DEAD-box: Function on Growth and Development in Arabidopsis thaliana
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摘要: 在RNA代谢过程中，需要许多蛋白和核酸的参与，其中一类蛋白就是RNA解旋酶。RNA解旋酶通过水解ATP获得能量来参与RNA代谢的多个方面，包括核内转录、pre-mRNA的剪切、核糖体发生、核质运输、蛋白质翻译、RNA降解、细胞器内基因的表达。DEAD-box蛋白家族是RNA解旋酶中最大的亚家族，它具有9个保守结构域，因motify Ⅱ的保守氨基酸序列Asp-Glu-Ala-Asp（DEAD）而命名。该家族在酵母、拟南芥（Arabidopsis thaliana Heynh.）和人类基因组中都有较多的家庭成员。近年来，研究者对拟南芥DEAD-box蛋白家族的结构和功能进行了一些研究，本文着重总结DEAD-box基因家族对拟南芥生长发育的影响。Abstract: Many RNA molecules require proteins and other nucleic acids to assist in RNA metabolism. RNA helicases are such proteins, and participate in nearly all aspects of RNA metabolism, including transcription, pre-mRNA splicing, ribosome biogenesis, transport between the nucleus and cytoplasm, protein translation, nonsense-mediated decay, and organelle-specific RNA metabolism, in an ATP-dependent manner. The DEAD-box protein family of RNA helicases belong to superfamily Ⅱ. They have nine conserved motifs, and are named for the conserved amino acid sequence Asp-Glu-Ala-Asp(D-E-A-D) in motif Ⅱ. DEAD-box families consist of abundant members in Saccharomyces cerevisiae, Arabidopsis thaliana, and humans. Recently, the functions of some DEAD-box proteins were revealed in Arabidopsis. This review focuses on the functions of DEAD-box proteins on the growth and development of A. thaliana.
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Keywords:
- DEAD-box /
- Arabidopsis thaliana /
- Development /
- RNA helicase
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[1] Rocak S, Linder P. DEAD-box proteins:the driving forces behind RNA metabolism[J]. Nat Rev Mol Cell Biol, 2004, 5(3):232-241.
[2] Cordin O, Banroques J, Tanner NK, Linder P. The DEAD-box protein family of RNA helicases[J]. Gene, 2006, 367:17-37.
[3] Gorbalenya AE, Koonin EV. Helicases:amino acid sequence comparisons and structure-function relationships[J]. Curr Biol, 1993, 3(3):419-429.
[4] Martin R, Straub AU, Doebele C, Bohnsack MT. DExD/H-box RNA helicases in ribosome biogenesis[J]. RNA Biol,2013, 10(1):4-18.
[5] Linder P. Birth of the DEAD box[J]. Nature, 1989, 337:121-122.
[6] Tanner NK, Cordin O, Banroques J, Doère M, Linder P. The Q motif:a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis[J]. Mol Cell, 2003, 11(1):127-138.
[7] Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, Murcko MA, Lin C, Caron PR. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide:the crystal structure provides insights into the mode of unwinding[J]. Structure, 1998, 6(1):89-100.
[8] Caruthers JM, McKay DB. Helicase structure and mechanism[J]. Curr Biol, 2002, 12(1):123-133.
[9] Fry DC, Kuby SA, Mildvan AS. ATP-binding site of adenylate kinase:mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins[J]. Proc Natl Acad Sci USA, 1986, 83(4):907-911.
[10] Pause A, Sonenberg N. Mutational analysis of a DEAD box RNA helicase:the mammalian translation initiation factor eIF-4A[J]. EMBO J, 1992, 11(7):2643.
[11] Schwer B, Meszaros T. RNA helicase dynamics in pre-mRNA splicing[J]. EMBO J,2000, 19(23):6582-6591.
[12] Linder P, Jankowsky E. From unwinding to clamping-the DEAD box RNA helicase family[J]. Nat Rev Mol Cell Biol, 2011, 12(8):505-516.
[13] Koroleva O, Brown JW, Shaw PE. Localization of eIF4A-III in the nucleolus and splicing speckles is an indicator of plant stress[J]. Plant Signal Behav, 2009, 4(12):1148-1151.
