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Thaker K, Patoliya J, Rabadiya K, Patel D, Ponnuchamy M, Rama Reddy NR, Joshi R. An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl. J Biomol Struct Dyn 2024; 42:3848-3861. [PMID: 37243697 DOI: 10.1080/07391102.2023.2216300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/13/2023] [Indexed: 05/29/2023]
Abstract
The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khushali Thaker
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jaimini Patoliya
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Khushbu Rabadiya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dhaval Patel
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Manivel Ponnuchamy
- ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India
| | | | - Rushikesh Joshi
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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102
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Khichi S, Morang S, Dhamija P, Handu S. A Multi-epitope Subunit Vaccine Identification and Development Against Scrub Typhus (Orientia tsutsugamushi) Using Immunoinformatics Approaches. Cureus 2024; 16:e61009. [PMID: 38910723 PMCID: PMC11194024 DOI: 10.7759/cureus.61009] [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] [Accepted: 05/24/2024] [Indexed: 06/25/2024] Open
Abstract
Background The pathogen Orientia tsutsugamushi, which causes scrub typhus, is rapidly spreading throughout the tropics. As a measure to improve public health, the development of a vaccine for human use is essential. Scrub typhus is listed as one of the underdiagnosed and underreported febrile infections. This vector-borne zoonotic infection appears as eschar on the patient's skin. Methods Immunoinformatics was employed to predict the multi-epitope subunit vaccine that will activate both B and T cells. The final vaccine includes lipoprotein LprA as an adjuvant at the N-terminus along with B-cell, helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL)-binding epitopes to boost immunogenicity. Assessing the vaccine's physiochemistry demonstrates that it is both antigenic and non-allergic. The vaccine structure was developed, enhanced, confirmed, and disulfide-engineered to provide the best possible model. Using molecular docking, the interaction of the produced vaccine with toll-like receptor 2 (TLR2) was analyzed, and the vaccine-receptor complex was stabilized by molecular dynamics (MD) simulation. According to in silico cloning, Escherichia coli can efficiently produce the recommended vaccine. Additionally, the efficacy of the in silico-developed vaccine must be evaluated in an in vitro and in vivo experiment. Results The developed vaccine successfully stimulates cellular and humoral immune responses. The vaccine, which has three B-cell epitopes, three HCL epitopes, and nine CTL epitopes, can bind firmly to immunological receptors. Dynamic investigations of the vaccine-receptor complex show a strong interaction and stable conformation. Conclusion In this study, the vaccine candidate demonstrated strong antigenicity, stability, and solubility while also being non-allergenic to host cells. The vaccine candidate's stability with the TLR2 immune receptor is established by binding studies, and in silico cloning verifies efficient and stable expression in the bacterial system.
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Affiliation(s)
- Shalini Khichi
- Pharmacology, All India Institute of Medical Sciences, Rishikesh, IND
| | - Sikha Morang
- Pharmacology, All India Institute of Medical Sciences, Rishikesh, IND
| | - Puneet Dhamija
- Pharmacology, All India Institute of Medical Sciences, Rishikesh, IND
| | - Shailendra Handu
- Pharmacology, All India Institute of Medical Sciences, Rishikesh, IND
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103
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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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104
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Morales-Quintana L, Rabert C, Mendez-Yañez A, Ramos P. Transcriptional and structural analysis of non-specific lipid transfer proteins modulated by fungal endophytes in Antarctic plants under drought. PHYSIOLOGIA PLANTARUM 2024; 176:e14359. [PMID: 38797943 DOI: 10.1111/ppl.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Lipid transfer proteins (LTPs) play crucial roles in various biological processes in plants, such as pollen tube adhesion, phospholipid transfer, cuticle synthesis, and response to abiotic stress. While a few members of the non-specific LTPs (nsLTPs) have been identified, their structural characteristics remain largely unexplored. Given the observed improvement in the performance of Antarctic plants facing water deficit when associated with fungal endophytes, this study aimed to assess the role of these symbiotic organisms in the transcriptional modulation of putative nsLTPs. The study focused on identifying and characterizing two nsLTP in the Antarctic plant Colobanthus quitensis that exhibit responsiveness to drought stress. Furthermore, we investigated the influence of Antarctic endophytic fungi on the expression profiles of these nsLTPs, as these fungi have been known to enhance plant physiological and biochemical performance under water deficit conditions. Through 3D modeling, docking, and molecular dynamics simulations with different substrates, the conducted structural and ligand-protein interaction analyses showed that differentially expressed nsLTPs displayed the ability to interact with various ligands, with a higher affinity towards palmitoyl-CoA. Overall, our findings suggest a regulatory mechanism for the expression of these two nsLTPs in Colobanthus quitensis under drought stress, further modulated by the presence of endophytic fungi.
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Affiliation(s)
- Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Claudia Rabert
- Instituto de Ciencias Biomédicas, Facultad Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Chile
| | - Angela Mendez-Yañez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Patricio Ramos
- Plant-microorganisms Interaction Laboratory, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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105
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Sharma N, Patel SN, Rai AK, Singh SP. Biochemical characterization of a novel acid-active endopolygalacturonase for pectin depolymerization, pectic-oligomer production, and fruit juice clarification. Int J Biol Macromol 2024; 267:131565. [PMID: 38614184 DOI: 10.1016/j.ijbiomac.2024.131565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/18/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Endopolygalacturonases are crucial pectinases known for their efficient and sustainable pectin depolymerization activities. The present study identified a novel gene encoding endopolygalacturonase from an acidic mine tailing metagenome. The putative gene showed a maximum identity of 67.55 % with an uncharacterized peptide sequence from Flavobacterium fluvii. The gene was cloned and expressed in a heterologous host, E. coli. Biochemical characterization of the novel endopolygalacturonase enzyme variant (EPHM) showed maximum activity at 60 °C and at 5.0 pH, while retaining 50 % activity under the temperature and pH range of 20 °C to 70 °C for 6 h, and 3.0 to 10.0 for 3 h, respectively. The enzyme exhibited tolerance to different metal ions. EPHM was characterized for the depolymerization of methylated pectin into pectic oligosaccharides. Further, its utility was established for fruit juice clarification, as endorsed by high transmittance, significant viscosity reduction, and release of reducing sugars in the treated fruit juice samples.
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Affiliation(s)
- Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India
| | - Satya N Patel
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India
| | - Amit Kumar Rai
- National Agri-Food Biotechnology Institute, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), SAS Nagar, Sector 81, Mohali, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India.
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106
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Ali EAA, Hussein NA, El-Hakim AE, Amer MA, Shahein YE. Cloning and catalytic profile of Hyalomma dromedarii leucine aminopeptidase. Int J Biol Macromol 2024; 268:131778. [PMID: 38657929 DOI: 10.1016/j.ijbiomac.2024.131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Ticks have harmful impacts on both human and animal health and cause considerable economic losses. Leucine aminopeptidase enzymes (LAP) play important roles during tick infestation to liberate vital amino acids necessary for growth. The aim of the current study is to identify, express and characterize the LAP from the hard tick Hyalomma dromedarii and elucidate its biochemical characteristics. We cloned an open reading frame of 1560 bp encoding a protein of 519 amino acids. The LAP full-length was expressed in Escherichia coli BL21 (DE3) and purified. The recombinant enzyme (H.d rLAP- 6×His) had a predicted molecular mass of approximately 55 kDa. Purification and the enzymatic characteristics of H.d rLAP- 6×His were studied. The purified enzyme showed maximum activity at 37 °C and pH 8.0-8.5 using Leu-p-nitroanilide as a substrate. The activity of H.d rLAP- 6×His was sensitive to β-mercaptoethanol, dl-dithiothreitol, 1,10- phenanthroline, bestatin HCl, and EDTA and completely abolished by 0.05 % SDS. In parallel, the enzymatic activity was enhanced by Ni2+, Mn2+ and Mg2+, partially inhibited by Na+, Cu2+, Ca2+ and completely inhibited by Zn2+.
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Affiliation(s)
- Esraa A A Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Nahla A Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
| | - Amr E El-Hakim
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Mahmoud A Amer
- Zoology Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
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107
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Gangurde SS, Korani W, Bajaj P, Wang H, Fountain JC, Agarwal G, Pandey MK, Abbas HK, Chang PK, Holbrook CC, Kemerait RC, Varshney RK, Dutta B, Clevenger JP, Guo B. Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters. BMC PLANT BIOLOGY 2024; 24:354. [PMID: 38693487 PMCID: PMC11061970 DOI: 10.1186/s12870-024-04950-8] [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: 02/15/2024] [Accepted: 03/26/2024] [Indexed: 05/03/2024]
Abstract
BACKGROUND Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes. RESULTS Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites. CONCLUSION In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.
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Affiliation(s)
- Sunil S Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
| | - Walid Korani
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Prasad Bajaj
- International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, Telangana, India
| | - Hui Wang
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Jake C Fountain
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Manish K Pandey
- International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, Telangana, India.
| | - Hamed K Abbas
- Biological Control of Pests Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Perng-Kuang Chang
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70124, USA
| | - C Corley Holbrook
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
| | - Robert C Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Rajeev K Varshney
- WA State Biotechnology Centre, Centre for Crop and Food innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Josh P Clevenger
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA.
