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Wu L, Zhao Z, Shin YJ, Yin Y, Raju A, Vaiyapuri TS, Idzham K, Son M, Lee Y, Sa JK, Chua JYH, Unal B, Zhai Y, Fan W, Huang L, Hu H, Gunaratne J, Nam DH, Jiang T, Tergaonkar V. Tumour microenvironment programming by an RNA-RNA-binding protein complex creates a druggable vulnerability in IDH-wild-type glioblastoma. Nat Cell Biol 2024; 26:1003-1018. [PMID: 38858501 PMCID: PMC11178504 DOI: 10.1038/s41556-024-01428-5] [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: 03/21/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Patients with IDH-wild-type glioblastomas have a poor five-year survival rate along with limited treatment efficacy due to immune cell (glioma-associated microglia and macrophages) infiltration promoting tumour growth and resistance. To enhance therapeutic options, our study investigated the unique RNA-RNA-binding protein complex LOC-DHX15. This complex plays a crucial role in driving immune cell infiltration and tumour growth by establishing a feedback loop between cancer and immune cells, intensifying cancer aggressiveness. Targeting this complex with blood-brain barrier-permeable small molecules improved treatment efficacy, disrupting cell communication and impeding cancer cell survival and stem-like properties. Focusing on RNA-RNA-binding protein interactions emerges as a promising approach not only for glioblastomas without the IDH mutation but also for potential applications beyond cancer, offering new avenues for developing therapies that address intricate cellular relationships in the body.
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Affiliation(s)
- Lele Wu
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yong Jae Shin
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yiyun Yin
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Anandhkumar Raju
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Khaireen Idzham
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Miseol Son
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yeri Lee
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Jason K Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joelle Yi Heng Chua
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Bilal Unal
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - You Zhai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wenhua Fan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijie Huang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Huimin Hu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jayantha Gunaratne
- Laboratory of Translational Biomedical Proteomics, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Do-Hyun Nam
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
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2
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Álvarez ÁL, Arboleya A, Abade dos Santos FA, García-Manso A, Nicieza I, Dalton KP, Parra F, Martín-Alonso JM. Highs and Lows in Calicivirus Reverse Genetics. Viruses 2024; 16:866. [PMID: 38932159 PMCID: PMC11209508 DOI: 10.3390/v16060866] [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: 03/24/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones.
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Affiliation(s)
- Ángel L. Álvarez
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Aroa Arboleya
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Fábio A. Abade dos Santos
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Nacional de Investigação Agrária e Veterinária, 2780-157 Oeiras, Portugal
| | - Alberto García-Manso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Inés Nicieza
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José M. Martín-Alonso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
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3
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Xie R, Yuan S, Hu G, Zhan J, Jin K, Tang Y, Fan J, Zhao Y, Wang F, Chen C, Wang DW, Li H. Nuclear AGO2 promotes myocardial remodeling by activating ANKRD1 transcription in failing hearts. Mol Ther 2024; 32:1578-1594. [PMID: 38475992 PMCID: PMC11081878 DOI: 10.1016/j.ymthe.2024.03.018] [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: 10/13/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024] Open
Abstract
Heart failure (HF) is manifested by transcriptional and posttranscriptional reprogramming of critical genes. Multiple studies have revealed that microRNAs could translocate into subcellular organelles such as the nucleus to modify gene expression. However, the functional property of subcellular Argonaute2 (AGO2), the core member of the microRNA machinery, has remained elusive in HF. AGO2 was found to be localized in both the cytoplasm and nucleus of cardiomyocytes, and robustly increased in the failing hearts of patients and animal models. We demonstrated that nuclear AGO2 rather than cytosolic AGO2 overexpression by recombinant adeno-associated virus (serotype 9) with cardiomyocyte-specific troponin T promoter exacerbated the cardiac dysfunction in transverse aortic constriction (TAC)-operated mice. Mechanistically, nuclear AGO2 activates the transcription of ANKRD1, encoding ankyrin repeat domain-containing protein 1 (ANKRD1), which also has a dual function in the cytoplasm as part of the I-band of the sarcomere and in the nucleus as a transcriptional cofactor. Overexpression of nuclear ANKRD1 recaptured some key features of cardiac remodeling by inducing pathological MYH7 activation, whereas cytosolic ANKRD1 seemed cardioprotective. For clinical practice, we found ivermectin, an antiparasite drug, and ANPep, an ANKRD1 nuclear location signal mimetic peptide, were able to prevent ANKRD1 nuclear import, resulting in the improvement of cardiac performance in TAC-induced HF.
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Affiliation(s)
- Rong Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Shuai Yuan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Guo Hu
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiabing Zhan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Kunying Jin
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yuyan Tang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiahui Fan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yanru Zhao
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Feng Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
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4
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Ottesen EW, Seo J, Luo D, Singh NN, Singh RN. A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes. Nucleic Acids Res 2024; 52:3547-3571. [PMID: 38214229 DOI: 10.1093/nar/gkad1259] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
Here we report a Survival Motor Neuron 2 (SMN2) super minigene, SMN2Sup, encompassing its own promoter, all exons, their flanking intronic sequences and the entire 3'-untranslated region. We confirm that the pre-mRNA generated from SMN2Sup undergoes splicing to produce a translation-competent mRNA. We demonstrate that mRNA generated from SMN2Sup produces more SMN than an identical mRNA generated from a cDNA clone. We uncover that overexpression of SMN triggers skipping of exon 3 of SMN1/SMN2. We define the minimal promoter and regulatory elements associated with the initiation and elongation of transcription of SMN2. The shortened introns within SMN2Sup preserved the ability of camptothecin, a transcription elongation inhibitor, to induce skipping of exons 3 and 7 of SMN2. We show that intron 1-retained transcripts undergo nonsense-mediated decay. We demonstrate that splicing factor SRSF3 and DNA/RNA helicase DHX9 regulate splicing of multiple exons in the context of both SMN2Sup and endogenous SMN1/SMN2. Prevention of SMN2 exon 7 skipping has implications for the treatment of spinal muscular atrophy (SMA). We validate the utility of the super minigene in monitoring SMN levels upon splicing correction. Finally, we demonstrate how the super minigene could be employed to capture the cell type-specific effects of a pathogenic SMN1 mutation.
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Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
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5
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Crosby HA, Keim K, Kwiecinski JM, Langouët-Astrié CJ, Oshima K, LaRivière WB, Schmidt EP, Horswill AR. Host-derived protease promotes aggregation of Staphylococcus aureus by cleaving the surface protein SasG. mBio 2024; 15:e0348323. [PMID: 38511930 PMCID: PMC11005337 DOI: 10.1128/mbio.03483-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Staphylococcus aureus is one of the leading causes of hospital-acquired infections, many of which begin following attachment and accumulation on indwelling medical devices or diseased tissue. These infections are often linked to the establishment of biofilms, but another often overlooked key characteristic allowing S. aureus to establish persistent infection is the formation of planktonic aggregates. Such aggregates are physiologically similar to biofilms and protect pathogens from innate immune clearance and increase antibiotic tolerance. The cell-wall-associated protein SasG has been implicated in biofilm formation via mechanisms of intercellular aggregation but the mechanism in the context of disease is largely unknown. We have previously shown that the expression of cell-wall-anchored proteins involved in biofilm formation is controlled by the ArlRS-MgrA regulatory cascade. In this work, we demonstrate that the ArlRS two-component system controls aggregation, by repressing the expression of sasG by activation of the global regulator MgrA. We also demonstrate that SasG must be proteolytically processed by a non-staphylococcal protease to induce aggregation and that strains expressing functional full-length sasG aggregate significantly upon proteolysis by a mucosal-derived host protease found in human saliva. We used fractionation and N-terminal sequencing to demonstrate that human trypsin within saliva cleaves within the A domain of SasG to expose the B domain and induce aggregation. Finally, we demonstrated that SasG is involved in virulence during mouse lung infection. Together, our data point to SasG, its processing by host proteases, and SasG-driven aggregation as important elements of S. aureus adaptation to the host environment.IMPORTANCEHere, we demonstrate that the Staphylococcus aureus surface protein SasG is important for cell-cell aggregation in the presence of host proteases. We show that the ArlRS two-component regulatory system controls SasG levels through the cytoplasmic regulator MgrA. We identified human trypsin as the dominant protease triggering SasG-dependent aggregation and demonstrated that SasG is important for S. aureus lung infection. The discovery that host proteases can induce S. aureus aggregation contributes to our understanding of how this pathogen establishes persistent infections. The observations in this study demonstrate the need to strengthen our knowledge of S. aureus surface adhesin function and processing, regulation of adhesin expression, and the mechanisms that promote biofilm formation to develop strategies for preventing chronic infections.
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Affiliation(s)
- Heidi A. Crosby
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Klara Keim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jakub M. Kwiecinski
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Christophe J. Langouët-Astrié
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kaori Oshima
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Wells B. LaRivière
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric P. Schmidt
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA
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6
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Wang S, Chen B, Ni S, Liang Y, Li Z. Efficient generation of recombinant eggplant mottled dwarf virus and expression of foreign proteins in solanaceous hosts. Virology 2024; 591:109980. [PMID: 38215560 DOI: 10.1016/j.virol.2024.109980] [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: 11/14/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024]
Abstract
Reverse genetics systems have only been successfully developed for a few plant rhabdoviruses. Additional systems are needed for molecular virology studies of these diverse viruses and development of viral vectors for biotechnological applications. Eggplant mottled dwarf virus (EMDV) is responsible for significant agricultural losses in various crops throughout the Mediterranean region and the Middle East. In this study, we report efficient recovery of infectious EMDV from cloned DNAs and engineering of EMDV-based vectors for the expression of foreign proteins in tobacco, eggplant, pepper, and potato plants. Furthermore, we show that the EMDV-based vectors are capable of simultaneously expressing multiple foreign proteins. The developed EMDV reverse genetics system offers a versatile tool for studying virus pathology and plant-virus interactions and for expressing foreign proteins in a range of solanaceous crops.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Binhuan Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuang Ni
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Liang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
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7
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Ma K, Cai L, Wang R, Wang J, Zhan H, Ni H, Lu B, Zhang Y, Gao J. Complete genome sequence of a novel mitovirus isolated from the fungus Fusarium oxysporum f. sp. ginseng causing ginseng root rot. Arch Virol 2024; 169:53. [PMID: 38381240 DOI: 10.1007/s00705-024-05962-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 02/22/2024]
Abstract
A novel mitovirus, tentatively designated as "Fusarium oxysporum mitovirus 2" (FoMV2), was isolated from the pathogenic Fusarium oxysporum f. sp. ginseng strain 0414 infecting Panax ginseng. The complete genome of FoMV2 is 2388 nt in length with a GC content of 30.57%. It contains a large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 713 amino acids with a molecular weight of 83.05 kDa. The sequence identity between FoMV2 and Botrytis cinerea mitovirus 8 and Fusarium verticillioides mitovirus 1 was 87.94% and 77.85%, respectively. Phylogenetic analysis showed that FoMV2 belongs to the genus Unuamitovirus in the family Mitoviridae. To the best of our knowledge, this is the first report of an unuamitovirus isolated from F. oxysporum f. sp. ginseng causing ginseng root rot.
