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Govindan G, Harini P, Alphonse V, Parani M. From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance. Mol Biol Rep 2024; 51:598. [PMID: 38683409 DOI: 10.1007/s11033-024-09539-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.
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Affiliation(s)
- Ganesan Govindan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, TN, 603203, India
| | - Prakash Harini
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, TN, 603203, India
| | - Vinoth Alphonse
- Department of Botany, St. Xavier's College (Autonomous), Palayamkottai, TN, 627 002, India
| | - Madasamy Parani
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, TN, 603203, India.
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Sharma B, Govindan G, Li Y, Sunkar R, Gregory BD. RNA N 6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana. Noncoding RNA 2024; 10:8. [PMID: 38392963 PMCID: PMC10892094 DOI: 10.3390/ncrna10010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, post-transcriptional regulation of mRNA mediated by N6-methyladenosine (m6A) has been found to have profound effects on transcriptome regulation during plant responses to various abiotic stresses. However, whether this RNA modification can affect an oxidative stress response in plants has not been studied. To assess the role of m6A modifications during copper-induced oxidative stress responses, m6A-IP-seq was performed in Arabidopsis seedlings exposed to high levels of copper sulfate. This analysis revealed large-scale shifts in this modification on the transcripts most relevant for oxidative stress. This altered epitranscriptomic mark is known to influence transcript abundance and translation; therefore we scrutinized these possibilities. We found an increased abundance of copper-enriched m6A-containing transcripts. Similarly, we also found increased ribosome occupancy of copper-enriched m6A-containing transcripts, specifically those encoding proteins involved with stress responses relevant to oxidative stressors. Furthermore, the significance of the m6A epitranscriptome on plant oxidative stress tolerance was uncovered by assessing germination and seedling development of the mta (N6-methyladenosine RNA methyltransferase A mutant complemented with ABI3:MTA) mutant exposed to high copper treatment. These analyses suggested hypersensitivity of the mta mutant compared to the wild-type plants in response to copper-induced oxidative stress. Overall, our findings suggest an important role for m6A in the oxidative stress response of Arabidopsis.
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Affiliation(s)
- Bishwas Sharma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (G.G.); (Y.L.)
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (G.G.); (Y.L.)
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (G.G.); (Y.L.)
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
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Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023; 24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
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Affiliation(s)
- David Payne
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Charles A Addo-Quaye
- Department of Computer Science and Cybersecurity, Metropolitan State University, Saint Paul, MN 55106, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Govindan G, Sharma B, Li Y, Armstrong CD, Merum P, Rohila JS, Gregory BD, Sunkar R. mRNA N 6 -methyladenosine is critical for cold tolerance in Arabidopsis. Plant J 2022; 111:1052-1068. [PMID: 35710867 PMCID: PMC9543165 DOI: 10.1111/tpj.15872] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 05/16/2023]
Abstract
Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m6 A, m5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m6 A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.
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Affiliation(s)
- Ganesan Govindan
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Bishwas Sharma
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Yong‐Fang Li
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | | | - Pandrangaiah Merum
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Jai S. Rohila
- Dale Bumpers National Rice Research CenterUnited States Department of Agriculture‐Agricultural Research ServicesStuttgartAR72160USA
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
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Natarajan P, Murugesan AK, Govindan G, Gopalakrishnan A, Kumar R, Duraisamy P, Balaji R, Tanuja, Shyamli PS, Parida AK, Parani M. A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina. Commun Biol 2021; 4:851. [PMID: 34239036 PMCID: PMC8266904 DOI: 10.1038/s42003-021-02384-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Water scarcity and salinity are major challenges facing agriculture today, which can be addressed by engineering plants to grow in the boundless seawater. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant agricultural crops. With this objective, we sequenced the genome of a salt-secreting and extraordinarily salt-tolerant mangrove species, Avicennia marina, that grows optimally in 75% seawater and tolerates >250% seawater. Our reference-grade ~457 Mb genome contains 31 scaffolds corresponding to its chromosomes. We identified 31,477 protein-coding genes and a salinome consisting of 3246 salinity-responsive genes and homologs of 614 experimentally validated salinity tolerance genes. The salinome provides a strong foundation to understand the molecular mechanisms of salinity tolerance in plants and breeding crops suitable for seawater farming.
