Al‐Hadid,, Q., Roy,, K., Chanfreau,, G., & Clarke,, S. G. (2016). Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity. RNA, 22(4), 489–498. https://doi.org/10.1261/rna.054569.115
Aravindan,, R. G., Kirn‐Safran,, C. B., Smith,, M. A., & Martin‐DeLeon,, P. A. (2014). Ultrastructural changes and asthenozoospermia in murine spermatozoa lacking the ribosomal protein L29/HIP gene. Asian Journal of Andrology, 16(6), 925–926. https://doi.org/10.4103/1008-682X.133318
Babaian,, A., Rothe,, K., Girodat,, D., Minia,, I., Djondovic,, S., Milek,, M., Spencer Miko,, S. E., Wieden,, H. J., Landthaler,, M., Morin,, G. B., & Mager,, D. L. (2020). Loss of m1acp3Ψ ribosomal RNA modification is a major feature of cancer. Cell Reports, 31(5), 107611. https://doi.org/10.1016/j.celrep.2020.107611
Bailey‐Serres,, J., & Freeling,, M. (1990). Hypoxic stress‐induced changes in ribosomes of maize seedling roots. Plant Physiology, 94(3), 1237–1243. https://doi.org/10.1104/pp.94.3.1237
Bailey‐Serres,, J., Vangala,, S., Szick,, K., & Lee,, C. H. (1997). Acidic phosphoprotein complex of the 60S ribosomal subunit of maize seedling roots. Components and changes in response to flooding. Plant Physiology, 114(4), 1293–1305. https://doi.org/10.1104/pp.114.4.1293
Bansal,, S. K., Gupta,, N., Sankhwar,, S. N., & Rajender,, S. (2015). Differential genes expression between fertile and infertile spermatozoa revealed by Transcriptome analysis. PLoS One, 10(5), e0127007. https://doi.org/10.1371/journal.pone.0127007
Barakat,, A., Szick‐Miranda,, K., Chang,, I. F., Guyot,, R., Blanc,, G., Cooke,, R., Delseny,, M., & Bailey‐Serres,, J. (2001). The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiology, 127(2), 398–415.
Berleth,, T., Krogan,, N. T., & Scarpella,, E. (2004). Auxin signals—Turning genes on and turning cells around. Current Opinion in Plant Biology, 7(5), 553–563. https://doi.org/10.1016/j.pbi.2004.07.016
Biever,, A., Glock,, C., Tushev,, G., Ciirdaeva,, E., Dalmay,, T., Langer,, J. D., & Schuman,, E. M. (2020). Monosomes actively translate synaptic mRNAs in neuronal processes. Science, 367(6477), eaay4991. https://doi.org/10.1126/science.aay4991
Blanc,, G., & Wolfe,, K. H. (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell, 16(7), 1679–1691. https://doi.org/10.1105/tpc.021410
Bouffard,, S., Dambroise,, E., Brombin,, A., Lempereur,, S., Hatin,, I., Simion,, M., Corre,, R., Bourrat,, F., Joly,, J. S., & Jamen,, F. (2018). Fibrillarin is essential for S‐phase progression and neuronal differentiation in zebrafish dorsal midbrain and retina. Developmental Biology, 437(1), 1–16. https://doi.org/10.1016/j.ydbio.2018.02.006
Boyer,, N. P., & Gupton,, S. L. (2018). Revisiting netrin‐1: One who guides (axons). Frontiers in Cellular Neuroscience, 12, 221. https://doi.org/10.3389/fncel.2018.00221
Bridges,, C. B., & Morgan,, T. H. (1923). Third‐chromosome group of mutant characters of Drosophila melanogaster. Carnegie Institution of Washington.
Briese,, M., Saal,, L., Appenzeller,, S., Moradi,, M., Baluapuri,, A., & Sendtner,, M. (2016). Whole transcriptome profiling reveals the RNA content of motor axons. Nucleic Acids Research, 44(4), e33. https://doi.org/10.1093/nar/gkv1027
Brooks,, S. S., Wall,, A. L., Golzio,, C., Reid,, D. W., Kondyles,, A., Willer,, J. R., Botti,, C., Nicchitta,, C. V., Katsanis,, N., & Davis,, E. E. (2014). A novel ribosomopathy caused by dysfunction of RPL10 disrupts neurodevelopment and causes X‐linked microcephaly in humans. Genetics, 198(2), 723–733. https://doi.org/10.1534/genetics.114.168211
Carroll,, A. J., Heazlewood,, J. L., Ito,, J., & Millar,, A. H. (2008). Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post‐translational modification. Molecular %26 Cellular Proteomics, 7(2), 347–369. https://doi.org/10.1074/mcp.M700052-MCP200
Casanova‐Sáez,, R., Candela,, H., & Micol,, J. L. (2014). Combined haploinsufficiency and purifying selection drive retention of RPL36a paralogs in Arabidopsis. Scientific Reports, 4, 4122. https://doi.org/10.1038/srep04122
Cenik,, E. S., Meng,, X., Tang,, N. H., Hall,, R. N., Arribere,, J. A., Cenik,, C., Jin,, Y., & Fire,, A. (2019). Maternal ribosomes are sufficient for tissue diversification during embryonic development in C. elegans. Developmental Cell, 48(6), 811–826.e816. https://doi.org/10.1016/j.devcel.2019.01.019
