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Beye A, Billot C, Ronfort J, McNally KL, Diouf D, Glaszmann JC. Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties. RICE (NEW YORK, N.Y.) 2023; 16:12. [PMID: 36853402 PMCID: PMC9975138 DOI: 10.1186/s12284-023-00625-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. METHODS We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. KEY RESULTS Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions.
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Affiliation(s)
- Abdoulaye Beye
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Claire Billot
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Joëlle Ronfort
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, The Philippines
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Jean Christophe Glaszmann
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France.
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France.
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2
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Stein RE, Nauerth BH, Binmöller L, Zühl L, Loreth A, Reinert M, Ibberson D, Schmidt A. RH17 restricts reproductive fate and represses autonomous seed coat development in sexual Arabidopsis. Development 2021; 148:272091. [PMID: 34495331 DOI: 10.1242/dev.198739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Plant sexual and asexual reproduction through seeds (apomixis) is tightly controlled by complex gene regulatory programs, which are not yet fully understood. Recent findings suggest that RNA helicases are required for plant germline development. This resembles their crucial roles in animals, where they are involved in controlling gene activity and the maintenance of genome integrity. Here, we identified previously unknown roles of Arabidopsis RH17 during reproductive development. Interestingly, RH17 is involved in repression of reproductive fate and of elements of seed development in the absence of fertilization. In lines carrying a mutant rh17 allele, development of supernumerary reproductive cell lineages in the female flower tissues (ovules) was observed, occasionally leading to formation of two embryos per seed. Furthermore, seed coat, and putatively also endosperm development, frequently initiated autonomously. Such induction of several features phenocopying distinct elements of apomixis by a single mutation is unusual and suggests that RH17 acts in regulatory control of plant reproductive development. Furthermore, an in-depth understanding of its action might be of use for agricultural applications.
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Affiliation(s)
- Ron Eric Stein
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Berit Helge Nauerth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Laura Binmöller
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anna Loreth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Maximilian Reinert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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3
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Particle bombardment technology and its applications in plants. Mol Biol Rep 2020; 47:9831-9847. [PMID: 33222118 DOI: 10.1007/s11033-020-06001-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Particle bombardment, or biolistics, has emerged as an excellent alternative approach for plant genetic transformation which circumvents the limitations of Agrobacterium-mediated genetic transformation. The method has no biological constraints and can transform a wide range of plant species. Besides, it has been the most efficient way to achieve organelle transformation (for both chloroplasts and mitochondria) so far. Along with the recent advances in genome editing technologies, conventional gene delivery tools are now being repurposed to deliver targeted gene editing reagents into the plants. One of the key advantages is that the particle bombardment allows DNA-free gene editing of the genome. It enables the direct delivery of proteins, RNAs, and RNPs into plants. Owing to the versatility and wide-range applicability of the particle bombardment, it will likely remain one of the major genetic transformation methods in the future. This article provides an overview of the current status of particle bombardment technology and its applications in the field of plant research and biotechnology.
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4
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Pandey S, Prasad A, Sharma N, Prasad M. Linking the plant stress responses with RNA helicases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110607. [PMID: 32900445 DOI: 10.1016/j.plantsci.2020.110607] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 05/21/2023]
Abstract
RNA helicases are omnipresent plant proteins across all kingdoms and have been demonstrated to play an essential role in all cellular processes involving nucleic acids. Currently, these proteins emerged as a new tool for plant molecular biologists to modulate plant stress responses. Here, we review the crucial role of RNA helicases triggered by biotic, abiotic, and multiple stress conditions. In this review, the emphasis has been given on the role of these proteins upon viral stress. Further, we have explored RNA helicase mediated regulation of RNA metabolism, starting from ribosome biogenesis to its decay upon stress induction. We also highlighted the cross-talk between RNA helicase, phytohormones, and ROS. Different overexpression and transgenic studies have been provided in the text to indicate the stress tolerance abilities of these proteins.
