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Mehla S, Singh Y, Kumar U, Balyan P, Singh KP, Dhankher OP. Overexpression of rice lectin receptor-like kinase, OsLec-RLK, confers salinity stress tolerance and increases seed yield in pigeon pea (Cajanus cajan (L.) Millsp.). PLANT CELL REPORTS 2024; 43:230. [PMID: 39251423 DOI: 10.1007/s00299-024-03314-8] [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: 05/16/2024] [Accepted: 08/10/2024] [Indexed: 09/11/2024]
Abstract
KEY MESSAGE OsLec-RLK overexpression enhances cell signalling and salt stress tolerance in pigeon pea, enhancing seed yield and harvest index and thus, enabling marginal lands to increase food and nutritional security. Lectin Receptor-like kinases (Lec-RLKs) are highly effective cell signaling molecules that counteract various stresses, including salt stress. We engineered pigeon pea by overexpressing OsLec-RLK gene for enhancing salt tolerance. The OsLec-RLK overexpression lines demonstrated superior performance under salt stress, from vegetative to reproductive phase, compared to wild types (WT). The overexpression lines had significantly higher K+/Na+ ratio than WT exposed to 100 mM NaCl. Under salt stress, transgenic lines showed higher levels of chlorophyll, proline, total soluble sugars, relative water content, and peroxidase and catalase activity than WT plants. Membrane injury index and lipid peroxidation were significantly reduced in transgenic lines. Analysis of phenological and yield attributes confirmed that the OsLec-RLK pigeon pea lines maintain plant vigor, with 10.34-fold increase in seed yield (per plant) and 4-5-fold increase in harvest index of overexpression lines, compared to wild type. Meanwhile, the overexpression of OsLec-RLK up-regulated the expression levels of histone deacetylase1, acyl CoA, ascorbate peroxidase, peroxidase, glutathione reductase and catalase, which were involved in the K+/Na+ homeostasis pathway. This study showed the potential of OsLec-RLK gene for increasing crop productivity and yields under salt stress and enabling the crops to be grown on marginal lands for increasing food and nutritional security.
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Affiliation(s)
- Sheetal Mehla
- Department of Molecular Biology and Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Yogita Singh
- Department of Molecular Biology and Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA
| | - Upendra Kumar
- Department of Molecular Biology and Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India.
- Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243006, India.
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University, Meerut, 245206, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, GB Pant University of Agriculture & Technology, Pantnagar, 263145, India
- Vice-Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA.
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Moore AFT, Berhie Y, Weislow IS, Koculi E. Substrate Specificities of DDX1: A Human DEAD-box protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.573566. [PMID: 38260591 PMCID: PMC10802426 DOI: 10.1101/2024.01.09.573566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DDX1 is a human protein which belongs to the DEAD-box protein family of enzymes and is involved in various stages of RNA metabolism from transcription to decay. Many members of the DEAD-box family of enzymes use the energy of ATP binding and hydrolysis to perform their cellular functions. On the other hand, a few members of the DEAD-box family of enzymes bind and/or hydrolyze other nucleotides in addition to ATP. Furthermore, the ATPase activity of DEAD-box family members is stimulated differently by nucleic acids of various structures. The identity of the nucleotides that the DDX1 hydrolyzes and the structure of the nucleic acids upon which it acts in the cell remain largely unknown. Identifying the DDX1 protein's in vitro substrates is important for deciphering the molecular roles of DDX1 in cells. Here we identify the nucleic acid sequences and structures supporting the nucleotide hydrolysis activity of DDX1 and its nucleotide specificity. Our data demonstrate that the DDX1 protein hydrolyzes only ATP and deoxy-ATP in the presence of RNA. The ATP hydrolysis activity of DDX1 is stimulated by multiple molecules: single-stranded RNA molecules as short as ten nucleotides, a blunt-ended double-stranded RNA molecule, a hybrid of a double-stranded DNA-RNA molecule, and a single-stranded DNA molecule. Under our experimental conditions, the single-stranded DNA molecule stimulates the ATPase activity of DDX1 at a significantly reduced extent when compared to the other investigated RNA constructs or the hybrid double-stranded DNA/RNA molecule.