Chalhoub,, B., Denoeud,, F., Liu,, S., Parkin,, I. A., Tang,, H., Wang,, X., Chiquet,, J., Belcram,, H., Tong,, C., Samans,, B., Corréa,, M., Da Silva,, C., Just,, J., Falentin,, C., Koh,, C. S., Le Clainche,, I., Bernard,, M., Bento,, P., Noel,, B., … Wincker,, P. (2014). Plant genetics. Early allopolyploid evolution in the post‐Neolithic Brassica napus oilseed genome. Science, 345(6199), 950–953. https://doi.org/10.1126/science.1253435
Chang,, I. F., Szick‐Miranda,, K., Pan,, S., & Bailey‐Serres,, J. (2005). Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes. Plant Physiology, 137(3), 848–862. https://doi.org/10.1104/pp.104.053637
Charneski,, C. A., & Hurst,, L. D. (2013). Positively charged residues are the major determinants of ribosomal velocity. PLoS Biology, 11(3), e1001508. https://doi.org/10.1371/journal.pbio.1001508
Chiocchetti,, A., Pakalapati,, G., Duketis,, E., Wiemann,, S., Poustka,, A., Poustka,, F., & Klauck,, S. M. (2011). Mutation and expression analyses of the ribosomal protein gene RPL10 in an extended German sample of patients with autism spectrum disorder. American Journal of Medical Genetics. Part A, 155A(6), 1472–1475. https://doi.org/10.1002/ajmg.a.33977
Creff,, A., Sormani,, R., & Desnos,, T. (2010). The two Arabidopsis RPS6 genes, encoding for cytoplasmic ribosomal proteins S6, are functionally equivalent. Plant Molecular Biology, 73(4–5), 533–546. https://doi.org/10.1007/s11103-010-9639-y
Degenhardt,, R. F., & Bonham‐Smith,, P. C. (2008a). Arabidopsis ribosomal proteins RPL23aA and RPL23aB are differentially targeted to the nucleolus and are disparately required for normal development. Plant Physiology, 147(1), 128–142. https://doi.org/10.1104/pp.107.111799
Degenhardt,, R. F., & Bonham‐Smith,, P. C. (2008b). Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog. Planta, 228(4), 627–640. https://doi.org/10.1007/s00425-008-0765-6
Devis,, D., Firth,, S. M., Liang,, Z., & Byrne,, M. E. (2015). Dosage sensitivity of RPL9 and concerted evolution of ribosomal protein genes in plants. Frontiers in Plant Science, 6, 1102. https://doi.org/10.3389/fpls.2015.01102
Dinman,, J. D. (2016). Pathways to specialized ribosomes: The Brussels lecture. Journal of Molecular Biology, 428(10 Pt B), 2186–2194. https://doi.org/10.1016/j.jmb.2015.12.021
D`Souza,, M. N., Gowda,, N. K. C., Tiwari,, V., Babu,, R. O., Anand,, P., Dastidar,, S. G., Singh,, R., James,, O. G., Selvaraj,, B., Pal,, R., Ramesh,, A., Chattarji,, S., Chandran,, S., Gulyani,, A., Palakodeti,, D., & Muddashetty,, R. S. (2018). FMRP interacts with C/D box snoRNA in the nucleus and regulates ribosomal RNA methylation. iScience, 9, 399–411. https://doi.org/10.1016/j.isci.2018.11.007
Dunn,, J. G., Foo,, C. K., Belletier,, N. G., Gavis,, E. R., & Weissman,, J. S. (2013). Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife, 2, e01179. https://doi.org/10.7554/eLife.01179
Falcone Ferreyra,, M. L., Casadevall,, R., Luciani,, M. D., Pezza,, A., & Casati,, P. (2013). New evidence for differential roles of l10 ribosomal proteins from Arabidopsis. Plant Physiology, 163(1), 378–391. https://doi.org/10.1104/pp.113.223222
Fatemi,, S. H., Halt,, A. R., Stary,, J. M., Realmuto,, G. M., & Jalali‐Mousavi,, M. (2001). Reduction in anti‐apoptotic protein Bcl‐2 in autistic cerebellum. Neuroreport, 12(5), 929–933. https://doi.org/10.1097/00001756-200104170-00013
Ferreyra,, M. L., Biarc,, J., Burlingame,, A. L., & Casati,, P. (2010). Arabidopsis L10 ribosomal proteins in UV‐B responses. Plant Signaling %26 Behavior, 5(10), 1222–1225. https://doi.org/10.4161/psb.5.10.12758
Friend,, K., Brooks,, H. A., Propson,, N. E., Thomson,, J. A., & Kimble,, J. (2015). Embryonic stem cell growth factors regulate eIF2α phosphorylation. PLoS One, 10(9), e0139076. https://doi.org/10.1371/journal.pone.0139076
Fujikura,, U., Horiguchi,, G., Ponce,, M. R., Micol,, J. L., & Tsukaya,, H. (2009). Coordination of cell proliferation and cell expansion mediated by ribosome‐related processes in the leaves of Arabidopsis thaliana. The Plant Journal, 59(3), 499–508. https://doi.org/10.1111/j.1365-313X.2009.03886.x
García‐Marcos,, A., Sánchez,, S. A., Parada,, P., Eid,, J., Jameson,, D. M., Remacha,, M., Gratton,, E., & Ballesta,, J. P. (2008). Yeast ribosomal stalk heterogeneity in vivo shown by two‐photon FCS and molecular brightness analysis. Biophysical Journal, 94(7), 2884–2890. https://doi.org/10.1529/biophysj.107.121822