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Affiliation(s)
- Kaige Ma
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Liping Cai
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Ruojin Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Jun Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Haoxin Zhan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Hechi Ni
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Baohui Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China
| | - Yanjing Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
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8
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Özbilen A, Sezer F, Taşkin KM. Identification and expression of strigolactone biosynthesis and signaling genes and the in vitro effects of strigolactones in olive ( Olea europaea L.). PLANT DIRECT 2024; 8:e568. [PMID: 38405354 PMCID: PMC10894696 DOI: 10.1002/pld3.568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/27/2024]
Abstract
Strigolactones (SLs), synthesized in plant roots, play a dual role in modulating plant growth and development, and in inducing the germination of parasitic plant seeds and arbuscular mycorrhizal fungi in the rhizosphere. As phytohormones, SLs are crucial in regulating branching and shaping plant architecture. Despite the significant impact of branching strategies on the yield performance of fruit crops, limited research has been conducted on SLs in these crops. In our study, we identified the transcript sequences of SL biosynthesis and signaling genes in olive (Olea europaea L.) using rapid amplification of cDNA ends. We predicted the corresponding protein sequences, analyzed their characteristics, and conducted molecular docking with bioinformatics tools. Furthermore, we quantified the expression levels of these genes in various tissues using quantitative real-time PCR. Our findings demonstrate the predominant expression of SL biosynthesis and signaling genes (OeD27, OeMAX3, OeMAX4, OeMAX1, OeD14, and OeMAX2) in roots and lateral buds, highlighting their importance in branching. Treatment with rac-GR24, an SL analog, enhanced the germination frequency of olive seeds in vitro compared with untreated embryos. Conversely, inhibition of SL biosynthesis with TIS108 increased lateral bud formation in a hard-to-root cultivar, underscoring the role of SLs as phytohormones in olives. These results suggest that modifying SL biosynthesis and signaling pathways could offer novel approaches for olive breeding, with potential applicability to other fruit crops.
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Affiliation(s)
- Aslıhan Özbilen
- Department of BiologyCanakkale Onsekiz Mart UniversityCanakkaleTurkey
| | - Fatih Sezer
- Department of Molecular Biology and GeneticsCanakkale Onsekiz Mart UniversityCanakkaleTurkey
| | - Kemal Melih Taşkin
- Department of Molecular Biology and GeneticsCanakkale Onsekiz Mart UniversityCanakkaleTurkey
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9
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Bo Z, Wang S, Xu K, Zhang C, Guo M, Cao Y, Zhang X, Wu Y. Isolation and genomic characteristics of the novel variant infectious bursal disease virus in China. Front Vet Sci 2023; 10:1314903. [PMID: 38146498 PMCID: PMC10749300 DOI: 10.3389/fvets.2023.1314903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023] Open
Abstract
The infectious bursal disease virus (IBDV) is a member of the viruses that can induce immunosuppression in chickens. In recent years, more and more IBDV-infected cases by the novel variant IBDV were reported in China, and it has been demonstrated that currently used vaccines could not provide complete protection against these new IBDV variants. However, a lack of comprehensive analysis of the genomic characteristics of the novel variant strain IBDV has hampered its vaccine development. In this study, a strain of IBDV, designated HB202201, was phylogenetically analyzed, and it was found that the hypervariable region (HVR) of VP2 belonged to the novel variant strain. Furthermore, the 5'- and 3'-ends of segments A and B were analyzed using the rapid amplification of cDNA end (RACE) method. After the full-length of segment A and segment B were determined, the phylogenetic analysis of the segment A and segment B showed that the isolated HB202201 belonged to A2dB1 genotype, which demonstrated the HB202201 belonged to the novel variant strain. In addition, the specific mutations in VP1-VP5 amino acids were analyzed, which showed that there were multiple typical mutations in novel variant IBDV proteins, including VP1 (G24, I141, V163, and E240), VP2 (K221, and I252), VP3 (Q167 and L196), and VP5 (R7, P44, R92, G104, and E147), whereas there was no typical mutation in VP4. This study provides insights into the genomic and antigenic characteristics of the novel variant IBDV, which will promote the development of novel vaccine against the novel variant IBDV.
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Affiliation(s)
- Zongyi Bo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shixu Wang
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Keke Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chengcheng Zhang
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mengjiao Guo
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yongzhong Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaorong Zhang
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yantao Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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10
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Ma Y, Zhao T, Wu X, Yang Z, Sun Y. Identification cloning and functional analysis of novel natural antisense lncRNA CFL1-AS1 in cattle. Epigenetics 2023; 18:2231707. [PMID: 37406176 DOI: 10.1080/15592294.2023.2231707] [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: 04/04/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
Long noncoding RNAs have been identified as important regulators of gene expression and animal development. The expression of natural antisense transcripts (NATs) transcribed in the opposite direction to protein-coding genes is usually positively correlated with the expression of homologous sense genes and is the key factor for expression. Here, we identified a conserved noncoding antisense transcript, CFL1-AS1, that plays an important role in muscle growth and development. CFL1-AS1 overexpression and knockout vectors were constructed and transfected into 293T and C2C12 cells. CFL1-AS1 positively regulated CFL1 gene expression, and the expression of CFL2 was also downregulated when CFL1-AS1 was knocked down. CFL1-AS1 promoted cell proliferation, inhibited apoptosis and participated in autophagy. This study expands the research on NATs in cattle and lays a foundation for the study of the biological function of bovine CFL1 and its natural antisense chain transcript CFL1-AS1 in bovine skeletal muscle development. The discovery of this NAT can provide a reference for subsequent genetic breeding and data on the characteristics and functional mechanisms of NATs.
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Affiliation(s)
- Yaoyao Ma
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianqi Zhao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinyi Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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11
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Lanave G, Diakoudi G, Pellegrini F, Lombardi R, Prioletti M, Circella E, Camarda A, Di Martino B, Camero M, Decaro N, Bányai K, Lavazza A, Buonavoglia C, Martella V. Novel parvovirus in an outbreak of fatal enteritis in European hedgehogs ( Erinaceus europaeus), Italy, 2022. Microbiol Spectr 2023; 11:e0249423. [PMID: 37728570 PMCID: PMC10581001 DOI: 10.1128/spectrum.02494-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023] Open
Abstract
Starting from June 2022, increased mortality associated with enteric signs was reported in European hedgehogs (Erinaceus europaeus) recovered at a regional wildlife rescue center, in Apulia, Italy. Cases of enteric disease were observed until the end of the breeding season, despite increased biosafety measures. A novel parvovirus was identified using metaviromic, and parvovirus-like particles were observed in the stools on electron microscopy observation. The virus was detected in the fecal samples of all the animals tested (n = 9) and in the internal organs (liver, spleen, and kidney) of three out of nine animals using a specific quantitative assay. In the full-length genome, the parvovirus was closely related (90.4% nt) to a chaphamaparvovirus identified in an Amur hedgehog (Erinaceus amurensis) in Asia and to chaphamaparvoviruses (≤ 70% nt) detected in bats and rodents. Since chaphamaparvoviruses are considered as pathogen in rodents, it will be important to investigate the pathogenic role, if any, of these parvoviruses in hedgehogs. IMPORTANCE European hedgehogs (Erinaceus europaeus) are common in Europe. This species has been shown to harbor occasionally zoonotic pathogens, including bacteria, fungi, and viruses. Exploring the virome of wildlife animals is important for animal conservation and also to assess zoonotic risks. Our metaviromic investigation identified a novel parvovirus from an outbreak of enteritis in European hedgehogs housed in a wildlife rescue center, extending the spectrum of potential viral pathogens in this species.
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Affiliation(s)
- Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Lombardi
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Michela Prioletti
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Elena Circella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Camarda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | | | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Krisztián Bányai
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Veterinary Medical Research Institute, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Canio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
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12
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Getz LJ, Brown JM, Sobot L, Chow A, Mahendrarajah J, Thomas N. Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus. Nucleic Acids Res 2023; 51:6156-6171. [PMID: 37158250 PMCID: PMC10325908 DOI: 10.1093/nar/gkad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/23/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Pathogenic Vibrio species account for 3-5 million annual life-threatening human infections. Virulence is driven by bacterial hemolysin and toxin gene expression often positively regulated by the winged helix-turn-helix (wHTH) HlyU transcriptional regulator family and silenced by histone-like nucleoid structural protein (H-NS). In the case of Vibrio parahaemolyticus, HlyU is required for virulence gene expression associated with type 3 Secretion System-1 (T3SS1) although its mechanism of action is not understood. Here, we provide evidence for DNA cruciform attenuation mediated by HlyU binding to support concomitant virulence gene expression. Genetic and biochemical experiments revealed that upon HlyU mediated DNA cruciform attenuation, an intergenic cryptic promoter became accessible allowing for exsA mRNA expression and initiation of an ExsA autoactivation feedback loop at a separate ExsA-dependent promoter. Using a heterologous E. coli expression system, we reconstituted the dual promoter elements which revealed that HlyU binding and DNA cruciform attenuation were strictly required to initiate the ExsA autoactivation loop. The data indicate that HlyU acts to attenuate a transcriptional repressive DNA cruciform to support T3SS1 virulence gene expression and reveals a non-canonical extricating gene regulation mechanism in pathogenic Vibrio species.