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Affiliation(s)
- Anthony F. T. Moore
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Yepeth Berhie
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Isaac S. Weislow
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
| | - Eda Koculi
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
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Singh RS, Vidhyasagar V, Yang S, Arna AB, Yadav M, Aggarwal A, Aguilera AN, Shinriki S, Bhanumathy KK, Pandey K, Xu A, Rapin N, Bosch M, DeCoteau J, Xiang J, Vizeacoumar FJ, Zhou Y, Misra V, Matsui H, Ross SR, Wu Y. DDX41 is required for cGAS-STING activation against DNA virus infection. Cell Rep 2022; 39:110856. [PMID: 35613581 PMCID: PMC9205463 DOI: 10.1016/j.celrep.2022.110856] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
Upon binding double-stranded DNA (dsDNA), cyclic GMP-AMP synthase (cGAS) is activated and initiates the cGAS-stimulator of IFN genes (STING)-type I interferon pathway. DEAD-box helicase 41 (DDX41) is a DEAD-box helicase, and mutations in DDX41 cause myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). Here, we show that DDX41-knockout (KO) cells have reduced type I interferon production after DNA virus infection. Unexpectedly, activations of cGAS and STING are affected in DDX41 KO cells, suggesting that DDX41 functions upstream of cGAS. The recombinant DDX41 protein exhibits ATP-dependent DNA-unwinding activity and ATP-independent strand-annealing activity. The MDS/AML-derived mutant R525H has reduced unwinding activity but retains normal strand-annealing activity and stimulates greater cGAS dinucleotide-synthesis activity than wild-type DDX41. Overexpression of R525H in either DDX41-deficient or -proficient cells results in higher type I interferon production. Our results have led to the hypothesis that DDX41 utilizes its unwinding and annealing activities to regulate the homeostasis of dsDNA and single-stranded DNA (ssDNA), which, in turn, regulates cGAS-STING activation. cGAS is activated by dsDNA. Singh et al. find DDX41 regulates cGAS activation through unwinding and annealing activities on dsDNA and ssDNA, respectively, and MDS/AML patient mutant R525H causes overactivation of innate immune response due to its unbalanced activities. This DDX41-cGAS-STING pathway may be related to molecular pathogenesis of MDS/AML.
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Affiliation(s)
- Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Aanchal Aggarwal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Kannupriya Pandey
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Aizhang Xu
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Noreen Rapin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Mark Bosch
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - John DeCoteau
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Jim Xiang
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada; Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Vikram Misra
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Susan R Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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Wu N, Yang J, Wang G, Ke H, Zhang Y, Liu Z, Ma Z, Wang X. Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum. BMC PLANT BIOLOGY 2022; 22:6. [PMID: 34979912 PMCID: PMC8722198 DOI: 10.1186/s12870-021-03382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The fiber yield and quality of cotton are greatly and periodically affected by water deficit. However, the molecular mechanism of the water deficit response in cotton fiber cells has not been fully elucidated. RESULTS In this study, water deficit caused a significant reduction in fiber length, strength, and elongation rate but a dramatic increase in micronaire value. To explore genome-wide transcriptional changes, fibers from cotton plants subjected to water deficit (WD) and normal irrigation (NI) during fiber development were analyzed by transcriptome sequencing. Analysis showed that 3427 mRNAs and 1021 long noncoding RNAs (lncRNAs) from fibers were differentially expressed between WD and NI plants. The maximum number of differentially expressed genes (DEGs) and lncRNAs (DERs) was identified in fibers at the secondary cell wall biosynthesis stage, suggesting that this is a critical period in response to water deficit. Twelve genes in cotton fiber were differentially and persistently expressed at ≥ five time points, suggesting that these genes are involved in both fiber development and the water-deficit response and could potentially be used in breeding to improve cotton resistance to drought stress. A total of 540 DEGs were predicted to be potentially regulated by DERs by analysis of coexpression and genomic colocation, accounting for approximately 15.76% of all DEGs. Four DERs, potentially acting as target mimics for microRNAs (miRNAs), indirectly regulated their corresponding DEGs in response to water deficit. CONCLUSIONS This work provides a comprehensive transcriptome analysis of fiber cells and a set of protein-coding genes and lncRNAs implicated in the cotton response to water deficit, significantly affecting fiber quality during the fiber development stage.
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Affiliation(s)
- Nan Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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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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SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China. FORESTS 2020. [DOI: 10.3390/f11010080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Chinese elm is an important tree ecologically; however, little is known about its genetic diversity and adaptation mechanisms. In this study, a total of 107 individuals collected from seven natural populations in eastern China were investigated by specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) detected by SLAF-seq, genetic diversity and markers associated with climate variables were identified. All seven populations showed medium genetic diversity, with PIC values ranging from 0.2632 to 0.2761. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Environmental association analyses with three climate variables (annual rainfall, annual average temperature, and altitude) resulted in, altogether, 43 and 30 putative adaptive loci by Bayenv2 and LFMM, respectively. Five adaptive genes were annotated, which were related to the functions of glycosylation, peroxisome synthesis, nucleic acid metabolism, energy metabolism, and signaling. This study was the first on the genetic diversity and local adaptation in Chinese elms, and the results will be helpful in future work on molecular breeding.