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108
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Shahbazi M, Majka J, Kubíková D, Zwierzykowski Z, Glombik M, Wendel JF, Sharbrough J, Hartmann S, Szecówka M, Doležel J, Bartoš J, Kopecký D, Kneřová J. Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1102-1118. [PMID: 38323852 DOI: 10.1111/tpj.16659] [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: 11/01/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.
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Affiliation(s)
- Mehrdad Shahbazi
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Denisa Kubíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, Iowa, USA
| | - Joel Sharbrough
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, 87801, USA
| | - Stephan Hartmann
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 4, 85354, Freising, Germany
| | - Marek Szecówka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
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109
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Liu K, Hou Q, Yu R, Deng H, Shen L, Wang Q, Wen X. Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple. Gene 2024; 904:148164. [PMID: 38224923 DOI: 10.1016/j.gene.2024.148164] [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: 10/26/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.
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Affiliation(s)
- Ke Liu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Luonan Shen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Institute for Forest Resources & Environment of Guizhou/ College of Forestry, Guizhou University, Guiyang 550025, China
| | - Qian Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
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Fan J, Chen N, Rao W, Ding W, Wang Y, Duan Y, Wu J, Xing S. Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus. PeerJ 2024; 12:e17371. [PMID: 38708338 PMCID: PMC11067905 DOI: 10.7717/peerj.17371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Background Platycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus. Methods P. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses. Conclusions Forty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus's ability to cope with environmental stresses during growth and development.
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Affiliation(s)
- Jizhou Fan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Na Chen
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- College of Pharmacy, Bozhou Vocational and Technical College, Bozhou, Anhui, China
| | - Weiyi Rao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
| | - Wanyue Ding
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuqing Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yingying Duan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
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111
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Qi T, Yang W, Hassan MJ, Liu J, Yang Y, Zhou Q, Li H, Peng Y. Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress. BMC PLANT BIOLOGY 2024; 24:346. [PMID: 38684940 PMCID: PMC11057079 DOI: 10.1186/s12870-024-05034-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored. RESULTS In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana. CONCLUSION These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiefang Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujiao Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Wubshet AK, Li GX, Li Q, Dai JF, Ding YZ, Zhou L, Qu M, Wang Y, Ma Z, Werid GM, Abera BH, Kebede AT, Sun Y, Yin X, Liu Y, Jie Z. Stability and integrity of self-assembled bovine parvovirus virus‑like particles (BPV‑VLPs) of VP2 and combination of VP1VP2 assisted by baculovirus-insect cell expression: a potential logistical platform for vaccine deployment. Virol J 2024; 21:87. [PMID: 38641833 PMCID: PMC11027344 DOI: 10.1186/s12985-024-02322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/20/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Bovine parvovirus (BPV) is an autonomous DNA virus with a smaller molecular size and subtle differences in its structural proteins, unlike other animal parvoviruses. More importantly, this virus has the potential to produce visible to silent economic catastrophes in the livestock business, despite receiving very little attention. Parvoviral virus-like particles (VLPs) as vaccines and as logistical platforms for vaccine deployment are well studied. However, no single experimental report on the role of VP1 in the assembly and stability of BPV-VLPs is available. Furthermore, the self-assembly, integrity and stability of the VLPs of recombinant BPV VP2 in comparison to VP1 VP2 Cap proteins using any expression method has not been studied previously. In this study, we experimentally evaluated the self-assembling ability with which BPV virus-like particles (VLPs) could be synthesized from a single structural protein (VP2) and by integrating both VP2 and VP1 amino acid sequences. METHODS In silico and experimental cloning methods were carried out. His-tagged and without-His-tag VP2 and V1VP2-encoding amino acid sequences were cloned and inserted into pFastbacdual, and insect cell-generated recombinant protein was evaluated by SDS‒PAGE and western blot. Period of infectivity and expression level were determined by IFA. The integrity and stability of the BPV VLPs were evaluated by transmission electron microscopy. The secondary structure of the BPV VLPs from both VP2 and V1VP2 was analyzed by circular dichroism. RESULTS Our findings show that VP2 alone was equally expressed and purified into detectable proteins, and the stability at different temperatures and pH values was not appreciably different between the two kinds of VLPs. Furthermore, BPV-VP2 VLPs were praised for their greater purity and integrity than BPV-VP1VP2 VLPs, as indicated by SDS‒PAGE. Therefore, our research demonstrates that the function of VP1 has no bearing on the stability or integrity of BPV-VLPs. CONCLUSIONS In summary, incredible physiochemically stable BPV VP2-derived VLPs have been found to be promising candidates for the development of multivalent vaccines and immunodiagnostic kits against enteric viruses and to carry heterogeneous epitopes for various economically important livestock diseases.
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Affiliation(s)
- Ashenafi Kiros Wubshet
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
- Department of Veterinary Basics and Diagnostic Sciences, College of Veterinary Science, Mekelle University, 2084, Mekelle, Tigray, Ethiopia
| | - Guo-Xiu Li
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Qian Li
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Jun-Fei Dai
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Yao-Zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Luoyi Zhou
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Min Qu
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Yang Wang
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Zhongyuan Ma
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Gebremeskel Mamu Werid
- Davies Livestock Research Centre, School of Animal & Veterinary Sciences, University of Adelaide, Roseworthy Campus, Roseworthy, SA, 5371, Australia
| | - Birhanu Hadush Abera
- Department of Veterinary Basics and Diagnostic Sciences, College of Veterinary Science, Mekelle University, 2084, Mekelle, Tigray, Ethiopia
| | - Asmelash Tassew Kebede
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
- Department of Animal Science, College of Agriculture and Natural Resources, Raya University, 92, Maychew, Tigray, Ethiopia
| | - Yuefeng Sun
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Xiangping Yin
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China.
- College of Animal Science & Technology (CAST), Hebei Normal University of Science & Technology (HNUST), Qinhuangdao, People's Republic of China.
| | - Zhang Jie
- State Key Laboratory of Veterinary Etiological Biology, National/OIE Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China.
- College of Animal Science & Technology (CAST), Hebei Normal University of Science & Technology (HNUST), Qinhuangdao, People's Republic of China.
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Zhang Y, Mo Y, Li J, Liu L, Gao Y, Zhang Y, Huang Y, Ren L, Zhu H, Jiang X, Ling Y. Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress. Sci Rep 2024; 14:8743. [PMID: 38627506 PMCID: PMC11021534 DOI: 10.1038/s41598-024-59341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.
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Affiliation(s)
- Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yanhu Gao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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Mei Z, Li B, Zhu S, Li Y, Yao J, Pan J, Zhang Y, Chen W. A Genome-Wide Analysis of the CEP Gene Family in Cotton and a Functional Study of GhCEP46-D05 in Plant Development. Int J Mol Sci 2024; 25:4231. [PMID: 38673820 PMCID: PMC11050269 DOI: 10.3390/ijms25084231] [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: 03/14/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
C-TERMINALLY ENCODED PEPTIDEs (CEPs) are a class of peptide hormones that have been shown in previous studies to play an important role in regulating the development and response to abiotic stress in model plants. However, their role in cotton is not well understood. In this study, we identified 54, 59, 34, and 35 CEP genes from Gossypium hirsutum (2n = 4x = 52, AD1), G. barbadense (AD2), G. arboreum (2n = 2X = 26, A2), and G. raimondii (2n = 2X = 26, D5), respectively. Sequence alignment and phylogenetic analyses indicate that cotton CEP proteins can be categorized into two subgroups based on the differentiation of their CEP domain. Chromosomal distribution and collinearity analyses show that most of the cotton CEP genes are situated in gene clusters, suggesting that segmental duplication may be a critical factor in CEP gene expansion. Expression pattern analyses showed that cotton CEP genes are widely expressed throughout the plant, with some genes exhibiting specific expression patterns. Ectopic expression of GhCEP46-D05 in Arabidopsis led to a significant reduction in both root length and seed size, resulting in a dwarf phenotype. Similarly, overexpression of GhCEP46-D05 in cotton resulted in reduced internode length and plant height. These findings provide a foundation for further investigation into the function of cotton CEP genes and their potential role in cotton breeding.
