oxidation of a cysteine pair to quinone reduction. Vertebrate VKOR and VKOR-like enzymes have gained the epoxide reductase activity to support blood coagulation. The core structures of DsbB and VKOR variants share the architecture of a four-transmembrane-helix bundle that supports the coupled redox reaction and a flexible region containing another cysteine pair for electron transfer. Despite considerable similarities, recent high-resolution crystal structures of DsbB and VKOR variants reveal significant differences. DsbB activates the cysteine thiolate by a catalytic triad of polar residues, a reminiscent of classical cysteine/serine proteases. In contrast, bacterial VKOR homologs create a hydrophobic pocket to activate the cysteine thiolate. Vertebrate VKOR and VKOR-like maintain this hydrophobic pocket and further evolved two strong hydrogen bonds to stabilize the reaction intermediates and increase the quinone redox potential. These hydrogen bonds are critical to overcome the higher energy barrier required for epoxide reduction. The electron transfer process of DsbB and VKOR variants uses slow and fast pathways, but their relative contribution may be different in prokaryotic and eukaryotic cells. The quinone is a tightly bound cofactor in DsbB and bacterial VKOR homologs, whereas vertebrate VKOR variants use transient substrate binding to trigger the electron transfer in the slow pathway. Overall, the catalytic mechanisms of DsbB and VKOR variants have fundamental differences.
Collapse
Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
5
|
Yang L, Yu C, Fan X, Zeng T, Yang W, Xia J, Wang J, Yao L, Hu C, Jin Y, Zhu Y, Chen J, Hu Z. Dual-dynamic-bond cross-linked injectable hydrogel of multifunction for intervertebral disc degeneration therapy. J Nanobiotechnology 2022; 20:433. [PMID: 36182921 PMCID: PMC9526989 DOI: 10.1186/s12951-022-01633-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Developing smart hydrogels with integrated and suitable properties to treat intervertebral disc degeneration (IVDD) by minimally invasive injection is of high desire in clinical application and still an ongoing challenge. In this work, an extraordinary injectable hydrogel PBNPs@OBG (Prussian blue nanoparticles@oxidized hyaluronic acid/borax/gelatin) with promising antibacterial, antioxidation, rapid gelation, and self-healing characteristics was designed via dual-dynamic-bond cross-linking among the oxidized hyaluronic acid (OHA), borax, and gelatin. The mechanical performance of the hydrogel was studied by dynamic mechanical analysis. Meanwhile, the swelling ratio and degradation level of the hydrogel was explored. Benefiting from its remarkable mechanical properties, sufficient tissue adhesiveness, and ideal shape-adaptability, the injectable PBNPs containing hydrogel was explored for IVDD therapy. Astoundingly, the as-fabricated hydrogel was able to alleviate H2O2-induced excessive ROS against oxidative stress trauma of nucleus pulposus, which was further revealed by theoretical calculations. Rat IVDD model was next established to estimate therapeutic effect of this PBNPs@OBG hydrogel for IVDD treatment in vivo. On the whole, combination of the smart multifunctional hydrogel and nanotechnology-mediated antioxidant therapy can serve as a fire-new general type of therapeutic strategy for IVDD and other oxidative stress-related diseases.
Collapse
Affiliation(s)
- Linjun Yang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Congcong Yu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Xuhui Fan
- Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, People's Republic of China
| | - Tianni Zeng
- Department of Oncology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, 453 Tiyuchang Road, Hangzhou, 310007, People's Republic of China
| | - Wentao Yang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Jiechao Xia
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Jianle Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Litao Yao
- Department of Dentistry, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Chuan Hu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Yang Jin
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Yutao Zhu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Jiaxin Chen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China
| | - Zhijun Hu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Key Laboratory of Musculoskeletal System Degeneration, Regeneration Translational Research of Zhejiang Province, Zhejiang University School of Medicine, 3 East Qing Chun Road, Hangzhou, 310002, People's Republic of China.
| |
Collapse
|
6
|
Wu SY, Wen Y, Serre NBC, Laursen CCH, Dietz AG, Taylor BR, Drobizhev M, Molina RS, Aggarwal A, Rancic V, Becker M, Ballanyi K, Podgorski K, Hirase H, Nedergaard M, Fendrych M, Lemieux MJ, Eberl DF, Kay AR, Campbell RE, Shen Y. A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life. PLoS Biol 2022; 20:e3001772. [PMID: 36067248 PMCID: PMC9481166 DOI: 10.1371/journal.pbio.3001772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/16/2022] [Accepted: 08/01/2022] [Indexed: 12/03/2022] Open
Abstract
Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice. Potassium ions play a critical role as an essential electrolyte in all biological systems. This study describes high performance genetically encoded potassium ion sensors to enable in vivo measurement of potassium ion concentrations across multiple model organisms.
