Plant Molecular Biology Reporter

, Volume 28, Issue 2, pp 239–252 | Cite as

Analysis of RPS15aE, an Isoform of a Plant-Specific Evolutionarily Distinct Ribosomal Protein in Arabidopsis thaliana, Reveals its Potential Role as a Growth Regulator

  • Kathleen Szick-Miranda
  • Ammar S. Zanial
  • Ali S. Zanial
  • Stacey Abidayo
  • Karie L. C. Slater
Article

Abstract

There is increasing evidence for ribosome heterogeneity in biological systems. In Arabidopsis thaliana, the ribosomal protein S15a is encoded by six separate genes, which fall into two evolutionarily distinct categories (Type I and Type II). Type I S15a is a universally conserved component of cytosolic ribosomes, whereas there is ambiguity as to the specific subcellular location of Type II S15a (cytosolic and/or mitochondrial ribosomes). In this study, we investigated the functional significance of the distinct form of ribosomal protein S15a (Type II) in Arabidopsis by examining: the evolutionary relationship of eukaryotic S15a proteins with respect to organellar homologs, the expression of individual Type II S15a genes during various developmental stages by RT-PCR, and the phenotypes of an insertional mutation into the RPS15aE gene. The Type II S15a proteins are plant specific, and the duplication event that gave rise to the Type II S15a genes appears to have occurred during the evolution of land plants. The genes encoding Type II S15a in Arabidopsis are differentially expressed, and mutant plants in which the gene encoding S15aE is knocked down produce larger leaves, longer roots, and possess larger cells than wild-type plants suggesting that the RPS15aE isoform of Type II S15a may act as a regulator of translational activity. Our results add significantly to the understanding of the protein constitution of plant ribosomes and the functional significance of ribosome heterogeneity.

Keywords

Arabidopsis Ribosome Ribosomal protein Protein synthesis Translational regulation 

Supplementary material

11105_2009_148_MOESM1_ESM.xls (20 kb)
Supplemental Table 1(XLS 20 kb)

