Translation machinery: the basis of translational control

Shu Yuan; Guilong Zhou; Guoyong Xu

doi:10.1016/j.jgg.2023.07.009

Translation machinery: the basis of translational control

doi: 10.1016/j.jgg.2023.07.009

a State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China;
b Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China

基金项目:

This study was supported by grants from the National Natural Science Foundation of China (32070284), the Major Project of Hubei Hongshan Laboratory (2022hszd016) and the Key Research and Development Program of Hubei Province (2022BFE003) to G. Xu.

详细信息

通讯作者:
Guoyong Xu,E-mail address:guoyong.xu@whu.edu.cn

计量
- 文章访问数: 75
- HTML全文浏览量: 35
- PDF下载量: 14
- 被引次数: 0
出版历程
- 收稿日期: 2023-06-25
- 录用日期: 2023-08-01
- 修回日期: 2023-07-23
- 网络出版日期: 2023-08-15

Translation machinery: the basis of translational control

Shu Yuan^a,
Guilong Zhou^a,
Guoyong Xu^{a,b
, ,}

a State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China;
b Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China

Funds:

摘要

摘要:
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
- Translational control /
- Ribosome /
- tRNA /
- Translation machinery /
- uORF /
- Phase separation /
- Immune response
Abstract:
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
- Translational control /
- Ribosome /
- tRNA /
- Translation machinery /
- uORF /
- Phase separation /
- Immune response

HTML全文

参考文献(171)

Adams, D.R., Ron, D.,Kiely, P.A., 2011. RACK1, A multifaceted scaffolding protein:Structure and function.Cell Commun. Signal. 9, 22.

Albar, L., Bangratz-Reyser, M., Hebrard, E., Ndjiondjop, M.N., Jones, M.,Ghesquiere, A., 2006. Mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus. Plant J. 47, 417-426.

An, H.,Harper, J.W., 2018. Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy. Nat. Cell Biol. 20, 135-143.

Archer, S.K., Shirokikh, N.E., Beilharz, T.H.,Preiss, T., 2016. Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature 535, 570-574.

Bailey-Serres, J.,Ma, W., 2017. Plant biology:An immunity boost combats crop disease. Nature 545, 420-421.

Bastet, A., Lederer, B., Giovinazzo, N., Arnoux, X., German-Retana, S., Reinbold, C., Brault, V., Garcia, D., Djennane, S., Gersch, S., et al., 2018. Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants. Plant Biotechnol. J. 16, 1569-1581

Behrens, A., Rodschinka, G.,Nedialkova, D.D., 2021. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol. Cell 81, 1802-1815.e1807.

Belostotsky, D.A., 2003. Unexpected complexity of poly(A)-binding protein gene families in flowering plants:three conserved lineages that are at least 200 million years old and possible auto- and cross-regulation. Genetics 163, 311-319.

Bieganowski, P., Shilinski, K., Tsichlis, P.N.,Brenner, C., 2004. Cdc123 and checkpoint forkhead associated with RING proteins control the cell cycle by controlling eIF2gamma abundance. J. Biol. Chem. 279, 44656-44666.

Bilgin, D.D., Liu, Y., Schiff, M.,Dinesh-Kumar, S.P., 2003. P58(IPK), a plant ortholog of double-stranded RNA-dependent protein kinase PKR inhibitor, functions in viral pathogenesis. Dev. Cell 4, 651-661.

Bird, J.G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J.K., et al., 2016. The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA. Nature 535, 444-447.

Bohlen, J., Fenzl, K., Kramer, G., Bukau, B.,Teleman, A.A., 2020. Selective 40s footprinting reveals cap-tethered ribosome scanning in human cells. Mol. Cell. 79, 561-574.e5

Brandman, O.,Hegde, R.S., 2016. Ribosome-associated protein quality control. Nat. Struct. Mol. Biol. 23, 7-15.

Browning, K.S., 2004. Plant translation initiation factors:It is not easy to be green. Biochem. Soc. Trans. 32, 589-591.

Browning, K.S.,Bailey-Serres, J., 2015. Mechanism of cytoplasmic mRNA translation. The Arabidopsis book 13, e0176.

Cao, R., Gkogkas, C.G., de Zavalia, N., Blum, I.D., Yanagiya, A., Tsukumo, Y., Xu, H., Lee, C., Storch, K.F., Liu, A.C., et al., 2015. Light-regulated translational control of circadian behavior by eIF4E phosphorylation. Nat. Neurosci. 18, 855-862.

Carroll, A.J., 2013. The arabidopsis cytosolic ribosomal proteome:From form to function. Front. Plant Sci. 4, 32.

Cencic, R., Desforges, M., Hall, D.R., Kozakov, D., Du, Y.H., Min, J., Dingledine, R., Fu, H.A., Vajda, S., Talbot, P.J., et al., 2011a. Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication. J. Virol. 85, 6381-6389.