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Affiliation(s)
- Saurabh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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5
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Xiaomei W, Rongrong K, Ting Z, Yuanyuan G, Jianlong X, Zhongze P, Gangseob L, Dongzhi L, Yanjun D. A DEAD-box RNA helicase TCD33 that confers chloroplast development in rice at seedling stage under cold stress. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153138. [PMID: 32213379 DOI: 10.1016/j.jplph.2020.153138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 05/24/2023]
Abstract
Cold stress is one of the most common unfavorable environmental factors affecting the growth, development, and survival of plants. The DEAD-box RNA helicases play important roles in all types of processes of RNA metabolism. However, the function of DEAD-box RNA helicase under cold stress is poorly explored in plants, especially in rice. This study reported the identification of a novel rice thermo-sensitive chlorophyll-deficient mutant, tcd33, which displayed an albino phenotype before the four-leaf stage, then withered and eventually died at 20 °C, while wild-type plants exhibited normal green coloration at 32 °C. The tcd33 seedlings also exhibited less chlorophyll contents and severe defects of chloroplast structure under 20 °C condition. Map-based cloning and complementation experiments suggested that TCD33 encodes a chloroplast-located DEAD-box RNA helicase protein. The transcript expression level of TCD33 indicated that the genes related to chlorophyll (Chl) biosynthesis, photosynthesis, and chloroplast development in tcd33 mutants were down-regulated at 20 °C, while the down-regulated genes were nearly recovered to or slightly higher than the WT level at 32 °C. Together, our results suggest that the cold-inducible TCD33 is essential for early chloroplast development and is important for cold-responsive gene regulation and cold tolerance in rice.
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Affiliation(s)
- Wang Xiaomei
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kong Rongrong
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhang Ting
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Gao Yuanyuan
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xu Jianlong
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China
| | - Piao Zhongze
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, 1000 Jingqi Road, Fengxian District, Shanghai 201403, China
| | - Lee Gangseob
- National Institute of Agricultural Science, Jeon Ju, 560-500 South Korea
| | - Lin Dongzhi
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Dong Yanjun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai 200234, China.
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Jaikishan I, Rajendrakumar P, Hariprasanna K, Balakrishna D, Bhat BV, Tonapi VA. Identification of differentially expressed transcripts at critical developmental stages in sorghum [ Sorghum bicolor (L.) Moench] in relation to grain yield heterosis. 3 Biotech 2019; 9:239. [PMID: 31168432 DOI: 10.1007/s13205-019-1777-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/23/2019] [Indexed: 12/22/2022] Open
Abstract
Evaluation of a set of 10 F1 hybrids along with their female (27A and 7A) and male parents (C 43, RS 673, RS 627, CB 26, and CB 29) for grain yield and its component traits revealed that grain yield/plant followed by panicle weight, primary branches/panicle, and 100-seed weight exhibited high levels of heterosis. Eight hybrids exhibited 50% or more mid-parent heterosis for grain yield/plant, of which, one hybrid (27A × RS673) recorded heterobeltiosis above 50% (73.61%). Differential display analysis generated about 2995 reproducible transcripts, which were categorized as UPF1-expressed in any one of the parents and F1 (10.53-14.76%), BPnF1-expressed in both parents but not in F1 (4.56-11.44%), UPnF1-expressed in either of the parents and not in F1 (17.95-27.40%), F1nBP-expressed only in F1 but not in either of the parents (14.39-20.54%), and UET-expressed in both parents and F1 (34.52-42.43%). A comparison between high and low heterotic hybrids revealed that the proportions of UPF1 and F1nBP transcript patterns were much higher in the former (21.31% and 45.24%) as compared to the latter (16.67% and 32.14%) at the booting and flowering stage, respectively, indicating the role of over-dominance and dominance in the manifestation of grain yield heterosis. Significant positive correlations were observed for differential transcript patterns with mid-parent and better-parent heterosis for the components of grain yield such as primary branches (0.63 and 0.61 at p < 0.01) and 100-seed weight (0.64 and 0.52 at p < 0.01). Cloning and sequence analysis of 16 transcripts that were differentially expressed in hybrids and their parental lines revealed that they code for genes involved in basic cellular processes, cellulose biosynthesis, and assimilate partitioning between various organs and allocation between various pathways, pyrimidine, and polyamine biosynthesis, enhancing ATP production and regulation of plant growth and development.
