miR482 and Its Isoforms in Plants

Abstract

In plants, miR482 family members are generally 22-nucleotide long, distinguishing from other microRNA (miRNA) families by their extraordinary and diverse sequence structures. Studies showed that miRNA482 is related to NBLRR (Nucleotide binding-site leucine-rich repeat) genes conferring resistance to disease in plants. There are different coded NB-LRR genes which are considered as the part immune response assisting the recognition of pathogens in plant genomes. NB-LRR proteins are mostly related to effector – triggering immune system against pathogens. The main immune receptors in plants are PRR (Pattern recoginition receptor) and R (Resistance) proteins. R proteins code for immune system proteins by NB-LRR activity. miR482, miR1448, slmiR2118 and ath-miR472 are disease resistance related miRNAs. In several studies, miR482 was found to be a homolog of miR1448 and phylogenetic analyses showed that miR1448 is formed by tandem duplication of miR482. While suppression of miR482 results in plant susceptibility to pathogens, miR482 was considered to play role in nodulation and mycorrhizal processes of soya roots. Increasing evidences exhibit that miR482 is critical in disease resistance against pathogen attacks.

Keywords

• miR482 family,NB-LRR,R gene,nodulation

miR482 ve Bitkilerdeki İzoformları

Abstract

Bitkilerdeki miR482 aile üyeleri genelde 22 nükleotid uzunluğunda diğer mikroRNA (miRNA) ailelerinden daha değişken ve sıra dışı dizilere sahiptir. Çalışmalar miR482’nin hastalık direnciyle ilişkili nükleotit-bağlayıcı lösince zengin tekrarlı (Nucleotide binding-site leucine-rich repeat, NB-LRR) genlerle ilgili olduğunu göstermektedir. Bitki genomlarında kodlanmış çeşitli NB-LRR’ler birçok patojen tanımayı sağlayan bir çeşit bağışıklık sistemidir. NB-LRR proteinleri normal patojenlere karşı efektör-tetikleme bağışıklıklığı ile ilişkilidir. Bitkide temelden gelen bağışıklık reseptörleri tanılayıcı reseptör yapıları (Pattern recoginition receptor, PRR) ve direnç (Resistance, R) proteinleridir. R genlerinin çoğu NB-LRR etki ile hücrede bağışıklık proteinlerini kodlarlar. miR482, miR1448, slmiR2118 ve ath-miR472 hastalık direnci ile ilişkili miRNA’lardır. Yapılan bazı çalışmalarda ise miR482’nin miR1448 homoloğu olduğu bildirilmiş ve filogenetik analizler miR482’nin tandem duplikasyon ürünü miR1448 olabileceğini göstermektedir. Evrimsel süreçte bu miRNA’lar aynı transkripti hedeflemişlerdir. miR482 izoformlarının baskılanması bitkiyi patojene karşı hassaslaştırırken miR482’nin soyada nodülasyon oluşumunda ve mikorizaların çalışma prensibinde etkili olabileceği düşünülmektedir. Giderek artan kanıtlar miRNA482’nın patojen saldırısında hastalık direnci tepkilerinde kritik roller oynadığını göstermektedir.

Keywords

• miR482 ailesi,NB-LRR,R geni,nodülasyon

References

1. Allen, E., Xie, Z., Gustafson, A.M., Sung, G.H., Spatafora, J.W., Carrington, J.C., 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics, 36(12): 1282-1290.
2. Barrera-Figueroa, B.E., Wu, Z., Liu, R., 2013. Abiotic stress-associated microRNAs in plants: Discovery, expression analysis, and evolution. Frontiers in Biology, 8(2): 189-197.
3. Boller, T., Felix, G., 2009. A renaissance of elicitors: Perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annual Review of Plant Biology, (60): 379-406.
4. Chisholm, S.T., Coaker, G., Day, B., Staskawicz, B.J., 2006. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell, 124(4): 803-814.
5. Cuperus, J.T., Fahlgren, N., Carrington, J.C., 2011. Evolution and functional diversification of MIRNA genes. Plant Cell, 23(2): 431-442.
6. Eckardt, N.A., 2012. A MicroRNA cascade in plant defense. Plant Cell, 24(3): 840-840.
7. Eitas, T.K., Dangl, J.L., 2010. NB-LRR proteins: Pairs, pieces, perception, partners, and pathways. Current Opinion in Plant Biology, 13(4): 472-477.
8. Eldem, V., Okay, S., Ünver, T., 2013. Plant microRNAs: New players in functional genomics. Turkish Journal of Agriculture and Forestry, 37(1): 1-21.