Cencic, R., Hall, D.R., Robert, F., Du, Y.H., Min, J., Li, L., Qui, M., Lewis, I., Kurtkaya, S., Dingledine, R., et al., 2011b. Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. P. Natl. Acad. Sci. U.S.A. 108, 6689-6689.

Chandrasekaran, J., Brumin, M., Wolf, D., Leibman, D., Klap, C., Pearlsman, M., Sherman, A., Arazi, T.,Gal-On, A., 2016. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol. Plant Pathol. 17, 1140-1153.

Chen, J.-G., 2015. Phosphorylation of RACK1 in plants. Plant Signal. Behav. 10, e1022013.

Chen, T., Xu, G., Mou, R., Greene, G.H., Liu, L., Motley, J.,Dong, X., 2023. Global translational induction during NLR-mediated immunity in plants is dynamically regulated by CDC123, an ATP-sensitive protein. Cell Host Microbe 31, 334-342.e335.

Cheng, Z.Y., Li, J.F., Niu, Y.J., Zhang, X.C., Woody, O.Z., Xiong, Y., Djonovic, S., Millet, Y., Bush, J., McConkey, B.J., et al., 2015. Pathogen-secreted proteases activate a novel plant immune pathway. Nature 521, 213-216.

Choe, J., Lin, S., Zhang, W., Liu, Q., Wang, L., Ramirez-Moya, J., Du, P., Kim, W., Tang, S., Sliz, P., et al., 2018. mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis.Nature 561, 556-560.

Collart, M.A.,Weiss, B., 2019. Ribosome pausing, a dangerous necessity for co-translational events.Nucleic Acids Res. 48, 1043-1055.

Crum, C.J., Hu, J., Hiddinga, H.J.,Roth, D.A., 1988. Tobacco mosaic virus infection stimulates the phosphorylation of a plant protein associated with double-stranded RNA-dependent protein kinase activity. J. Biol. Chem. 263, 13440-13443.

Cullen, B.R., 2009. Viral RNAs:Lessons from the enemy. Cell 136, 592-597.

Decker, C.J.,Parker, R., 2012. P-bodies and stress granules:Possible roles in the control of translation and mRNA degradation. Cold Spring Harb. Perspect. Biol. 4, a012286.

Derry, M.C., Yanagiya, A., Martineau, Y.,Sonenberg, N., 2006. Regulation of poly(A)-binding protein through PABP-interacting proteins. Cold Spring Harb. Sym. 71, 537-543.

Dinkova, T.D., Zepeda, H., Martinez-Salas, E., Martinez, L.M., Nieto-Sotelo, J.,de Jimenez, E.S., 2005. Cap-independent translation of maize Hsp101. Plant J. 41, 722-731.

Dorokhov, Y.L., Skulachev, M.V., Ivanov, P.A., Zvereva, S.D., Tjulkina, L.G., Merits, A., Gleba, Y.Y., Hohn, T.,Atabekov, J.G., 2002. Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. P. Natl. Acad. Sci. U.S.A. 99, 5301-5306.

Dresios, J., Chappell, S.A., Zhou, W.,Mauro, V.P., 2006. An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 13, 30-34.

Duan, H.-C., Wei, L.-H., Zhang, C., Wang, Y., Chen, L., Lu, Z., Chen, P.R., He, C.,Jia, G., 2017. Alkbh10b is an RNA N6-methyladenosine demethylase affecting arabidopsis floral transition. The Plant cell 29, 2995-3011.

Dufresne, P.J., Ubalijoro, E., Fortin, M.G.,Laliberte, J.F., 2008. Arabidopsis thaliana class II poly(A)-binding proteins are required for efficient multiplication of turnip mosaic virus. J. Gen. Virol. 89, 2339-2348.

Eliseeva, I.A., Lyabin, D.N.,Ovchinnikov, L.P., 2013. Poly(A)-binding proteins:Structure, domain organization, and activity regulation. Biochemistry (Moscow) 78, 1377-1391.

Farache, D., Antine, S.P.,Lee, A.S.Y., 2022. Moonlighting translation factors:Multifunctionality drives diverse gene regulation. Trends Cell Biol. 32, 762-772

Fawaz, M.V., Topper, M.E.,Firestine, S.M., 2011. The ATP-grasp enzymes. Bioorg. Chem. 39, 185-191.

Gallie, D.R., 2014. The role of the poly(A) binding protein in the assembly of the cap-binding complex during translation initiation in plants. Translation (Austin) 2, e959378.

Genuth, N.R.,Barna, M., 2018. The discovery of ribosome heterogeneity and its implications for gene regulation and organismal life. Mol. Cell 71, 364-374.

Gerashchenko, M.V.,Gladyshev, V.N., 2017. Ribonuclease selection for ribosome profiling. Nucleic Acids Res. 45, e6.

Gerbasi, V.R., Weaver, C.M., Hill, S., Friedman, D.B.,Link, A.J., 2004. Yeast Asc1p and mammalian RACK1are functionally orthologous core 40s ribosomal proteins that repress gene expression. Mol.Cell Biol. 24, 8276-8287.