Gebauer,, F., & Hentze,, M. W. (2004). Molecular mechanisms of translational control. Nature Reviews. Molecular Cell Biology, 5(10), 827–835. https://doi.org/10.1038/nrm1488
Genuth,, N. R., & Barna,, M. (2018). The discovery of ribosome heterogeneity and its implications for gene regulation and organismal life. Molecular Cell, 71(3), 364–374. https://doi.org/10.1016/j.molcel.2018.07.018
Ghosh,, S., & Lasko,, P. (2015). Loss‐of‐function analysis reveals distinct requirements of the translation initiation factors eIF4E, eIF4E‐3, eIF4G and eIF4G2 in Drosophila spermatogenesis. PLoS One, 10(4), e0122519. https://doi.org/10.1371/journal.pone.0122519
Giavalisco,, P., Wilson,, D., Kreitler,, T., Lehrach,, H., Klose,, J., Gobom,, J., & Fucini,, P. (2005). High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome. Plant Molecular Biology, 57(4), 577–591. https://doi.org/10.1007/s11103-005-0699-3
Gilbert,, W. V. (2011). Functional specialization of ribosomes? Trends in Biochemical Sciences, 36(3), 127–132. https://doi.org/10.1016/j.tibs.2010.12.002
Goering, R., Hudish, L. I., Guzman, B. B., Raj, N., Bassell, G. J., Russ, H. A., Dominguez, D., & Taliaferro, J. M. (2010). FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G‐quadruplex RNA sequences. Elife, 9. https://doi.org/10.7554/eLife.52621
Guimaraes,, J. C., & Zavolan,, M. (2016). Patterns of ribosomal protein expression specify normal and malignant human cells. Genome Biology, 17(1), 236. https://doi.org/10.1186/s13059-016-1104-z
Guo,, H. (2018). Specialized ribosomes and the control of translation. Biochemical Society Transactions, 46(4), 855–869. https://doi.org/10.1042/BST20160426
Hafner,, A. S., Donlin‐Asp,, P. G., Leitch,, B., Herzog,, E., & Schuman,, E. M. (2019). Local protein synthesis is a ubiquitous feature of neuronal pre‐ and postsynaptic compartments. Science, 364(6441), eaau3644. https://doi.org/10.1126/science.aau3644
Hagerman, R. J., Berry‐Kravis, E., Hazlett, H. C., Bailey, D. B., Moine, H., Kooy, R. F., Tassone, F., Gantois, I., Sonenberg, N., Mandel, J. L., & Hagerman, P. J. (2017). Fragile X syndrome. Nat Rev Dis Primers, 3, 17065. https://doi.org/10.1038/nrdp.2017.65
Hebras,, J., Krogh,, N., Marty,, V., Nielsen,, H., & Cavaillé,, J. (2020). Developmental changes of rRNA ribose methylations in the mouse. RNA Biology, 17(1), 150–164. https://doi.org/10.1080/15476286.2019.1670598
Henderson,, M. A., Cronland,, E., Dunkelbarger,, S., Contreras,, V., Strome,, S., & Keiper,, B. D. (2009). A germline‐specific isoform of eIF4E (IFE‐1) is required for efficient translation of stored mRNAs and maturation of both oocytes and sperm. Journal of Cell Science, 122(Pt 10), 1529–1539. https://doi.org/10.1242/jcs.046771
Hernández,, G., Han,, H., Gandin,, V., Fabian,, L., Ferreira,, T., Zuberek,, J., Sonenberg,, N., Brill,, J. A., & Lasko,, P. (2012). Eukaryotic initiation factor 4E‐3 is essential for meiotic chromosome segregation, cytokinesis and male fertility in Drosophila. Development, 139(17), 3211–3220. https://doi.org/10.1242/dev.073122
Herrera, S. C., & Bach, E. A. (2018). JNK signaling triggers spermatogonial dedifferentiation during chronic stress to maintain the germline stem cell pool in the Elife, 7. https://doi.org/10.7554/eLife.36095
Hertz,, M. I., Landry,, D. M., Willis,, A. E., Luo,, G., & Thompson,, S. R. (2013). Ribosomal protein S25 dependency reveals a common mechanism for diverse internal ribosome entry sites and ribosome shunting. Molecular and Cellular Biology, 33(5), 1016–1026. https://doi.org/10.1128/MCB.00879-12
Hetman,, M., & Slomnicki,, L. P. (2019). Ribosomal biogenesis as an emerging target of neurodevelopmental pathologies. Journal of Neurochemistry, 148(3), 325–347. https://doi.org/10.1111/jnc.14576
Holland,, M. L., Lowe,, R., Caton,, P. W., Gemma,, C., Carbajosa,, G., Danson,, A. F., Carpenter,, A. A., Loche,, E., Ozanne,, S. E., & Rakyan,, V. K. (2016). Early‐life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. Science, 353(6298), 495–498. https://doi.org/10.1126/science.aaf7040
Horiguchi,, G., Mollá‐Morales,, A., Pérez‐Pérez,, J. M., Kojima,, K., Robles,, P., Ponce,, M. R., Micol,, J. L., & Tsukaya,, H. (2011). Differential contributions of ribosomal protein genes to Arabidopsis thaliana leaf development. The Plant Journal, 65(5), 724–736. https://doi.org/10.1111/j.1365-313X.2010.04457.x