[14] Kovalev N, Nagy PD. The expanding functions of cellular helicases:the tombusvirus RNA replication enhancer co-opts the plant eIF4AIII-like AtRH2 and the DDX5-like AtRH5 DEAD-box RNA helicases to promote viral asymmetric RNA replication[J]. PLoS Pathog, 2014, 10(4):e1004051.
[15] Asakura Y, Galarneau E, Watkins KP, Barkan A, van Wijk KJ. Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific groupⅡ[STXFZ] introns and affect chloroplast ribosome biogenesis[J]. Plant Physiol, 2012, 159(3):961-974.
[16] Lee KH, Park J, Williams DS, Xiong Y, Hwang I, Kang BH. Defective chloroplast development inhibits maintenance of normal levels of abscisic acid in a mutant of the Arabidopsis RH3 DEAD-box protein during early post-germination growth[J]. Plant J, 2013, 73(5):720-732.
[17] Gu L, Xu T, Lee K, Lee KH, Kang H. A chloroplast-loca-lized DEAD-box RNA helicase AtRH3 is essential for intron splicing and plays an important role in the growth and stress response in Arabidopsis thaliana[J]. Plant Physiol Biochem, 2014, 82:309-318.
[18] Khan A, Garbelli A, Grossi S, Florentin A, Batelli G, Acuna T, Zolla G, Kaye Y, Paul LK, Zhu JK,Maga G, Grafi G, Barak S. The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar-and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing[J]. Plant J, 2014, 79(1):28-43.
[19] Kant P, Kant S, Gordon M, Shaked R, Barak S.[STXFX]STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2,[STXFZ] two DEAD-box RNA helicases that atte-nuate Arabidopsis responses to multiple abiotic stresses[J]. Plant Physiol, 2007, 145(3):814-830.
[20] Nayak NR, Putnam AA, Addepalli B, Lowenson JD, Chen T, Jankowsky E, Perry SE, Dinkins RD, Limbach PA, Clarke SG,Downie AB. An Arabidopsis ATP-dependent, DEAD-box RNA helicase loses activity upon IsoAsp formation but is restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE[J]. Plant Cell, 2013, 25(7):2573-2586.
[21] Huang TS, Wei T, Laliberte JF, Wang A. A host RNA helicase-like protein, AtRH8, interacts with the potyviral genome-linked protein, VPg, associates with the virus accumulation complex, and is essential for infection[J]. Plant Physiol, 2010, 152(1):255-266.
[22] Matthes A, Schmidt-Gattung S, Kohler D, Forner J, Wildum S, Raabe M, Urlaub H, Binder S. Two DEAD-box proteins may be part of RNA-dependent high-molecular-mass protein complexes in Arabidopsis mitochondria[J]. Plant Physiol, 2007, 145(4):1637-1646.
[23] Kim JS, Kim KA, Oh TR, Park CM, Kang H. Functional characterization of DEAD-box RNA helicases in Arabidopsis thaliana under abiotic stress conditions[J]. Plant Cell Physiol, 2008, 49(10):1563-1571.
[24] Kammel C, Thomaier M, Sorensen BB, Schubert T, Langst G, Grasser M, Grasser KD. Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and DNA as well as with mRNA export factors[J]. PLoS One, 2013, 8(3):e60644.
[25] Pan H, Liu S, Tang D. The THO/TREX complex functions in disease resistance in Arabidopsis[J]. Plant Signal Behav, 2012, 7(3):422-424.
[26] Servet C, Benhamed M, Latrasse D, Kim W, Delarue M, Zhou DX. Characterization of a phosphatase 2C protein as an interacting partner of the histone acetyltransferase GCN5 in Arabidopsis[J]. Biochim Biophys Acta, 2008, 1779(6-7):376-382.
[27] Chi W, He B, Mao J, Li Q, Ma J, Ji D, Zou M, Zhang L. The function of RH22, a DEAD RNA helicase, in the biogenesis of the 50S ribosomal subunits of Arabidopsis chloroplasts[J]. Plant Physiol, 2012, 158(2):693-707.