Gilbert, W.V., Zhou, K.H., Butler, T.K.,Doudna, J.A., 2007. Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317, 1224-1227.

Goss, D.J.,Kleiman, F.E., 2013. Poly(A) binding proteins:Are they all created equal? Wiley Interdiscip.Rev. RNA. 4, 167-179.

Gu, H., Lian, B., Yuan, Y., Kong, C., Li, Y., Liu, C.,Qi, Y., 2022. A 5' tRNA-Ala-derived small RNA regulates anti-fungal defense in plants. Sci. China Life Sci. 65, 1-15.

Guo, H., 2018. Specialized ribosomes and the control of translation. Biochem. Soc. Trans. 46, 855-869.

Hellen, C.U.T., 2018. Translation termination and ribosome recycling in eukaryotes. Cold Spring Harb.Perspect. Biol. 10 a032656.

Hernandez-Alias, X., Katanski, C.D., Zhang, W., Assari, M., Watkins, Christopher P., Schaefer, Martin H., Serrano, L.,Pan, T., 2022. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res. 51, e17-e17.

Hiddinga, H.J., Crum, C.J., Hu, J.,Roth, D.A., 1988. Viroid-induced phosphorylation of a host protein related to a dsRNA-dependent protein-kinase. Science 241, 451-453.

Hu, W., Zeng, H., Shi, Y., Zhou, C., Huang, J., Jia, L., Xu, S., Feng, X., Zeng, Y., Xiong, T., et al., 2022. Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation. Nat. Commun. 13, 5114.

Immanuel, T.M., Greenwood, D.R.,MacDiarmid, R.M., 2012. A critical review of translation initiation factor eIF2α kinases in plants-regulating protein synthesis during stress. Funct. Plant Biol. 39, 717-735.

Ingolia, N.T., Ghaemmaghami, S., Newman, J.R.S.,Weissman, J.S., 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223.

Iwakawa, H.O., Tajima, Y., Taniguchi, T., Kaido, M., Mise, K., Tomari, Y., Taniguchi, H.,Okunoa, T., 2012.Poly(A)-binding protein facilitates translation of an uncapped/nonpolyadenylated viral RNA by binding to the 3' untranslated region. J. Virol. 86, 7836-7849.

Jackson, R.J., Hellen, C.U.,Pestova, T.V., 2010. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113-127.

Jiang, J.,Laliberte, J.F., 2011. The genome-linked protein VPg of plant viruses-a protein with many partners. Curr. Opin. Virol. 1, 347-354.

Jiao, X., Doamekpor, S.K., Bird, J.G., Nickels, B.E., Tong, L., Hart, R.P.,Kiledjian, M., 2017. 5' end nicotinamide adenine dinucleotide cap in human cells promotes RNA decay through dxo-mediated denadding. Cell 168, 1015-1027 e1010.

Kang, B.C., Yeam, I.,Jahn, M.M., 2005. Genetics of plant virus resistance. Annu. Rev. Phytopathol. 43, 581-621.

Kang, B.C., Yeam, I., Li, H., Perez, K.W.,Jahn, M.M., 2007. Ectopic expression of a recessive resistance gene generates dominant potyvirus resistance in plants. Plant Biotechnol. J. 5, 526-536.

Kariko, K., Buckstein, M., Ni, H.,Weissman, D., 2005. Suppression of RNA recognition by toll-like receptors:The impact of nucleoside modification and the evolutionary origin of RNA. Immunity 23, 165-175.

Kawahara, H., Imai, T., Imataka, H., Tsujimoto, M., Matsumoto, K.,Okano, H., 2008. Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP. J. Cell Biol. 181, 639-653.

Kazibwe, Z., Liu, A.-Y., MacIntosh, G.C.,Bassham, D.C., 2019. The ins and outs of autophagic ribosome turnover. Cells 8, 1603.

Khan, M.A., Yumak, H.,Goss, D.J., 2009. Kinetic mechanism for the binding of eIF4F and tobacco etch virus internal ribosome entry site RNA:Effects of eIF4B and poly(A)-binding protein. J. Biol.Chem. 284, 35461-35470.

Kim, J., Kang, W.H., Hwang, J., Yang, H.B., Dosun, K., Oh, C.S.,Kang, B.C., 2014. Transgenic brassica rapa plants over-expressing eIF(iso)4E variants show broad-spectrum turnip mosaic virus (tumv)resistance. Mol. Plant Pathol. 15, 615-626.

Kneller, E.L.P., Rakotondrafara, A.M.,Miller, W.A., 2006. Cap-independent translation of plant viral RNAs.Virus Res. 119, 63-75.

Komar, A.A.,Hatzoglou, M., 2011. Cellular IRES-mediated translation:The war of ITAFs in pathophysiological states. Cell Cycle 10, 229-240.

