Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis
The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tro...
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MDPI AG
2023-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/16/12925 |
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| author | Chenyu Lin Xin Guo Xiaohui Yu Shuxia Li Wenbin Li Xiaoling Yu Feng An Pingjuan Zhao Mengbin Ruan |
| author_facet | Chenyu Lin Xin Guo Xiaohui Yu Shuxia Li Wenbin Li Xiaoling Yu Feng An Pingjuan Zhao Mengbin Ruan |
| author_sort | Chenyu Lin |
| collection | DOAJ |
| description | The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H<sub>2</sub>O<sub>2</sub>), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T23:52:11Z |
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| spelling | doaj.art-30a69f4db5d1452394d582e5193460fc2023-11-19T01:32:22ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-08-0124161292510.3390/ijms241612925Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional AnalysisChenyu Lin0Xin Guo1Xiaohui Yu2Shuxia Li3Wenbin Li4Xiaoling Yu5Feng An6Pingjuan Zhao7Mengbin Ruan8School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaSchool of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaSchool of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaKey Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaKey Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaKey Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaHainan Danzhou Agro-Ecosystem National Observation and Research Station, Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, ChinaKey Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaKey Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaThe plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H<sub>2</sub>O<sub>2</sub>), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava.https://www.mdpi.com/1422-0067/24/16/12925cassavanodule inception-like proteinsRWP-RK domain proteinsabiotic stressphylogenetic relationshipsgene expression patterns |
| spellingShingle | Chenyu Lin Xin Guo Xiaohui Yu Shuxia Li Wenbin Li Xiaoling Yu Feng An Pingjuan Zhao Mengbin Ruan Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis International Journal of Molecular Sciences cassava nodule inception-like proteins RWP-RK domain proteins abiotic stress phylogenetic relationships gene expression patterns |
| title | Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis |
| title_full | Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis |
| title_fullStr | Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis |
| title_full_unstemmed | Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis |
| title_short | Genome-Wide Survey of the <i>RWP-RK</i> Gene Family in Cassava (<i>Manihot esculenta</i> Crantz) and Functional Analysis |
| title_sort | genome wide survey of the i rwp rk i gene family in cassava i manihot esculenta i crantz and functional analysis |
| topic | cassava nodule inception-like proteins RWP-RK domain proteins abiotic stress phylogenetic relationships gene expression patterns |
| url | https://www.mdpi.com/1422-0067/24/16/12925 |
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