Hummel,, M., Cordewener,, J. H., de Groot,, J. C., Smeekens,, S., America,, A. H., & Hanson,, J. (2012). Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. Proteomics, 12(7), 1024–1038. https://doi.org/10.1002/pmic.201100413
Hummel,, M., Dobrenel,, T., Cordewener,, J. J., Davanture,, M., Meyer,, C., Smeekens,, S. J., Bailey‐Serres,, J., America,, T. A., & Hanson,, J. (2015). Proteomic LC‐MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re‐annotation of the ribosomal protein genes. Journal of Proteomics, 128, 436–449. https://doi.org/10.1016/j.jprot.2015.07.004
Imai,, A., Komura,, M., Kawano,, E., Kuwashiro,, Y., & Takahashi,, T. (2008). A semi‐dominant mutation in the ribosomal protein L10 gene suppresses the dwarf phenotype of the acl5 mutant in Arabidopsis thaliana. The Plant Journal, 56(6), 881–890. https://doi.org/10.1111/j.1365-313X.2008.03647.x
Ingolia,, N. T., Lareau,, L. F., & Weissman,, J. S. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147(4), 789–802. https://doi.org/10.1016/j.cell.2011.10.002
Ito,, T., Kim,, G. T., & Shinozaki,, K. (2000). Disruption of an Arabidopsis cytoplasmic ribosomal protein S13‐homologous gene by transposon‐mediated mutagenesis causes aberrant growth and development. The Plant Journal, 22(3), 257–264. https://doi.org/10.1046/j.1365-313x.2000.00728.x
Jiang,, L., Li,, T., Zhang,, X., Zhang,, B., Yu,, C., Li,, Y., Fan,, S., Jiang,, X., Khan,, T., Hao,, Q., Xu,, P., Nadano,, D., Huleihel,, M., Lunenfeld,, E., Wang,, P. J., Zhang,, Y., & Shi,, Q. (2017). RPL10L is required for male meiotic division by compensating for RPL10 during meiotic sex chromosome inactivation in mice. Current Biology, 27(10), 1498–1505.e1496. https://doi.org/10.1016/j.cub.2017.04.017
Jiao,, Y., Wickett,, N. J., Ayyampalayam,, S., Chanderbali,, A. S., Landherr,, L., Ralph,, P. E., Tomsho,, L. P., Hu,, Y., Liang,, H., Soltis,, P. S., Soltis,, D. E., Clifton,, S. W., Schlarbaum,, S. E., Schuster,, S. C., Ma,, H., Leebens‐Mack,, J., & de Pamphilis,, C. W. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature, 473(7345), 97–100. https://doi.org/10.1038/nature09916
Kampen,, K. R., Sulima,, S. O., Verbelen,, B., Girardi,, T., Vereecke,, S., Rinaldi,, G., Verbeeck,, J., Op de Beeck,, J., Uyttebroeck,, A., Meijerink,, J. P. P., Moorman,, A. V., Harrison,, C. J., Spincemaille,, P., Cools,, J., Cassiman,, D., Fendt,, S. M., Vermeersch,, P., & De Keersmaecker,, K. (2019). The ribosomal RPL10 R98S mutation drives IRES‐dependent BCL‐2 translation in T‐ALL. Leukemia, 33(2), 319–332. https://doi.org/10.1038/s41375-018-0176-z
Kearse,, M. G., Chen,, A. S., & Ware,, V. C. (2011). Expression of ribosomal protein L22e family members in Drosophila melanogaster: rpL22‐like is differentially expressed and alternatively spliced. Nucleic Acids Research, 39(7), 2701–2716. https://doi.org/10.1093/nar/gkq1218
Klauck,, S. M., Felder,, B., Kolb‐Kokocinski,, A., Schuster,, C., Chiocchetti,, A., Schupp,, I., Wellenreuther,, R., Schmötzer,, G., Poustka,, F., Breitenbach‐Koller,, L., & Poustka,, A. (2006). Mutations in the ribosomal protein gene RPL10 suggest a novel modulating disease mechanism for autism. Molecular Psychiatry, 11(12), 1073–1084. https://doi.org/10.1038/sj.mp.4001883
Kleene,, K. C. (2003). Patterns, mechanisms, and functions of translation regulation in mammalian spermatogenic cells. Cytogenetic and Genome Research, 103(3–4), 217–224. https://doi.org/10.1159/000076807
Komili,, S., Farny,, N. G., Roth,, F. P., & Silver,, P. A. (2007). Functional specificity among ribosomal proteins regulates gene expression. Cell, 131(3), 557–571. https://doi.org/10.1016/j.cell.2007.08.037
Kondrashov,, N., Pusic,, A., Stumpf,, C. R., Shimizu,, K., Hsieh,, A. C., Xue,, S., Ishijima,, J., Shiroishi,, T., & Barna,, M. (2011). Ribosome‐mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell, 145(3), 383–397. https://doi.org/10.1016/j.cell.2011.03.028
Kong,, J., Han,, H., Bergalet,, J., Bouvrette,, L. P. B., Hernández,, G., Moon,, N. S., Vali,, H., Lécuyer,, É., & Lasko,, P. (2019). A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster. Scientific Reports, 9(1), 13779. https://doi.org/10.1038/s41598-019-50357-z
Kongsuwan, K., Yu, Q., Vincent, A., Frisardi, M. C., Rosbash, M., Lengyel, J. A., & Merriam, J., (1985). A Drosophila Minute gene encodes a ribosomal protein. Nature, 317(6037), 555–558.