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7
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Nidumukkala S, Tayi L, Chittela RK, Vudem DR, Khareedu VR. DEAD box helicases as promising molecular tools for engineering abiotic stress tolerance in plants. Crit Rev Biotechnol 2019; 39:395-407. [DOI: 10.1080/07388551.2019.1566204] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Lavanya Tayi
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, India
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8
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Nguyen LV, Seok HY, Woo DH, Lee SY, Moon YH. Overexpression of the DEAD-Box RNA Helicase Gene AtRH17 Confers Tolerance to Salt Stress in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123777. [PMID: 30486488 PMCID: PMC6321491 DOI: 10.3390/ijms19123777] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 01/13/2023] Open
Abstract
Plants adapt to abiotic stresses by complex mechanisms involving various stress-responsive genes. Here, we identified a DEAD-box RNA helicase (RH) gene, AtRH17, in Arabidopsis, involved in salt-stress responses using activation tagging, a useful technique for isolating novel stress-responsive genes. AT895, an activation tagging line, was more tolerant than wild type (WT) under NaCl treatment during germination and seedling development, and AtRH17 was activated in AT895. AtRH17 possesses nine well-conserved motifs of DEAD-box RHs, consisting of motifs Q, I, Ia, Ib, and II-VI. Although at least 12 orthologs of AtRH17 have been found in various plant species, no paralog occurs in Arabidopsis. AtRH17 protein is subcellularily localized in the nucleus. AtRH17-overexpressing transgenic plants (OXs) were more tolerant to high concentrations of NaCl and LiCl compared with WT, but no differences from WT were detected among seedlings exposed to mannitol and freezing treatments. Moreover, in the mature plant stage, AtRH17 OXs were also more tolerant to NaCl than WT, but not to drought, suggesting that AtRH17 is involved specifically in the salt-stress response. Notably, transcriptions of well-known abscisic acid (ABA)-dependent and ABA-independent stress-response genes were similar or lower in AtRH17 OXs than WT under salt-stress treatments. Taken together, our findings suggest that AtRH17, a nuclear DEAD-box RH protein, is involved in salt-stress tolerance, and that its overexpression confers salt-stress tolerance via a pathway other than the well-known ABA-dependent and ABA-independent pathways.
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Affiliation(s)
- Linh Vu Nguyen
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Hye-Yeon Seok
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Dong-Hyuk Woo
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Sun-Young Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Yong-Hwan Moon
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
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Zhang HY, Lei G, Zhou HW, He C, Liao JL, Huang YJ. Quantitative iTRAQ-based proteomic analysis of rice grains to assess high night temperature stress. Proteomics 2017; 17. [PMID: 28101936 PMCID: PMC5811895 DOI: 10.1002/pmic.201600365] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/23/2016] [Accepted: 01/13/2017] [Indexed: 12/13/2022]
Abstract
Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat‐tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat‐tolerant and ‐sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database. These proteins were then classified into seven functional subgroups, which include signal transduction, transcript regulation, oxidation, defense response, transport, energy metabolism, and biosynthesis. Further analysis indicated that HNT stress could disrupt the redox equilibrium of plant cells, which in turn triggers the calcium‐dependent protein kinase and COP9 signalosome, thereby regulating downstream genes/proteins that are involved in the HNT response. The candidate proteins may provide genetic resources for the improvement of heat‐tolerant characteristics in rice, and the proposed model for signal transduction and transcriptional regulation may facilitate in the elucidation of the molecular mechanism underlying the response to HNT stress in rice.