References

  1. Adams K, Daley D, Whelan J, Palmer J (2002) Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast of cytosolic counterparts. Plant Cell 14:931–943CrossRefPubMedGoogle Scholar
  2. Alonso J et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657CrossRefPubMedGoogle Scholar
  3. Amsterdam A, Sadler KC, Lai K, Farrington S, Bronson RT, Lees JA, Hopkins N (2004) Many ribosomal protein genes are cancer genes in zebrafish. PLoS Biology 2(5):690–698CrossRefGoogle Scholar
  4. 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 Physiol 127(2):398–415CrossRefPubMedGoogle Scholar
  5. Bilanges B, Stokoe D (2007) Mechanisms of translational deregulation in human tumors and therapeutic intervention strategies. Oncogene 26:5973–5990CrossRefPubMedGoogle Scholar
  6. Boyes D, Zayed A, Ascenzi R, McCaskill A, Hoffman N, Davis K, Gorlach J (2001) Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 13:1499–1510CrossRefPubMedGoogle Scholar
  7. Branco-Price C, Kawaguchi R, Ferriera R, Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96:647–660CrossRefPubMedGoogle Scholar
  8. Branco-Price C, Hamersky KA, Jang CJH, Larive CK, Bailey-Serres J (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to hypoxia and reoxygenation in Arabidopsis thaliana. Plant J 56(5):743–755CrossRefPubMedGoogle Scholar
  9. Brodersen DE, Clemons WM Jr, Carter AP, Wimberly BT, Ramakrishnan V (2002) Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. J Mol Biol 316(3):725–768CrossRefPubMedGoogle Scholar
  10. Cammarano P, Pons S, Romeo A, Galdieri M, Gualerzi C (1972) Characterization of unfolded and compact ribosomal subunits from plants and their relationship to those of lower and higher animals: evidence for physicochemical heterogeneity among eucaryotic ribosomes. Biochim Biophys Acta 281(4):571–596PubMedGoogle Scholar
  11. Carroll AJ, Heazlewood JL, Ito J, Millar AH (2008) Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification. Mol Cell Proteomics 7(2):347–369PubMedGoogle Scholar
  12. Chandramouli P, Topf M, Menetret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW (2008) Structure of the mammalian 80S ribosome at 8.7 Å resolution. Structure 16:535–548CrossRefPubMedGoogle Scholar
  13. 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 Physiol 137:848–862CrossRefPubMedGoogle Scholar
  14. Davies C, Ramakrishnan V, White SW (1996) Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 Å resolution. Structure 4(9):1093–1104CrossRefPubMedGoogle Scholar
  15. Dean D, Yates JL, Nomura M (1981) Escherichia coli ribosomal protein S8 feedback regulates part of spc operon. Nature 289(5793):89–91CrossRefPubMedGoogle Scholar
  16. Degenhardt RF, Bonham-Smith PC (2008a) Arabidopsis ribosomal proteins RPL23aA and RPL23aB are differentially targeted to the nucleolus and are disparately required for normal development. Plant Physiol 147:128–142CrossRefPubMedGoogle Scholar
  17. Degenhardt RF, Bonham-Smith PC (2008b) Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog. Planta 228:627–640CrossRefPubMedGoogle Scholar
  18. Dresselhaus T, Cordts S, Heuer S, Sauter M, Loerz H, Kranz E (1999) Novel ribosomal genes from maize are differentially expressed in the zygotic and somatic cell cycles. Mol Gen Genet 261(2):416–427CrossRefPubMedGoogle Scholar
  19. 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 Mol Biol 57:577–591CrossRefPubMedGoogle Scholar
  20. Graack HR, WittmannLiebold B (1998) Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 329(PT3):433–448PubMedGoogle Scholar
  21. Heazlewood J, Tonti-Filippini J, Gout A, Day D, Whelan J, Millar AH (2004) Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulator components, provides assessment of targeting prediction programs and indicates plant-specific mitochondrial proteins. Plant Cell 16:241–256CrossRefPubMedGoogle Scholar
  22. Heazlewood JL, Millar AH (2005) Arabidopsis mitochondrial proteomics. Methods Mol Biol 372:559–571CrossRefGoogle Scholar
  23. Held WA, Ballou B, Mizushima S, Nomura M (1974) Assembly mapping of 30S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem 249(10):3103–3111PubMedGoogle Scholar
  24. Hershey JW (1991) Translational control in mammalian cells. Annu Rev Biochem 60(25):717–755CrossRefPubMedGoogle Scholar