Collapse
Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yurong Wen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Nelson B. C. Serre
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Andrea Grostøl Dietz
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Brian R. Taylor
- Department of Physics, University of California at San Diego, La Jolla, California, United States of America
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Rosana S. Molina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Abhi Aggarwal
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Vladimir Rancic
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Becker
- GM/CA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hajime Hirase
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Alan R. Kay
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- * E-mail: (REC); (YS)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail: (REC); (YS)
| |
Collapse
|
7
|
Liu S, Shen G, Li W. Structural and cellular basis of vitamin K antagonism. J Thromb Haemost 2022; 20:1971-1983. [PMID: 35748323 DOI: 10.1111/jth.15800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022]
Abstract
Vitamin K antagonists (VKAs), such as warfarin, are oral anticoagulants widely used to treat and prevent thromboembolic diseases. Therapeutic use of these drugs requires frequent monitoring and dose adjustments, whereas overdose often causes severe bleeding. Addressing these drawbacks requires mechanistic understandings at cellular and structural levels. As the target of VKAs, vitamin K epoxide reductase (VKOR) generates the active, hydroquinone form of vitamin K, which in turn drives the γ-carboxylation of several coagulation factors required for their activity. Crystal structures revealed that VKAs inhibit VKOR via mimicking its catalytic process. At the active site, two strong hydrogen bonds that facilitate the catalysis also afford the binding specificity for VKAs. Binding of VKAs induces a global change from open to closed conformation. Similar conformational change is induced by substrate binding to promote an electron transfer process that reduces the VKOR active site. In the cellular environment, reducing partner proteins or small reducing molecules may afford electrons to maintain the VKOR activity. The catalysis and VKA inhibition require VKOR in different cellular redox states, explaining the complex kinetics behavior of VKAs. Recent studies also revealed the mechanisms underlying warfarin resistance, warfarin dose variation, and antidoting by vitamin K. These mechanistic understandings may lead to improved anticoagulation strategies targeting the vitamin K cycle.
Collapse
Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Guomin Shen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, China
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
8
|
Protein Fusion Strategies for Membrane Protein Stabilization and Crystal Structure Determination. CRYSTALS 2022. [DOI: 10.3390/cryst12081041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of membrane proteins are highly desired for their use in the mechanistic understanding of their functions and the designing of new drugs. However, obtaining the membrane protein structures is difficult. One way to overcome this challenge is with protein fusion methods, which have been successfully used to determine the structures of many membrane proteins, including receptors, enzymes and adhesion molecules. Existing fusion strategies can be categorized into the N or C terminal fusion, the insertion fusion and the termini restraining. The fusions facilitate protein expression, purification, crystallization and phase determination. Successful applications often require further optimization of protein fusion linkers and interactions, whose design can be facilitated by a shared helix strategy and by AlphaFold prediction in the future.
Collapse
|
9
|
Killer M, Finocchio G, Mertens HDT, Svergun DI, Pardon E, Steyaert J, Löw C. Cryo-EM Structure of an Atypical Proton-Coupled Peptide Transporter: Di- and Tripeptide Permease C. Front Mol Biosci 2022; 9:917725. [PMID: 35898305 PMCID: PMC9309889 DOI: 10.3389/fmolb.2022.917725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the most promiscuous class of MFS transporters, with the potential to transport more than 8400 unique substrates. Over the past two decades, transport assays and biophysical studies have shown that various orthologues and paralogues display differences in substrate selectivity. The E. coli genome codes for four different POTs, known as Di- and tripeptide permeases A-D (DtpA-D). DtpC was shown previously to favor positively charged peptides as substrates. In this study, we describe, how we determined the structure of the 53 kDa DtpC by cryogenic electron microscopy (cryo-EM), and provide structural insights into the ligand specificity of this atypical POT. We collected and analyzed data on the transporter fused to split superfolder GFP (split sfGFP), in complex with a 52 kDa Pro-macrobody and with a 13 kDa nanobody. The latter sample was more stable, rigid and a significant fraction dimeric, allowing us to reconstruct a 3D volume of DtpC at a resolution of 2.7 Å. This work provides a molecular explanation for the selectivity of DtpC, and highlights the value of small and rigid fiducial markers such as nanobodies for structure determination of low molecular weight integral membrane proteins lacking soluble domains.
