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Yang T, Dong J, Zhao J, Zhang L, Zhou L, Yang W, Ma Y, Wang J, Fu H, Chen J, Li W, Hu H, Jiang X, Liu Z, Liu B, Zhang S. Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:251. [PMID: 37985474 PMCID: PMC10661777 DOI: 10.1007/s00122-023-04497-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
KEY MESSAGE Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.
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Affiliation(s)
- Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xianya Jiang
- Yangjiang Institute of Agricultural Science, Yangjiang, 529500, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. Proteome Changes Resulting from Malting in Hordein-Reduced Barley Lines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14079-14091. [PMID: 37712129 PMCID: PMC10540200 DOI: 10.1021/acs.jafc.3c02292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Hordeum vulgare L., commonly known as barley, is primarily used for animal feed and malting. The major storage proteins in barley are hordeins, known triggers of celiac disease (CD). Here, sequential window acquisition of all theoretical mass spectra (SWATH)-MS proteomics was employed to investigate the proteome profile of grain and malt samples from the malting barley cultivar Sloop and single-, double-, and triple hordein-reduced lines bred in a Sloop background. Using a discovery proteomics approach, 2688 and 3034 proteins were detected from the grain and malt samples, respectively. By utilizing label-free relative quantitation through SWATH-MS, a total of 2654 proteins have been quantified from grain and malt. The comparative analyses between the barley grain and malt samples revealed that the C-hordein-reduced lines have a more significant impact on proteome level changes due to malting than B- and D-hordein-reduced lines. Upregulated proteins in C-hordein-reduced lines were primarily involved in the tricarboxylic acid cycle and fatty acid peroxidation processes to provide more energy for seed germination during malting. By applying proteomics approaches after malting in hordein-reduced barley lines, we uncovered additional changes in the proteome driven by the genetic background that were not apparent in the sound grain. Our findings offer valuable insights for barley breeders and maltsters seeking to understand and optimize the performance of gluten-free grains in malt products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
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3
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Li Y, Wang W, Zhang N, Cheng Y, Hussain S, Wang Y, Tian H, Hussain H, Lin R, Yuan Y, Wang C, Wang T, Wang S. Antagonistic Regulation of ABA Responses by Duplicated Tandemly Repeated DUF538 Protein Genes in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:2989. [PMID: 37631202 PMCID: PMC10459309 DOI: 10.3390/plants12162989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
The plant hormone ABA (abscisic acid) regulates plant responses to abiotic stresses by regulating the expression of ABA response genes. However, the functions of a large portion of ABA response genes have remained unclear. We report in this study the identification of ASDs (ABA-inducible signal peptide-containing DUF538 proteins), a subgroup of DUF538 proteins with a signal peptide, as the regulators of plant responses to ABA in Arabidopsis. ASDs are encoded by four closely related DUF538 genes, with ASD1/ASD2 and ASD3/ASD4 being two pairs of duplicated tandemly repeated genes. The quantitative RT-PCR (qRT-PCR) results showed that the expression levels of ASDs increased significantly in response to ABA as well as NaCl and mannitol treatments, with the exception that the expression level of ASD2 remained largely unchanged in response to NaCl treatment. The results of Arabidopsis protoplast transient transfection assays showed that ASDs were localized on the plasma membrane and in the cytosol and nucleus. When recruited to the promoter of the reporter gene via a fused GD domain, ASDs were able to slightly repress the expression of the co-transfected reporter gene. Seed germination and cotyledon greening assays showed that ABA sensitivity was increased in the transgenic plants that were over-expressing ASD1 or ASD3 but decreased in the transgenic plants that were over-expressing ASD2 or ASD4. On the other hand, ABA sensitivity was increased in the CRISPR/Cas9 gene-edited asd2 single mutants but decreased in the asd3 single mutants. A transcriptome analysis showed that differentially expressed genes in the 35S:ASD2 transgenic plant seedlings were enriched in several different processes, including in plant growth and development, the secondary metabolism, and plant hormone signaling. In summary, our results show that ASDs are ABA response genes and that ASDs are involved in the regulation of plant responses to ABA in Arabidopsis; however, ASD1/ASD3 and ASD2/ASD4 have opposite functions.
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Affiliation(s)
- Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Wei Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (W.W.); (S.H.)
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Yuxin Cheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Saddam Hussain
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (W.W.); (S.H.)
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Hadia Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Yuan Yuan
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Chen Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (Y.L.); (N.Z.); (Y.C.); (Y.W.); (H.T.); (H.H.); (R.L.); (Y.Y.); (C.W.); (T.W.)
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (W.W.); (S.H.)