[28] Kanai M, Hayashi M, Kondo M, Nishimura M. The plasti-dic DEAD-box RNA helicase 22, HS3, is essential for plastid functions both in seed development and in seedling growth[J]. Plant Cell Physiol, 2013, 54(9):1431-1440.
[29] Barak S, Singh Yadav N, Khan A. DEAD-box RNA helicases and epigenetic control of abiotic stress-responsive gene expression[J]. Plant Signal Behav, 2014, 9(12):e977729.
[30] Liu M, Shi DQ, Yuan L, Liu J, Yang WC.[STXFX]SLOW WALKER3,[STXFZ] encoding a putative DEAD-box RNA helicase, is essential for female gametogenesis in Arabidopsis[J]. J Integr Plant Biol, 2010, 52(9):817-828.
[31] Huang CK, Huang LF, Huang JJ, Wu SJ, Yeh CH, Lu CA. A DEAD-box protein, AtRH36, is essential for female gametophyte development and is involved in rRNA biogenesis in Arabidopsis[J]. Plant Cell Physiol, 2010, 51(5):694-706.
[32] Huang CK, Yu SM, Lu CA. A rice DEAD-box protein, OsRH36, can complement an Arabidopsis[STXFX]atrh36[STXFZ] mutant, but cannot functionally replace its yeast homolog Dbp8p[J]. Plant Mol Biol, 2010, 74(1-2):119-128.
[33] Gong Z, Dong CH, Lee H, Zhu J, Xiong L, Gong D, Stevenson B, Zhu JK. A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis[J]. Plant Cell, 2005, 17(1):256-267.
[34] Braud C, Zheng W, Xiao W.[STXFX]LONO1[STXFZ] encoding a nucleoporin is required for embryogenesis and seed viability in Arabidopsis[J]. Plant Physiol, 2012, 160(2):823-836.
[35] Nishimura K, Ashida H, Ogawa T, Yokota A. A DEAD box protein is required for formation of a hidden break in Arabidopsis chloroplast 23S rRNA[J]. Plant J, 2010, 63(5):766-777.
[36] Guan Q, Wu J, Zhang Y, Jiang C, Liu R, Chai C, Zhu J. A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis[J]. Plant Cell, 2013, 25(1):342-356.
[37] Stonebloom S, Burch-Smith T, Kim I, Meinke D, Mindrinos M, Zambryski P. Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata[J]. Proc Natl Acad Sci USA, 2009, 106(40):17229-17234.
[38] Burch-Smith TM, Zambryski PC. Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata[J]. Curr Biol, 2010, 20(11):989-993.
[39] Burch-Smith TM, Brunkard JO, Choi YG, Zambryski PC. Organelle-nucleus cross-talk regulates plant intercellular communication via plasmodesmata[J]. Proc Natl Acad Sci USA, 2011, 108(51):E1451-1460.
[40] Kohler D, Schmidt-Gattung S, Binder S. The DEAD-box protein PMH2 is required for efficient groupⅡ[STXFZ] intron splicing in mitochondria of Arabidopsis thaliana[J]. Plant Mol Biol, 2010, 72(4-5):459-467.
[41] Hsu YF, Chen YC, Hsiao YC, Wang BJ, Lin SY, Cheng WH, Jauh GY, Harada JJ, Wang CS. AtRH57, a DEAD-box RNA helicase, is involved in feedback inhibition of glucose-mediated abscisic acid accumulation during seedling development and additively affects pre-ribosomal RNA processing with high glucose[J]. Plant J, 2014, 77(1):119-135.
[42] 黄洁, 李鑫波, 严海龙, 陈丹, 孙蒙祥, 彭雄波. 快速筛选拟南芥受精和早期胚胎发生相关基因的方法[J]. 植物科学学报, 2015, 33(4):564-571. Huang J, Li XB, Yan HL, Chen D, Sun MX, Peng XB. A convenient methed for screening genes related to fertilization and embryogenesis in Arabidopsis[J]. Plant Science Journal, 2015, 33(4):564-571.
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