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Affiliation(s)
- Zhenyu Mei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Bei Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shouhong Zhu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yan Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jinbo Yao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jingwen Pan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yongshan Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wei Chen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Tullius MV, Bowen RA, Back PS, Masleša-Galić S, Nava S, Horwitz MA. LVS Δ capB-vectored multiantigenic melioidosis vaccines protect against lethal respiratory Burkholderia pseudomallei challenge in highly sensitive BALB/c mice. mBio 2024; 15:e0018624. [PMID: 38511933 PMCID: PMC11005352 DOI: 10.1128/mbio.00186-24] [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: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
Melioidosis, caused by the intracellular bacterial pathogen and Tier 1 select agent Burkholderia pseudomallei (Bp), is a highly fatal disease endemic in tropical areas. No licensed vaccine against melioidosis exists. In preclinical vaccine studies, demonstrating protection against respiratory infection in the highly sensitive BALB/c mouse has been especially challenging. To address this challenge, we have used a safe yet potent live attenuated platform vector, LVS ΔcapB, previously used successfully to develop vaccines against the Tier 1 select agents of tularemia, anthrax, and plague, to develop a melioidosis vaccine. We have engineered melioidosis vaccines (rLVS ΔcapB/Bp) expressing multiple immunoprotective Bp antigens among type VI secretion system proteins Hcp1, Hcp2, and Hcp6, and membrane protein LolC. Administered intradermally, rLVS ΔcapB/Bp vaccines strongly protect highly sensitive BALB/c mice against lethal respiratory Bp challenge, but protection is overwhelmed at very high challenge doses. In contrast, administered intranasally, rLVS ΔcapB/Bp vaccines remain strongly protective against even very high challenge doses. Under some conditions, the LVS ΔcapB vector itself provides significant protection against Bp challenge, and consistent with this, both the vector and vaccines induce humoral immune responses to Bp antigens. Three-antigen vaccines expressing Hcp6-Hcp1-Hcp2 or Hcp6-Hcp1-LolC are among the most potent and provide long-term protection and protection even with a single intranasal immunization. Protection via the intranasal route was either comparable to or statistically significantly better than the single-deletional Bp mutant Bp82, which served as a positive control. Thus, rLVS ΔcapB/Bp vaccines are exceptionally promising safe and potent melioidosis vaccines. IMPORTANCE Melioidosis, a major neglected disease caused by the intracellular bacterial pathogen Burkholderia pseudomallei, is endemic in many tropical areas of the world and causes an estimated 165,000 cases and 89,000 deaths in humans annually. Moreover, B. pseudomallei is categorized as a Tier 1 select agent of bioterrorism, largely because inhalation of low doses can cause rapidly fatal pneumonia. No licensed vaccine is available to prevent melioidosis. Here, we describe a safe and potent melioidosis vaccine that protects against lethal respiratory challenge with B. pseudomallei in a highly sensitive small animal model-even a single immunization is highly protective, and the vaccine gives long-term protection. The vaccine utilizes a highly attenuated replicating intracellular bacterium as a vector to express multiple key proteins of B. pseudomallei; this vector platform has previously been used successfully to develop potent vaccines against other Tier 1 select agent diseases including tularemia, anthrax, and plague.
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Affiliation(s)
- Michael V. Tullius
- Division of Infectious Diseases, Department of Medicine, Center for Health Sciences, School of Medicine, University of California, Los Angeles, California, USA
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Peter S. Back
- Division of Infectious Diseases, Department of Medicine, Center for Health Sciences, School of Medicine, University of California, Los Angeles, California, USA
| | - Saša Masleša-Galić
- Division of Infectious Diseases, Department of Medicine, Center for Health Sciences, School of Medicine, University of California, Los Angeles, California, USA
| | - Susana Nava
- Division of Infectious Diseases, Department of Medicine, Center for Health Sciences, School of Medicine, University of California, Los Angeles, California, USA
| | - Marcus A. Horwitz
- Division of Infectious Diseases, Department of Medicine, Center for Health Sciences, School of Medicine, University of California, Los Angeles, California, USA
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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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Zeng Q, Gu J, Cai M, Wang Y, Xie Q, Han Y, Zhang S, Lu L, Chen Y, Zeng Y, Chen T. Genome-Wide Identification and Expression Analysis of TGA Family Genes Associated with Abiotic Stress in Sunflowers ( Helianthus annuus L.). Int J Mol Sci 2024; 25:4097. [PMID: 38612905 PMCID: PMC11012525 DOI: 10.3390/ijms25074097] [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: 03/09/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Sunflower (Helianthus annuus L.) is an important, substantial global oil crop with robust resilience to drought and salt stresses. The TGA (TGACG motif-binding factor) transcription factors, belonging to the basic region leucine zipper (bZIP) family, have been implicated in orchestrating multiple biological processes. Despite their functional significance, a comprehensive investigation of the TGA family's abiotic stress tolerance in sunflowers remains elusive. In the present study, we identified 14 TGA proteins in the sunflower genome, which were unequally distributed across 17 chromosomes. Employing phylogenetic analysis encompassing 149 TGA members among 13 distinct species, we revealed the evolutionary conservation of TGA proteins across the plant kingdom. Collinearity analysis suggested that both HaTGA01 and HaTGA03 were generated due to HaTGA08 gene duplication. Notably, qRT-PCR analysis demonstrated that HaTGA04, HaTGA05, and HaTGA14 genes were remarkably upregulated under ABA, MeJA, and salt treatments, whereas HaTGA03, HaTGA06, and HaTGA07 were significantly repressed. This study contributes valuable perspectives on the potential roles of the HaTGA gene family under various stress conditions in sunflowers, thereby enhancing our understanding of TGA gene family dynamics and function within this agriculturally significant species.
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Affiliation(s)
- Qinzong Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Jiafeng Gu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Maohong Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Yingwei Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Qinyu Xie
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Yuliang Han
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Siqi Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Lingyue Lu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Youheng Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Youling Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
| | - Tao Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
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118
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Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588023. [PMID: 38617253 PMCID: PMC11014511 DOI: 10.1101/2024.04.03.588023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis with subsequent detection with High Performance Liquid Chromatography (HPLC). This method can be performed in anaerobic glove bag settings, requires readily available HPLC instrumentation for subsequent detection, and is adaptable to meet the needs of a variety of substrate affinity measurements.
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Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
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119
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Reena G, Ranjani R, Goutham D, Sangeetha K. In silico screening of potential plant peptides against the non-structural proteins of dengue virus. J Vector Borne Dis 2024; 61:211-219. [PMID: 38922655 DOI: 10.4103/jvbd.jvbd_47_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/06/2023] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND OBJECTIVES Peptides isolated from different sources of plants have the advantages of specificity, lower toxicity, and increased therapeutic effects; hence, it is necessary to search for newer antivirals from plant sources for the treatment of dengue viral infections. METHODS In silico screening of selected plant peptides against the non-structural protein 1, NS3 protease domain (NS2B-NS3Pro) with the cofactor and ATPase/helicase domain (NS3 helicase domain/NS3hel) of dengue virus was performed. The physicochemical characteristics of the peptides were calculated using Protparam tools, and the allergenicity and toxicity profiles were assessed using allergenFP and ToxinPred, respectively. RESULTS Among the tested compounds, Ginkbilobin demonstrated higher binding energy against three tested nonstructural protein targets. Kalata B8 demonstrated maximum binding energy against NSP-1 and NSP-2, whereas Circulin A acted against the NSP3 protein of dengue virus. INTERPRETATION CONCLUSION The three compounds identified by in silico screening can be tested in vitro, which could act as potential leads as they are involved in hampering the replication of the dengue virus by interacting with the three prime non-structural proteins.
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Affiliation(s)
- G Reena
- Saveetha School of Engineering, SIMATS, Thandalam, Chennai, India
| | - R Ranjani
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh, India
| | - D Goutham
- Department of Computer Science, College of Engineering & Sri Venkateswara University, Tirupathi, Andhra Pradesh, India
| | - K Sangeetha
- Saveetha School of Engineering, SIMATS, Thandalam, Chennai, India
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120
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Jain U, Johari S, Srivastava P. Current Insights of Nanocarrier-Mediated Gene Therapeutics to Treat Potential Impairment of Amyloid Beta Protein and Tau Protein in Alzheimer's Disease. Mol Neurobiol 2024; 61:1969-1989. [PMID: 37831361 DOI: 10.1007/s12035-023-03671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Alzheimer's disease (AD), is the major type of dementia and most progressive, irreversible widespread neurodegenerative disorder affecting the elderly worldwide. The prime hallmarks of Alzheimer's disease (AD) are beta-amyloid plaques (Aβ) and neurofibrillary tangles (NFT). In spite of recent advances and developments in targeting the hallmarks of AD, symptomatic medications that promise neuroprotective activity against AD are currently unable to treat degenerating brain clinically or therapeutically and show little efficacy. The extensive progress of AD therapies over time has resulted in the advent of disease-modifying medications with the potential to alleviate AD. However, due to the presence of a defensive connection between the vascular system and the neural tissues known as the blood-brain barrier (BBB), directing these medications to the site of action in the degenerating brain is the key problem. BBB acts as a highly selective semipermeable membrane that prevents any type of foreign substance from entering the microenvironment of neurons. To overcome this limitation, the revolutionary approach of nanoparticle(NP)/nanocarrier-mediated drug delivery system has marked the era with its unique property to cross, avoid, or disrupt the defensive BBB efficiently and release the modified drug at the target site of action. After comprehensive data mining, this review focuses on the detailed understanding of different types of nanoparticle(NP)/nanocarrier-mediated drug delivery system like liposomes, micelles, gold nanoparticles(NP), polymeric NPs, etc. which have promising potential in carrying the desired drug(cargo) to the location in the degenerated brain thus mitigating the Alzheimer's disease.
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Affiliation(s)
- Unnati Jain
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India
| | - Surabhi Johari
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India.
| | - Priyanka Srivastava
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India.