Koster, T.,Meyer, K., 2018. Plant ribonomics:Proteins in rearch of RNA partners. Trends in plant science.

Kumar, P., Kuscu, C.,Dutta, A., 2016. Biogenesis and function of transfer RNA-related fragments (tRFs).Trends Biochem. Sci. 41, 679-689.

Lageix, S., Lanet, E., Pouch-Pelissier, M.N., Espagnol, M.C., Robaglia, C., Deragon, J.M.,Pelissier, T., 2008.Arabidopsis eIF2 alpha kinase GCN2 is essential for growth in stress conditions and is activated by wounding. BMC Plant Biol. 8.

Lapointe, C.P., Wilinski, D., Saunders, H.A.J.,Wickens, M., 2015. Protein-RNA networks revealed through covalent RNA marks. Nat. Methods 12, 1163-70

Le, H., Browning, K.S.,Gallie, D.R., 2000. The phosphorylation state of poly(A)-binding protein specifies its binding to poly(A) RNA and its interaction with eukaryotic initiation factor (eIF) 4F, eIFiso4F, and eIF4B. J. Biol. Chem. 275, 17452-17462.

Lee, J.H., Muhsin, M., Atienza, G.A., Kwak, D.Y., Kim, S.M., De Leon, T.B., Angeles, E.R., Coloquio, E., Kondoh, H., Satoh, K., et al., 2010. Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to rice tungro spherical virus. Cell Commun. Signal. 23, 29-38.

Leonard, S., Viel, C., Beauchemin, C., Daigneault, N., Fortin, M.G.,Laliberte, J.F., 2004. Interaction of VPg-Pro of turnip mosaic virus with the translation initiation factor 4E and the poly(A)-binding protein in planta. J. Gen. Virol. 85, 1055-1063.

Li, G.-B., He, J.-X., Wu, J.-L., Wang, H., Zhang, X., Liu, J., Hu, X.-H., Zhu, Y., Shen, S., Bai, Y.-F., et al., 2022.Overproduction of OsRACK1A, an effector-targeted scaffold protein promoting OsRBOHB-mediated ros production, confers rice floral resistance to false smut disease without yield penalty. Mol. Plant 15, 1790-1806.

Li, J.J.,Xie, D., 2015. RACK1, a versatile hub in cancer. Oncogene 34, 1890-1898.

Li, W.Y., Ma, M.D., Feng, Y., Li, H.J., Wang, Y.C., Ma, Y.T., Li, M.Z., An, F.Y.,Guo, H.W., 2015. EIN2-directed translational regulation of ethylene signaling in Arabidopsis. Cell 163, 670-683.

Li, Y., Wang, X., Li, C., Hu, S., Yu, J.,Song, S., 2014. Transcriptome-wide N6-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification. RNA Biol. 11, 1180-1188.

Lin, C.Y.,Miles, W.O., 2019. Beyond clip:Advances and opportunities to measure RBP-RNA and RNA-RNA interactions. Nucleic Acids Res. 47, 5490-5501.

Lin, Y.,Fang, X., 2021. Phase separation in RNA biology. J. Genet. Genomics. 48, 872-880.

Lin, Y., Li, F., Huang, L., Polte, C., Duan, H., Fang, J., Sun, L., Xing, X., Tian, G., Cheng, Y., et al., 2020. eIF3associates with 80s ribosomes to promote translation elongation, mitochondrial homeostasis, and muscle health. Mol. Cell. 79, 575-587.e7.

Liu, X., Afrin, T.,Pajerowska-Mukhtar, K.M., 2019. Arabidopsis GCN2 kinase contributes to ABA homeostasis and stomatal immunity. Commun. Biol. 2, 302.

Lokdarshi, A., Guan, J., Urquidi Camacho, R.A., Cho, S.K., Morgan, P.W., Leonard, M., Shimono, M., Day, B.,von Arnim, A.G., 2020a. Light activates the translational regulatory kinase GCN2 via reactive oxygen species emanating from the chloroplast. The Plant cell 32, 1161-1178.

Lokdarshi, A., Morgan, P.W., Franks, M., Emert, Z., Emanuel, C.,von Arnim, A.G., 2020b. Light-dependent activation of the GCN2 kinase under cold and salt stress is mediated by the photosynthetic status of the chloroplast. Front. Plant Sci. 11, 431.

Long, Y.-P., Xie, D.-J., Zhao, Y.-Y., Shi, D.-Q.,Yang, W.-C., 2019. BICELLULAR POLLEN 1 is a modulator of DNA replication and pollen development in Arabidopsis. New Phytol. 222, 588-603.

Lopez, M.D.,Samuelsson, T., 2008. Early evolution of histone mRNA 3' end processing. RNA 14, 1-10.

Lucas, M.C., Pryszcz, L.P., Medina, R., Milenkovic, I., Camacho, N., Marchand, V., Motorin, Y., Ribas de Pouplana, L.,Novoa, E.M., 2023. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol. doi: 10.1038/s41587-023-01743-6.