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Affiliation(s)
- Landon J Getz
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Justin M Brown
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Lauren Sobot
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Alexandra Chow
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Jastina Mahendrarajah
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Nikhil A Thomas
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
- Department of Medicine, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
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13
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Wang X, Cheng R, Xu D, Huang R, Li H, Jin L, Wu Y, Tang J, Sun C, Peng D, Chu C, Guo X. MG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode. Nat Commun 2023; 14:3354. [PMID: 37291108 PMCID: PMC10250356 DOI: 10.1038/s41467-023-39080-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
The rice root-knot nematode (Meloidogyne graminicola) is one of the most destructive pests threatening rice (Oryza sativa L.) production in Asia; however, no rice resistance genes have been cloned. Here, we demonstrate that M. GRAMINICOLA-RESISTANCE GENE 1 (MG1), an R gene highly expressed at the site of nematode invasion, determines resistance against the nematode in several rice varieties. Introgressing MG1 into susceptible varieties increases resistance comparable to resistant varieties, for which the leucine-rich repeat domain is critical for recognizing root-knot nematode invasion. We also report transcriptome and cytological changes that are correlated with a rapid and robust response during the incompatible interaction that occurs in resistant rice upon nematode invasion. Furthermore, we identified a putative protease inhibitor that directly interacts with MG1 during MG1-mediated resistance. Our findings provide insight into the molecular basis of nematode resistance as well as valuable resources for developing rice varieties with improved nematode resistance.
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Affiliation(s)
- Xiaomin Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daochao Xu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Renliang Huang
- Nanchang Subcenter of Rice National Engineering Laboratory, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Haoxing Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Jin
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, 625014, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoli Guo
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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14
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Ye Q, Wang DJ, Lan B, Mao JH. T-cell and B-cell repertoire diversity are selectively skewed in children with idiopathic nephrotic syndrome revealed by high-throughput sequencing. World J Pediatr 2023; 19:273-282. [PMID: 36449136 DOI: 10.1007/s12519-022-00640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/12/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Clinical studies suggest that the dysfunction of T cells and B cells may play an essential role in the pathogenesis of idiopathic nephrotic syndrome (INS), but laboratory evidence is lacking. Therefore, this study explored T-cell receptor (TCR) and B-cell receptor (BCR) profiling in children with idiopathic nephrotic syndrome. METHODS High-throughput sequencing technology was used to profile the TCR and BCR repertoires in children with INS. Peripheral blood was collected from ten INS patients, including five vinculin autoantibody-positive patients and five vinculin autoantibody-negative patients, before and after treatment. TCR and BCR libraries were constructed by 5'-RACE and sequenced by a DNBSEQ-T7 sequencer, and sequence analyses were performed using ReSeqTools, FastP, MiXCR, and VDJtools. RESULTS The TRA (T-cell receptor α), TRG (T-cell receptor γ), and IGH (immunoglobulin heavy chain) repertoires of the INS group were occupied by highly abundant clonotypes, whereas small clonotypes occupied the healthy group, especially TRA. A significant increase in the Shannon-Weaver index was observed for the TRA and TRG repertoires after treatment in vinculin autoantibody-negative patients, but a significant increase in the IGH repertoire after treatment was observed in vinculin autoantibody-positive patients. The frequency of some V-J pairs was significantly enriched in steroid-sensitive nephrotic syndrome patients. The usage frequency of the V and J genes was skewed in patients, which seemed not related to immunosuppressive therapy. However, after effective treatment, dynamic changes in the size of the individual clonotype were observed. CONCLUSION T-cell and B-cell immunity contribute to the pathogenesis of different INSs. Video: (MP4 99,786 KB).
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Affiliation(s)
- Qing Ye
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Dong-Jie Wang
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Bing Lan
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Jian-Hua Mao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China.
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15
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Fu M, Eimes JA, Waldman B. Divergent allele advantage in the MHC and amphibian emerging infectious disease. INFECTION, GENETICS AND EVOLUTION 2023; 111:105429. [PMID: 36990307 DOI: 10.1016/j.meegid.2023.105429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Genetic variation in the major histocompatibility complex (MHC) may be associated with resistance to the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). The pathogen originated in Asia, then spread worldwide, causing amphibian population declines and species extinctions. We compared the expressed MHC IIβ1 alleles of a Bd-resistant toad species, Bufo gargarizans, from South Korea with those of a Bd-susceptible Australasian frog species, Litoria caerulea. We found at least six expressed MHC IIβ1 loci in each of the two species. Amino acid diversity encoded by these MHC alleles was similar between species, but the genetic divergence of those alleles known for broader pathogen-derived peptide binding was greater in the Bd-resistant species. In addition, we found a potentially rare allele in one resistant individual from the Bd-susceptible species. Deep next-generation sequencing recovered approximately triple the genetic resolution accessible from traditional cloning-based genotyping. Targeting more than one MHC IIβ1 expressed locus enables us to better understand how host MHC may adapt to emerging infectious diseases.
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16
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Fang Z, Fan M, Yuan D, Jin L, Wang Y, Ding L, Xu S, Tu J, Zhang E, Wu X, Chen ZB, Huang W. Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice. Commun Biol 2023; 6:105. [PMID: 36707678 PMCID: PMC9883214 DOI: 10.1038/s42003-023-04483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging important epigenetic regulators in metabolic processes. Whether they contribute to the metabolic effects of vertical sleeve gastrectomy (VSG), one of the most effective treatments for sustainable weight loss and metabolic improvement, is unknown. Herein, we identify a hepatic lncRNA Gm19619, which is strongly repressed by VSG but highly up-regulated by diet-induced obesity and overnight-fasting in mice. Forced transcription of Gm19619 in the mouse liver significantly promotes hepatic gluconeogenesis with the elevated expression of G6pc and Pck1. In contrast, AAV-CasRx mediated knockdown of Gm19619 in high-fat diet-fed mice significantly improves hepatic glucose and lipid metabolism. Mechanistically, Gm19619 is enriched along genomic regions encoding leptin receptor (Lepr) and transcription factor Foxo1, as revealed in chromatin isolation by RNA purification (ChIRP) assay and is confirmed to modulate their transcription in the mouse liver. In conclusion, Gm19619 may enhance gluconeogenesis and lipid accumulation in the liver.
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Affiliation(s)
- Zhipeng Fang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Mingjie Fan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Department of Pediatric, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lihua Jin
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Yangmeng Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lili Ding
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Senlin Xu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Jui Tu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Eryun Zhang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrated Genomic Core, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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17
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An SY, Kim KS, Cho JH, Kim HD, Kim CH, Lee YC. Curcumin-mediated transcriptional regulation of human N-acetylgalactosamine-α2,6-sialyltransferase which synthesizes sialyl-Tn antigen in HCT116 human colon cancer cells. Front Mol Biosci 2022; 9:985648. [PMID: 36172045 PMCID: PMC9510914 DOI: 10.3389/fmolb.2022.985648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Human N-acetylgalactosamine-α2,6-sialyltransferase (hST6GalNAc I) is the major enzyme involved in the biosynthesis of sialyl-Tn antigen (sTn), which is known to be expressed in more than 80% of human carcinomas and correlated with poor prognosis in cancer patients. Athough high expression of hST6GalNAc I is associated with augmented proliferation, migration and invasion in various cancer cells, transcriptional mechanism regulating hST6GalNAc I gene expression remains largely unknown. In this study, we found that hST6GalNAc I gene expression was markedly augmented by curcumin in HCT116 human colon carcinoma cells. To understand the molecular mechanism for the upregulation of hST6GalNAc I gene expression by curcumin in HCT116 cells, we first determined the transcriptional start site of hST6GalNAc I gene by 5′-RACE and cloned the proximal hST6GalNAc I 5′-flanking region spanning about 2 kb by PCR. Functional analysis of the hST6GalNAc I 5′ flanking region of hST6GalNAc I by sequential 5′-deletion, transient transfection of reporter gene constructs and luciferase reporter assays showed that -378/-136 region is essential for maximal activation of transcription in response to curcumin in HCT 116 cells. This region includes putative binding sites for transcription factors c-Ets-1, NF-1, GATA-1, ER-α, YY1, and GR-α. ChIP analysis and site-directed mutagenesis demonstrated that estrogen receptor α (ER-α) binding site (nucleotides -248/-238) in this region is crucial for hST6GalNAc I gene transcription in response to curcumin stimulation in HCT116 cells. The transcription activity of hST6GalNAc I gene induced by curcumin in HCT116 cells was strongly inhibited by PKC inhibitor (Gö6983) and ERK inhibitor (U0126). These results suggest that curcumin-induced hST6GalNAc I gene expression in HCT116 cells is modulated through PKC/ERKs signal pathway.
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Affiliation(s)
- So-Young An
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan, South Korea
| | - Kyoung-Sook Kim
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan, South Korea
| | - Jong-Hyun Cho
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan, South Korea
| | - Hee-Do Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Kyunggi-Do, South Korea
| | - Cheorl-Ho Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Kyunggi-Do, South Korea
- *Correspondence: Cheorl-Ho Kim, ; Young-Choon Lee,
| | - Young-Choon Lee
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan, South Korea
- *Correspondence: Cheorl-Ho Kim, ; Young-Choon Lee,
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18
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Zhang W, Deng R, Shi W, Li Z, Larkin RM, Fan Q, Duanmu D. Heme oxygenase-independent bilin biosynthesis revealed by a hmox1 suppressor screening in Chlamydomonas reinhardtii. Front Microbiol 2022; 13:956554. [PMID: 36003942 PMCID: PMC9393634 DOI: 10.3389/fmicb.2022.956554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Bilins are open-chain tetrapyrroles synthesized in phototrophs by successive enzymic reactions catalyzed by heme oxygenases (HMOXs/HOs) and ferredoxin-dependent biliverdin reductases (FDBRs) that typically serve as chromophore cofactors for phytochromes and phycobiliproteins. Chlamydomonas reinhardtii lacks both phycobiliproteins and phytochromes. Nonetheless, the activity and stability of photosystem I (PSI) and the catalytic subunit of magnesium chelatase (MgCh) named CHLH1 are significantly reduced and phototropic growth is significantly attenuated in a hmox1 mutant that is deficient in bilin biosynthesis. Consistent with these findings, previous studies on hmox1 uncovered an essential role for bilins in chloroplast retrograde signaling, maintenance of a functional photosynthetic apparatus, and the direct regulation of chlorophyll biosynthesis. In this study, we generated and screened a collection of insertional mutants in a hmox1 genetic background for suppressor mutants with phototropic growth restored to rates observed in wild-type 4A+ C. reinhardtii cells. Here, we characterized a suppressor of hmox1 named ho1su1 with phototrophic growth rates and levels of CHLH1 and PSI proteins similar to 4A+. Tetrad analysis indicated that a plasmid insertion co-segregated with the suppressor phenotype of ho1su1. Results from TAIL-PCR and plasmid rescue experiments demonstrated that the plasmid insertion was located in exon 1 of the HMOX1 locus. Heterologous expression of the bilin-binding reporter Nostoc punctiforme NpF2164g5 in the chloroplast of ho1su1 indicated that bilin accumulated in the chloroplast of ho1su1 despite the absence of the HMOX1 protein. Collectively, our study reveals the presence of an alternative bilin biosynthetic pathway independent of HMOX1 in the chloroplasts of Chlamydomonas cells.
