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Luo D, Huguet-Tapia JC, Raborn RT, White FF, Brendel VP, Yang B. The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. PLANT COMMUNICATIONS 2021; 2:100164. [PMID: 34027391 PMCID: PMC8132128 DOI: 10.1016/j.xplc.2021.100164] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Many plant disease resistance (R) genes function specifically in reaction to the presence of cognate effectors from a pathogen. Xanthomonas oryzae pathovar oryzae (Xoo) uses transcription activator-like effectors (TALes) to target specific rice genes for expression, thereby promoting host susceptibility to bacterial blight. Here, we report the molecular characterization of Xa7, the cognate R gene to the TALes AvrXa7 and PthXo3, which target the rice major susceptibility gene SWEET14. Xa7 was mapped to a unique 74-kb region. Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element (EBE) in its promoter and encoded a 113-amino-acid peptide of unknown function. Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains. Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana. The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility. Ectopic expression of Xa7 triggers cell death in N. benthamiana. Xa7 is prevalent in indica rice accessions from 3000 rice genomes. Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.
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Affiliation(s)
- Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - R. Taylor Raborn
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Current address: Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Volker P. Brendel
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Corresponding author
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Liu Q, Jiang F, Zhang J, Li X, Kang L. Transcription initiation of distant core promoters in a large-sized genome of an insect. BMC Biol 2021; 19:62. [PMID: 33785021 PMCID: PMC8011201 DOI: 10.1186/s12915-021-01004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Core promoters have a substantial influence on various steps of transcription, including initiation, elongation, termination, polyadenylation, and finally, translation. The characterization of core promoters is crucial for exploring the regulatory code of transcription initiation. However, the current understanding of insect core promoters is focused on those of Diptera (especially Drosophila) species with small genome sizes. Results Here, we present an analysis of the transcription start sites (TSSs) in the migratory locust, Locusta migratoria, which has a genome size of 6.5 Gb. The genomic differences, including lower precision of transcription initiation and fewer constraints on the distance from transcription factor binding sites or regulatory elements to TSSs, were revealed in locusts compared with Drosophila insects. Furthermore, we found a distinct bimodal log distribution of the distances from the start codons to the core promoters of locust genes. We found stricter constraints on the exon length of mRNA leaders and widespread expression activity of the distant core promoters in locusts compared with fruit flies. We further compared core promoters in seven arthropod species across a broad range of genome sizes to reinforce our results on the emergence of distant core promoters in large-sized genomes. Conclusions In summary, our results provide novel insights into the effects of genome size expansion on distant transcription initiation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01004-5.
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Affiliation(s)
- Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiao Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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Sada M, Saraya T, Ishii H, Okayama K, Hayashi Y, Tsugawa T, Nishina A, Murakami K, Kuroda M, Ryo A, Kimura H. Detailed Molecular Interactions of Favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza Virus Polymerases In Silico. Microorganisms 2020; 8:E1610. [PMID: 33092045 PMCID: PMC7589801 DOI: 10.3390/microorganisms8101610] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 12/20/2022] Open
Abstract
Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions underlying its potential impact on the coronaviruses including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) remain unclear. We performed in silico studies to elucidate detailed molecular interactions between favipiravir and the SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus RNA-dependent RNA polymerases (RdRp). As a result, no interactions between favipiravir ribofuranosyl-5'-triphosphate (F-RTP), the active form of favipiravir, and the active sites of RdRps (PB1 proteins) from influenza A (H1N1)pdm09 virus were found, yet the agent bound to the tunnel of the replication genome of PB1 protein leading to the inhibition of replicated RNA passage. In contrast, F-RTP bound to the active sites of coronavirus RdRp in the presence of the agent and RdRp. Further, the agent bound to the replicated RNA terminus in the presence of agent, magnesium ions, nucleotide triphosphate, and RdRp proteins. These results suggest that favipiravir exhibits distinct mechanisms of action against influenza virus and various coronaviruses.
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Affiliation(s)
- Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University, Shibukawa, Gunma 377-0008, Japan;
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Takeshi Saraya
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Haruyuki Ishii
- Department of Respiratory medicine, Kyorin University Hospital of medicine, Mitaka, Tokyo 181-8611, Japan; (T.S.); (H.I.)
| | - Kaori Okayama
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Yuriko Hayashi
- School of Medical Technology, Faculty of Health Science, Gumma Paz University, Takasaki, Gunma 370-0006, Japan; (K.O.); (Y.H.)
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan;
| | - Atsuyoshi Nishina
- College of Science and Technology, Nihon University, Tokyo 101-0062, Japan;
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
| | - Hirokazu Kimura
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki, Gunma 370-0006, Japan
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