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Giraud G, Terrone S, Bourgeois CF. Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep 2019. [PMID: 30293550 PMCID: PMC6330936 DOI: 10.5483/bmbrep.2018.51.12.234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA helicases DDX5 and DDX17 are multitasking proteins that regulate gene expression in different biological contexts through diverse activities. Special attention has long been paid to their function as coregulators of transcription factors, providing insight about their functional association with a number of chromatin modifiers and remodelers. However, to date, the variety of described mechanisms has made it difficult to understand precisely how these proteins work at the molecular level, and the contribution of their ATPase domain to these mechanisms remains unclear as well. In light of their association with long noncoding RNAs that are key epigenetic regulators, an emerging view is that DDX5 and DDX17 may act through modulating the activity of various ribonucleoprotein complexes that could ensure their targeting to specific chromatin loci. This review will comprehensively describe the current knowledge on these different mechanisms. We will also discuss the potential roles of DDX5 and DDX17 on the 3D chromatin organization and how these could impact gene expression at the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Guillaume Giraud
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Sophie Terrone
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
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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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Tao S, Jiao Z, Wen G, Zhang L, Wang G. Cloning and expression analysis of the DEAD-box/RNA helicase Oslaf-1 in Ovomermis sinensis. PLoS One 2018; 13:e0192101. [PMID: 29408876 PMCID: PMC5800602 DOI: 10.1371/journal.pone.0192101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/18/2018] [Indexed: 11/28/2022] Open
Abstract
Ovomermis sinensis is a potentially-valuable nematode for controlling insect pests. The parasitic stage of the nematode absorbs nutrients in its host’s hemolymph to maintain its growth development and then kills the host when it emerges. At present, little known about its reproductive development, particularly the responsible molecular mechanism. More detailed research on the genes of reproductive development will not only help us understand the mechanisms underlying sex differentiation in the nematode, but would also be valuable for successfully cultivating them in vitro and using them for biocontrol. In this study, we used the homology cloning method to clone the full-length cDNA of a DEAD-box family gene (Oslaf-1) from O. sinensis. Then, using qRT-PCR technology to detect the expression pattern of the Oslaf-1 gene at different development stages and tissues, the gene was found to be highly expressed in the post-parasitic stage (P < 0.01) and ovarian (P < 0.05) of O. sinensis. Western blot analysis showed the same result that the gene is associated with gonadal development and function, but is not gonad-specific. In situ hybridization further demonstrated that the gene is widely expressed in early embryos and is mainly distributed in the gonadal area. However, the signal was mainly concentrated in the reproductive primordia in pre-parasitic juveniles. RNA interference (RNAi) studies revealed that the sex ratio of O. sinensis soaked in dsRNA of Oslaf-1 was not statistically different than the gfp dsRNA treated groups. Our results suggest that Oslaf-1 may play a vital role in the reproductive systems of the nematode. In addition, we speculate that the Oslaf-1 gene plays an important role during embryonic development and that it occurs and develops in the gonads of pre-parasitic juveniles of O. sinensis.
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Affiliation(s)
- Siying Tao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhenlong Jiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guigui Wen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Lihong Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guoxiu Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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Alam Z, Roncal J, Peña-Castillo L. Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea. BMC Genomics 2018; 19:4. [PMID: 29291734 PMCID: PMC5748963 DOI: 10.1186/s12864-017-4396-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically increased worldwide demand due to its numerous health benefits. Genetic markers can facilitate the selection of berries with desirable climatic adaptations, agronomic and nutritious characteristics to improve cultivation programs. However, no genomic resources are available for this species. Results We used Genotyping-by-Sequencing (GBS) to analyze the genetic variation of 56 lingonberry samples from across Newfoundland and Labrador, Canada. To elucidate a potential adaptation to environmental conditions we searched for genotype-environment associations by applying three distinct approaches to screen the identified single nucleotide polymorphisms (SNPs) for correlation with six environmental variables. We also searched for an association between the identified SNPs and two phenotypic traits: the total phenolic content (TPC) and antioxidant capacity (AC) of fruit. We identified 1586 high-quality putative SNPs using the UNEAK pipeline available in TASSEL. We found 132 SNPs likely associated with at least one of the environmental or phenotypic variables. To obtain insights on the function of the genomic sequences containing the SNPs likely to be associated with the environmental or phenotypic variables, we performed a sequence-based functional annotation and identified homologous protein-coding sequences with functional roles related to abiotic stress response, pathogen defense, RNA metabolism, and, most interestingly, phenolic compound biosynthesis. Conclusions The putative SNPs discovered are the first genomic resource for lingonberry. This resource might prove useful in high-density quantitative trait locus analysis, and association mapping. The identified candidate genes containing the SNPs need further studies on their potential role in local adaptation of lingonberry. Altogether, the present study provides new resources that can be used to breed for desirable traits in lingonberry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4396-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zobayer Alam