Krogh,, N., Jansson,, M. D., Häfner,, S. J., Tehler,, D., Birkedal,, U., Christensen‐Dalsgaard,, M., Lund,, A. H., & Nielsen,, H. (2016). Profiling of 2′‐O‐Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Research, 44(16), 7884–7895. https://doi.org/10.1093/nar/gkw482
Lambertsson,, A. (1998). The minute genes in Drosophila and their molecular functions. Advances in Genetics, 38, 69–134.
Landry,, D. M., Hertz,, M. I., & Thompson,, S. R. (2009). RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes %26 Development, 23(23), 2753–2764. https://doi.org/10.1101/gad.1832209
Lasko,, P. (2012). mRNA localization and translational control in Drosophila oogenesis. Cold Spring Harbor Perspectives in Biology, 4(10), a012294. https://doi.org/10.1101/cshperspect.a012294
Lee,, A. S., Burdeinick‐Kerr,, R., & Whelan,, S. P. (2013). A ribosome‐specialized translation initiation pathway is required for cap‐dependent translation of vesicular stomatitis virus mRNAs. Proceedings of the National Academy of Sciences of the United States of America, 110(1), 324–329. https://doi.org/10.1073/pnas.1216454109
Locati,, M. D., Pagano,, J. F., Ensink,, W. A., van Olst,, M., van Leeuwen,, S., Nehrdich,, U., Zhu,, K., Spaink,, H. P., Girard,, G., Rauwerda,, H., Jonker,, M. J., Dekker,, R. J., & Breit,, T. M. (2017). Linking maternal and somatic 5S rRNA types with different sequence‐specific non‐LTR retrotransposons. RNA, 23(4), 446–456. https://doi.org/10.1261/rna.059642.116
Locati,, M. D., Pagano,, J. F. B., Girard,, G., Ensink,, W. A., van Olst,, M., van Leeuwen,, S., Nehrdich,, U., Spaink,, H. P., Rauwerda,, H., Jonker,, M. J., Dekker,, R. J., & Breit,, T. M. (2017). Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA, 23(8), 1188–1199. https://doi.org/10.1261/rna.061515.117
Lopes,, A. M., Miguel,, R. N., Sargent,, C. A., Ellis,, P. J., Amorim,, A., & Affara,, N. A. (2010). The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis. BMC Molecular Biology, 11, 33. https://doi.org/10.1186/1471-2199-11-33
Luo,, A., Zhan,, H., Zhang,, X., Du,, H., Zhang,, Y., & Peng,, X. (2020). Cytoplasmic ribosomal protein L14B is essential for fertilization in Arabidopsis. Plant Science, 292, 110394. https://doi.org/10.1016/j.plantsci.2019.110394
Mageeney,, C. M., Kearse,, M. G., Gershman,, B. W., Pritchard,, C. E., Colquhoun,, J. M., & Ware,, V. C. (2018). Functional interplay between ribosomal protein paralogues in the eRpL22 family in Drosophila melanogaster. Fly (Austin), 12(3–4), 143–163. https://doi.org/10.1080/19336934.2018.1549419
Mageeney,, C. M., & Ware,, V. C. (2019). Specialized eRpL22 paralogue‐specific ribosomes regulate specific mRNA translation in spermatogenesis in. Molecular Biology of the Cell, 30(17), 2240–2253. https://doi.org/10.1091/mbc.E19-02-0086
Martinez‐Seidel,, F., Beine‐Golovchuk,, O., Hsieh,, Y. C., & Kopka,, J. (2020). Systematic review of plant ribosome heterogeneity and specialization. Frontiers in Plant Science, 11, 948. https://doi.org/10.3389/fpls.2020.00948
Marygold,, S. J., Roote,, J., Reuter,, G., Lambertsson,, A., Ashburner,, M., Millburn,, G. H., Harrison,, P. M., Yu,, Z., Kenmochi,, N., Kaufman,, T. C., Leevers,, S. J., & Cook,, K. R. (2007). The ribosomal protein genes and minute loci of Drosophila melanogaster. Genome Biology, 8(10), R216. https://doi.org/10.1186/gb-2007-8-10-r216
Mauro,, V. P., & Edelman,, G. M. (2002). The ribosome filter hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 99(19), 12031–12036. https://doi.org/10.1073/pnas.192442499
Moin,, M., Bakshi,, A., Saha,, A., Dutta,, M., Madhav,, S. M., & Kirti,, P. B. (2016). Rice ribosomal protein large subunit genes and their spatio‐temporal and stress regulation. Frontiers in Plant Science, 7, 1284. https://doi.org/10.3389/fpls.2016.01284
Nadano,, D., Notsu,, T., Matsuda,, T., & Sato,, T. (2002). A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells. Biochimica et Biophysica Acta, 1577(3), 430–436. https://doi.org/10.1016/s0167-4781(02)00445-1
Narla,, A., & Ebert,, B. L. (2010). Ribosomopathies: Human disorders of ribosome dysfunction. Blood, 115(16), 3196–3205. https://doi.org/10.1182/blood-2009-10-178129
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(7681), 472–477. https://doi.org/10.1038/nature24482
Nishimura,, T., Wada,, T., Yamamoto,, K. T., & Okada,, K. (2005). The Arabidopsis STV1 protein, responsible for translation reinitiation, is required for auxin‐mediated gynoecium patterning. Plant Cell, 17(11), 2940–2953. https://doi.org/10.1105/tpc.105.036533
Palade,, G. E. (1958). Microsomes and ribonucleoproteins. In Microsomal particles and protein synthesis, New York: Washington Academy of Sciences.