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Wagner C, Urquiza-Garcia U, Zurbriggen MD, Beyer HM. GMOCU: Digital Documentation, Management, and Biological Risk Assessment of Genetic Parts. Adv Biol (Weinh) 2024; 8:e2300529. [PMID: 38263723 DOI: 10.1002/adbi.202300529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
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Affiliation(s)
- Christoph Wagner
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Uriel Urquiza-Garcia
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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122
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Werth EG, Roos D, Philip ET. Immunocapture LC-MS methods for pharmacokinetics of large molecule drugs. Bioanalysis 2024; 16:165-177. [PMID: 38348660 DOI: 10.4155/bio-2023-0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Implementation of immunocapture LC-MS methods to characterize the pharmacokinetic profile of large molecule drugs has become a widely used technique over the past decade. As the pharmaceutical industry strives for speediness into clinical development without jeopardizing quality, robust assays with generic application across the pipeline are becoming instrumental in bioanalysis, especially in early-stage development. This review highlights the capabilities and challenges involved in hybrid immunocapture LC-MS techniques and its continued applications in nonclinical and clinical pharmacokinetic assay design. This includes a comparison of LC-MS-based approaches to conventional ligand-binding assays and the driving demands in large molecule drug portfolios including growing sensitivity requirements and the unique challenges of new modalities requiring innovation in the bioanalytical laboratory.
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Affiliation(s)
- Emily G Werth
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - David Roos
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Elsy T Philip
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
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123
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Tirado TC, Machado KC, Shigunov P, Batista M, Figueiredo FB. A peptide dataset for target analysis of human complement system proteins. Data Brief 2024; 53:110217. [PMID: 38445196 PMCID: PMC10912339 DOI: 10.1016/j.dib.2024.110217] [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: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The targeted LC-MS/MS method has been widely applied for peptide quantification, offering sensibility, specificity, and reproducibility to the analysis. However, it requires the prior selection of targets, including the construction of a spectral library. Here, we present a dataset comprising peptide mass spectra for targeted LC-MS/MS method setup, applied to a set of human complement system proteins. Additionally, we selected a group of peptides and demonstrated their stability and reproducibility in quantification. This dataset is invaluable for studies aiming at the quantification of the complement system proteins by targeted LC-MS/MS, as it provides data for spectral library construction and a list of selected peptides.
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Affiliation(s)
- Thais Cristina Tirado
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
- Laboratório de Referência em Leishmanioses, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Kelly Cavalcanti Machado
- Plataforma de Espectrometria de Massas RPT02H, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Patrícia Shigunov
- Laboratório de Biologia Básica de Células-Tronco, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Michel Batista
- Plataforma de Espectrometria de Massas RPT02H, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Fabiano Borges Figueiredo
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
- Laboratório de Referência em Leishmanioses, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
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Li G, Zhu W, Tian M, Liu R, Ruan Y, Liu C. Genome-Wide Identification of the SPP/SPPL Gene Family and BnaSPPL4 Regulating Male Fertility in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:3936. [PMID: 38612746 PMCID: PMC11012144 DOI: 10.3390/ijms25073936] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, the functions of SPP/SPPL in rapeseed (Brassica napus L.) have not been reported. In this study, 26 SPP/SPPLs were identified in rapeseed and categorized into three groups: SPP, SPPL2, and SPPL3. These members mainly contained the Peptidase_A22 and PA domains, which were distributed on 17 out of 19 chromosomes. Evolutionary analyses indicated that BnaSPP/SPPLs evolved with a large number of whole-genome duplication (WGD) events and strong purifying selection. Members are widely expressed and play a key role in the growth and development of rapeseed. The regulation of rapeseed pollen fertility by the BnaSPPL4 gene was further validated through experiments based on bioinformatics analysis, concluding that BnaSPPL4 silencing causes male sterility. Cytological observation showed that male infertility caused by loss of BnaSPPL4 gene function occurs late in the mononucleate stage due to microspore dysplasia.
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Affiliation(s)
- Guangze Li
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Wenjun Zhu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Minyu Tian
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Rong Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Ying Ruan
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
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Pan X, Deng Z, Wu R, Yang Y, Akher SA, Li W, Zhang Z, Guo Y. Identification of CEP peptides encoded by the tobacco (Nicotiana tabacum) genome and characterization of their roles in osmotic and salt stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 209:108525. [PMID: 38518396 DOI: 10.1016/j.plaphy.2024.108525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Members of the CEP (C-terminally Encoded Peptide) gene family have been shown to be involved in various developmental processes and stress responses in plants. In order to understand the roles of CEP peptides in stress response, a comprehensive bioinformatics approach was employed to identify NtCEP genes in tobacco (Nicotiana tabacum L.) and to analyze their potential roles in stress responses. Totally 21 NtCEP proteins were identified and categorized into two subgroups based on their CEP domains. Expression changes of the NtCEP genes in response to various abiotic stresses were analyzed via qRT-PCR and the results showed that a number of NtCEPs were significant up-regulated under drought, salinity, or temperature stress conditions. Furthermore, application of synthesized peptides derived from NtCEP5, NtCEP13, NtCEP14, and NtCEP17 enhanced plant tolerance to different salt stress treatments. NtCEP5, NtCEP9 and NtCEP14, and NtCEP17 peptides were able to promote osmotic tolerance of tobacco plants. The results from this study suggest that NtCEP peptides may serve as important signaling molecules in tobacco's response to abiotic stresses.
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Affiliation(s)
- Xiaolu Pan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Rongrong Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China; Qingdao Agricultural University, Qingdao, China
| | - Yalun Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China; Qingdao Agricultural University, Qingdao, China
| | - Sayed Abdul Akher
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China.
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China.
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McGary LC, Fetter CM, Gu M, Hamilton MC, Kumar H, Kuehm OP, Douglas CD, Bearne SL. Interrogating l-fuconate dehydratase with tartronate and 3-hydroxypyruvate reveals subtle differences within the mandelate racemase-subgroup of the enolase superfamily. Arch Biochem Biophys 2024; 754:109924. [PMID: 38354877 DOI: 10.1016/j.abb.2024.109924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Enzymes of the enolase superfamily share a conserved structure and a common partial reaction (i.e., metal-assisted, Brønsted base-catalyzed enol(ate) formation). The architectures of the enolization apparatus at the active sites of the mandelate racemase (MR)-subgroup members MR and l-fuconate dehydratase (FucD) are almost indistinguishable at the structural level. Tartronate and 3-hydroxypyruvate (3-HP) recognize the enolization apparatus and can be used to interrogate the active sites for differences that may not be apparent from structural data. We report a circular dichroism-based assay of FucD activity that monitors the change in ellipticity at 216 nm (Δ[Θ]S-P = 8985 ± 87 deg cm2 mol-1) accompanying the conversion of l-fuconate to 2-keto-3-deoxy-l-fuconate. Tartronate was a linear mixed-type inhibitor of FucD (Ki = 8.4 ± 0.7 mM, αKi = 63 ± 11 mM), binding 18-fold weaker than l-fuconate, compared with 2-fold weaker binding of tartronate by MR relative to mandelate. 3-HP irreversibly inactivated FucD (kinact/KI = 0.018 ± 0.002 M-1s-1) with an efficiency that was ∼4.6 × 103-fold less than that observed with MR. The inactivation arose predominantly from modifications at multiple sites and Tris-HCl, but not l-fuconate, afforded protection against inactivation. Similar to the reaction of 3-HP with MR, 3-HP modified the Brønsted base catalyst (Lys 220) at the active site of FucD, which was facilitated by the Brønsted acid catalyst His 351. Thus, the interactions of tartronate and 3-HP with MR and FucD revealed differences in binding affinity and reactivity that differentiated between the enzymes' enolization apparatuses.
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Affiliation(s)
- Laura C McGary
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Christopher M Fetter
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Minglu Gu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Meghan C Hamilton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Himank Kumar
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Oliver P Kuehm
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Colin D Douglas
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Ganji M, Bakhshi S, Ahmadi K, Shoari A, Moeini S, Ghaemi A. Rational design of B-cell and T-cell multi epitope-based vaccine against Zika virus, an in silico study. J Biomol Struct Dyn 2024; 42:3426-3440. [PMID: 37190978 DOI: 10.1080/07391102.2023.2213339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
The Zika virus (ZKV) is a single-stranded positive-sense, enveloped RNA virus. Zika infection during pregnancy can cause congenital microcephaly, Guillain-Barré syndrome, miscarriage, and other CNS abnormalities. The world needs safe and effective vaccinations to fight against ZIKV infection since vaccination is generally regarded as one of the most effective ways to prevent infectious diseases. In the present work, we used immunoinformatics and docking studies to construct a vaccine containing multi-epitopes using the structural and non-structural proteins of ZKV. The structural models of ZKV proteins (PrE, PrM, NS1, and NS2A) were constructed using Pyre2 and RaptorX servers. The epitopes of B-cell, T-cell (HTL and CTL), and IFN-γ were predicted, and each epitope's immunogenic nature and physiochemical properties were confirmed. As an adjuvant, the CPG-Oligodeoxynucleotide, an agonist of Toll-like receptor 9 (TLR9), is associated to cytotoxic T-lymphocytes (CTL) epitopes via PAPAP linker. To assess the binding affinity and the tendency of the designed vaccine to induce an immune response through TLR9, molecular docking was done. In the next step, molecular dynamics (MD) simulation to 100 nanoseconds (ns) was used to evaluate the stability of the interaction of the designed vaccine with TLR9. The designed vaccine is predicted to be highly antigenic, non-toxic, soluble, and stable with low flexibility in MD simulation. MD studies indicated that the finalized vaccine-TLR9 docked complex was stable during simulation time. The vaccine construct is able to stimulate both humoral and cellular immune responses. We suppose that our constructed model of the vaccine may have the ability to induce the host immune response against ZKV. Further studies, including in vitro and in vivo experimental analyses, are needed to prove the constructed vaccine's efficacy with multi-epitopes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shohreh Bakhshi
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Shoari
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Soheila Moeini
- Department of Surgery, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Delihas N. Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer. Int J Mol Sci 2024; 25:3924. [PMID: 38612733 PMCID: PMC11011693 DOI: 10.3390/ijms25073924] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues.