Luna, E., van Hulten, M., Zhang, Y.H., Berkowitz, O., Lopez, A., Petriacq, P., Sellwood, M.A., Chen, B.N., Burrell, M., van de Meene, A., et al., 2014. Plant perception of beta-aminobutyric acid is mediated by an aspartyl-tRNA synthetase. Nat. Chem. Biol. 10, 450-456.

Luo, G.Z., MacQueen, A., Zheng, G., Duan, H., Dore, L.C., Lu, Z., Liu, J., Chen, K., Jia, G., Bergelson, J., et al., 2014. Unique features of the m6A methylome in Arabidopsis thaliana. Nat. commun. 5, 5630.

Lyabin, D.N., Eliseeva, I.A.,Ovchinnikov, L.P., 2014. YB-1 protein:functions and regulation. Wires RNA 5, 95-110.

Ma, X., Liu, C.,Cao, X., 2021. Plant transfer RNA-derived fragments:Biogenesis and functions. J. Integr.Plant Biol. 63, 1399-1409.

Macovei, A., Sevilla, N.R., Cantos, C., Jonson, G.B., Slamet-Loedin, I., Cermak, T., Voytas, D.F., Choi, I.R.,Chadha-Mohanty, P., 2018. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnol. J. 16, 1918-1927.

Mandadi, K.K.,Scholthof, K.B.G., 2013. Plant immune responses against viruses:How does a virus cause disease? The Plant cell 25, 1489-1505.

Mauer, J., Luo, X., Blanjoie, A., Jiao, X., Grozhik, A.V., Patil, D.P., Linder, B., Pickering, B.F., Vasseur, J.J., Chen, Q., et al., 2017. Reversible methylation of m6Am in the 5' cap controls mRNA stability.Nature 541, 371-375.

Merchante, C., Brumos, J., Yun, J., Hu, Q.W., Spencer, K.R., Enriquez, P., Binder, B.M., Heber, S., Stepanova, A.N.,Alonso, J.M., 2015. Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2. Cell 163, 684-697.

Meyer, K.D., Patil, D.P., Zhou, J., Zinoviev, A., Skabkin, M.A., Elemento, O., Pestova, T.V., Qian, S.B.,Jaffrey, S.R., 2015. 5' UTR m(6)A promotes cap-independent translation. Cell 163, 999-1010.

Miller, W.A., Wang, Z.,Treder, K., 2007. The amazing diversity of cap-independent translation elements in the 3'-untranslated regions of plant viral RNAs. Biochem. Soc. Trans. 35, 1629-1633.

Mitchell, S.A., Spriggs, K.A., Bushell, M., Evans, J.R., Stoneley, M., Le Quesne, J.P.C., Spriggs, R.V.,Willis, A.E., 2005. Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Gene Dev. 19, 1556-1571.

Mitchell, S.F.,Parker, R., 2015. Modifications on translation initiation. Cell 163, 796-798.

Mohr, I.,Sonenberg, N., 2012. Host translation at the nexus of infection and immunity. Cell Host Microbe 12, 470-483.

Nakashima, A., Chen, L.T., Thao, N.P., Fujiwara, M., Wong, H.L., Kuwano, M., Umemura, K., Shirasu, K., Kawasaki, T.,Shimamoto, K., 2008. RACK1 functions in rice innate immunity by interacting with the RAC1 immune complex. The Plant cell 20, 2265-2279.

Natchiar, S.K., Myasnikov, A.G., Kratzat, H., Hazemann, I.,Klaholz, B.P., 2017. Visualization of chemical modifications in the human 80s ribosome structure. Nature 551, 472-477.

Nicaise, V., 2014. Crop immunity against viruses:Outcomes and future challenges. Front. Plant Sci. 5, 660.

Niu, R., Zhou, Y., Zhang, Y., Mou, R., Tang, Z., Wang, Z., Zhou, G., Guo, S., Yuan, M.,Xu, G., 2020. uORFlight:A vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes. Database 2020.

Ozadam, H., Tonn, T., Han, C.M., Segura, A., Hoskins, I., Rao, S., Ghatpande, V., Tran, D., Catoe, D., Salit, M., et al., 2023. Single-cell quantification of ribosome occupancy in early mouse development.Nature 618, 1057-1064.

Pakos-Zebrucka, K., Koryga, I., Mnich, K., Ljujic, M., Samali, A.,Gorman, A.M., 2016. The integrated stress response. EMBO Rep. 17, 1374-1395.

Panvert, M., Dubiez, E., Arnold, L., Perez, J., Mechulam, Y., Seufert, W.,Schmitt, E., 2015. Cdc123, a cell cycle regulator needed for eIF2 assembly, is an ATP-Grasp protein with unique features.Structure 23, 1596-1608.

Patel, G.P., Ma, S.,Bag, J., 2005. The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex. Nucleic Acids Res. 33, 7074-7089.