Collapse
Affiliation(s)
- Maxime Killer
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Giada Finocchio
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Haydyn D. T. Mertens
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Dmitri I. Svergun
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| |
Collapse
|
10
|
Carbon dioxide photoreduction in prebiotic environments. Photochem Photobiol Sci 2022; 21:863-878. [PMID: 35107790 DOI: 10.1007/s43630-021-00168-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
The reduction of carbon dioxide is one of the hottest topics due to the concern of global warming. Carbon dioxide reduction is also an essential step for life's origins as photoautotrophs arose soon after Earth formation. Both the topics are of high general interest, and possibly, there could be a fruitful cross-fertilization of the two fields. Herein, we selected and collected papers related to photoreduction of carbon dioxide using compounds easily available on the Earth and considered of prebiotic relevance. This work might be useful also to scientists interested in carbon dioxide photoreduction and/or to have an overview of the techniques available.
Collapse
|
11
|
Liu S, Li S, Krezel AM, Li W. Stabilization and structure determination of integral membrane proteins by termini restraining. Nat Protoc 2022; 17:540-565. [PMID: 35039670 DOI: 10.1038/s41596-021-00656-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Integral membrane proteins isolated from cellular environment often lose activity and native conformation required for functional analyses and structural studies. Even in their native state, they lack sufficient surfaces to form crystal contacts. Furthermore, most of them are too small for cryogenic electron microscopy detection and too big for solution NMR. To overcome these difficulties, we recently developed a strategy to stabilize the folded state of membrane proteins by restraining their two termini with a self-assembling protein coupler. The termini-restrained membrane proteins from distinct functional families retain their activities and show increased stability and yield. This strategy enables their structure determination at near-atomic resolution by facilitating the entire pipeline from crystallization, crystal identification, diffraction enhancement and phase determination, to electron density improvement. Furthermore, stabilization of membrane proteins enables their biochemical and biophysical characterization. Here we present the protocol of membrane protein engineering (2 weeks), quality assessment (1-2 weeks), protein production (1-6 weeks), crystallization (1-2 weeks), diffraction improvement (1-3 months) and crystallographic data analysis (1 week). This protocol is intended not only for structural biologists, but also for biochemists, biophysicists and pharmaceutical scientists whose research focuses on membrane proteins.
Collapse
Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrzej M Krezel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
12
|
Dai C, Waduge P, Ji L, Huang C, He Y, Tian H, Zuniga-Sanchez E, Bhatt A, Pang IH, Su G, Webster KA, Li W. Secretogranin III stringently regulates pathological but not physiological angiogenesis in oxygen-induced retinopathy. Cell Mol Life Sci 2022; 79:63. [PMID: 35006382 PMCID: PMC9007175 DOI: 10.1007/s00018-021-04111-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 01/12/2023]
Abstract
Conventional angiogenic factors, such as vascular endothelial growth factor (VEGF), regulate both pathological and physiological angiogenesis indiscriminately, and their inhibitors may elicit adverse side effects. Secretogranin III (Scg3) was recently reported to be a diabetes-restricted VEGF-independent angiogenic factor, but the disease selectivity of Scg3 in retinopathy of prematurity (ROP), a retinal disease in preterm infants with concurrent pathological and physiological angiogenesis, was not defined. Here, using oxygen-induced retinopathy (OIR) mice, a surrogate model of ROP, we quantified an exclusive binding of Scg3 to diseased versus healthy developing neovessels that contrasted sharply with the ubiquitous binding of VEGF. Functional immunohistochemistry visualized Scg3 binding exclusively to disease-related disorganized retinal neovessels and neovascular tufts, whereas VEGF bound to both disorganized and well-organized neovessels. Homozygous deletion of the Scg3 gene showed undetectable effects on physiological retinal neovascularization but markedly reduced the severity of OIR-induced pathological angiogenesis. Furthermore, anti-Scg3 humanized antibody Fab (hFab) inhibited pathological angiogenesis with similar efficacy to anti-VEGF aflibercept. Aflibercept dose-dependently blocked physiological angiogenesis in neonatal retinas, whereas anti-Scg3 hFab was without adverse effects at any dose and supported a therapeutic window at least 10X wider than that of aflibercept. Therefore, Scg3 stringently regulates pathological but not physiological angiogenesis, and anti-Scg3 hFab satisfies essential criteria for development as a safe and effective disease-targeted anti-angiogenic therapy for ROP.