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4
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Lv P, Wan J, Zhang C, Hina A, Al Amin GM, Begum N, Zhao T. Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective. Int J Mol Sci 2023; 24:ijms24044187. [PMID: 36835600 PMCID: PMC9966272 DOI: 10.3390/ijms24044187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Wan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - G M Al Amin
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
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5
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Joshi V, Shi A, Mishra AK, Gill H, DiPiazza J. Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach. Sci Rep 2022; 12:13751. [PMID: 35962022 PMCID: PMC9374745 DOI: 10.1038/s41598-022-18134-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Efficient partitioning of above and below-ground biomass in response to nitrogen (N) is critical to the productivity of plants under sub-optimal conditions. It is particularly essential in vegetable crops like spinach with shallow root systems, a short growth cycle, and poor nitrogen use efficiency. In this study, we conducted a genome-wide association study (GWAS) to explore N-induced changes using spinach accessions with diverse genetic backgrounds. We evaluated phenotypic variations as percent changes in the shoot and root biomass in response to N using 201 spinach accessions grown in randomized complete blocks design in a soilless media under a controlled environment. A GWAS was performed for the percent changes in the shoot and root biomass in response to N in the 201 spinach accessions using 60,940 whole-genome resequencing generated SNPs. Three SNP markers, chr4_28292655, chr6_1531056, and chr6_37966006 on chromosomes 4 and 6, were significantly associated with %change in root weight, and two SNP markers, chr2_18480277 and chr4_47598760 on chromosomes 2 and 4, were significantly associated with % change shoot weight. The outcome of this study established a foundation for genetic studies needed to improve the partitioning of total biomass and provided a resource to identify molecular markers to enhance N uptake via marker-assisted selection or genomic selection in spinach breeding programs.
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Affiliation(s)
- Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA. .,Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Amit Kumar Mishra
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA.,Department of Botany, School of Life Sciences, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Haramrit Gill
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - James DiPiazza
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA
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Tian X, Niu X, Chang Z, Zhang X, Wang R, Yang Q, Li G. DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia. Front Genet 2022; 13:807293. [PMID: 35422842 PMCID: PMC9001952 DOI: 10.3389/fgene.2022.807293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins with a domain of unknown function (DUF) represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. In particular, members of the DUF1005 family in plants have a 411-amino-acid conserved domain, and this family has not been described previously. In this study, a total of 302 high-confidence DUF1005 family members were identified from 58 plant species, and none were found in the four algae that were selected. Thus, this result showed that DUF1005s might belong to a kind of plant-specific gene family, and this family has not been evolutionarily expanded. Phylogenetic analysis showed that the DUF1005 family genes could be classified into four subgroups in 58 plant species. The earliest group to emerge was Group I, including a total of 100 gene sequences, and this group was present in almost all selected species spanning from mosses to seed plants. Group II and Group III, with 69 and 74 members, respectively, belong to angiosperms. Finally, with 59 members, Group IV was the last batch of genes to emerge, and this group is unique to dicotyledons. Expression pattern analysis of the CiDUF1005, a member of the DUF1005 family from Caragana intermedia, showed that CiDUF1005 genes were differentially regulated under various treatments. Compared to the wild type, transgenic lines with heterologous CiDUF1005 expression in Arabidopsis thaliana had longer primary roots and more lateral roots. These results expanded our knowledge of the evolution of the DUF1005 family in plants and will contribute to elucidating biological functions of the DUF1005 family in the future.
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Affiliation(s)
- Xiaona Tian
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaocui Niu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ziru Chang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Zhang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
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7
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Yu CY, Sharma O, Nguyen PHT, Hartono CD, Kanehara K. A pair of DUF538 domain-containing proteins modulates plant growth and trichome development through the transcriptional regulation of GLABRA1 in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:992-1004. [PMID: 34496091 DOI: 10.1111/tpj.15487] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
SMALLER TRICHOMES WITH VARIABLE BRANCHES (SVB) is an emerging plant growth regulator in trichome development, endoplasmic reticulum stress response, and phosphoinositide signaling, and belongs to the land plant-specific DUF538 domain-containing protein family. Despite its multifaceted roles, the functions of this protein family are poorly understood in plant growth and development. Here, we report that SVB-like (SVBL), the closest homolog of SVB, modulates plant growth and trichome development with SVB in Arabidopsis thaliana. Although none of the single mutants showed an obvious growth defect, the double mutants of svb svbl exhibited dwarfed plant growth. In trichome development, the defects in svb mutant were greatly enhanced by the additional mutation in SVBL, despite the single knockout of SVBL showing the mild defects. The double mutation reduced the transcript level of one of the central hub genes for trichome development, GLABRA1 (GL1), which in turn affects the other downstream genes, GLABRA2 (GL2), TRANSPARENT TESTA GLABRA2 (TTG2), TRIPTYCHON (TRY), CAPRICE (CPC), and ENHANCER OF TRY AND CPC1 (ETC1). In situ translational reporter assays showed that SVB and SVBL share highly similar localization patterns both at tissue and subcellular levels. The present study suggests that SVB and SVBL play a pivotal role in plant growth and trichome development by affecting a specific subset of known trichome developmental regulators, highlighting the importance of the DUF538 protein family in higher plants.
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Affiliation(s)
- Chao-Yuan Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Oshin Sharma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Phong H T Nguyen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chynthia D Hartono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kazue Kanehara
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
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8
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Pinski A, Betekhtin A, Skupien-Rabian B, Jankowska U, Jamet E, Hasterok R. Changes in the Cell Wall Proteome of Leaves in Response to High Temperature Stress in Brachypodium distachyon. Int J Mol Sci 2021; 22:6750. [PMID: 34201710 PMCID: PMC8267952 DOI: 10.3390/ijms22136750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non-redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over-accumulated and 42 were under-accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over- and 12 under-accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature.
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Affiliation(s)
- Artur Pinski
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
| | - Bozena Skupien-Rabian
- Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland; (B.S.-R.); (U.J.)
| | - Urszula Jankowska
- Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland; (B.S.-R.); (U.J.)
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Auzeville Tolosane, France;
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
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