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.,Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
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Talwar T, Vidhyasagar V, Qing J, Guo M, Kariem A, Lu Y, Singh RS, Lukong KE, Wu Y. The DEAD-box protein DDX43 (HAGE) is a dual RNA-DNA helicase and has a K-homology domain required for full nucleic acid unwinding activity. J Biol Chem 2017; 292:10429-10443. [PMID: 28468824 DOI: 10.1074/jbc.m117.774950] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/25/2017] [Indexed: 11/06/2022] Open
Abstract
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins but has not been reported in helicases. DDX43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box protein family. It contains a helicase core domain in its C terminus and a potential KH domain in its N terminus. DDX43 is highly expressed in many tumors and is, therefore, considered a potential target for immunotherapy. Despite its potential as a therapeutic target, little is known about its activities. Here, we purified recombinant DDX43 protein to near homogeneity and found that it exists as a monomer in solution. Biochemical assays demonstrated that it is an ATP-dependent RNA and DNA helicase. Although DDX43 was active on duplex RNA regardless of the orientation of the single-stranded RNA tail, it preferred a 5' to 3' polarity on RNA and a 3' to 5' direction on DNA. Truncation mutations and site-directed mutagenesis confirmed that the KH domain in DDX43 is responsible for nucleic acid binding. Compared with the activity of the full-length protein, the C-terminal helicase domain had no unwinding activity on RNA substrates and had significantly reduced unwinding activity on DNA. Moreover, the full-length DDX43 protein, with single amino acid change in the KH domain, had reduced unwinding and binding activates on RNA and DNA substrates. Our results demonstrate that DDX43 is a dual helicase and the KH domain is required for its full unwinding activity.
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Affiliation(s)
- Tanu Talwar
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | | | - Jennifer Qing
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Manhong Guo
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Ahmad Kariem
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yi Lu
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Ravi Shankar Singh
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Kiven Erique Lukong
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yuliang Wu
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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Rakei A, Maali-Amiri R, Zeinali H, Ranjbar M. DNA methylation and physio-biochemical analysis of chickpea in response to cold stress. PROTOPLASMA 2016; 253:61-76. [PMID: 25820678 DOI: 10.1007/s00709-015-0788-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/27/2015] [Indexed: 05/27/2023]
Abstract
Cold stress (CS) signals are translated into physiological changes as products of direct and/or indirect of gene expression regulated by different factors like DNA methylation. In this study, some of these factors were comparatively studied in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold-tolerant genotype, and ILC533, cold susceptible one) under control (23 °C) and days 1, 3, and 6 after exposing the seedlings to CS (4 °C). Under CS, tolerant genotype prevented H2O2 accumulation which led to a decrease in damage indices (malondialdehyde and electrolyte leakage index) compared to susceptible one. The significant activities of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase) along with a significant proportion of change in DNA methylation/demethylation patterns were often effective factors in preserving cell against cold-induced oxidative stress. Chickpea cells in response to CS changed access to their genome as the number of bands without change from day 1 to day 6 of exposure to CS particularly in tolerant genotype was decreased. During CS, the methylation level was higher compared to demethylation (29.05 vs 19.79 %) in tolerant genotype and (27.92 vs 22.09 %) in susceptible one. However, for prolonged periods of CS, changes in demethylated bands in tolerant genotype were higher than that of in susceptible one (9.24 vs 4.13 %), indicating higher potential for activation of CS responsive genes. Such a status along with higher activity of antioxidants and less damage indices could be related to cold tolerance (CT) mechanisms in chickpea. Sequencing analysis confirmed the important role of some specific DNA sequences in creating CT with possible responsive components involved in CS. Thus, dynamic assessment using multi-dimensional approaches allows us to progressively fill in the gaps between physio-biochemical and molecular events in creating CT, to comprehend better the nature of the plant stress response and molecular mechanisms behind.