Collapse
Affiliation(s)
- Chang Dai
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA
| | - Prabuddha Waduge
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA
| | - Liyang Ji
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA
| | - Chengchi Huang
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Ye He
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA
| | - Hong Tian
- Everglades Biopharma, LLC, Houston, Texas, USA
| | - Elizabeth Zuniga-Sanchez
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Amit Bhatt
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Iok-Hou Pang
- Dept. of Pharmaceutical Sciences, North Texas Eye Research Institute, University of North Texas, Fort Worth, Texas, USA
| | - Guanfang Su
- Department of Ophthalmology, The Second Hospital of Jilin University, #218 Ziqiang Street, Changchun, Jilin, China
| | - Keith A. Webster
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA.,Everglades Biopharma, LLC, Houston, Texas, USA
| | - Wei Li
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida, USA
| |
Collapse
|
13
|
Pielhop TP, Popp C, Knierim D, Margaria P, Maiß E. Three new mycoviruses identified in the apple replant disease (ARD)-associated fungus Rugonectria rugulosa. Virus Genes 2022; 58:423-435. [PMID: 35841525 PMCID: PMC9477930 DOI: 10.1007/s11262-022-01924-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/25/2022] [Indexed: 02/05/2023]
Abstract
In this study, three new mycoviruses were identified co-infecting the apple replant disease (ARD)-associated root endophyte Rugonectria rugulosa. After dsRNA extraction, six viral fragments were visualized. Four fragments belong to a quadrivirus, which has a genome size of 17,166 bp. Each of the fragments of this quadrivirus has a single ORF encoding a protein. Two of these proteins are coat protein subunits, one ORF encodes the RdRp, and one protein has an unknown function. This virus was tentatively named rugonectria rugulosa quadrivirus 1 (RrQV1) as a member of the proposed new species Quadrivirus rugonectria. Another fragment represents the dsRNA intermediate form of a + ssRNA mitovirus with a genome size of 2410 nt. This virus encodes an RdRp and is tentatively called rugonectria rugulosa mitovirus 1 (RrMV1). RrMV1 is suggested as a member of a new species with the proposed name Mitovirus rugonectria. The sixth fragment belongs to the genome of an unclassified dsRNA virus tentatively called rugonectria rugulosa dsRNA virus 1 (RrV1). The monopartite dsRNA genome of RrV1 has a length of 8964 bp and contains two ORFs encoding a structure/gag protein and an RdRp. Full genomic sequences were determined and the genome structure as well as molecular properties are presented. After phylogenetic studies and sequence identity analyses, all three isolates are proposed as new mycoviruses. The results help to improve the understanding of the complexity of the factors involved in ARD and support the interest in mycoviral research. Subsequent analyses need to focus on the impact of mycoviruses on the biology and pathogenicity of ARD-associated fungi. The results of such studies could contribute to the development of mitigation strategies against the disease.
Collapse
Affiliation(s)
- Tom P. Pielhop
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Carolin Popp
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Brunswick, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Brunswick, Germany
| | - Edgar Maiß
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| |
Collapse
|
14
|
Du J, Li Q, Liu M, Wang Y, Xue Z, Huo F, Zhang X, Shang Y, Li S, Huang H, Pang Y. Distinguishing Relapse From Reinfection With Whole-Genome Sequencing in Recurrent Pulmonary Tuberculosis: A Retrospective Cohort Study in Beijing, China. Front Microbiol 2021; 12:754352. [PMID: 34956119 PMCID: PMC8693897 DOI: 10.3389/fmicb.2021.754352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Tuberculosis recurrence is still a major problem for the control of tuberculosis, and the cause of the recurrence is still unclear. Methods: We retrospectively recruited 68 pairs of samples of Mycobacterium tuberculosis (MTB) from recurrent TB cases in Beijing Chest Hospital between January 2008 and December 2019. The whole-genome sequencing was conducted to analyze single-nucleotide polymorphism (SNP) and to identify whether recurrent disease was due to relapse or reinfection. The BACTEC MGIT was performed to compare differences in drug susceptibility profiles between two episodes. Results: 62 (91.2%) out of 68 confirmed recurrence were due to relapse, whereas the remaining six (8.8%) were due to reinfection. And there was a strong association between earlier relapse and underlying chronic diseases. In addition, the MTB isolates from non-diabetic patients had a higher mutation rate than those from diabetic patients. A community transmission was also identified in our cohort. Levofloxacin resistance was the most frequently observed drug resistance for 12.9% relapse cases. Conclusion: The relapse of a previous episode in Beijing. The underlying chronic diseases are associated with an earlier TB relapse. MTB isolates were more prone to develop levofloxacin resistance than moxifloxacin resistance after FQ exposure. The patients at high-risk for relapses deserve more careful investigation.