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Affiliation(s)
- Weiqing Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Rui Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Weida Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Zheng Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Qiuling Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Deqiang Duanmu,
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Zhang Y, Wang K, Huang Q, Shu S. Molecular cloning and characterization of an alpha-amylase inhibitor (TkAAI) gene from Trichosanthes kirilowii Maxim. Biotechnol Lett 2022; 44:1127-1138. [PMID: 35925526 DOI: 10.1007/s10529-022-03277-4] [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: 12/22/2021] [Accepted: 06/21/2022] [Indexed: 12/01/2022]
Abstract
Trichosanthes kirilowii Maxim taxonomically belongs to the Cucurbitaceae family and Trichosanthes genus. Its whole fruit, fruit peel, seed and root are widely used in traditional Chinese medicines. A ribosome-inactivating protein with RNA N-glycosidase activity called Trichosanthrip was isolated and purified from the seeds of T. kirilowii in our recent previous research. To further explore the biological functions of Trichosanthrip, the cDNA of T. kirilowii alpha-amylase inhibitor (TkAAI) was cloned through rapid-amplification of cDNA ends and its sequence was analyzed. Also, the heterologous protein was expressed in Escherichia coli and its alpha-amylase activity was further measured under optimized conditions. The full-length cDNA of TkAAI was 613 bp. The speculated open reading frame sequence encoded 141 amino acids with a molecular weight of 16.14 kDa. Phylogenetic analysis demonstrated that the Alpha-Amylase Inhibitors Seed Storage domain sequence of TkAAI revealed significant evolutionary homology with the 2S albumin derived from the other plants in the Cucurbitaceae group. In addition, TkAAI was assembled into pET28a with eGFP to generate a prokaryotic expression vector and was induced to express in E. coli. The TkAAI-eGFP infusion protein was proven to exhibit alpha-amylase inhibitory activity against porcine pancreatic amylase in a suitable reaction system. Analysis of gene expression patterns proved that the relative expression level of TkAAI in seeds is highest. The results presented here forecasted that the TkAAI might play a crucial role during the development of T. kirilowii seeds and provided fundamental insights into the possibility of T. kirilowii derived medicine to treat diabetes related diseases.
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Affiliation(s)
- Yipeng Zhang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China.
| | - Keyue Wang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
| | - Qiyuan Huang
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
| | - Shaohua Shu
- College of Plant Science and Technology, HUAZHONG Agricultural University, Shizishan Street 1#, Hongshan District, Wuhan, Hubei, People's Republic of China
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Prakashrao AS, Beuerle T, Simões ARG, Hopf C, Çiçek SS, Stegemann T, Ober D, Kaltenegger E. The long road of functional recruitment-The evolution of a gene duplicate to pyrrolizidine alkaloid biosynthesis in the morning glories (Convolvulaceae). PLANT DIRECT 2022; 6:e420. [PMID: 35865076 PMCID: PMC9295680 DOI: 10.1002/pld3.420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In plants, homospermidine synthase (HSS) is a pathway-specific enzyme initiating the biosynthesis of pyrrolizidine alkaloids (PAs), which function as a chemical defense against herbivores. In PA-producing Convolvulaceae ("morning glories"), HSS originated from deoxyhypusine synthase at least >50 to 75 million years ago via a gene duplication event and subsequent functional diversification. To study the recruitment of this ancient gene duplicate to PA biosynthesis, the presence of putative hss gene copies in 11 Convolvulaceae species was analyzed. Additionally, various plant parts from seven of these species were screened for the presence of PAs. Although all of these species possess a putative hss copy, PAs could only be detected in roots of Ipomoea neei (Spreng.) O'Donell and Distimake quinquefolius (L.) A.R.Simões & Staples in this study. A precursor of PAs was detected in roots of Ipomoea alba L. Thus, despite sharing high sequence identities, the presence of an hss gene copy does not correlate with PA accumulation in particular species of Convolvulaceae. In vitro activity assays of the encoded enzymes revealed a broad spectrum of enzyme activity, further emphasizing a functional diversity of the hss gene copies. A recently identified HSS specific amino acid motif seems to be important for the loss of the ancestral protein function-the activation of the eukaryotic initiation factor 5A (eIF5A). Thus, the motif might be indicative for a change of function but allows not to predict the new function. This emphasizes the challenges in annotating functions for duplicates, even for duplicates from closely related species.
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Affiliation(s)
- Arunraj Saranya Prakashrao
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
- Present address:
Heart Research Center GöttingenUniversity Medical Center GöttingenGöttingenGermany.
| | - Till Beuerle
- Institute of Pharmaceutical BiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Ana Rita G. Simões
- Royal Botanic Gardens, KewRichmondUK
- Systematic and Evolutionary Botany LabGhent UniversityGhentBelgium
| | - Christina Hopf
- Department of Structural Biology, Zoological InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Serhat Sezai Çiçek
- Department of Pharmaceutical Biology, Pharmaceutical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Thomas Stegemann
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Dietrich Ober
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
| | - Elisabeth Kaltenegger
- Department Biochemical Ecology and Molecular Evolution, Botanical InstituteChristian‐Albrechts‐UniversityKielGermany
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Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
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Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
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22
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Cengher L, Manna AC, Cho J, Theprungsirikul J, Sessions K, Rigby W, Cheung AL. Regulation of neutrophil myeloperoxidase inhibitor SPIN by the small RNA Teg49 in Staphylococcus aureus. Mol Microbiol 2022; 117:1447-1463. [PMID: 35578788 PMCID: PMC9880452 DOI: 10.1111/mmi.14919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 01/31/2023]
Abstract
Teg49 is a Staphylococcus aureus trans-acting regulatory sRNA derived from cleavage of the sarA P3 transcript. We showed by RNA-Seq here that the 5' trident-like structure in Teg49 regulates transcriptionally (direct and indirect) 22 genes distinct from sarA. Among these, Teg49 was noted to repress spn, encoding a 102 residue preprotein which yields the mature 73 residue peptide which inhibits the catalytic activity of myeloperoxidase in human neutrophils. Teg49 was found to regulate spn mRNA post-transcriptionally in strain SH1000 through 9-nt base-pairing between hairpin loop 2 of Teg49 and an exposed bulge of the spn mRNA. Mutations of the Teg49 binding site disrupted the repression of spn, leading to reduced degradation, and increased half-life of spn mRNA in the Teg49 mutant. The spn-Teg49 interaction was also confirmed with a synonymous spn mutation to yield enhanced spn expression in the mutant vs. the parent. The Teg49 mutant with increased spn expression exhibited enhanced resistance to MPO activity in vitro. Killing assays with human neutrophils showed that the Teg49 mutant was more resistant to killing after phagocytosis. Altogether, this study shows that Teg49 in S. aureus has a distinct and important regulatory profile whereby this sRNA modulates resistance to myeloperoxidase-mediated killing by human neutrophils.
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Affiliation(s)
- Liviu Cengher
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - Junho Cho
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - Jomkuan Theprungsirikul
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - Katherine Sessions
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - William Rigby
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
| | - Ambrose L. Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine Dartmouth College Hanover New Hampshire USA
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Ma L, Ouyang H, Su A, Zhang Y, Pang D, Zhang T, Sun R, Wang W, Xie Z, Lv D. AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level. ACS Synth Biol 2022; 11:1856-1864. [PMID: 35503752 DOI: 10.1021/acssynbio.2c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoclonal antibody (mAb) has been widely used in immunity research and disease diagnosis and therapy. Antibody sequence and epitope are the prerequisites and basis of mAb applications, which determine the properties of antibodies and make the preparation of antibody-based molecules controllable and reliable. Here, we present the antibody sequence and epitope identification (AbSE) workflow, a time-saving and cost-effective route for rapid determination of antibody sequence and linear epitope of mAb even at the single-cell level. The feasibility and accuracy of the AbSE workflow were demonstrated through the identification and validation of the coding sequence and epitope of antihuman serum albumin (antiHSA) mAb. It can be inferred that the AbSE workflow is a powerful and universal approach for paired antibody-epitope sequence identification. It may characterize antibodies not only on a single hybridoma cell but also on any other antibody-secreting cells.