9. Eren, H., Pekmezci, M.Y., Okay, S., Türktaş, M., İnal, B., İlhan, E., Atak, M., Erayman, M., Ünver, T., 2015. Hexaploid wheat (Triticum aestivum) root miRNome analysis in response to salt stress. Annals of Applied Biology, 167(2): 208-216.
10. Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L., Carrington, J.C., 2007. High-throughput sequencing of Arabidopsis microRNAs: Evidence for frequent birth and death of MIRNA genes. Plos One, 2(2): 1-14.
11. Fahlgren, N., Jogdeo, S., Kasschau, K.D., Sullivan, C.M., Chapman, E.J., Laubinger, S., Smith, L.M., Dasenko, M., Givan, S.A., Weigel, D., Carrington, J.C., 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 22(4): 1074-1089.
12. Fei, Q.L., Xia, R., Meyers, B.C., 2013. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. The Plant Cell, 25(7): 2400-2415.
13. Goettel, W., Xia, E., Upchurch, R., Wang, M.L., Chen, P.Y., An, Y.Q.C., 2014. Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. Bmc Genomics, 15(1): 1-17.
14. Han, J., Fang, J.G., Wang, C., Yin, Y.L., Sun, X., Leng, X.P., Song, C.N., 2014. Grapevine microRNAs responsive to exogenous gibberellin. Bmc Genomics, 15(1): 111.
15. Hassan, N.M., El-Bastawisy, Z.M., El-Sayed, A.K., Ebeed, H.T., Alla, M.M.N., 2015. Roles of dehydrin genes in wheat tolerance to drought stress. Journal of Advanced Research, 6(2): 179-188.
16. İlhan, E., Eren, A.H., Erayman, M., 2013. Serin iklim tahıllarında virüs kaynaklı gen susturma: BSMV kullanımı. Atatürk Üniversitesi Ziraat Fakültesi Dergisi, 44(1): 91-97.
17. İnal, B., Türktaş, M., Eren, H., İlhan, E., Okay, S., Atak, M., Erayman, M., Ünver, T., 2014. Genome-wide fungal stress responsive miRNA expression in wheat. Planta, 240(6): 1287-1298.
18. Jones-Rhoades, M.W., 2012. Conservation and divergence in plant microRNAs. Plant Molecular Biology, 80(1): 3-16.
19. Jones, J.D.G., Dangl, J.L., 2006. The plant immune system. Nature, 444(7117): 323-329.
20. Karlova, R., Van Haarst, J.C., Maliepaard, C., Van de Geest, H., Bovy, A.G., Lammers, M., Angenent, G.C., De Maagd, R.A., 2013. Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. Journal of Experimental Botany, 64(7): 1863-1878.
21. King, S.W., Joshi, C.P., Nguyen, H.T., 1992. DNA-Sequence of an aba-responsive gene (Rab-15) from water-stressed wheat roots. Plant Molecular Biology, 18(1): 119-121.
22. Koptekin, D., Aktaş, L.Y., 2013. Bitki mikroRNA’ları: Biyogenezi, köken ve evrimi. Türk Bilimsel Derlemeler Dergisi, 6(2): 140-148.
23. Kwak, P.B., Wang, Q.Q., Chen, X.S., Qiu, C.X., Yang, Z.M., 2009. Enrichment of a set of microRNAs during the cotton fiber development. Bmc Genomics, 10(1): 1-11.
24. Li, F., Pignatta, D., Bendix, C., Brunkard, J.O., Cohn, M.M., Tung, J., Sun, H.Y., Kumar, P., Baker, B., 2012. MicroRNA regulation of plant innate immune receptors. Proceedings of the National Academy of Sciences, 109(5): 1790-1795.
25. Li, H., Deng, Y., Wu, T.L., Subramanian, S., Yu, O., 2010. Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiology, 153(4): 1759-1770.
26. Lu, S.F., Sun, Y.H., Chiang, V.L., 2008. Stress-responsive microRNAs in populus. The Plant Journal, 55(1): 131-151.
27. Meyers, B.C., Kozik, A., Griego, A., Kuang, H.H., Michelmore, R.W., 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. The Plant Cell, 15(7): 1683-1683.
28. Mohorianu, I., Schwach, F., Jing, R.C., Lopez-Gomollon, S., Moxon, S., Szittya, G., Sorefan, K., Moulton, V., Dalmay, T., 2011. Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. The Plant Journal, 67(2): 232-246.