Patrick, R.M.,Browning, K.S., 2012. The eIF4F and eIFiso4F complexes of plants:An evolutionary perspective. Comp. Funct. Genom. 2012, 287814.

Perzlmaier, A.F., Richter, F.,Seufert, W., 2013. Translation initiation requires cell division cycle 123(CDC123) to facilitate biogenesis of the eukaryotic initiation factor 2 (eIF2). J. Biol. Chem. 288, 21537-21546.

Prall, W., Ganguly, D.R.,Gregory, B.D., 2023. The covalent nucleotide modifications within plant mRNAs:What we know, how we find them, and what should be done in the future. The Plant cell, koad044.

Proud, C.G., 2018. Phosphorylation and signal transduction pathways in translational control. Cold Spring Harb. Perspect. Biol. 11, a033050.

Pyott, D.E., Sheehan, E.,Molnar, A., 2016. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free arabidopsis plants. Mol. Plant Pathol. 17, 1276-1288.

Ramanathan, M., Porter, D.F.,Khavari, P.A., 2019. Methods to study RNA-protein interactions. Nat.Methods 16, 225-234.

Ren, B., Wang, X., Duan, J.,Ma, J., 2019. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation. Science 365, 919-922.

Rhine, K., Vidaurre, V.,Myong, S., 2020. RNA droplets. Annu. Rev. Biophys. 49, 247-265.

Roobol, A., Roobol, J., Bastide, A., Knight, J.R.P., Willis, A.E.,Smales, C.M., 2015. P58(IPK) is an inhibitor of the eIF2 alpha kinase GCN2 and its localization and expression underpin protein synthesis and ER processing capacity. Biochem. J. 465, 213-225.

Schleich, S., Strassburger, K., Janiesch, P.C., Koledachkina, T., Miller, K.K., Haneke, K., Cheng, Y.S., Kuchler, K., Stoecklin, G., Duncan, K.E., et al., 2014. DENR-MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth. Nature 512, 208-212.

Schmitt, K., Smolinski, N., Neumann, P., Schmaul, S., Hofer-Pretz, V., Braus, G.H.,Valerius, O., 2017.Asc1p/RACK1 connects ribosomes to eukaryotic phosphosignaling. Mol. Cell Biol. 37, e00279-00216.

Schuller, A.P., Wu, C.C.-C., Dever, T.E., Buskirk, A.R.,Green, R., 2017. eIF5A functions globally in translation elongation and termination. Mol. Cell 66, 194-205.e195.

She, R., Luo, J.,Weissman, J.S., 2023. Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity. Nucleic Acids Res. 51, 6355-6369.

Shor, B., Calaycay, J., Rushbrook, J.,McLeod, M., 2003. Cpc2/RACK1 is a ribosome-associated protein that promotes efficient translation in Schizosaccharomyces pombe. J. Biol. Chem. 278, 49119-49128.

Shore, D.,Albert, B., 2022. Ribosome biogenesis and the cellular energy economy. Curr. Biol. 32, R611-R617.

Simsek, D.,Barna, M., 2017. An emerging role for the ribosome as a nexus for post-translational modifications. Curr. Opin. Cell Biol. 45, 92-101.

Simsek, D., Tiu, G.C., Flynn, R.A., Byeon, G.W., Leppek, K., Xu, A.F., Chang, H.Y.,Barna, M., 2017. The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity. Cell 169, 1051-1065.e1018.

Skabkin, M.A., Skabkina, O.V., Dhote, V., Komar, A.A., Hellen, C.U.,Pestova, T.V., 2010. Activities of ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. Gene Dev. 24, 1787-1801.

Smorag, L., Xu, X.B., Engel, W.,Pantakani, D.V.K., 2014. The roles of DAZL in RNA biology and development. Wires RNA 5, 527-535.

Sonenberg, N.,Hinnebusch, A.G., 2009. Regulation of translation initiation in eukaryotes:Mechanisms and biological targets. Cell 136, 731-745.

Speth, C., Willing, E.M., Rausch, S., Schneeberger, K.,Laubinger, S., 2013. RACK1 scaffold proteins influence miRNA abundance in Arabidopsis. Plant J. 76, 433-445.

Srivastava, T., Fortin, D.A., Nygaard, S., Kaech, S., Sonenberg, N., Edelman, A.M.,Soderling, T.R., 2012.Regulation of neuronal mRNA translation by CaM-kinase I phosphorylation of eIF4GII. J.Neurosci. 32, 5620-5630.

Stern-Ginossar, N., Thompson, S.R., Mathews, M.B.,Mohr, I., 2018. Translational control in virus-infected cells. Cold Spring Harb. Perspect. Biol. 11, a033001.

Suzuki, T., 2021. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol.Cell Biol. 22, 375-392.

Tahmasebi, S., Khoutorsky, A., Mathews, M.B.,Sonenberg, N., 2018. Translation deregulation in human disease. Nat. Rev. Mol. Cell Biol. 19, 791-807.