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Affiliation(s)
- Lerong Ma
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - HongSheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
- Shenzhen Kingsino Technology Co., Ltd., Shenzhen 518100, China
| | - Ang Su
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
| | - Tao Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Ruize Sun
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wentao Wang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zicong Xie
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Dongmei Lv
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
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Griego A, Douché T, Gianetto QG, Matondo M, Manina G. RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness. iScience 2022; 25:104233. [PMID: 35521527 PMCID: PMC9062218 DOI: 10.1016/j.isci.2022.104233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although RNase E is essential for RNA turnover in several species, its role in mycobacterial single-cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that RNase E forms dynamic foci, which are associated with cellular homeostasis and fate, and we discover a versatile molecular interactome. We show a likely interaction between RNase E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where phenotypic diversity increases. Disruption of RNase E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication, and host spread. Our work lays the foundation for targeting the RNase E and its partner HupB, aiming to undermine M. tuberculosis cellular balance, diversification capacity, and persistence. Single mycobacterial cells exhibit phenotypic variation in RNase E expression RNase E is implicated in the maintenance of mycobacterial cell growth homeostasis RNase E and HupB show a functional interplay in single mycobacterial cells RNase E-HupB disruption impairs Mycobacterium tuberculosis fate under drug and in macrophages
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Abstract
Rhabdoviruses are ubiquitous and diverse viruses that propagate owing to bidirectional interactions with their vertebrate, arthropod, and plant hosts, and some of them could pose global health or agricultural threats. However, rhabdoviruses have rarely been reported in fungi. Here, two newly identified fungal rhabdoviruses, Rhizoctonia solani rhabdovirus 1 (RsRhV1) and RsRhV2, were discovered and molecularly characterized from the phytopathogenic fungus Rhizoctonia solani. The genomic organizations of RsRhV1 and RsRhV2 are 11,716 and 11,496 nucleotides (nt) in length, respectively, and consist of five open reading frames (ORFs) (ORFs I to V). ORF I, ORF IV, and ORF V encode the viral nucleocapsid (N), glycoprotein (G), and RNA polymerase (L), respectively. The putative protein encoded by ORF III has a lower level of identity with the matrix protein of rhabdoviruses. ORF II encodes a hypothetical protein with unknown function. Phylogenetic trees based on multiple alignments of N, L, and G proteins revealed that RsRhV1 and RsRhV2 are new members of the family Rhabdoviridae, but they form an independent evolutionary branch significantly distinct from other known nonfungal rhabdoviruses, suggesting that they represent a novel viral evolutionary lineage within Rhabdoviridae. Compared to strains lacking rhabdoviruses, strains harboring RsRhV2 and RsRhV1 showed hypervirulence, suggesting that RsRhV1 and RsRhV2 might be associated with the virulence of R. solani. Taken together, this study enriches our understanding of the diversity and host range of rhabdoviruses. IMPORTANCE Mycoviruses have been attracting an increasing amount of attention due to their impact on important medical, agricultural, and industrial fungi. Rhabdoviruses are prevalent across a wide spectrum of hosts, from plants to invertebrates and vertebrates. This study molecularly characterized two novel rhabdoviruses from four Rhizoctonia solani strains, based on their genomic structures, transcription strategy, phylogenetic relationships, and biological impact on their host. Our study makes a significant contribution to the literature because it not only enriches the mycovirus database but also expands the known host range of rhabdoviruses. It also offers insight into the evolutionary linkage between animal viruses and mycoviruses and the transmission of viruses from one host to another. Our study will also help expand the contemporary knowledge of the classification of rhabdoviruses, as well as providing a new model to study rhabdovirus-host interactions, which will benefit the agriculture and medical areas of human welfare.
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Zhong X, Xu P, Chen K, Yang D, Wang F, Ni H, Wu Y, Xia D, Ye J, Wu H. A novel lncRNA lnc-PPRL promotes pterygium development by activating PI3K/PDK1 signaling pathway. Exp Eye Res 2022; 219:109034. [PMID: 35304111 DOI: 10.1016/j.exer.2022.109034] [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: 09/07/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
Abstract
A sight threatening, pterygium is a common proliferative and degenerative disease of the ocular surface. LncRNAs have been widely studied in the occurrence and development of various diseases, however, the study of lncRNAs in pterygium has just relatively lacking. In the present study, we performed the high-throughput RNA sequencing (HTS) technology to identify differentially expressed lncRNAs in pterygium. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out to forecast the regulatory and functional role of lncRNAs in pterygium. Notably, we identified a novel lncRNA, LOC102724238, which we named pterygium positively-related lncRNA (lnc-PPRL), was up-regulated in pterygium. Lnc-PPRL showed to be preferentially accumulated in cytoplasm, and it can promote cell proliferation, migration and invasion of human pterygium epithelium cells (hPECs). Further study of underlying mechanisms demonstrated that lnc-PPRL may exert its biological effect by activating canonical PI3K/PDK1 pathway, and subsequently promoting the activation of Akt/mTOR signaling pathway and its downstream effectors. Interestingly, lnc-PPRL was also proved to influence YAP nuclear localization. Taken together, our study firstly suggested that the "big molecule" lnc-PPRL have potential as a novel therapeutic target for the prevention and treatment of pterygium.
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Affiliation(s)
- Xincao Zhong
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Peifang Xu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Kelie Chen
- Department of Toxicology of School of Public Health, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Gynecologic Oncology of Women's Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Dexin Yang
- Department of Toxicology of School of Public Health, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fang Wang
- Department of Toxicology of School of Public Health, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Heng Ni
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Yihua Wu
- Department of Toxicology of School of Public Health, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Gynecologic Oncology of Women's Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Dajing Xia
- Department of Toxicology of School of Public Health, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Gynecologic Oncology of Women's Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Juan Ye
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China.
| | - Han Wu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China.
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Adamopoulos PG, Tsiakanikas P, Stolidi I, Scorilas A. A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs. BMC Genomics 2022; 23:163. [PMID: 35219290 PMCID: PMC8881849 DOI: 10.1186/s12864-022-08386-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5′ rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5′ ends of cDNAs. In the current study, we developed a 5′ RACE-seq method by coupling a custom template-switching and 5′ RACE assay with targeted nanopore sequencing, to accurately unveil 5′ termini of mRNA targets. Results The optimization of the described 5′ RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5′ RACE. Collectively, our results support the existence of two distinct 5′ termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5′ RACE-seq methodology to investigate the 5′ UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5′ UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones. Conclusions In this work we present an in-house developed 5′ RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5′ UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08386-y.
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Raz A, Manafi M, Ilbeigi Khamseh Nejad M. Molecular Characterization of a Vector-Based Candidate Antigen Using the 3'-RACE and Genome Walking Methods and In Silico Analysis of the Correspondent Protein for Vaccine Design and Development. Methods Mol Biol 2022; 2410:567-579. [PMID: 34914068 DOI: 10.1007/978-1-0716-1884-4_29] [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: 06/14/2023]
Abstract
The main objectives of developing vaccines to prevent malaria transmission are malaria control and preventing the reemergence of the disease in endemic regions. Molecular and in silico characterization of a candidate molecule is the first step in the vaccine design process. Determining the sequence and amplification of full-length cDNA copies from the mRNA transcripts is often challenging. The methods in this chapter provide a protocol for the rapid amplification of cDNA ends (RACE) and genome walking. Carboxypeptidase B2 enzyme from A. stephensi (CPBAs-2) was selected as the target molecule and the steps in its characterization and in silico analysis are explained in this chapter.
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Affiliation(s)
- Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Mahdieh Manafi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
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Capozza P, Martella V, Lanave G, Catella C, Diakoudi G, Beikpour F, Camero M, Di Martino B, Fusco G, Balestrieri A, Campanile G, Banyai K, Buonavoglia C. An outbreak of neonatal enteritis in buffalo calves associated with astrovirus. J Vet Sci 2021; 22:e84. [PMID: 34854267 PMCID: PMC8636656 DOI: 10.4142/jvs.2021.22.e84] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 12/18/2022] Open
Abstract
Background Enteritis of an infectious origin is a major cause of productivity and economic losses to cattle producers worldwide. Several pathogens are believed to cause or contribute to the development of calf diarrhea. Astroviruses (AstVs) are neglected enteric pathogens in ruminants, but they have recently gained attention because of their possible association with encephalitis in humans and various animal species, including cattle. Objectives This paper describes a large outbreak of neonatal diarrhea in buffalo calves (Bubalus bubalis), characterized by high mortality, which was associated with an AstV infection. Methods Following an enteritis outbreak characterized by high morbidity (100%) and mortality (46.2%) in a herd of Mediterranean buffaloes (B. bubalis) in Italy, 16 samples from buffalo calves were tested with the molecular tools for common and uncommon enteric pathogens, including AstV, kobuvirus, and torovirus. Results The samples tested negative for common enteric viral agents, including Rotavirus A, coronavirus, calicivirus, pestivirus, kobuvirus, and torovirus, while they tested positive for AstV. Overall, 62.5% (10/16) of the samples were positive in a single round reverse transcription polymerase chain reaction (PCR) assay for AstV, and 100% (16/16) were positive when nested PCR was performed. The strains identified in the outbreak showed a clonal origin and shared the closest genetic relationship with bovine AstVs (up to 85% amino acid identity in the capsid). Conclusions This report indicates that AstVs should be included in a differential diagnosis of infectious diarrhea in buffalo calves.
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Affiliation(s)
- Paolo Capozza
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy.
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Farzad Beikpour
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, University of Teramo, Teramo 64100, Italy
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici 80055, Italy
| | - Anna Balestrieri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici 80055, Italy
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Production, University of Naples, Naples 80137, Italy
| | - Krisztian Banyai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest 1143, Hungary
| | - Canio Buonavoglia
- Department of Veterinary Medicine, University of Bari, Valenzano 70010, Italy
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Sauder AB, Kendall MM. A pathogen-specific sRNA influences enterohemorrhagic Escherichia coli fitness and virulence in part by direct interaction with the transcript encoding the ethanolamine utilization regulatory factor EutR. Nucleic Acids Res 2021; 49:10988-11004. [PMID: 34591974 PMCID: PMC8565329 DOI: 10.1093/nar/gkab863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 relies on sRNAs to coordinate expression of metabolic and virulence factors to colonize the host. Here, we focus on the sRNA, named MavR (metabolism and virulence regulator), that is conserved among pathogenic Enterobacteriaceae. MavR is constitutively expressed under in vitro conditions that promote EHEC virulence gene expression. Using MS2-affinity purification coupled with RNA sequencing, the eutR transcript was identified as a putative target of MavR. EutR is a transcription factor that promotes expression of genes required for ethanolamine metabolism as well as virulence factors important for host colonization. MavR binds to the eutR coding sequence to protect the eutR transcript from RNase E-mediated degradation. Ultimately, MavR promotes EutR expression and in turn ethanolamine utilization and ethanolamine-dependent growth. RNAseq analyses revealed that MavR also affected expression of genes important for other metabolic pathways, motility, oxidative stress and attaching and effacing lesion formation, which contribute to EHEC colonization of the gastrointestinal tract. In support of the idea that MavR-dependent gene expression affects fitness during infection, deletion of mavR resulted in significant (∼10- to 100-fold) attenuation in colonization of the mammalian intestine. Altogether, these studies reveal an important, extensive, and robust phenotype for a bacterial sRNA in host-pathogen interactions.