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Affiliation(s)
- Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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129
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Shen H, Hou Y, Wang X, Li Y, Wu J, Lou H. Genome-Wide Identification, Expression Analysis under Abiotic Stress and Co-Expression Analysis of MATE Gene Family in Torreya grandis. Int J Mol Sci 2024; 25:3859. [PMID: 38612669 PMCID: PMC11012001 DOI: 10.3390/ijms25073859] [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: 02/03/2024] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis.
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Affiliation(s)
| | | | | | | | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (H.S.); (Y.H.); (X.W.); (Y.L.)
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Devi R, Goyal P, Verma B, Hussain S, Chowdhary F, Arora P, Gupta S. A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L. BMC Genomics 2024; 25:315. [PMID: 38532362 DOI: 10.1186/s12864-024-10227-z] [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: 10/20/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein-Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.
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Affiliation(s)
- Ritu Devi
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Goyal
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Bhawna Verma
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Fariha Chowdhary
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Suphla Gupta
- Plant Biotechnology Division, Jammu, India.
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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131
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Jangra J, Bajad NG, Singh R, Kumar A, Singh SK. Identification of novel potential cathepsin-B inhibitors through pharmacophore-based virtual screening, molecular docking, and dynamics simulation studies for the treatment of Alzheimer's disease. Mol Divers 2024:10.1007/s11030-024-10821-z. [PMID: 38517648 DOI: 10.1007/s11030-024-10821-z] [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: 11/28/2023] [Accepted: 02/03/2024] [Indexed: 03/24/2024]
Abstract
Cathepsin B is a cysteine protease lysosomal enzyme involved in several physiological functions. Overexpression of the enzyme enhances its proteolytic activity and causes the breakdown of amyloid precursor protein (APP) into neurotoxic amyloid β (Aβ), a characteristic hallmark of Alzheimer's disease (AD). Therefore, inhibition of the enzyme is a crucial therapeutic aspect for treating the disease. Combined structure and ligand-based drug design strategies were employed in the current study to identify the novel potential cathepsin B inhibitors. Five different pharmacophore models were developed and used for the screening of the ZINC-15 database. The obtained hits were analyzed for the presence of duplicates, interfering PAINS moieties, and structural similarities based on Tanimoto's coefficient. The molecular docking study was performed to screen hits with better target binding affinity. The top seven hits were selected and were further evaluated based on their predicted ADME properties. The resulting best hits, ZINC827855702, ZINC123282431, and ZINC95386847, were finally subjected to molecular dynamics simulation studies to determine the stability of the protein-ligand complex during the run. ZINC123282431 was obtained as the virtual lead compound for cathepsin B inhibition and may be a promising novel anti-Alzheimer agent.
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Affiliation(s)
- Jatin Jangra
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Nilesh Gajanan Bajad
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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132
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Li JM, Shi K, Li AT, Zhang ZJ, Yu HL, Xu JH. Development of a Thermodynamically Favorable Multi-enzyme Cascade Reaction for Efficient Sustainable Production of ω-Amino Fatty Acids and α,ω-Diamines. CHEMSUSCHEM 2024; 17:e202301477. [PMID: 38117609 DOI: 10.1002/cssc.202301477] [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: 10/12/2023] [Revised: 11/25/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Aliphatic ω-amino fatty acids (ω-AFAs) and α,ω-diamines (α,ω-DMs) are essential monomers for the production of nylons. Development of a sustainable biosynthesis route for ω-AFAs and α,ω-DMs is crucial in addressing the challenges posed by climate change. Herein, we constructed an unprecedented thermodynamically favorable multi-enzyme cascade (TherFavMEC) for the efficient sustainable biosynthesis of ω-AFAs and α,ω-DMs from cheap α,ω-dicarboxylic acids (α,ω-DAs). This TherFavMEC was developed by incorporating bioretrosynthesis analysis tools, reaction Gibbs free energy calculations, thermodynamic equilibrium shift strategies and cofactor (NADPH&ATP) regeneration systems. The molar yield of 6-aminohexanoic acid (6-ACA) from adipic acid (AA) was 92.3 %, while the molar yield from 6-ACA to 1,6-hexanediamine (1,6-HMD) was 96.1 %, which were significantly higher than those of previously reported routes. Furthermore, the biosynthesis of ω-AFAs and α,ω-DMs from 20.0 mM α,ω-DAs (C6-C9) was also performed, giving 11.2 mM 1,6-HMD (56.0 % yield), 14.8 mM 1,7-heptanediamine (74.0 % yield), 17.4 mM 1,8-octanediamine (87.0 % yield), and 19.7 mM 1,9-nonanediamine (98.5 % yield), respectively. The titers of 1,9-nonanediamine, 1,8-octanediamine, 1,7-heptanediamine and 1,6-HMD were improved by 328-fold, 1740-fold, 87-fold and 3.8-fold compared to previous work. Therefore, this work holds great potential for the bioproduction of ω-AFAs and α,ω-DMs.
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Affiliation(s)
- Ju-Mou Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Kun Shi
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ai-Tao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan, 430062, P.R. China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
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133
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Ozsahin DU, Ameen ZS, Hassan AS, Mubarak AS. Enhancing explainable SARS-CoV-2 vaccine development leveraging bee colony optimised Bi-LSTM, Bi-GRU models and bioinformatic analysis. Sci Rep 2024; 14:6737. [PMID: 38509174 PMCID: PMC10954760 DOI: 10.1038/s41598-024-55762-7] [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: 08/05/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus that caused the outbreak of the coronavirus disease 2019 (COVID-19). The COVID-19 outbreak has led to millions of deaths and economic losses globally. Vaccination is the most practical solution, but finding epitopes (antigenic peptide regions) in the SARS-CoV-2 proteome is challenging, costly, and time-consuming. Here, we proposed a deep learning method based on standalone Recurrent Neural networks to predict epitopes from SARS-CoV-2 proteins easily. We optimised the standalone Bidirectional Long Short-Term Memory (Bi-LSTM) and Bidirectional Gated Recurrent Unit (Bi-GRU) with a bioinspired optimisation algorithm, namely, Bee Colony Optimization (BCO). The study shows that LSTM-based models, particularly BCO-Bi-LSTM, outperform all other models and achieve an accuracy of 0.92 and AUC of 0.944. To overcome the challenge of understanding the model predictions, explainable AI using the Shapely Additive Explanations (SHAP) method was employed to explain how Blackbox models make decisions. Finally, the predicted epitopes led to the development of a multi-epitope vaccine. The multi-epitope vaccine effectiveness evaluation is based on vaccine toxicity, allergic response risk, and antigenic and biochemical characteristics using bioinformatic tools. The developed multi-epitope vaccine is non-toxic and highly antigenic. Codon adaptation, cloning, gel electrophoresis assess genomic sequence, protein composition, expression and purification while docking and IMMSIM servers simulate interactions and immunological response, respectively. These investigations provide a conceptual framework for developing a SARS-CoV-2 vaccine.