Park, H. S., Himmelbach, A., Browning, K. S., Hohn, T., & Ryabova, L. A. (2001). A plant viral "reinitiation" factor interacts with the host translational machinery. Cell, 106(6), 723‐733. https://doi.org/10.1016/s0092-8674(01)00487-1
Peshkin,, L., Wühr,, M., Pearl,, E., Haas,, W., Freeman,, R. M., Gerhart,, J. C., Klein,, A. M., Horb,, M., Gygi,, S. P., & Kirschner,, M. W. (2015). On the relationship of protein and mRNA dynamics in vertebrate embryonic development. Developmental Cell, 35(3), 383–394. https://doi.org/10.1016/j.devcel.2015.10.010
Peterson,, R. C., Doering,, J. L., & Brown,, D. D. (1980). Characterization of two xenopus somatic 5S DNAs and one minor oocyte‐specific 5S DNA. Cell, 20(1), 131–141. https://doi.org/10.1016/0092-8674(80)90241-x
Pinon,, V., Etchells,, J. P., Rossignol,, P., Collier,, S. A., Arroyo,, J. M., Martienssen,, R. A., & Byrne,, M. E. (2008). Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins. Development, 135(7), 1315–1324. https://doi.org/10.1242/dev.016469
Raikhel,, A. S., & Dhadialla,, T. S. (1992). Accumulation of yolk proteins in insect oocytes. Annual Review of Entomology, 37, 217–251. https://doi.org/10.1146/annurev.en.37.010192.001245
Ramly,, B., Afiqah‐Aleng,, N., & Mohamed‐Hussein,, Z. A. (2019). Protein–protein interaction network analysis reveals several diseases highly associated with polycystic ovarian syndrome. International Journal of Molecular Sciences, 20(12), 2959. https://doi.org/10.3390/ijms20122959
Richter,, J. D., & Lasko,, P. (2011). Translational control in oocyte development. Cold Spring Harbor Perspectives in Biology, 3(9), a002758. https://doi.org/10.1101/cshperspect.a002758
Rosado,, A., Li,, R., van de Ven,, W., Hsu,, E., & Raikhel,, N. V. (2012). Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors. Proceedings of the National Academy of Sciences of the United States of America, 109(48), 19537–19544. https://doi.org/10.1073/pnas.1214774109
Rosado,, A., & Raikhel,, N. V. (2010). Application of the gene dosage balance hypothesis to auxin‐related ribosomal mutants in Arabidopsis. Plant Signaling %26 Behavior, 5(4), 450–452. https://doi.org/10.4161/psb.5.4.11341
Rosado,, A., Sohn,, E. J., Drakakaki,, G., Pan,, S., Swidergal,, A., Xiong,, Y., Kang,, B. H., Bressan,, R. A., & Raikhel,, N. V. (2010). Auxin‐mediated ribosomal biogenesis regulates vacuolar trafficking in Arabidopsis. Plant Cell, 22(1), 143–158. https://doi.org/10.1105/tpc.109.068320
Sanchez,, C. G., Teixeira,, F. K., Czech,, B., Preall,, J. B., Zamparini,, A. L., Seifert,, J. R. K., Malone,, C. D., Hannon,, G. J., & Lehmann,, R. (2016). Regulation of ribosome biogenesis and protein synthesis controls germline stem cell differentiation. Cell Stem Cell, 18(2), 276–290. https://doi.org/10.1016/j.stem.2015.11.004
Shi,, Z., & Barna,, M. (2015). Translating the genome in time and space: Specialized ribosomes, RNA regulons, and RNA‐binding proteins. Annual Review of Cell and Developmental Biology, 31, 31–54. https://doi.org/10.1146/annurev-cellbio-100814-125346
Shi,, Z., Fujii,, K., Kovary,, K. M., Genuth,, N. R., Röst,, H. L., Teruel,, M. N., & Barna,, M. (2017). Heterogeneous ribosomes preferentially translate distinct subpools of mRNAs genome‐wide. Molecular Cell, 67(1), 71–83.e7. https://doi.org/10.1016/j.molcel.2017.05.021
Shigeoka,, T., Koppers,, M., Wong,, H. H., Lin,, J. Q., Cagnetta,, R., Dwivedy,, A., de Freitas Nascimento,, J., van Tartwijk,, F. W., Ströhl,, F., Cioni,, J. M., Schaeffer,, J., Carrington,, M., Kaminski,, C. F., Jung,, H., Harris,, W. A., & Holt,, C. E. (2019). On‐site ribosome remodeling by locally synthesized ribosomal proteins in axons. Cell Reports, 29(11), 3605–3619.e3610. https://doi.org/10.1016/j.celrep.2019.11.025
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(6), 1051–1065 e1018. https://doi.org/10.1016/j.cell.2017.05.022
Slavov,, N., Semrau,, S., Airoldi,, E., Budnik,, B., & van Oudenaarden,, A. (2015). Differential stoichiometry among core ribosomal proteins. Cell Reports, 13(5), 865–873. https://doi.org/10.1016/j.celrep.2015.09.056
Stefani,, G., Fraser,, C. E., Darnell,, J. C., & Darnell,, R. B. (2004). Fragile X mental retardation protein is associated with translating polyribosomes in neuronal cells. The Journal of Neuroscience, 24(33), 7272–7276. https://doi.org/10.1523/JNEUROSCI.2306-04.2004
Stirnberg,, P., Liu,, J. P., Ward,, S., Kendall,, S. L., & Leyser,, O. (2012). Mutation of the cytosolic ribosomal protein‐encoding RPS10B gene affects shoot meristematic function in Arabidopsis. BMC Plant Biology, 12, 160. https://doi.org/10.1186/1471-2229-12-160