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Affiliation(s)
- Purushothaman Natarajan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ashok Kumar Murugesan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ganesan Govindan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ayyaru Gopalakrishnan
- grid.411408.80000 0001 2369 7742Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, Tamil Nadu India
| | - Ravichandiran Kumar
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Purushothaman Duraisamy
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Raju Balaji
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Tanuja
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Puhan Sushree Shyamli
- grid.418782.00000 0004 0504 0781Institute of Life Sciences, NALCO Square, Bhubaneswar, India
| | - Ajay K. Parida
- grid.418782.00000 0004 0504 0781Institute of Life Sciences, NALCO Square, Bhubaneswar, India
| | - Madasamy Parani
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
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Saini A, Rohila JS, Govindan G, Li YF, Sunkar R. Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses. Int J Mol Sci 2021; 22:ijms22083997. [PMID: 33924430 PMCID: PMC8068833 DOI: 10.3390/ijms22083997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/11/2021] [Indexed: 01/02/2023] Open
Abstract
The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. The rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2, and MSD) that encode seven constitutive transcripts. Of these, five (CSD2, CSD3, CSD4, FSD1, and MSD) utilizes an alternative splicing (AS) strategy and generate seven additional splice variants (SVs) or mRNA variants, i.e., three for CSD3, and one each for CSD2, CSD4, FSD1, and MSD. The exon-intron organization of these SVs revealed variations in the number and length of exons and/or untranslated regions (UTRs). We determined the expression patterns of SVs along with their constitutive forms of SODs in rice seedlings exposed to salt, osmotic, cold, heavy metal (Cu+2) stresses, as well as copper-deprivation. The results revealed that all seven SVs were transcriptionally active in both roots and shoots. When compared to their corresponding constitutive transcripts, the profiles of five SVs were almost similar, while two specific SVs (CSD3-SV4 and MSD-SV2) differed significantly, and the differences were also apparent between shoots and roots suggesting that the specific SVs are likely to play important roles in a tissue-specific and stress-specific manner. Overall, the present study has provided a comprehensive analysis of the SVs of SODs and their responses to stress conditions in shoots and roots of rice seedlings.
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Affiliation(s)
- Ajay Saini
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (A.S.); (G.G.); (Y.-F.L.)
- Bhabha Atomic Research Centre, Molecular Biology Division, Trombay, Mumbai, Maharashtra 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra 400094, India
| | - Jai S. Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Services, Stuttgart, AR 72160, USA;
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (A.S.); (G.G.); (Y.-F.L.)
| | - Yong-Fang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (A.S.); (G.G.); (Y.-F.L.)
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (A.S.); (G.G.); (Y.-F.L.)
- Correspondence:
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Harb A, Simpson C, Guo W, Govindan G, Kakani VG, Sunkar R. The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance. Front Plant Sci 2020; 11:618491. [PMID: 33424910 PMCID: PMC7786106 DOI: 10.3389/fpls.2020.618491] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/27/2020] [Indexed: 05/21/2023]
Abstract
Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.
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Affiliation(s)
- Amal Harb
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, Jordan
- *Correspondence: Amal Harb ;
| | - Craig Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Informatics and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
| | - Vijaya Gopal Kakani
- Department of Plant and Soil Science, Oklahoma State University, Stillwater, OK, United States
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Ramanjulu Sunkar
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Li YF, Zheng Y, Vemireddy LR, Panda SK, Jose S, Ranjan A, Panda P, Govindan G, Cui J, Wei K, Yaish MW, Naidoo GC, Sunkar R. Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress. BMC Genomics 2018; 19:935. [PMID: 30598105 PMCID: PMC6311934 DOI: 10.1186/s12864-018-5279-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of these genotypes may offer a better understanding of the salinity tolerance mechanisms in rice. Although most stress-responsive genes are regulated at the transcriptional level, in many cases, changes at the transcriptional level are not always accompanied with the changes in protein abundance, which suggests that the transcriptome needs to be studied in conjunction with the proteome to link the phenotype of stress tolerance or sensitivity. Published reports have largely underscored the importance of transcriptional regulation during salt stress in these genotypes, but the regulation at the translational level has been rarely studied. Using RNA-Seq, we simultaneously analyzed the transcriptome and translatome from control and salt-exposed Pok and IR29 seedlings to unravel molecular insights into gene regulatory mechanisms that differ between these genotypes. Results Clear differences were evident at both transcriptional and translational levels between the two genotypes even under the control condition. In response to salt stress, 57 differentially expressed genes (DEGs) were commonly upregulated at both transcriptional and translational levels in both genotypes; the overall number of up/downregulated DEGs in IR29 was comparable at both transcriptional and translational levels, whereas in Pok, the number of upregulated DEGs was considerably higher at the translational level (544 DEGs) than at the transcriptional level (219 DEGs); in contrast, the number of downregulated DEGs (58) was significantly less at the translational level than at the transcriptional level (397 DEGs). These results imply that Pok stabilizes mRNAs and also efficiently loads mRNAs onto polysomes for translation during salt stress. Conclusion Under salt stress, Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis. The present study confirmed the known salt stress-associated genes and also identified a number of putative new salt-responsive genes. Most importantly, the study revealed that the translational regulation under salinity plays an important role in salt-tolerant Pok, but such regulation was less evident in the salt-sensitive IR29. Electronic supplementary material The online version of this article (10.1186/s12864-018-5279-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China. .,Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Yun Zheng