Collapse
Affiliation(s)
- Jian Du
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qing Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Min Liu
- Provincial Center for Tuberculosis Control and Prevention, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Yufeng Wang
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Zhongtan Xue
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| |
Collapse
|
15
|
Avalos-Calleros JA, Pastor-Palacios G, Bolaños-Martínez OC, Mauricio-Castillo A, Gregorio-Jorge J, Martínez-Marrero N, Bañuelos-Hernández B, Méndez-Lozano J, Arguello-Astorga GR. Two strains of a novel begomovirus encoding Rep proteins with identical β1 strands but different β5 strands are not compatible in replication. Arch Virol 2021; 166:1691-1709. [PMID: 33852083 DOI: 10.1007/s00705-021-05066-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
Geminiviruses have genomes composed of single-stranded DNA molecules and encode a rolling-circle replication (RCR) initiation protein ("Rep"), which has multiple functions. Rep binds to specific repeated DNA motifs ("iterons"), which are major determinants of virus-specific replication. The particular amino acid (aa) residues that determine the preference of a geminivirus Rep for specific iterons (i.e., the trans-acting replication "specificity determinants", or SPDs) are largely unknown, but diverse lines of evidence indicate that most of them are closely associated with the so-called RCR motif I (FLTYP), located in the first 12-19 aa residues of the protein. In this work, we characterized two strains of a novel begomovirus, rhynchosia golden mosaic Sinaloa virus (RhGMSV), that were incompatible in replication in pseudorecombination experiments. Systematic comparisons of the Rep proteins of both RhGMSV strains in the DNA-binding domain allowed the aa residues at positions 71 and 74 to be identified as the residues most likely to be responsible for differences in replication specificity. Residue 71 is part of the β-5 strand structural element, which was predicted in previous studies to contain Rep SPDs. Since the Rep proteins encoded by both RhGMSV strains are identical in their first 24 aa residues, where other studies have mapped potential SPDs, this is the first study lending direct support to the notion that geminivirus Rep proteins contain separate SPDs in their N-terminal domain.
Collapse
Affiliation(s)
- Jesús Aarón Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Guillermo Pastor-Palacios
- CONACYT-Consorcio de Investigación Innovación y Desarrollo para las Zonas Áridas, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a La Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Omayra C Bolaños-Martínez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | | | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala (UPTx)., Av. Insurgentes Sur 1582, Col. Crédito Constructor, Del. Benito Juárez, 03940, Mexico City, Mexico
| | - Nadia Martínez-Marrero
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Bernardo Bañuelos-Hernández
- Facultad de Agronomia y Veterinaria, Universidad De La Salle Bajio, Avenida Universidad 602, Lomas del Campestre, 37150, León Guanajuato, Mexico
| | - Jesús Méndez-Lozano
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
| | - Gerardo Rafael Arguello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico.
| |
Collapse
|
16
|
Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
Collapse
Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
| |
Collapse
|
17
|
The transcriptome of anterior regeneration in earthworm Eudrilus eugeniae. Mol Biol Rep 2020; 48:259-283. [PMID: 33306150 DOI: 10.1007/s11033-020-06044-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/28/2020] [Indexed: 12/25/2022]
Abstract
The oligochaete earthworm, Eudrilus eugeniae is capable of regenerating both anterior and posterior segments. The present study focuses on the transcriptome analysis of earthworm E. eugeniae to identify and functionally annotate the key genes supporting the anterior blastema formation and regulating the anterior regeneration of the worm. The Illumina sequencing generated a total of 91,593,182 raw reads which were assembled into 105,193 contigs using CLC genomics workbench. In total, 40,946 contigs were annotated against the NCBI nr and SwissProt database and among them, 15,702 contigs were assigned to 14,575 GO terms. Besides a total of 9389 contigs were mapped to 416 KEGG biological pathways. The RNA-Seq comparison study identified 10,868 differentially expressed genes (DEGs) and of them, 3986 genes were significantly upregulated in the anterior regenerated blastema tissue samples of the worm. The GO enrichment analysis showed angiogenesis and unfolded protein binding as the top enriched functions and the pathway enrichment analysis denoted TCA cycle as the most significantly enriched pathway associated with the upregulated gene dataset of the worm. The identified DEGs and their function and pathway information can be effectively utilized further to interpret the key cellular, genetic and molecular events associated with the regeneration of the worm.
Collapse
|