Sugihara,, Y., Honda,, H., Iida,, T., Morinaga,, T., Hino,, S., Okajima,, T., Matsuda,, T., & Nadano,, D. (2010). Proteomic analysis of rodent ribosomes revealed heterogeneity including ribosomal proteins L10‐like, L22‐like 1, and L39‐like. Journal of Proteome Research, 9(3), 1351–1366. https://doi.org/10.1021/pr9008964
Szakonyi,, D., & Byrne,, M. E. (2011). Ribosomal protein L27a is required for growth and patterning in Arabidopsis thaliana. The Plant Journal, 65(2), 269–281. https://doi.org/10.1111/j.1365-313X.2010.04422.x
Tahmasebi,, S., Amiri,, M., & Sonenberg,, N. (2018). Translational control in stem cells. Frontiers in Genetics, 9, 709. https://doi.org/10.3389/fgene.2018.00709
Tcherkezian,, J., Brittis,, P. A., Thomas,, F., Roux,, P. P., & Flanagan,, J. G. (2010). Transmembrane receptor DCC associates with protein synthesis machinery and regulates translation. Cell, 141(4), 632–644. https://doi.org/10.1016/j.cell.2010.04.008
Teixeira,, F. K., & Lehmann,, R. (2019). Translational control during developmental transitions. Cold Spring Harbor Perspectives in Biology, 11(6), a032987. https://doi.org/10.1101/cshperspect.a032987
Terashima,, J., & Bownes,, M. (2005). A microarray analysis of genes involved in relating egg production to nutritional intake in Drosophila melanogaster. Cell Death and Differentiation, 12(5), 429–440. https://doi.org/10.1038/sj.cdd.4401587
Theunissen,, T. W., & Jaenisch,, R. (2017). Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development, 144(24), 4496–4509. https://doi.org/10.1242/dev.157404
Thomas,, B. C., Pedersen,, B., & Freeling,, M. (2006). Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose‐sensitive genes. Genome Research, 16(7), 934–946. https://doi.org/10.1101/gr.4708406
Turkina,, M. V., Klang Årstrand,, H., & Vener,, A. V. (2011). Differential phosphorylation of ribosomal proteins in Arabidopsis thaliana plants during day and night. PLoS One, 6(12), e29307. https://doi.org/10.1371/journal.pone.0029307
Turner,, J. M. (2015). Meiotic silencing in mammals. Annual Review of Genetics, 49, 395–412. https://doi.org/10.1146/annurev-genet-112414-055145
van de Waterbeemd,, M., Tamara,, S., Fort,, K. L., Damoc,, E., Franc,, V., Bieri,, P., Itten,, M., Makarov,, A., Ban,, N., & Heck,, A. J. R. (2018). Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nature Communications, 9(1), 2493. https://doi.org/10.1038/s41467-018-04853-x
Van Lijsebettens,, M., Vanderhaeghen,, R., De Block,, M., Bauw,, G., Villarroel,, R., & Van Montagu,, M. (1994). An S18 ribosomal protein gene copy at the Arabidopsis PFL locus affects plant development by its specific expression in meristems. The EMBO Journal, 13(14), 3378–3388.
Vision,, T. J., Brown,, D. G., & Tanksley,, S. D. (2000). The origins of genomic duplications in Arabidopsis. Science, 290(5499), 2114–2117. https://doi.org/10.1126/science.290.5499.2114
Wang,, X., Wang,, H., Wang,, J., Sun,, R., Wu,, J., Liu,, S., Bai,, Y., Mun,, J. H., Bancroft,, I., Cheng,, F., Huang,, S., Li,, X., Hua,, W., Freeling,, M., Pires,, J. C., Paterson,, A. H., Chalhoub,, B., Wang,, B., Hayward,, A., … Brassica rapa Genome Sequencing Project Consortium. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics, 43(10), 1035–1039. https://doi.org/10.1038/ng.919
Weijers,, D., Franke‐van Dijk,, M., Vencken,, R. J., Quint,, A., Hooykaas,, P., & Offringa,, R. (2001). An Arabidopsis Minute‐like phenotype caused by a semi‐dominant mutation in a RIBOSOMAL PROTEIN S5 gene. Development, 128(21), 4289–4299.
Whittle,, C. A., & Krochko,, J. E. (2009). Transcript profiling provides evidence of functional divergence and expression networks among ribosomal protein gene paralogs in Brassica napus. Plant Cell, 21(8), 2203–2219. https://doi.org/10.1105/tpc.109.068411
Williams,, M. E., & Sussex,, I. M. (1995). Developmental regulation of ribosomal protein L16 genes in Arabidopsis thaliana. The Plant Journal, 8(1), 65–76. https://doi.org/10.1046/j.1365-313x.1995.08010065.x
Witt,, E., Benjamin,, S., Svetec,, N., & Zhao,, L. (2019). Testis single‐cell RNA‐seq reveals the dynamics of de novo gene transcription and germline mutational bias in. eLife, 8, e47138. https://doi.org/10.7554/eLife.47138
Wong,, Q. W.‐L., Li,, J., Ng,, S. R., Lim,, S. G., Yang,, H., & Vardy,, L. A. (2014). RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors. RNA Biology, 11(1), 33–41.