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Affiliation(s)
- Dilber Uzun Ozsahin
- Department of Medical Diagnostic Imaging, College of Health Science, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
| | - Zubaida Said Ameen
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Biochemistry, Yusuf Maitama Sule University, Kano, Nigeria
| | - Abdurrahman Shuaibu Hassan
- Department of Electrical Electronics and Automation Systems Engineering, Kampala International University, Kampala, Uganda.
| | - Auwalu Saleh Mubarak
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia, 99138, Turkey
- Department of Electrical Engineering, Aliko Dangote University of Science and Technology, Wudil, Kano, Nigeria
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134
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Zeng X, Luo G, Fan Z, Xiao Z, Lu Y, Xiao Q, Hou Z, Tang Q, Zhou Y. Whole genome identification, molecular docking and expression analysis of enzymes involved in the selenomethionine cycle in Cardamine hupingshanensis. BMC PLANT BIOLOGY 2024; 24:199. [PMID: 38500044 PMCID: PMC10949594 DOI: 10.1186/s12870-024-04898-9] [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: 10/11/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND The selenomethionine cycle (SeMTC) is a crucial pathway for the metabolism of selenium. The basic bioinformatics and functions of four enzymes involved in the cycle including S-adenosyl-methionine synthase (MAT), SAM-dependent methyltransferase (MTase), S-adenosyl-homocysteine hydrolase (SAHH) and methionine synthase (MTR), have been extensively reported in many eukaryotes. The identification and functional analyses of SeMTC genes/proteins in Cardamine hupingshanensis and their response to selenium stress have not yet been reported. RESULTS In this study, 45 genes involved in SeMTC were identified in the C. hupingshanensis genome. Phylogenetic analysis showed that seven genes from ChMAT were clustered into four branches, twenty-seven genes from ChCOMT were clustered into two branches, four genes from ChSAHH were clustered into two branches, and seven genes from ChMTR were clustered into three branches. These genes were resided on 16 chromosomes. Gene structure and homologous protein modeling analysis illustrated that proteins in the same family are relatively conserved and have similar functions. Molecular docking showed that the affinity of SeMTC enzymes for selenium metabolites was higher than that for sulfur metabolites. The key active site residues identified for ChMAT were Ala269 and Lys273, while Leu221/231 and Gly207/249 were determined as the crucial residues for ChCOMT. For ChSAHH, the essential active site residues were found to be Asn87, Asp139 and Thr206/207/208/325. Ile204, Ser111/329/377, Asp70/206/254, and His329/332/380 were identified as the critical active site residues for ChMTR. In addition, the results of the expression levels of four enzymes under selenium stress revealed that ChMAT3-1 genes were upregulated approximately 18-fold, ChCOMT9-1 was upregulated approximately 38.7-fold, ChSAHH1-2 was upregulated approximately 11.6-fold, and ChMTR3-2 genes were upregulated approximately 28-fold. These verified that SeMTC enzymes were involved in response to selenium stress to varying degrees. CONCLUSIONS The results of this research are instrumental for further functional investigation of SeMTC in C. hupingshanensis. This also lays a solid foundation for deeper investigations into the physiological and biochemical mechanisms underlying selenium metabolism in plants.
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Affiliation(s)
- Xixi Zeng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Enshi, China, Enshi
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Enshi, China, 44500
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, China, 44500
| | - Guoqiang Luo
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China, 44500
| | - Zhucheng Fan
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China, 44500
| | - Zhijing Xiao
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Enshi, China, Enshi
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China, 44500
| | - Yanke Lu
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Enshi, China, Enshi
| | - Qiang Xiao
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, China, 44500
| | - Zhi Hou
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China, 44500
| | - Qiaoyu Tang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Enshi, China, Enshi.
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, China, 44500.
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology, Enshi, China, 44500.
| | - Yifeng Zhou
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Enshi, China, 44500.
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China, 44500.
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135
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Mu F, Zheng H, Zhao Q, Zhu M, Dong T, Kai L, Li Z. Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato. BMC PLANT BIOLOGY 2024; 24:193. [PMID: 38493089 PMCID: PMC10944623 DOI: 10.1186/s12870-024-04824-z] [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: 10/03/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.
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Affiliation(s)
- Fangfang Mu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Hao Zheng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Qiaorui Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
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136
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Akintubosun MO, Higgins MA. A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A. Beilstein J Org Chem 2024; 20:589-596. [PMID: 38505238 PMCID: PMC10949010 DOI: 10.3762/bjoc.20.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Hygromycin A is a broad-spectrum antibiotic that contains a furanose, cinnamic acid, and aminocyclitol moieties. The biosynthesis of the aminocyclitol has been proposed to proceed through six enzymatic steps from glucose 6-phosphate through myo-inositol to the final methylenedioxy-containing aminocyclitol. Although there is some in vivo evidence for this proposed pathway, biochemical support for the individual enzyme activities is lacking. In this study, we verify the activity for one enzyme in this pathway. We show that Hyg17 is a myo-inositol dehydrogenase that has a unique substrate scope when compared to other myo-inositol dehydrogenases. Furthermore, we analyze sequences from the protein family containing Hyg17 and discuss genome mining strategies that target this protein family to identify biosynthetic clusters for natural product discovery.
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Affiliation(s)
- Michael O Akintubosun
- Department of Biological Sciences, The University of Alabama, 3314 Science and Engineering Complex, Tuscaloosa, AL 35487, USA
| | - Melanie A Higgins
- Department of Biological Sciences, The University of Alabama, 3314 Science and Engineering Complex, Tuscaloosa, AL 35487, USA
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137
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Parveen K, Saddique MAB, Ali Z, Ur Rehman S, Zaib-Un-Nisa, Khan Z, Waqas M, Munir MZ, Hussain N, Muneer MA. Genome-wide analysis of Glutathione peroxidase (GPX) gene family in Chickpea (Cicer arietinum L.) under salinity stress. Gene 2024; 898:148088. [PMID: 38104951 DOI: 10.1016/j.gene.2023.148088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Chickpea is the second most widely grown legume in the world. Its cultivation is highly affected by saline soils. Salt stress damages its all growth stages from germination to maturity. It has a huge genetic diversity containing adaptation loci that can help produce salt-tolerant cultivars. The glutathione peroxidase (GPX) gene family plays an important role in regulating plant response to abiotic stimuli and protects cells from oxidative damage. In current research, the role of GPX genes is studied for inducing salt tolerance in chickpea. This study identifies the GPX gene family in Cicer arietinum. In response to the NaCl stress, the gene expression profiles of CaGPX3 were examined using real-time qRT-PCR. The results of phylogenetic analysis show that CaGPX genes have an evolutionary relationship with monocots, dicots, chlorophytes, and angiosperms. Gene structure analysis showed that CaGPX3, CaGPX4, and CaGPX5 have six, CaGPX2 has five, and CaGPX1 contains 9 exons. According to the Ka and Ks analysis chickpea has one pair of duplicated genes of GPX and the duplication was tandem with negative (purifying) selection Ka < Ks (<1). In-silico gene expression analysis revealed that CaGPX3 is a salt stress-responsive gene among all other five GPX members in chickpea. The qRT-PCR results showed that the CaGPX3 gene expression was co-ordinately regulated under salt stress conditions, confirming CaGPX3's key involvement in salt tolerance.
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Affiliation(s)
- Kauser Parveen
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | | | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan; Programs and Projects Department, Islamic Organization for Food Security, Astana, Kazakhstan
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan; SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan.
| | - Zaib-Un-Nisa
- Cotton Research Institute, Multan, Punjab, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | - Muhammad Waqas
- Pakistan Agricultural Research Council, Arid Zone Research Center, Pakistan Agricultural Research Council, Dera Ismail Khan, Pakistan
| | - Muhammad Zeeshan Munir
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd., Shenzhen 518055, China
| | - Niaz Hussain
- Arid Zone Research Institute Bhakkar, Punjab, Pakistan
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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138
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Guan H, Zhang Y, Li J, Zhu Z, Chang J, Bakari A, Chen S, Zheng K, Cao S. Analysis of the UDP-Glucosyltransferase ( UGT) Gene Family and Its Functional Involvement in Drought and Salt Stress Tolerance in Phoebe bournei. PLANTS (BASEL, SWITZERLAND) 2024; 13:722. [PMID: 38475568 DOI: 10.3390/plants13050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
Uridine diphosphate glycosyltransferases (UDP-GTs, UGTs), which are regulated by UGT genes, play a crucial role in glycosylation. In vivo, the activity of UGT genes can affect the availability of metabolites and the rate at which they can be eliminated from the body. UGT genes can exert their regulatory effects through mechanisms such as post-transcriptional modification, substrate subtype specificity, and drug interactions. Phoebe bournei is an economically significant tree species that is endemic to southern China. Despite extensive studies on the UGT gene family in various species, a comprehensive investigation of the UGT family in P. bournei has not been reported. Therefore, we conducted a systematic analysis to identify 156 UGT genes within the entire P. bournei genome, all of which contained the PSPG box. The PbUGT family consists of 14 subfamilies, consistent with Arabidopsis thaliana. We observed varying expression levels of PbUGT genes across different tissues in P. bournei, with the following average expression hierarchy: leaf > stem xylem > stem bark > root xylem > root bark. Covariance analysis revealed stronger covariance between P. bournei and closely related species. In addition, we stressed the seedlings with 10% NaCl and 10% PEG-6000. The PbUGT genes exhibited differential expression under drought and salt stresses, with specific expression patterns observed under each stress condition. Our findings shed light on the transcriptional response of PbUGT factors to drought and salt stresses, thereby establishing a foundation for future investigations into the role of PbUGT transcription factors.