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Affiliation(s)
- Aida Rakei
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran.
| | - Hassan Zeinali
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Mojtaba Ranjbar
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, 46168-49767, Iran
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Tuteja N, Tarique M, Trivedi DK, Sahoo RK, Tuteja R. Stress-induced Oryza sativa BAT1 dual helicase exhibits unique bipolar translocation. PROTOPLASMA 2015; 252:1563-1574. [PMID: 25772680 DOI: 10.1007/s00709-015-0791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
HLA-B associated transcript 1 (BAT1) protein, also named as spliceosome RNA helicase UAP56, is a member of the DExD/H-box family of helicases. However, regulation under stress, biochemical properties, and functions of plant homologue of BAT1 are poorly understood. Here, we report the purification and detailed biochemical characterization of the Oryza sativa homologue of BAT1 (OsBAT1/UAP56) protein (52 kDa) and regulation of its transcript under abiotic stress. OsBAT1 transcript levels are enhanced in rice seedlings in response to abiotic stress including salt stress and abscisic acid. Purified OsBAT1 protein exhibits the DNA- and RNA-dependent ATPase, RNA helicase, and DNA- and RNA-binding activities. Interestingly OsBAT1 also exhibits unique DNA helicase activity, which has not been reported so far in any BAT1 homologue. Moreover, OsBAT1 translocates in both the 3' to 5' and 5' to 3' directions, which is also a unique property. The K m value for OsBAT1 DNA helicase is 0.9753 nM and for RNA helicase is 1.7536 nM, respectively. This study demonstrates several unique characteristics of OsBAT1 especially its ability to unwind both DNA and RNA duplexes; bipolar translocation and its transcript upregulation under abiotic stresses indicate that it is a multifunctional protein. Overall, this study represents significant contribution in advancing our knowledge regarding functions of OsBAT1 in RNA and DNA metabolism and its putative role in abiotic stress signaling in plants.
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Affiliation(s)
- Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Mohammed Tarique
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dipesh Kumar Trivedi
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ranjan Kumar Sahoo
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Renu Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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15
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Tuteja N, Tarique M, Tuteja R. Rice SUV3 is a bidirectional helicase that binds both DNA and RNA. BMC PLANT BIOLOGY 2014; 14:283. [PMID: 25311683 PMCID: PMC4207899 DOI: 10.1186/s12870-014-0283-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 10/09/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Helicases play crucial role in almost all the nucleic acid metabolism including replication, repair, recombination, transcription, translation, ribosome biogenesis and splicing and these processes regulate plant growth and development. It is suggested that helicases play essential roles in stabilizing growth in plants under stress because their presence in the stress-induced ORFs has been identified. Moreover in a recent study we have reported that SUV3 helicase from Oryza sativa (OsSUV3) functions in salinity stress tolerance in transgenic rice by improving the antioxidant machinery. SUV3 helicase has been identified and characterized from yeast and human systems but the properties and functions of plant SUV3 are poorly understood. RESULTS In this study, the purification and extensive characterization of recombinant OsSUV3 protein (67 kDa) is presented. OsSUV3 binds to DNA and RNA and exhibits DNA as well as RNA-dependent ATPase activities. It also contains the characteristic DNA and RNA helicase activity. OsSUV3 can use mainly ATP or dATP as energy source for the unwinding activity and it cannot unwind the blunt-end duplex DNA substrate. It is interesting to note that OsSUV3 unwinds DNA in both the 5'-3' and 3'-5 directions and thus its activity is bipolar in vitro. The Km values of OsSUV3 are 0.51 nM and 0.95 nM for DNA helicase and RNA helicase, respectively. CONCLUSIONS This study is the first direct evidence to show the bipolar DNA helicase activity of OsSUV3 protein. The unique properties of OsSUV3 including its dual helicase activity imply that it could be a multifunctional protein involved in biologically significant process of DNA and RNA metabolisms. These results should make significant contribution towards better understanding of SUV3 protein in plants.
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Affiliation(s)
- Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Mohammed Tarique
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Renu Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
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Mallam AL, Sidote DJ, Lambowitz AM. Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. eLife 2014; 3:e04630. [PMID: 25497230 PMCID: PMC4383044 DOI: 10.7554/elife.04630] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/10/2014] [Indexed: 01/07/2023] Open
Abstract
How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.
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Affiliation(s)
- Anna L Mallam
- Institute for Cellular
and Molecular Biology, University of Texas at
Austin, Austin, United States,Department of Molecular
Biosciences, University of Texas at
Austin, Austin, United States
| | - David J Sidote
- Institute for Cellular
and Molecular Biology, University of Texas at
Austin, Austin, United States,Department of Molecular
Biosciences, University of Texas at
Austin, Austin, United States
| | - Alan M Lambowitz
- Institute for Cellular
and Molecular Biology, University of Texas at
Austin, Austin, United States,Department of Molecular
Biosciences, University of Texas at
Austin, Austin, United States,For correspondence:
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