Urano, D., Czarnecki, O., Wang, X., Jones, A.M.,Chen, J.-G., 2015. Arabidopsis receptor of activated C kinase1 phosphorylation by WITH NO LYSINE8 KINASE. Plant Physiol. 167, 507-516.

Van Nostrand, E.L., Freese, P., Pratt, G.A., Wang, X., Wei, X., Xiao, R., Blue, S.M., Chen, J.-Y., Cody, N.A.L., Dominguez, D., et al., 2020. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711-719.

Vanderhaeghen, R., De Clercq, R., Karimi, M., Van Montagu, M., Hilson, P.,Van Lijsebettens, M., 2006.Leader sequence of a plant ribosomal protein gene with complementarity to the 18s rRNA triggers in vitro cap-independent translation. FEBS letters 580, 2630-2636.

VanInsberghe, M., van den Berg, J., Andersson-Rolf, A., Clevers, H.,van Oudenaarden, A., 2021. Single-cell ribo-seq reveals cell cycle-dependent translational pausing. Nature 597, 561-565.

Wagner, S., Herrmannová, A., Hronová, V., Gunišová, S., Sen, N.D., Hannan, R.D., Hinnebusch, A.G., Shirokikh, N.E., Preiss, T.,Valášek, L.S., 2020. Selective translation complex profiling reveals staged initiation and co-translational assembly of initiation factor complexes. Mol. Cell. 79, 546-560.e7.

Walsh, D., Mathews, M.B.,Mohr, I., 2013. Tinkering with translation:Protein synthesis in virus-infected cells. Cold Spring Harb. Perspect. Biol. 5, a012351.

Walsh, D.,Mohr, I., 2011. Viral subversion of the host protein synthesis machinery. Nat. Rev. Microbiol. 9, 860-875.

Walters, R.W., Matheny, T., Mizoue, L.S., Rao, B.S., Muhlrad, D.,Parker, R., 2017. Identification of NAD+capped mRNAs in Saccharomyces cerevisiae. P. Natl. Acad. Sci. U.S.A. 114, 480-485.

Wang, A.,Krishnaswamy, S., 2012. Eukaryotic translation initiation factor 4E-mediated recessive resistance to plant viruses and its utility in crop improvement. Mol. Plant Pathol. 13, 795-803.

Wang, B.S., Yu, J.J., Zhu, D.Y., Chang, Y.J.,Zhao, Q., 2014a. Maize ZmRACK1 is involved in the plant response to fungal phytopathogens. Int. J. Mol. Sci. 15, 9343-9359.

Wang, H., Niu, R., Zhou, Y., Tang, Z., Xu, G.,Zhou, G., 2023. ECT9 condensates with ECT1 and regulates plant immunity. Front. Plant Sci. 14.

Wang, J., Zhang, X., Greene, G.H., Xu, G.,Dong, X., 2022. PABP/purine-rich motif as an initiation module for cap-independent translation in pattern-triggered immunity. Cell 185, 3186-3200.e3117.

Wang, X., Lu, Z., Gomez, A., Hon, G.C., Yue, Y., Han, D., Fu, Y., Parisien, M., Dai, Q., Jia, G., et al., 2014b.N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117-120.

Wang, X., Zhao, B.S., Roundtree, I.A., Lu, Z., Han, D., Ma, H., Weng, X., Chen, K., Shi, H.,He, C., 2015.N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388-1399.

Wang, Y., Li, S., Zhao, Y., You, C., Le, B., Gong, Z., Mo, B., Xia, Y.,Chen, X., 2019. NAD+-capped RNAs are widespread in the arabidopsis transcriptome and can probably be translated. P. Natl. Acad. Sci.U.S.A., 201903682.

Wei, L.-H., Song, P., Wang, Y., Lu, Z., Tang, Q., Yu, Q., Xiao, Y., Zhang, X., Duan, H.-C.,Jia, G., 2018. The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in arabidopsis. The Plant cell 30, 968-985.

Wek, R.C., 2018. Role of eIF2alpha kinases in translational control and adaptation to cellular stress. Cold Spring Harb. Perspect. Biol. 10.

Wyant, G.A., Abu-Remaileh, M., Frenkel, E.M., Laqtom, N.N., Dharamdasani, V., Lewis, C.A., Chan, S.H., Heinze, I., Ori, A.,Sabatini, D.M., 2018. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science 360, 751-758.

Xiong, Z., Xu, K., Lin, Z., Kong, F., Wang, Q., Quan, Y., Sha, Q.-q., Li, F., Zou, Z., Liu, L., et al., 2022.Ultrasensitive ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat. Cell Biol. 24, 968-980.

Xu, G., Greene, G.H., Yoo, H., Liu, L., Marques, J., Motley, J.,Dong, X., 2017a. Global translational reprogramming is a fundamental layer of immune regulation in plants. Nature 545, 487-490.