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Affiliation(s)
- Hengfeng Guan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzi Zhang
- Center for Plant Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingshu Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhening Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiarui Chang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Almas Bakari
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kehui Zheng
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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139
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Dhondge HV, Barvkar VT, Dastager SG, Dharne MS, Rajput V, Pable AA, Henry RJ, Nadaf AB. Genome sequencing and protein modeling unraveled the 2AP biosynthesis in Bacillus cereus DB25. Int J Food Microbiol 2024; 413:110600. [PMID: 38281435 DOI: 10.1016/j.ijfoodmicro.2024.110600] [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: 05/16/2023] [Revised: 11/24/2023] [Accepted: 01/20/2024] [Indexed: 01/30/2024]
Abstract
2-Acetyl-1-pyrroline (2AP) is an important and major flavor aroma compound responsible for the fragrance of basmati rice, cheese, wine, and several other food products. Biosynthesis of 2AP in aromatic rice and a few other plant species is associated with a recessive Betaine aldehyde dehydrogenase 2 (BADH2) gene. However, the literature is scant on the relationship between the functional BADH2 gene and 2AP biosynthesis in prokaryotic systems. Therefore, in the present study, we aimed to explore the functionality of the BADH2 gene for 2AP biosynthesis in 2AP synthesizing rice rhizobacterial isolate Bacillus cereus DB25 isolated from the rhizosphere of basmati rice (Oryza sativa L.). Full-length BcBADH2 sequence was obtained through whole genome sequencing (WGS) and further confirmed through traditional PCR and Sanger sequencing. Then the functionality of the BcBADH2 gene was evaluated in-silico through bioinformatics analysis and protein docking studies and further experimentally validated through enzyme assay. The sequencing and bioinformatics analysis results revealed a full-length 1485 bp BcBADH2 coding sequence without any deletion or premature stop codons. Full-length BcBADH2 was found to encode a fully functional protein of 54.08 kDa with pI of 5.22 and showed the presence of the conserved amino acids responsible for enzyme activity. The docking studies confirmed a good affinity between the protein and its substrate whereas the presence of BcBADH2 enzyme activity confirmed the functionality of BADH2 enzyme in B. cereus DB25. In conclusion, the findings of the present study suggest that B. cereus DB25 is able to synthesize 2AP despite a functional BADH2 gene and there may be a different molecular mechanism responsible for 2AP biosynthesis in bacterial systems, unlike that found in aromatic rice and other eukaryotic plant species.
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Affiliation(s)
- Harshal V Dhondge
- Department of Botany, Savitribai Phule Pune University, Pune 411 007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune 411 007, India.
| | - Syed G Dastager
- NCIM Resource Center, Biochemical Sciences Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411 008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahesh S Dharne
- NCIM Resource Center, Biochemical Sciences Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411 008, India
| | - Vinay Rajput
- NCIM Resource Center, Biochemical Sciences Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411 008, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune 411 007, India
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Altafhusain B Nadaf
- Department of Botany, Savitribai Phule Pune University, Pune 411 007, India.
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140
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Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, Shen Z, Rao K. Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome. Genome Biol Evol 2024; 16:evae037. [PMID: 38408866 PMCID: PMC10919887 DOI: 10.1093/gbe/evae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024] Open
Abstract
The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong Province 510300, China
| | - Danilo Malara
- Stazione Zoologica Anton Dohrn, Integrated Marine Ecology Department, CRIMAC, Calabria Marine Centre, Amendolara 87071, Italy
| | - Pietro Battaglia
- Integrated Marine Ecology Department, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina 98168, Italy
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21300, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden 11900, Malaysia
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - D Allen Davis
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36830, USA
| | - Yu Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Zhongyuan Shen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Ke Rao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
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141
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Muthukumar VC. Escherichia coli FtsZ molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:2653-2666. [PMID: 37158088 DOI: 10.1080/07391102.2023.2206917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
Earlier molecular dynamics studies of the FtsZ protein revealed that the protein has high intrinsic flexibility which the crystal structures cannot reveal. However, the input structure in these simulation studies was based on the available crystal structure data and therefore, the effect of the C-terminal Intrinsically Disordered Region (IDR) of FtsZ could not be observed in any of these studies. Recent investigations have revealed that the C-terminal IDR is crucial for FtsZ assembly in vitro and Z ring formation in vivo. Therefore, in this study, we simulated FtsZ with the IDR. Simulations of the FtsZ monomer in different nucleotide bound forms (without nucleotide, GTP, GDP) were performed. In the conformations of FtsZ monomer with GTP, GTP binds variably with the protein. Such a variable interaction with the monomer has not been observed in any previous simulation studies of FtsZ and not observed in crystal structures. We found that central helix bends towards the C-terminal domain in the GTP bound form, hence, making way for polymerization. A nucleotide dependent shift/rotation of the C-terminal domain was observed in simulation time averaged structures.Communicated by Ramaswamy H. Sarma.
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142
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Northcote HM, Wititkornkul B, Cutress DJ, Allen ND, Brophy PM, Wonfor RE, Morphew RM. A dominance of Mu class glutathione transferases within the equine tapeworm Anoplocephala perfoliata. Parasitology 2024; 151:282-294. [PMID: 38200699 PMCID: PMC11007280 DOI: 10.1017/s0031182024000015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
The most common equine tapeworm, Anoplocephala perfoliata, has often been neglected amongst molecular investigations and has been faced with limited treatment options. However, the recent release of a transcriptome dataset has now provided opportunities for in-depth analysis of A. perfoliata protein expression. Here, global, and sub-proteomic approaches were utilized to provide a comprehensive characterization of the A. perfoliata soluble glutathione transferases (GST) (ApGST). Utilizing both bioinformatics and gel-based proteomics, GeLC and 2D-SDS PAGE, the A. perfoliata ‘GST-ome’ was observed to be dominated with Mu class GST representatives. In addition, both Sigma and Omega class GSTs were identified, albeit to a lesser extent and absent from affinity chromatography approaches. Moreover, 51 ApGSTs were localized across somatic (47 GSTs), extracellular vesicles (EVs) (Whole: 1 GST, Surface: 2 GSTs) and EV depleted excretory secretory product (ESP) (9 GSTs) proteomes. In related helminths, GSTs have shown promise as novel anthelmintic or vaccine targets for improved helminth control. Thus, provides potential targets for understanding A. perfoliata novel infection mechanisms, host–parasite relationships and anthelmintic treatments.
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Affiliation(s)
- Holly M. Northcote
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | - Boontarikaan Wititkornkul
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
- Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat 80240, Thailand
| | - David J. Cutress
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | - Nathan D. Allen
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | - Peter M. Brophy
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | - Ruth E. Wonfor
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | - Russell M. Morphew
- Department of Life Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
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143
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Yao X, Meng F, Wu L, Guo X, Sun Z, Jiang W, Zhang J, Wu J, Wang S, Wang Z, Su X, Dai X, Qu C, Xing S. Genome-wide identification of R2R3-MYB family genes and gene response to stress in ginger. THE PLANT GENOME 2024; 17:e20258. [PMID: 36209364 DOI: 10.1002/tpg2.20258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Ginger (Zingiber officinale Roscoe) is an important plant used worldwide for medicine and food. The R2R3-MYB transcription factor (TF) family has essential roles in plant growth, development, and stresses resistance, and the number of genes in the family varies greatly among different types of plants. However, genome-wide discovery of ZoMYBs and gene responses to stresses have not been reported in ginger. Therefore, genome-wide analysis of R2R3-MYB genes in ginger was conducted in this study. Protein phylogenetic relations and conserved motifs and chromosome localization and duplication, structure, and cis-regulatory elements were analyzed. In addition, the expression patterns of selected genes were analyzed under two different stresses. A total of 299 candidate ZoMYB genes were discovered in ginger. Based on groupings of R2R3-MYB genes in the model plant Arabidopsis thaliana (L.) Heynh., ZoMYBs were divided into eight groups. Genes were distributed across 22 chromosomes at uneven densities. In gene duplication analysis, 120 segmental duplications were identified in the ginger genome. Gene expression patterns of 10 ZoMYBs in leaves of ginger under abscisic acid (ABA) and low-temperature stress treatments were different. The results will help to determine the exact roles of ZoMYBs in anti-stress responses in ginger.
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Affiliation(s)
- Xiaoyan Yao
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Fei Meng
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Liping Wu
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Zongping Sun
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal Univ., Fuyang, 236037, China
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal Univ., Hengyang, Hunan, 421008, China
| | - Jing Zhang
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, 230038, China
| | - Shuting Wang
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Zhaojian Wang
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Xinglong Su
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
| | - Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural Univ., Tai'an, 271018, China
| | - Changqing Qu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal Univ., Fuyang, 236037, China
| | - Shihai Xing
- College of Pharmacy, Anhui Univ. of Chinese Medicine, Hefei, 230012, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
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144
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Monica P, Ranjan R, Kapoor M. Family 3 CBM improves the biochemical properties, substrate hydrolysis and coconut oil extraction by hemicellulolytic and holocellulolytic chimeras. Enzyme Microb Technol 2024; 174:110375. [PMID: 38157781 DOI: 10.1016/j.enzmictec.2023.110375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/10/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
To understand the influence of family 3 Carbohydrate Binding Module (hereafter CBM3), single (GH5 cellulase; CelB, CelBΔCBM), bi-chimeric [GH26 endo-mannanase (ManB-1601) and GH11 endo-xylanase (XynB); ManB-XynB [1], ManB-XynB-CBM] and tri-chimeric [ManB-XynB-CelB [1], ManB-XynB-CelBΔCBM] enzyme variants (fused or deleted of CBM) were produced and purified to homogeneity. CBM3 did not alter the pH and temperature optima of bi- and tri-chimeric enzymes but improved the pH and temperature stability of ManB in CBM variants of bi-/tri-chimeric enzymes. Truncation of CBM in CelB shifted the pH optimum and increased the melting temperature (Tm 65 ℃). CBM3 improved both substrate affinity (Km) and catalytic efficiency (kcat/Km) of fused enzymes in tri-chimera and CelB but only Km for bi-chimera. Far-UV CD of CelB and bi- and tri-chimeric enzymes suggested that CBM3 improved the α-helical content and compactness in the native state but did not prevent disintegration of secondary structural contents at acidic pH. Steady-state fluorescence studies suggested that under acidic conditions CBM3 prevented the exposure of hydrophobic patches in bi-chimeric protein but could not avert the opening up of chimeric enzyme structure. Aqueous enzyme assisted treatment of mature coconut kernel using single, bi- and tri-chimeric enzymes led to cracks, peeling and fracturing of the matrix and improved the oil yield by up to 22%.