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Affiliation(s)
- Amber B Sauder
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Melissa M Kendall
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Lv X, Sun Y, Hao P, Zhang C, Tian J, Fu M, Xu Z, Wang Y, Zhang X, Xu X, Wu T, Han Z. RBP differentiation contributes to selective transmissibility of OPT3 mRNAs. PLANT PHYSIOLOGY 2021; 187:1587-1604. [PMID: 34618059 PMCID: PMC8566248 DOI: 10.1093/plphys/kiab366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Long-distance mobile mRNAs play key roles in gene regulatory networks that control plant development and stress tolerance. However, the mechanisms underlying species-specific delivery of mRNA still need to be elucidated. Here, the use of grafts involving highly heterozygous apple (Malus) genotypes allowed us to demonstrate that apple (Malus domestica) oligopeptide transporter3 (MdOPT3) mRNA can be transported over a long distance, from the leaf to the root, to regulate iron uptake; however, the mRNA of Arabidopsis (Arabidopsis thaliana) oligopeptide transporter 3 (AtOPT3), the MdOPT3 homolog from A. thaliana, does not move from shoot to root. Reciprocal heterologous expression of the two types of mRNAs showed that the immobile AtOPT3 became mobile and moved from the shoot to the root in two woody species, Malus and Populus, while the mobile MdOPT3 became immobile in two herbaceous species, A. thaliana and tomato (Solanum lycopersicum). Furthermore, we demonstrated that the different transmissibility of OPT3 in A. thaliana and Malus might be caused by divergence in RNA-binding proteins between herbaceous and woody plants. This study provides insights into mechanisms underlying differences in mRNA mobility and validates the important physiological functions associated with this process.
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Affiliation(s)
- Xinmin Lv
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yaqiang Sun
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Pengbo Hao
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Cankui Zhang
- Department of Agronomy and Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Ji Tian
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Mengmeng Fu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhen Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
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Phosphorus Starvation- and Zinc Excess-Induced Astragalus sinicus AsZIP2 Zinc Transporter Is Suppressed by Arbuscular Mycorrhizal Symbiosis. J Fungi (Basel) 2021; 7:jof7110892. [PMID: 34829181 PMCID: PMC8623892 DOI: 10.3390/jof7110892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Zinc (Zn) is one of the most essential micronutrients for plant growth and metabolism, but Zn excess can impair many basic metabolic processes in plant cells. In agriculture, crops often experience low phosphate (Pi) and high Zn double nutrient stresses because of inordinate agro-industrial activities, while the dual benefit of arbuscular mycorrhizal (AM) fungi protects plants from experiencing both deficient and toxic nutrient stresses. Although crosstalk between Pi and Zn nutrients in plants have been extensively studied at the physiological level, the molecular basis of how Pi starvation triggers Zn over-accumulation in plants and how AM plants coordinately modulate the Pi and Zn nutrient homeostasis remains to be elucidated. Here, we report that a novel AsZIP2 gene, a Chinese milk vetch (Astragalus sinicus) member of the ZIP gene family, participates in the interaction between Pi and Zn nutrient homeostasis in plants. Phylogenetic analysis revealed that this AsZIP2 protein was closely related to the orthologous Medicago MtZIP2 and Arabidopsis AtZIP2 transporters. Gene expression analysis indicated that AsZIP2 was highly induced in roots by Pi starvation or Zn excess yet attenuated by arbuscular mycorrhization in a Pi-dependent manner. Subcellular localization and heterologous expression experiments further showed that AsZIP2 encoded a functional plasma membrane-localized transporter that mediated Zn uptake in yeast. Moreover, overexpression of AsZIP2 in A. sinicus resulted in the over-accumulation of Zn concentration in roots at low Pi or excessive Zn concentrations, whereas AsZIP2 silencing lines displayed an even more reduced Zn concentration than control lines under such conditions. Our results reveal that the AsZIP2 transporter functioned in Zn over-accumulation in roots during Pi starvation or high Zn supply but was repressed by AM symbiosis in a Pi-dependent manner. These findings also provide new insights into the AsZIP2 gene acting in the regulation of Zn homeostasis in mycorrhizal plants through Pi signal.
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Do HQ, Nguyen VG, Chung CU, Jeon YS, Shin S, Jang KC, Pham LBH, Kong A, Kim CU, Park YH, Park BK, Chung HC. Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020. Viruses 2021; 13:v13102041. [PMID: 34696471 PMCID: PMC8540747 DOI: 10.3390/v13102041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.
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Affiliation(s)
- Hai-Quynh Do
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam;
| | - Chul-Un Chung
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Yong-Shin Jeon
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
| | - Sook Shin
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Kuem-Chan Jang
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Le Bich Hang Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam;
| | - Aeri Kong
- Department of Medical Science, University of California, Los Angeles, CA 90095, USA;
| | - Cheong-Ung Kim
- Department of Veterinary Medicine Microbology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Yong-Ho Park
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Bong-Kyun Park
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Hee-Chun Chung
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
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Mu F, Li B, Cheng S, Jia J, Jiang D, Fu Y, Cheng J, Lin Y, Chen T, Xie J. Nine viruses from eight lineages exhibiting new evolutionary modes that co-infect a hypovirulent phytopathogenic fungus. PLoS Pathog 2021; 17:e1009823. [PMID: 34428260 PMCID: PMC8415603 DOI: 10.1371/journal.ppat.1009823] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/03/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Mycoviruses are an important component of the virosphere, but our current knowledge of their genome organization diversity and evolution remains rudimentary. In this study, the mycovirus composition in a hypovirulent strain of Sclerotinia sclerotiorum was molecularly characterized. Nine mycoviruses were identified and assigned into eight potential families. Of them, six were close relatives of known mycoviruses, while the other three had unique genome organizations and evolutionary positions. A deltaflexivirus with a tripartite genome has evolved via arrangement and horizontal gene transfer events, which could be an evolutionary connection from unsegmented to segmented RNA viruses. Two mycoviruses had acquired a second helicase gene by two different evolutionary mechanisms. A rhabdovirus representing an independent viral evolutionary branch was the first to be confirmed to occur naturally in fungi. The major hypovirulence-associated factor, an endornavirus, was finally corroborated. Our study expands the diversity of mycoviruses and potential virocontrol agents, and also provides new insights into virus evolutionary modes including virus genome segmentation. Identification of mycoviruses in phytopathogenic fungi is necessary for understanding the origin of viruses and developing virocontrol strategies to protect plants. Nine mycoviruses with RNA genomes were identified in a hypovirulent strain of Sclerotinia sclerotiorum and were classified into eight potential viral families, suggesting that the composition of mycoviral communities was complex in this single fungal strain. They included four previously characterized mycoviruses and three distant relatives of known mycoviruses, as well as the first reports of a deltaflexivirus with a tripartite genome, and a fungal rhabdovirus. In addition, we found an endornavirus associated with hypovirulence in a phytopathogenic fungus. Our study makes a significant contribution because it not only expands the diversity-related knowledge of mycoviruses and potential virocontrol agents, but also provides new insights into mycovirus evolution.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shufen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Schramm S, Rozhon W, Adedeji-Badmus AN, Liang Y, Nayem S, Winkelmann T, Poppenberger B. The Orphan Crop Crassocephalum crepidioides Accumulates the Pyrrolizidine Alkaloid Jacobine in Response to Nitrogen Starvation. FRONTIERS IN PLANT SCIENCE 2021; 12:702985. [PMID: 34394157 PMCID: PMC8355542 DOI: 10.3389/fpls.2021.702985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Crassocephalum crepidioides is an African orphan crop that is used as a leafy vegetable and medicinal plant. Although it is of high regional importance in Sub-Saharan Africa, the plant is still mainly collected from the wild and therefore efforts are made to promote its domestication. However, in addition to beneficial properties, there was first evidence that C. crepidioides can accumulate the highly toxic pyrrolizidine alkaloid (PA) jacobine and here it was investigated, how jacobine production is controlled. Using ecotypes from Africa and Asia that were characterized in terms of their PA profiles, it is shown that the tetraploid C. crepidioides forms jacobine, an ability that its diploid close relative Crassocephalum rubens appears to lack. Evidence is provided that nitrogen (N) deficiency strongly increases jacobine in the leaves of C. crepidioides, that this capacity depends more strongly on the shoot than the root system, and that homospermidine synthase (HSS) activity is not rate-limiting for this reaction. A characterization of HSS gene representation and transcription showed that C. crepidioides and C. rubens possess two functional versions, one of which is conserved, that the HSS transcript is mainly present in roots and that its abundance is not controlled by N deficiency. In summary, this work improves our understanding of how environmental cues impact PA biosynthesis in plants and provides a basis for the development of PA-free C. crepidioides cultivars, which will aid its domestication and safe use.
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Affiliation(s)
- Sebastian Schramm
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Adebimpe N. Adedeji-Badmus
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yuanyuan Liang
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Shahran Nayem
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Gottfried Wilhelm Leibniz University Hannover, Hanover, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Disruption of the odorant coreceptor Orco impairs foraging and host finding behaviors in the New World screwworm fly. Sci Rep 2021; 11:11379. [PMID: 34059738 PMCID: PMC8167109 DOI: 10.1038/s41598-021-90649-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/12/2021] [Indexed: 12/03/2022] Open
Abstract
The evolution of obligate ectoparasitism in blowflies (Diptera: Calliphoridae) has intrigued scientists for over a century, and surprisingly, the genetics underlying this lifestyle remain largely unknown. Blowflies use odors to locate food and oviposition sites; therefore, olfaction might have played a central role in niche specialization within the group. In insects, the coreceptor Orco is a required partner for all odorant receptors (ORs), a major gene family involved in olfactory-evoked behaviors. Hence, we characterized the Orco gene in the New World screwworm, Cochliomyia hominivorax, a blowfly that is an obligate ectoparasite of warm-blooded animals. In contrast, most of the closely related blowflies are scavengers that lay their eggs on dead animals. We show that the screwworm Orco orthologue (ChomOrco) is highly conserved within Diptera, showing signals of strong purifying selection. Expression of ChomOrco is broadly detectable in chemosensory appendages, and is related to morphological, developmental, and behavioral aspects of the screwworm biology. We used CRISPR/Cas9 to disrupt ChomOrco and evaluate the consequences of losing the OR function on screwworm behavior. In two-choice assays, Orco mutants displayed an impaired response to floral-like and animal host-associated odors, suggesting that OR-mediated olfaction is involved in foraging and host-seeking behaviors in C. hominivorax. These results broaden our understanding of the chemoreception basis of niche occupancy by blowflies.