Xu, G., Yuan, M., Ai, C., Liu, L., Zhuang, E., Karapetyan, S., Wang, S.,Dong, X., 2017b. uORF-mediated translation allows engineered plant disease resistance without fitness costs. Nature 545, 491-494.

Xu, W., Biswas, J., Singer, R.H.,Rosbash, M., 2021. Targeted RNA editing:Novel tools to study post-transcriptional regulation. Mol. Cell. 82, 389-403

Yin, S., Chen, Y., Chen, Y., Xiong, L.,Xie, K., 2023. Genome-wide profiling of rice double-stranded RNA-binding protein 1-associated RNAs by targeted RNA editing. Plant Physiol. 192, 805-820.

Yoshii, M., Nishikiori, M., Tomita, K., Yoshioka, N., Kozuka, R., Naito, S.,Ishikawa, M., 2004. The arabidopsis cucumovirus multiplication 1 and 2 loci encode tip translation initiation factors 4E and 4G. J. Virol. 78, 6102-6111.

Youn, J.Y., Dyakov, B.J.A., Zhang, J., Knight, J.D.R., Vernon, R.M., Forman-Kay, J.D.,Gingras, A.C., 2019.Properties of stress granule and P-body proteomes. Mol. Cell 76, 286-294.

Yue, Y., Liu, J.,He, C., 2015. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 29, 1343-1355.

Zavaliev, R., Mohan, R., Chen, T.,Dong, X., 2020. Formation of NPR1 condensates promotes cell survival during the plant immune response. Cell 182, 1093-1108 e1018.

Zeng, H., Huang, J., Ren, J., Wang, C.K., Tang, Z., Zhou, H., Zhou, Y., Shi, H., Aditham, A., Sui, X., et al., 2023. Spatially resolved single-cell translatomics at molecular resolution. Science 380, eadd3067.

Zhang, H., Zhong, H., Zhang, S., Shao, X., Ni, M., Cai, Z., Chen, X.,Xia, Y., 2019. NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in arabidopsis. P. Natl. Acad. Sci. U.S.A., 201903683.

Zhang, Y., Wang, Y., Kanyuka, K., Parry, M.A.J., Powers, S.J.,Halford, N.G., 2008. GCN2-dependent phosphorylation of eukaryotic translation initiation factor-2α in Arabidopsis. J. Exp. Bot. 59, 3131-3141.

Zhao, T., Chen, Y.-M., Li, Y., Wang, J., Chen, S., Gao, N.,Qian, W., 2021. Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. Genome Biol. 22, 16.

Zhao, T., Huan, Q., Sun, J., Liu, C., Hou, X., Yu, X., Silverman, I.M., Zhang, Y., Gregory, B.D., Liu, C.-M., et al., 2019. Impact of poly(A)-tail g-content on arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biol. 20, 189.

Zhao, Y., Zhu, X.B., Chen, X.W.,Zhou, J.M., 2022. From plant immunity to crop disease resistance. J. Genet.Genomics. 49, 693-703.

Zheng, G., Qin, Y., Clark, W.C., Dai, Q., Yi, C., He, C., Lambowitz, A.M.,Pan, T., 2015. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835-837.

Zhigailov, A.V., Alexandrova, A.M., Nizkorodova, A.S., Stanbekova, G.E., Kryldakov, R.V., Karpova, O.V., Polimbetova, N.S., Halford, N.G.,Iskakov, B.K., 2020. Evidence that phosphorylation of the α-subunit of eIF2 does not essentially inhibit mRNA translation in wheat germ cell-free system.Front. Plant Sci. 11.

Zhong, S., Li, H., Bodi, Z., Button, J., Vespa, L., Herzog, M.,Fray, R.G., 2008. MTA is an arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. The Plant Cell 20, 1278-1288.

Zhou, G., Niu, R., Zhou, Y., Luo, M., Peng, Y., Wang, H., Wang, Z.,Xu, G., 2021. Proximity editing to identify RNAs in phase-separated RNA binding protein condensates. Cell Discov. 7, 72.

Zhou, J., Wan, J., Gao, X.W., Zhang, X.Q., Jaffrey, S.R.,Qian, S.B., 2015. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature 526, 591-U332.

Zhou, Y., Niu, R., Tang, Z., Mou, R., Wang, Z., Zhu, S., Yang, H., Ding, P.,Xu, G., 2023. Plant HEM1 specifies a condensation domain to control immune gene translation. Nat. Plants 9, 289-301.

Zhu, S., Estévez, J.M., Liao, H., Zhu, Y., Yang, T., Li, C., Wang, Y., Li, L., Liu, X., Pacheco, J.M., et al., 2020.The RALF1-FERONIA complex phosphorylates eIF4E1 to promote protein synthesis and polar root hair growth. Mol. Plant 13, 698-716.

Zlobin, N.,Taranov, V., 2023. Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses. Front. Plant Sci. 14.

施引文献

资源附件(0)

访问统计