Xie,, F., Yan,, H., Sun,, Y., Wang,, Y., Chen,, H., Mao,, W., Zhang,, L., Sun,, M., & Peng,, X. (2018). RPL18aB helps maintain suspensor identity during early embryogenesis. Journal of Integrative Plant Biology, 60(4), 266–269. https://doi.org/10.1111/jipb.12616
Xiong,, W., Chen,, X., Zhu,, C., Zhang,, J., Lan,, T., & Liu,, L. (2020). Arabidopsis ribosomal proteins RPL23aA and RPL23aB are functionally equivalent. Research Square, 20, 463. https://doi.org/10.21203/rs.3.rs-18215/v1
Xue,, S., & Barna,, M. (2012). Specialized ribosomes: A new frontier in gene regulation and organismal biology. Nature Reviews. Molecular Cell Biology, 13(6), 355–369. https://doi.org/10.1038/nrm3359
Xue,, S., Tian,, S., Fujii,, K., Kladwang,, W., Das,, R., & Barna,, M. (2015). RNA regulons in Hox 5` UTRs confer ribosome specificity to gene regulation. Nature, 517(7532), 33–38. https://doi.org/10.1038/nature14010
Yamada,, K., Lim,, J., Dale,, J. M., Chen,, H., Shinn,, P., Palm,, C. J., Southwick,, A. M., Wu,, H. C., Kim,, C., Nguyen,, M., Pham,, P., Cheuk,, R., Karlin‐Newmann,, G., Liu,, S. X., Lam,, B., Sakano,, H., Wu,, T., Yu,, G., Miranda,, M., … Ecker,, J. R. (2003). Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302(5646), 842–846. https://doi.org/10.1126/science.1088305
Yamashita,, T., Wada,, R., Sasaki,, T., Deng,, C., Bierfreund,, U., Sandhoff,, K., & Proia,, R. L. (1999). A vital role for glycosphingolipid synthesis during development and differentiation. Proceedings of the National Academy of Sciences of the United States of America, 96(16), 9142–9147. https://doi.org/10.1073/pnas.96.16.9142
Yan,, H., Chen,, D., Wang,, Y., Sun,, Y., Zhao,, J., Sun,, M., & Peng,, X. (2016). Ribosomal protein L18aB is required for both male gametophyte function and embryo development in Arabidopsis. Scientific Reports, 6, 31195. https://doi.org/10.1038/srep31195
Yao,, Y., Ling,, Q., Wang,, H., & Huang,, H. (2008). Ribosomal proteins promote leaf adaxial identity. Development, 135(7), 1325–1334. https://doi.org/10.1242/dev.017913
Yewdell,, J. W., & Nicchitta,, C. V. (2006). The DRiP hypothesis decennial: Support, controversy, refinement and extension. Trends in Immunology, 27(8), 368–373. https://doi.org/10.1016/j.it.2006.06.008
Yu,, J., Lan,, X., Chen,, X., Yu,, C., Xu,, Y., Liu,, Y., Xu,, L., Fan,, H. Y., & Tong,, C. (2016). Protein synthesis and degradation are essential to regulate germline stem cell homeostasis in Drosophila testes. Development, 143(16), 2930–2945. https://doi.org/10.1242/dev.134247
Zhang,, Y., O`Leary,, M. N., Peri,, S., Wang,, M., Zha,, J., Melov,, S., Kappes,, D. J., Feng,, Q., Rhodes,, J., Amieux,, P. S., Morris,, D. R., Kennedy,, B. K., & Wiest,, D. L. (2017). Ribosomal proteins Rpl22 and Rpl22l1 control morphogenesis by regulating pre‐mRNA splicing. Cell Reports, 18(2), 545–556. https://doi.org/10.1016/j.celrep.2016.12.034
Zhang,, Y., Wölfle,, T., & Rospert,, S. (2013). Interaction of nascent chains with the ribosomal tunnel proteins Rpl4, Rpl17, and Rpl39 of Saccharomyces cerevisiae. The Journal of Biological Chemistry, 288(47), 33697–33707. https://doi.org/10.1074/jbc.M113.508283
Zhao,, Y., Li,, Q., Yao,, C., Wang,, Z., Zhou,, Y., Wang,, Y., Liu,, L., Wang,, L., & Qiao,, Z. (2006). Characterization and quantification of mRNA transcripts in ejaculated spermatozoa of fertile men by serial analysis of gene expression. Human Reproduction, 21(6), 1583–1590. https://doi.org/10.1093/humrep/del027
Zivraj,, K. H., Tung,, Y. C., Piper,, M., Gumy,, L., Fawcett,, J. W., Yeo,, G. S., & Holt,, C. E. (2010). Subcellular profiling reveals distinct and developmentally regulated repertoire of growth cone mRNAs. The Journal of Neuroscience, 30(46), 15464–15478. https://doi.org/10.1523/JNEUROSCI.1800-10.2010
Zsögön,, A., Szakonyi,, D., Shi,, X., & Byrne,, M. E. (2014). Ribosomal protein RPL27a promotes female gametophyte development in a dose‐dependent manner. Plant Physiology, 165(3), 1133–1143. https://doi.org/10.1104/pp.114.241778