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Affiliation(s)
- P Monica
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India
| | - Ritesh Ranjan
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India
| | - Mukesh Kapoor
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, UP, India.
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145
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Colomina-Alfaro L, Sist P, Marchesan S, Urbani R, Stamboulis A, Bandiera A. A Versatile Elastin-Like Carrier for Bioactive Antimicrobial Peptide Production and Delivery. Macromol Biosci 2024; 24:e2300236. [PMID: 37698188 DOI: 10.1002/mabi.202300236] [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: 05/24/2023] [Revised: 08/07/2023] [Indexed: 09/13/2023]
Abstract
Elastin-like polypeptides are biotechnological protein and peptide carriers that offer a vast scope of applicability. This work aims to build a model for the expression of antimicrobial peptides (AMPs) by genetically engineering the Human Elastin-like Polypeptide platform developed in the lab. The well-characterized AMP indolicidin is selected as an example of an antimicrobial domain for the recombinant fusion at the C-terminus of the carrier. The fusion construct has been designed to allow the release of the antimicrobial domain. The expression product has been purified and its physicochemical and antimicrobial properties has been characterized. Taking advantage of the self-assembling and matrix-forming properties of the recombinant biopolymer, the materials that are obtained have been evaluated for antimicrobial activity toward bacterial-strain models. This approach represents a cost-effective strategy for the production of smart components and materials endowed with antimicrobial capacity triggered by external stimuli.
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Affiliation(s)
- Laura Colomina-Alfaro
- Department of Life Sciences, University of Trieste, via L. Giorgieri, 1, Trieste, 34127, Italy
| | - Paola Sist
- Department of Life Sciences, University of Trieste, via L. Giorgieri, 1, Trieste, 34127, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri, 1, Trieste, 34127, Italy
| | - Ranieri Urbani
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri, 1, Trieste, 34127, Italy
| | - Artemis Stamboulis
- School of Metallurgy and Materials, Biomaterials Research Group, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Antonella Bandiera
- Department of Life Sciences, University of Trieste, via L. Giorgieri, 1, Trieste, 34127, Italy
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146
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Wang Q, Clark KM, Tiwari R, Raju N, Tharp GK, Rogers J, Harris RA, Raveendran M, Bosinger SE, Burdo TH, Silvestri G, Shan L. The CARD8 inflammasome dictates HIV/SIV pathogenesis and disease progression. Cell 2024; 187:1223-1237.e16. [PMID: 38428396 PMCID: PMC10919936 DOI: 10.1016/j.cell.2024.01.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this depletion remain incompletely understood, with most cell death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause CD4+ depletion and AIDS despite high-level viremia. Here, we report that the CARD8 inflammasome is activated immediately after HIV entry by the viral protease encapsulated in incoming virions. Sensing of HIV protease activity by CARD8 leads to rapid pyroptosis of quiescent cells without productive infection, while T cell activation abolishes CARD8 function and increases permissiveness to infection. In humanized mice reconstituted with CARD8-deficient cells, CD4+ depletion is delayed despite high viremia. Finally, we discovered loss-of-function mutations in CARD8 from "natural hosts," which may explain the peculiarly non-pathogenic nature of these infections. Our study suggests that CARD8 drives CD4+ T cell depletion during pathogenic HIV/SIV infections.
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Affiliation(s)
- Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ritudhwaj Tiwari
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nagarajan Raju
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven E Bosinger
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Tricia H Burdo
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
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147
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Siriatcharanon AK, Sutheeworapong S, Baramee S, Waeonukul R, Pason P, Kosugi A, Uke A, Ratanakhanokchai K, Tachaapaikoon C. Discovery of a Novel Cellobiose Dehydrogenase from Cellulomonas palmilytica EW123 and Its Sugar Acids Production. J Microbiol Biotechnol 2024; 34:457-466. [PMID: 38044713 PMCID: PMC10940743 DOI: 10.4014/jmb.2307.07004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023]
Abstract
Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30°C), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 x 105 and 9.06 x 104 (M-1 s-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.
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Affiliation(s)
- Ake-kavitch Siriatcharanon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sawannee Sutheeworapong
- Division of Bioinformatics and Systems Biology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sirilak Baramee
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
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148
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Zhai T, Lan S, Xv L, Zhang X, Ma X, Li Z, Gao J, Chen Y, Lai Z, Lin Y. Genome-Wide Identification and Expression Analysis Reveal bZIP Transcription Factors Mediated Hormones That Functions during Early Somatic Embryogenesis in Dimocarpus longan. PLANTS (BASEL, SWITZERLAND) 2024; 13:662. [PMID: 38475508 DOI: 10.3390/plants13050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The basic leucine zip (bZIP) transcription factors (TFs) are a group of highly conserved gene families that play important roles in plant growth and resistance to adversity stress. However, studies on hormonal regulatory pathways and functional analysis during somatic embryogenesis (SE) in Dimocarpus longan is still unavailable. In this study, a total of 51 bZIP family members were systematically identified in the whole genome of longan, a comprehensive bioinformatics analysis of DlbZIP (bZIP family members of D. longan) was performed, and subcellular localization and profiles patterns after transiently transformed DlbZIP60 were analyzed. The combined analysis of RNA-seq, ATAC-seq and ChIP-seq showed that four members have different H3K4me1 binding peaks in early SE and differentially expressed with increased chromatin accessibility. Comparative transcriptome analysis of bZIPs expression in early SE, different tissues and under 2,4-D treatment revealed that DlbZIP family might involved in growth and development during longan early SE. The qRT-PCR results implied that DlbZIP family were subjected to multiple hormonal responses and showed different degrees of up-regulated expression under indole-3-acetic acid (IAA), abscisic acid (ABA) and methyl jasmonate (MeJA) treatments, which indicated that they played an important role in the hormone synthesis pathways associated with the early SE of longan. Subcellular localization showed that DlbZIP60 was located in the nucleus, and the contents of endogenous IAA, MeJA and ABA were up-regulated in transiently DlbZIP60 overexpressed cell lines. These results suggest that DlbZIP60 may mediate hormones pathways that functions the development during early SE in longan.
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Affiliation(s)
- Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuoxian Lan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Luzhen Xv
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangwei Ma
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuoyun Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Gao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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149
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Goodell DJ, Whitby FG, Mellem JE, Lei N, Brockie PJ, Maricq AJ, Eckert DM, Hill CP, Madsen DM, Maricq AV. Mechanistic and structural studies reveal NRAP-1-dependent coincident activation of NMDARs. Cell Rep 2024; 43:113694. [PMID: 38265937 DOI: 10.1016/j.celrep.2024.113694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/27/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
N-methyl-D-aspartate (NMDA)-type ionotropic glutamate receptors have essential roles in neurotransmission and synaptic plasticity. Previously, we identified an evolutionarily conserved protein, NRAP-1, that is required for NMDA receptor (NMDAR) function in C. elegans. Here, we demonstrate that NRAP-1 was sufficient to gate NMDARs and greatly enhanced glutamate-mediated NMDAR gating, thus conferring coincident activation properties to the NMDAR. Intriguingly, vertebrate NMDARs-and chimeric NMDARs where the amino-terminal domain (ATD) of C. elegans NMDARs was replaced by the ATD from vertebrate receptors-were spontaneously active when ectopically expressed in C. elegans neurons. Thus, the ATD is a primary determinant of NRAP-1- and glutamate-mediated gating of NMDARs. We determined the crystal structure of NRAP-1 at 1.9-Å resolution, which revealed two distinct domains positioned around a central low-density lipoprotein receptor class A domain. The NRAP-1 structure, combined with chimeric and mutational analyses, suggests a model where the three NRAP-1 domains work cooperatively to modify the gating of NMDARs.
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Affiliation(s)
- Dayton J Goodell
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Jerry E Mellem
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Ning Lei
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Penelope J Brockie
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | | | - Debra M Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - David M Madsen
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA
| | - Andres V Maricq
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112-9458, USA.
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150
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Cardoso DC, Baldez BCL, Pereira AH, Kalapothakis E, Rosse IC, Cristiano MP. De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes. Mol Genet Genomics 2024; 299:16. [PMID: 38411741 DOI: 10.1007/s00438-024-02099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/10/2023] [Indexed: 02/28/2024]
Abstract
Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.
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Affiliation(s)
- Danon Clemes Cardoso
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil.
| | - Brenda Carla Lima Baldez
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
| | - Adriana Heloísa Pereira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Izinara Cruz Rosse
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Maykon Passos Cristiano
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
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