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Affiliation(s)
- Hong-Yu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Gang Lei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Hui-Wen Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Chao He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province, P. R. China.,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Province, P. R. China
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Khatri N, Singh S, Hakim N, Mudgil Y. Comparative expression profiling of AtRAD5B and AtNDL1: Hints towards a role in G protein mediated signaling. Gene Expr Patterns 2017; 25-26:167-174. [PMID: 28865954 DOI: 10.1016/j.gep.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
Arabidopsis AtRAD5B encodes for a putative helicase of the class SWItch/Sucrose Non-Fermentable (SWI/SNF) ATPases. We identified AtRAD5B as an interactor of N-MYC DOWNREGULATED-LIKE1 (AtNDL1) in a yeast two-hybrid screen. AtNDL1 is a G protein signaling component which regulates auxin transport and gradients together with GTP binding protein beta 1 (AGB1). Auxin gradients are known to recruit SWI/SNF remodeling complexes to the chromatin and regulate expression of genes involved in flower and leaf formation. In current study, a comparative spatial and temporal co-expression/localization analysis of AtNDL1, AGB1 with AtRAD5B was carried out in order to explore the possibility of their coexistence in a common signaling network. Translational fusion (GUS) of AtNDL1 and AtRAD5B in seedlings and reproductive organs revealed that both shared similar expression patterns with the highest expression observed in male reproductive organs. Moreover, they shared similar domains of localization in roots, suggesting their potential functioning together in reproductive and root development processes. This study predicts the existence of a signaling network involving AtNDL1, AGB1 with AtRAD5B.
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Affiliation(s)
- Nisha Khatri
- Department of Botany, University of Delhi, Delhi, India
| | - Swati Singh
- Department of Botany, University of Delhi, Delhi, India
| | - Nasmeen Hakim
- Department of Botany, University of Delhi, Delhi, India
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Mittal A, Tandon S, Singla SK, Tandon C. Mechanistic Insights into the Antilithiatic Proteins from Terminalia arjuna: A Proteomic Approach in Urolithiasis. PLoS One 2016; 11:e0162600. [PMID: 27649531 PMCID: PMC5029924 DOI: 10.1371/journal.pone.0162600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/25/2016] [Indexed: 11/23/2022] Open
Abstract
Kidney stone formation during hyperoxaluric condition is inherently dependent on the interaction between renal epithelial cells and calcium oxalate (CaOx) crystals. Although modern medicine has progressed in terms of removal of these stones, recurrence and persistent side effects restricts their use. Strategies involving plant based agents which could be used as adjunct therapy is an area which needs to be explored. Plant proteins having antilithiatic activity is a hitherto unexplored area and therefore, we conducted a detailed identification and characterization of antilithiatic proteins from Terminalia arjuna (T. arjuna). Proteins were isolated from the dried bark of T. arjuna and those having molecular weights > 3 kDa were subjected to anion exchange chromatography followed by gel filtration chromatography. Four proteins were identified exhibiting inhibitory activity against CaOx crystallization and crystal growth kinetics The cytoprotective and anti-apoptotic efficacy of these purified proteins was further investigated on oxalate injured renal epithelial cells (MDCK and NRK-52E) wherein, injury due to oxalate was significantly attenuated and led to a dose dependent increase in viability of these cells. These proteins also prevented the interaction of the CaOx crystals to the cell surface and reduced the number of apoptotic cells. Identification of these 4 anionic proteins from the bark of T. arjuna was carried out by Matrix-assisted laser desorption/ionization-time of flight Mass spectrometry (MALDI-TOF MS). This was followed by database search with the MASCOT server and sequence similarity was found with Nuclear pore anchor, DEAD Box ATP-dependent RNA helicase 45, Lon protease homolog 1 and Heat shock protein 90–3. These novel proteins isolated from T. arjuna have the potential to inhibit CaOx crystallization and promote cell survival and therefore, offer novel avenues which need to be explored further for the medical management of urolithiasis.
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Affiliation(s)
- Amisha Mittal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
| | | | - Chanderdeep Tandon
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
- * E-mail:
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12
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Upadhyaya HD, Bajaj D, Narnoliya L, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK. Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:302. [PMID: 27047499 PMCID: PMC4803732 DOI: 10.3389/fpls.2016.00302] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/25/2016] [Indexed: 05/17/2023]
Abstract
Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150-200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10-20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21-22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.
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Affiliation(s)
- Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Deepak Bajaj
- National Institute of Plant Genome ResearchNew Delhi, India
| | | | - Shouvik Das
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | | | - Swarup K. Parida
- National Institute of Plant Genome ResearchNew Delhi, India
- *Correspondence: Swarup K. Parida, ;
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