- Yunnan Key Lab of Primate Biomedicine Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | | | - Sanjib Kumar Panda
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smitha Jose
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Alok Ranjan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Piyalee Panda
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Junxia Cui
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | | | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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Natarajan P, Murugesan AK, Govindan G, Madasamy P. De novo transcriptome analysis of pneumatophores (modified roots) in the true mangrove species Avicennia marina and identification of the genes related to root gas exchange. Can J Biotech 2017. [DOI: 10.24870/cjb.2017-a178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Govindan G, Ramalingam S. Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes. J Cell Physiol 2016; 231:2380-92. [PMID: 26945523 DOI: 10.1002/jcp.25367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 01/12/2023]
Abstract
Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ganesan Govindan
- Department of Biotechnology, Molecular Biology Laboratory, MS Swaminathan Research Foundation, Taramani, Chennai, India
| | - Sivaprakash Ramalingam
- Department of Biotechnology, Molecular Biology Laboratory, MS Swaminathan Research Foundation, Taramani, Chennai, India
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Dixit S, Kumar Biswal A, Min A, Henry A, Oane RH, Raorane ML, Longkumer T, Pabuayon IM, Mutte SK, Vardarajan AR, Miro B, Govindan G, Albano-Enriquez B, Pueffeld M, Sreenivasulu N, Slamet-Loedin I, Sundarvelpandian K, Tsai YC, Raghuvanshi S, Hsing YIC, Kumar A, Kohli A. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL. Sci Rep 2015; 5:15183. [PMID: 26507552 PMCID: PMC4623671 DOI: 10.1038/srep15183] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/21/2015] [Indexed: 02/06/2023] Open
Abstract
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
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Affiliation(s)
- Shalabh Dixit
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Akshaya Kumar Biswal
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Aye Min
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Amelia Henry
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Rowena H. Oane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Manish L. Raorane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Toshisangba Longkumer
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Isaiah M. Pabuayon
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Sumanth K. Mutte
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Adithi R. Vardarajan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Berta Miro
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ganesan Govindan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Blesilda Albano-Enriquez
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Mandy Pueffeld
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Nese Sreenivasulu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Inez Slamet-Loedin
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | | | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Yue-Ie C. Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
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Govindan G, Sambandan TG, Govindan M, Sinskey A, Vanessendelft J, Adenan I, Rha CK. A bioactive polyacetylene compound isolated from Centella asiatica. Planta Med 2007; 73:597-9. [PMID: 17520525 DOI: 10.1055/s-2007-981521] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A polyacetylene compound was isolated from the aerial parts of Centella asiatica. The chemical structure of this new compound was identified as methyl 5-[(E)-9-hydroxy-1-(1-hydroxyhexyl)-2-methoxyundeca-3,10-diene-5,7-diynyloxy]pentanoate (cadiyenol). This compound induces apoptosis (63%) independent of cell cycle regimen in mouse lymphoma cells (P388D1) at 28 microM (IC (50) = 24 +/- 2 microM) in 24 hours. The compound also reduces nitric oxide production by 70 +/- 2% in lipopolysacharride-activated mouse macrophages at 24 microM with no measurable cytotoxicity.
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Affiliation(s)
- G Govindan
- Biomaterials Science and Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
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Abstract
Goldenseal (Hydrastis canadensis) has emerged as one of the top five herbal supplements in the world-wide market. A convenient method for the determination of the quality and possible adulteration of goldenseal products is thin-layer chromatography (TLC). TLC analysis of 10 goldenseal samples using two solvent systems and spray reagents was conducted. Five of these samples contained both hydrastine and berberine, four contained berberine and one did not contain either of these alkaloids. These TLC results were verified by HPLC analysis.
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Affiliation(s)
- M Govindan
- Department of Chemistry, Fitchburg State College, Fitchburg, MA 01420, USA.
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