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Yang L, Li RC, Xiang B, Li YC, Wang LP, Guo YB, Liang JH, Wang XT, Hou T, Xing X, Zhou ZQ, Ye H, Feng RQ, Lakatta EG, Chai Z, Wang SQ. Transcriptional regulation of intermolecular Ca 2+ signaling in hibernating ground squirrel cardiomyocytes: The myocardin-junctophilin axis. Proc Natl Acad Sci U S A 2021; 118:e2025333118. [PMID: 33785600 PMCID: PMC8040632 DOI: 10.1073/pnas.2025333118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The contraction of heart cells is controlled by the intermolecular signaling between L-type Ca2+ channels (LCCs) and ryanodine receptors (RyRs), and the nanodistance between them depends on the interaction between junctophilin-2 (JPH2) in the sarcoplasmic reticulum (SR) and caveolin-3 (CAV3) in the transversal tubule (TT). In heart failure, decreased expression of JPH2 compromises LCC-RyR communication leading to deficient blood-pumping power. In the present study, we found that JPH2 and CAV3 transcription was concurrently regulated by serum response factor (SRF) and myocardin. In cardiomyocytes from torpid ground squirrels, compared with those from euthermic counterparts, myocardin expression was up-regulated, which boosted both JPH2 and CAV3 expression. Transmission electron microscopic imaging showed that the physical coupling between TTs and SRs was tightened during hibernation and after myocardin overexpression. Confocal Ca2+ imaging under the whole-cell patch clamp condition revealed that these changes enhanced the efficiency of LCC-RyR intermolecular signaling and fully compensated the adaptive down-regulation of LCCs, maintaining the power of heart contraction while avoiding the risk of calcium overload during hibernation. Our finding not only revealed an essential molecular mechanism underlying the survival of hibernating mammals, but also demonstrated a "reverse model of heart failure" at the molecular level, suggesting a strategy for treating heart diseases.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Rong-Chang Li
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Bin Xiang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yi-Chen Li
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Peng Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yun-Bo Guo
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing-Hui Liang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiao-Ting Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Tingting Hou
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Xing
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Zeng-Quan Zhou
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Haihong Ye
- Beijing Key Laboratory of Neural Regeneration and Repair, Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Ren-Qing Feng
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Edward G Lakatta
- Laboratory of Cardiovascular Science, National Institute on Aging, Baltimore, MD 21224
| | - Zhen Chai
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shi-Qiang Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China;
- Chinese Institute for Brain Research, Beijing 102206, China
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38
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Miller RV, Neme R, Clay DM, Pathmanathan JS, Lu MW, Yerlici VT, Khurana JS, Landweber LF. Transcribed germline-limited coding sequences in Oxytricha trifallax. G3-GENES GENOMES GENETICS 2021; 11:6192809. [PMID: 33772542 PMCID: PMC8495736 DOI: 10.1093/g3journal/jkab092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/26/2021] [Indexed: 01/13/2023]
Abstract
The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination.
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Affiliation(s)
- Richard V Miller
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rafik Neme
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Derek M Clay
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jananan S Pathmanathan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Michael W Lu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - V Talya Yerlici
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jaspreet S Khurana
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Laura F Landweber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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39
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Wang Y, Song Y, Wang Y, Cao M, Hu T, Zhou X. Discovery and Characterization of a Novel Ampelovirus on Firespike. Viruses 2020; 12:E1452. [PMID: 33339381 PMCID: PMC7766885 DOI: 10.3390/v12121452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
A novel RNA virus was identified in firespike (Odontonema tubaeforme) plants exhibiting leaf curling and chlorosis. The molecular features of the viral genomic RNA and proteins resemble those of ampeloviruses. Based on sequence comparisons and phylogenetic analysis, we propose a new species in the genus Ampelovirus, which we have tentatively named Firespike leafroll-associated virus (FLRaV). Bioassays showed that the virus is mechanically transmissible to Nicotiana benthamiana. In addition, a full-length cDNA clone of FLRaV could successfully infect N. benthamiana via agroinfiltration.
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Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Yu Song
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Yongzhi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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40
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Di Martino B, Sarchese V, Di Profio F, Palombieri A, Melegari I, Fruci P, Aste G, Bányai K, Fulvio M, Martella V. Genetic heterogeneity of canine bufaviruses. Transbound Emerg Dis 2020; 68:802-812. [PMID: 32688446 DOI: 10.1111/tbed.13746] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 11/30/2022]
Abstract
Canine bufavirus (CBuV) is a protoparvovirus, genetically related to human and non-human primate bufaviruses and distantly related to canine parvovirus type 2 (CPV-2). CBuV was initially identified from young dogs with respiratory signs but subsequent studies revealed that this virus is also a common component of the canine enteric virome. In this survey, by assessing archival and recent collections of dogs faecal samples, CBuV DNA was detected with a higher prevalence rate (8.8%) in animals with enteritis than in control animals (5.0%), although this difference was not statistically significant. The rate of co-infections with other enteric viruses in diarrhoeic dogs was high (84.6%), mostly in association with canine parvovirus CPV-2 (90.1%). The complete ORF2 gene was determined in five samples, and the nearly full-length genome was reconstructed for three strains, 62/2017/ITA, 9AS/2005/ITA and 35/2018/ITA. Upon sequence comparison, the viruses appeared highly conserved in the NS1 (97.2%-97.9% nt and 97.5%-98.1% aa identities). In the complete VP2 coding region, three strains were similar to the prototype viruses (99.7-99.8 nt and 99.6%-99.8% aa) whilst strains 9AS/2005/ITA and 35/2016/ITA were distantly related (87.6%-89.3% nt and 93.9%-95.1% aa identities). Interestingly, genetic diversification occurred downstream conserved regions such as the VP1/VP2 splicing signals and/or the G-rich motif in the N terminus of the VP2, suggesting a potential recombination nature. Upon phylogenetic analysis, the two divergent CBuV strains formed a distinct cluster/genotype.
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Affiliation(s)
- Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Giovanni Aste
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Krisztián Bányai
- Hungarian Academy of Sciences Centre for Agricultural Research Institute for Veterinary Medical Research, Budapest, Hungary
| | - Marsilio Fulvio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
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41
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Complete Genome Sequence of a Novel Putative RNA Virus, RiPV-2, from the Bean Bug Riptortus pedestris. Microbiol Resour Announc 2020; 9:9/21/e01584-19. [PMID: 32439683 PMCID: PMC7242685 DOI: 10.1128/mra.01584-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel putative single-stranded RNA virus was discovered from the transcriptome of a bean bug, Riptortus pedestris, infected with the entomopathogenic fungus Beaveria bassiana JEF-007. The complete genome sequence was 9,915 nucleotides long and encoded a 2,916-amino-acid polyprotein. This virus belonged to Iflaviridae based on phylogenetic analysis and was named RiPV-2.
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42
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Hu T, Song Y, Wang Y, Zhou X. Functional analysis of a novel βV1 gene identified in a geminivirus betasatellite. SCIENCE CHINA. LIFE SCIENCES 2020; 63:688-696. [PMID: 32107688 DOI: 10.1007/s11427-020-1654-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023]
Abstract
Betasatellites (DNA β) are circular ssDNA molecules that are associated with monopartite geminiviruses and exert a positive effect on the viral infection. Betasatellites encode one protein, named βC1, on the complementary strand; βC1 functions as a pathogenicity factor and RNA silencing suppressor. In this report, we describe the identification of another betasatellite-encoded protein, βVl, which also contributes to symptom development. The βVl open reading frame can be found on the viral strand of approximately 40% of reported betasatellite sequences, and is conserved in position and sequence. The presence of the βVl transcript was observed in plants infected with Tomato yellow leaf curl China virus (TYTCCNV) along with its associated betasatellite Tomato yellow leaf curl China betasatellite (TYTCCNB). Mutant viruses unable to produce βVl showed reduced virulence and decreased viral load. Ectopic expression of the TYTCCNB-PV1 gene in Nicotiana benthamiana plants from a PVX-based vector resulted in leaf mosaic and chlorosis. We further demonstrated that the βVl protein could elicit hypersensitive response (HR)-type cell death in N. benthamiana leaves. Our results uncover a novel betasatellite-encoded protein that contributes to the virus infection, and this discover gives us a more complete view of the plant-geminivirus interaction landscape.
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Affiliation(s)
- Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yu Song
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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43
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Characterisation of recombinant thermostable manganese-superoxide dismutase (NeMnSOD) from Nerium oleander. Mol Biol Rep 2020; 47:3251-3270. [DOI: 10.1007/s11033-020-05374-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/07/2020] [Indexed: 12/17/2022]
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44
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Naro C, Pellegrini L, Jolly A, Farini D, Cesari E, Bielli P, de la Grange P, Sette C. Functional Interaction between U1snRNP and Sam68 Insures Proper 3' End Pre-mRNA Processing during Germ Cell Differentiation. Cell Rep 2020; 26:2929-2941.e5. [PMID: 30865884 DOI: 10.1016/j.celrep.2019.02.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/15/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Male germ cells express the widest repertoire of transcript variants in mammalian tissues. Nevertheless, factors and mechanisms underlying such pronounced diversity are largely unknown. The splicing regulator Sam68 is highly expressed in meiotic cells, and its ablation results in defective spermatogenesis. Herein, we uncover an extensive splicing program operated by Sam68 across meiosis, primarily characterized by alternative last exon (ALE) regulation in genes of functional relevance for spermatogenesis. Lack of Sam68 preferentially causes premature transcript termination at internal polyadenylation sites, a feature observed also upon depletion of the spliceosomal U1snRNP in somatic cells. Notably, Sam68-regulated ALEs are characterized by proximity between U1snRNP and Sam68 binding motifs. We demonstrate a physical association between Sam68 and U1snRNP and show that U1snRNP recruitment to Sam68-regulated ALEs is impaired in Sam68-/- germ cells. Thus, our study reveals an unexpected cooperation between Sam68 and U1snRNP that insures proper processing of transcripts essential for male fertility.
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Affiliation(s)
- Chiara Naro
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Livia Pellegrini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ariane Jolly
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Eleonora Cesari
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pierre de la Grange
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.