29. Nozawa, M., Miura, S., Nei, M., 2012. Origins and evolution of microRNA genes in plant species. Genome Biology and Evolution, 4(3): 230-239.
30. Omidvar, V., Mohorianu, I., Dalmay, T., Fellner, M., 2015. MicroRNA Regulation of abiotic stress response in 7B-1 male-sterile tomato mutant. Plant Genome, 8(3): 878-835.
31. Ouyang, S.Q., Park, G., Atamian, H.S., Han, C.S., Stajich, J.E., Kaloshian, I., Borkovich, K.A., 2014. MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum. Plos Pathog, 10(10): 1-15.
32. Pang, M.X., Woodward, A.W., Agarwal, V., Guan, X.Y., Ha, M., Ramachandran, V., Chen, X.M., Triplett, B.A., Stelly, D.M., Chen, Z.J., 2009. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biology, 10(11): 1-21.
33. Qiu, D.Y., Xiao, J., Ding, X.H., Xiong, M., Cai, M., Cao, C.L., Li, X.H., Xu, C.G., Wang, S.P., 2007. OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate- and jasmonate-dependent signaling. Molecular Plant-Microbe Interactions, 20(5): 492-499.
34. Rajagopalan, R., Vaucheret, H., Trejo, J., Bartel, D.P., 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Development, 20(24): 3407-3425.
35. Shivaprasad, P.V., Chen, H.M., Patel, K., Bond, D.M., Santos, B.A.C.M., Baulcombe, D.C., 2012. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell, 24(3): 859-874.
36. Shuai, P., Liang, D., Zhang, Z.J., Yin, W.L., Xia, X.L., 2013. Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis. Bmc Genomics, 14(1): 1-14.
37. Wan, H.J., Yuan, W., Ye, Q.J., Wang, R.Q., Ruan, M.Y., Li, Z.M., Zhou, G.Z., Yao, Z.P., Zhao, J., Liu, S.J., Yang, Y.J., 2012. Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: Characterization, genetic variation, functional divergence and expression patterns. Bmc Genomics, 13(1): 1-15.
38. Xiao, Y., Xia, W., Yang, Y.D., Mason, A.S., Lei, X.T., Ma, Z.L., 2013. Characterization and evolution of conserved microRNA through duplication events in date palm (Phoenix dactylifera). Plos One, 8(8): 1-10.
39. Xu, Q., Liu, Y.L., Zhu, A.D., Wu, X.M., Ye, J.L., Yu, K.Q., Guo, W.W., Deng, X.X., 2010. Discovery and comparative and profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. Bmc Genomics, 11(246): 1-17.
40. Yang, L., Mu, X.Y., Liu, C., Cai, J.H., Shi, K., Zhu, W.J., Yang, Q., 2015. Overexpression of potato miR482e enhanced plant sensitivity to Verticillium dahliae infection. Journal of Integrative Plant Biology, 57(12): 1078-1088.
41. Yang, S.M., Tang, F., Gao, M.Q., Krishnan, H.B., Zhu, H.Y., 2010. R gene-controlled host specificity in the legume-rhizobia symbiosis. Proceedings of the National Academy of Sciences, 107(43): 18735-18740.
42. Zhai, J.X., Jeong, D.H., De Paoli, E., Park, S., Rosen, B.D., Li, Y.P., Gonzalez, A.J., Yan, Z., Kitto, S.L., Grusak, M.A., Jackson, S.A., Stacey, G., Cook, D.R., Green, P.J., Sherrier, D.J., Meyers, B.C., 2011. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development, 25(23): 2540-2553.
43. Zhang, L.F., Chia, J.M., Kumari, S., Stein, J.C., Liu, Z.J., Narechania, A., Maher, C.A., Guill, K., McMullen, M.D., Ware, D., 2009. A genome-wide characterization of microRNA genes in maize. Plos Genetics, 5(11): e1000716. (doi:10.1371/journal. pgen.1000716).
44. Zhao, J.P., Diao, S., Zhang, B.Y., Niu, B.Q., Wang, Q.L., Wan, X.C., Luo, Y.Q., 2012. Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L. Plos One, 7(10): e4781110.
45. Zhu, Q.H., Fan, L.J., Liu, Y., Xu, H., Llewellyn, D., Wilson, I., 2013. miR482 regulation of NBS-LRR defense genes during fungal pathogen ınfection in cotton. Plos One, 8(12): e8439010.