  25. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, GruissemW, Zimmermann P (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008, Article ID 420747. doi:10.1155/2008/420747
  26. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754–755CrossRefPubMedGoogle Scholar
  27. Hulm J, McIntosh K, Bonham-Smith P (2005) Variation in transcript abundance among the four members of the Arabidopsis thaliana ribosomal protein s15a gene family. Plant Sci 169:267–278CrossRefGoogle Scholar
  28. 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. Plant J 22(3):257–264CrossRefPubMedGoogle Scholar
  29. Kawaguchi R, Bailey-Serres J (2005) mRNA sequence features responsible for translational regulation in Arabidopsis. Nucleic Acids Res 33(3):955–965CrossRefPubMedGoogle Scholar
  30. Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38:823–839CrossRefPubMedGoogle Scholar
  31. Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL (2000) A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J Biol Chem 275(42):32585–32591CrossRefPubMedGoogle Scholar
  32. Koc EC, Burkhart W, Blackburn K, Moseley A, Spremulli LL (2001) The small subunit of the mammalian mitochondrial ribosome: identification of the full complement of ribosomal proteins present. J Biol Chem 276(22):19363–19374CrossRefGoogle Scholar
  33. Lambertsson A (1998) The minute genes in Drosophila and their molecular functions. Adv Genet 38:69–134CrossRefPubMedGoogle Scholar
  34. Larkin JC, Hunsperger JP, Culley D, Rubenstein I, Silflow CD (1989) The organization and expression of a maize ribosomal protein gene family. Genes Dev 3(4):500–509CrossRefPubMedGoogle Scholar
  35. Lavoie C, Tam R, Clark M, Lee H, Sonenberg N, Lasko P (1994) Suppression of a temperature-sensitive cdc33 mutation of yeast by a multicopy plasmid expressing a Drosophila ribosomal protein. J Biol Chem 269(20):14625–14630PubMedGoogle Scholar
  36. Lee SW, Berger SJ, Martinovic S, Pasa-Tolic L, Andereson GA, Shen Y, Zhao R, Smith RD (2002) Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/TFICR. Proc Natl Acad Sci USA 99:5942–5947CrossRefPubMedGoogle Scholar
  37. Louie DF, Resing KA, Lewis TS, Ahn NG (1996) Mass spectrometric analysis of 40S ribosomal proteins from rat-1 fibroblasts. J Biol Chem 271:28189–28198CrossRefPubMedGoogle Scholar
  38. McIntosh KB, Bonham-Smith PC (2005) The two ribosomal protein L23A genes are differentially transcribed in Arabidopsis thaliana. Genome 48:443–454CrossRefPubMedGoogle Scholar
  39. Manuell AL, Yamaguchi K, Haynes PA, Milligan RA, Mayfield SP (2005) Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conversed in plants and animals. J Mol Biol 351:266–279CrossRefPubMedGoogle Scholar
  40. Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR (2007) The ribosomal protein genes and minute loci of Drosophila. Genome Biol 8(10):R216. doi:10.1186/gb-2007-8-10-r216 CrossRefPubMedGoogle Scholar
  41. Matheson AT, Auer J, Ramierez C, Bock A (1990) Structure and evolution of archaebacterial ribosomal proteins. In: Hill WE, Dahlberg A, Garrett RE, Moore PB, Schlessinger D, Warner DC (eds) The ribosome: structure, function and evolution. American Society of Microbiologists, Wasington, D.C, pp 617–633Google Scholar
  42. Merchant SS et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848):245–250CrossRefPubMedGoogle Scholar
  43. Merrick WC, Hershey JWB (1996) The pathway and mechanism of eukaryotic protein synthesis. In: Hershey JWB, Mathews MB, Sonenberg N (eds) Translational control. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 31–69Google Scholar
  44. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio-assays with tobacco tissue cultures. Physiol Plant 15(3):473–497CrossRefGoogle Scholar
  45. Nicolaï M, Roncato MA, Canoy AS, Rouquie D, Sarda X, Freyssinet G, Robaglia C (2006) Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 141(2):663–673CrossRefPubMedGoogle Scholar
  46. Nygård O, Nilsson L (1990) Translational dynamics. Interactions between the translational factors, tRNA and ribosomes during eukaryotic protein synthesis. Eur J Biochem 191(1):1–17CrossRefPubMedGoogle Scholar