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45
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Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host. ISME JOURNAL 2020; 14:1755-1767. [PMID: 32286546 PMCID: PMC7305300 DOI: 10.1038/s41396-020-0642-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Abstract
Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S. solidus, controlled experimental infections and field sampling, we demonstrate that five of these viruses are vertically transmitted, and persist throughout the S. solidus complex life cycle. Moreover, we show that one of the viruses, named Schistocephalus solidus rhabdovirus (SsRV1), is excreted by the parasite and transmitted to parasitized hosts indicating that it may impact S. solidus-host interactions. In addition, SsRV1 has a basal phylogenetic position relative to vertebrate rhabdoviruses suggesting that parasitic flatworms could have contributed to virus emergence. Viruses similar to four of the S. solidus viruses identified here were found in geographically distant S. solidus populations through data mining. Further studies are necessary to determine if flatworm viruses can replicate in parasitized hosts, how they contribute to parasite infection dynamics and if these viruses could be targeted for treatment of parasitic disease.
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46
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Palavecino CE, Carrasco-Véliz N, Quest AFG, Garrido MP, Valenzuela-Valderrama M. The 5' untranslated region of the anti-apoptotic protein Survivin contains an inhibitory upstream AUG codon. Biochem Biophys Res Commun 2020; 526:898-905. [PMID: 32279998 DOI: 10.1016/j.bbrc.2020.03.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/28/2020] [Indexed: 12/20/2022]
Abstract
Survivin (BIRC5) is an anti-apoptotic protein that is important in cancer. Mechanisms responsible for controlling Survivin levels in cells include transcriptional regulation and modulation of protein stability via post-translational modifications; however to date, translational control has been poorly studied. Here, we focused particularly on the primary control elements present in the Survivin 5' untranslated region (5'UTR). Bioinformatic analysis of ribosome occupancy on the Survivin 5'UTR revealed the presence of elongating ribosomes upstream of the canonical initiator AUG, suggesting an alternative upstream initiator AUG (uAUG) might exist. This uAUG was found out-of-frame at position -71 and appeared as a conserved element in mammals. RACE analysis revealed different transcriptional start sites for BIRC5, which indicated that translational control by this uAUG is restricted to longer 5'UTR variants. We studied the activity of the uAUG in different cell types by cloning the Survivin 5'UTR DNA sequence (wild-type and mutated variants) upstream of renilla luciferase (RLuc) into a pcDNA3 plasmid. Changes in RLuc activity were determined by luminescence assays and Western blotting. Results showed that when this uAUG was mutated to AUU or AGG in the cloned Survivin 5'UTR, RLuc activity was significantly increased. Similar results were obtained when uAUG was positioned inframe with the RLuc initiator AUG. Immunodetection of Renilla (35 kDa) by Western blotting revealed the presence of a second band (37 kDa approximately) in cells transfected with the Inframe reporter constructs, indicating that the uAUG was functional in our experimental conditions. In conclusion, our experimental data demonstrate the presence of an alternative and inhibitory initiator uAUG in the Survivin 5' UTR. This inhibitory uAUG may help understanding how Survivin expression is downregulated under physiological or pathological conditions.
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Affiliation(s)
- Christian E Palavecino
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Nicolás Carrasco-Véliz
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Andrew F G Quest
- Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile; Laboratorio de Comunicaciones Celulares, Centro de Estudios en Ejercicio, Metabolismo y Cáncer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Avenida Independencia 1027, Independencia, 8380453, Chile
| | - Maritza P Garrido
- Laboratorio de Endocrinología y Biología de la Reproducción, Departamento de Obstetricia y Ginecología, Hospital Clínico Universidad de Chile, Avenida Santos Dumont 999, Independencia, 8380456, Chile
| | - Manuel Valenzuela-Valderrama
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile; Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile.
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47
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Wang Q, Mu F, Xie J, Cheng J, Fu Y, Jiang D. A Single ssRNA Segment Encoding RdRp Is Sufficient for Replication, Infection, and Transmission of Ourmia-Like Virus in Fungi. Front Microbiol 2020; 11:379. [PMID: 32256466 PMCID: PMC7093599 DOI: 10.3389/fmicb.2020.00379] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/20/2020] [Indexed: 01/07/2023] Open
Abstract
Recently, an increasing number of ourmia-like viruses have been found in fungi; however, the features of these viruses remain unknown. Here, we report a novel ourmia-like virus isolated from Sclerotinia sclerotiorum. This virus, named S. sclerotiorum ourmia-like virus 4 (SsOLV4), has a genome 2,982 nt in length with a G-pentamer (GGGGG) at the 5'-terminus and a C-pentamer (CCCCC) at the 3'-terminus. The SsOLV4 genome has only one large putative open reading frame (ORF) predicted with both standard codes and mitochondrial codes and encodes an RNA-dependent RNA polymerase (RdRp). SsOLV4 is closely phylogenetically related to Pyricularia oryzae ourmia-like virus 1, with 42% identity between the RdRp amino acid sequences. We constructed full-length cDNA of SsOLV4 and synthesized RNA in vitro using the T7 RNA polymerase. The synthesized RNA could transfect S. sclerotiorum protoplasts efficiently. We further found that viral RNA could infect mycelia when mixed with PEG buffer. Our study suggests that a novel genus in family Botourmiaviridae should be established for SsOLV4 and other related viruses and demonstrates that one single-stranded RNA segment encoding RdRp is sufficient for ourmia-like viruses in fungi.
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Affiliation(s)
- Qihua Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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48
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Yu Y, Zhou Y, Feng Y, He H, Lian J, Yang Y, Lei M, Zhang Y, Chen Y. Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:679-690. [PMID: 31419052 PMCID: PMC7004900 DOI: 10.1111/pbi.13234] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 05/16/2023]
Abstract
Plant defence is multilayered and is essential for surviving in a changing environment. The discovery of long noncoding RNAs (lncRNAs) has dramatically extended our understanding of post-transcriptional gene regulation in diverse biological processes. However, the expression profile and function of lncRNAs in disease resistance are still largely unknown, especially in monocots. Here, we performed strand-specific RNA sequencing of rice leaves infected by Xanthomonas oryzae pv. Oryzae (Xoo) in different time courses and systematically identified 567 disease-responsive rice lncRNAs. Target analyses of these lncRNAs showed that jasmonate (JA) pathway was significantly enriched. To reveal the interaction between lncRNAs and JA-related genes, we studied the coexpression of them and found 39 JA-related protein-coding genes to be interplayed with 73 lncRNAs, highlighting the potential modulation of lncRNAs in JA pathway. We subsequently identified an lncRNA, ALEX1, whose expression is highly induced by Xoo infection. A T-DNA insertion line constructed using enhancer trap system showed a higher expression of ALEX1 and exerted a significant resistance to rice bacterial blight. Functional study revealed that JA signalling is activated and the endogenous content of JA and JA-Ile is increased. Overexpressing ALEX1 in rice further confirmed the activation of JA pathway and resistance to bacterial blight. Our findings reveal the expression of pathogen-responsive lncRNAs in rice and provide novel insights into the connection between lncRNAs and JA pathway in the regulation of plant disease resistance.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yan‐Fei Zhou
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yan‐Zhao Feng
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Huang He
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Jian‐Ping Lian
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yu‐Wei Yang
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Meng‐Qi Lei
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yu‐Chan Zhang
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yue‐Qin Chen
- Guangdong Provincial Key Laboratory of Plant ResourcesState Key Laboratory for BiocontrolSchool of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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49
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Genome sequence of an aichivirus detected in a common pipistrelle bat (Pipistrellus pipistrellus). Arch Virol 2020; 165:1019-1022. [PMID: 32056001 DOI: 10.1007/s00705-020-04548-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/11/2020] [Indexed: 12/23/2022]
Abstract
The family Picornaviridae includes important human and animal pathogens that are associated with a wide range of diseases and, in some cases, have zoonotic potential. During epidemiological surveillance of bats, we identified, by next-generation sequencing (NGS) techniques, the presence of picornavirus RNA in a common pipistrelle bat (Pipistrellus pipistrellus). By coupling NGS, primer-walking strategies, and sequence-independent protocols to obtain the sequences of the 5' and 3' termini, we reconstructed the genome sequence of picornavirus strain ITA/2017/189/18-155. The genome of the bat picornavirus is 8.2 kb in length and encodes a polyprotein of 2462 amino acids. A comparison of polyprotein sequences revealed that this virus is distantly related (65.1% and 70.9% sequence identity at the nucleotide and amino acid level, respectively) to a bat aichivirus identified in 2010. Phylogenetic analysis showed that this picornavirus clustered closely with members of the genus Kobuvirus, which also includes human and animal aichiviruses. The identification of aichiviruses in several animal hosts is providing hints that will lead to an understanding of their origin and evolutionary patterns.
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Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice. Mamm Genome 2020; 31:2-16. [PMID: 31912264 PMCID: PMC7060167 DOI: 10.1007/s00335-019-09824-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022]
Abstract
Stabilin2 (Stab2) encodes a large transmembrane protein which is predominantly expressed in the liver sinusoidal endothelial cells (LSECs) and functions as a scavenger receptor for various macromolecules including hyaluronans (HA). In DBA/2J mice, plasma HA concentration is ten times higher than in 129S6 or C57BL/6J mice, and this phenotype is genetically linked to the Stab2 locus. Stab2 mRNA in the LSECs was significantly lower in DBA/2J than in 129S6, leading to reduced STAB2 proteins in the DBA/2J LSECs. We found a retrovirus-derived transposable element, intracisternal A particle (IAP), in the promoter region of Stab2DBA which likely interferes with normal expression in the LSECs. In contrast, in other tissues of DBA/2J mice, the IAP drives high ectopic Stab2DBA transcription starting within the 5′ long terminal repeat of IAP in a reverse orientation and continuing through the downstream Stab2DBA. Ectopic transcription requires the Stab2-IAP element but is dominantly suppressed by the presence of loci on 59.7–73.0 Mb of chromosome (Chr) 13 from C57BL/6J, while the same region in 129S6 requires additional loci for complete suppression. Chr13:59.9–73 Mb contains a large number of genes encoding Krüppel-associated box-domain zinc-finger proteins that target transposable elements-derived sequences and repress their expression. Despite the high amount of ectopic Stab2DBA transcript in tissues other than liver, STAB2 protein was undetectable and unlikely to contribute to the plasma HA levels of DBA/2J mice. Nevertheless, the IAP insertion and its effects on the transcription of the downstream Stab2DBA exemplify that stochastic evolutional events could significantly influence susceptibility to complex but common diseases.
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