  47. Odintsova TI, Muller EC, Ivanov AV, Egorov TA, Bienert R, Vladimirov SN, Kostka S, Otto A, Wittmann-Liebold B, Karapova GG (2003) Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing. J Protein Chem 22:249–258CrossRefPubMedGoogle Scholar
  48. Pinon V, Etchells JP, Rossignol P, Collier SA, Arroyo JM, Martienssen RA, Byrne ME (2008) Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins. Development 135(7):1315–1324CrossRefPubMedGoogle Scholar
  49. Popescu SC, Tumer NE (2004) Silencing of ribosomal protein L3 genes in N. tabacum reveals coordinate expression and significant alterations in plant growth, development and ribosome biogenesis. Plant J 39:29–44CrossRefPubMedGoogle Scholar
  50. Proud CG (2007) Signalling to translation: how signal transduction pathways control the protein synthetic machinery. Biochem J 403:217–234CrossRefPubMedGoogle Scholar
  51. Rensing et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319(5859):64–69CrossRefPubMedGoogle Scholar
  52. Revenkova E, Masson J, Koncz C, Afsar K, Jakovleva L, Paszkowski J (1999) Involvement of Arabidopsis thaliana ribosomal protein S27 in mRNA degradation triggered by genotoxic stress. EMBO J 18(2):490–499CrossRefPubMedGoogle Scholar
  53. Skinner DJ, Baker SC, Meister RJ, Broadhvest J, Schneitz K, Gasser CS (2001) The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. Plant Cell 13(12):2719–2730CrossRefPubMedGoogle Scholar
  54. Svensson P, Changchien LM, Craven GR, Noller HF (1988) Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16S ribosomal RNA. J Mol Biol 200(2):301–308CrossRefPubMedGoogle Scholar
  55. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J (2001) Structure of 80 S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit–subunit interactions. Cell 107:3733–3786CrossRefGoogle Scholar
  56. Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jorgensen R, Andersen GR, Bechmann R, Penczek PA, Ballesta JPG, Frank J (2004) Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J 23:1008–1019CrossRefPubMedGoogle Scholar
  57. Tishchenko SV, Vassilieva JM, Platonova OB, Serganov AA, Fomenkova NP, Mudrik ES, Piendl W, Ehresmann C, Ehresmann B, Garber MB (2001) Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin. Biochemistry (Moscow) 66(9):948–953CrossRefGoogle Scholar
  58. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680CrossRefPubMedGoogle Scholar
  59. Uechi T, Nakajima Y, Nakao A, Torihara H, Chakraborty A, Inoue K, Kenmochi N (2006) Ribosomal protein gene knockdown causes developmental defects in zebrafish. PLoS ONE 1:e37CrossRefPubMedGoogle Scholar
  60. Weijers D, Dijk MF, Vencken RJ, 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 128:4289–4299PubMedGoogle Scholar
  61. Williams ME, Sussex IM (1995) Developmental regulation of ribosomal protein L16 genes in Arabidopsis thaliana. Plant J 8(1):65–76CrossRefPubMedGoogle Scholar
  62. Wittmann-Leibold B, Kopke AKE, Arndt E, Kromer W, Hatakeyama T, Wittmann H-G (1990) Sequence comparison and evolution of ribosomal proteins and their genes. In: Hill WE, Dahlberg A, Garrett RE, Moore PB, Schlessinger D, Warner DC (eds) The ribosome: structure, function and evolution. American Society of Microbiologists, Washington, D.C., pp 598–616Google Scholar
  63. Wool IG, Chan Y-L, Gluck A (1995) Structure and evolution of mammalian ribosomal proteins. Biochem Cell Biol 73(11–12):933–947CrossRefPubMedGoogle Scholar
  64. 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. EMBO J 13(14):3378–3388PubMedGoogle Scholar
  65. Verschoor A, Srivastava S, Grassucci R, Frank J (1996) Native 3D structure of eukaryotic 80S ribosome: morphological homology with E. coli 70S ribosome. J Cell Biol 133:495–505CrossRefPubMedGoogle Scholar
  66. Yamaguchi K, Subramanian AR (2000) The plastid ribosomal proteins - Identification of all the proteins in the 50S subunit of an organelle ribosome (chloroplast). J Biol Chem 275(37):28466–28482CrossRefPubMedGoogle Scholar
  67. Yamaguchi K, von Knoblauch K, Subramanian AR (2000) The plastid ribosomal proteins—identification of all the proteins in the 30S subunit of an organelle ribosome (chloroplast). J Biol Chem 275(37):28455–28465CrossRefPubMedGoogle Scholar
  68. Yao Y, Ling Q, Wang H, Haung H (2008) Ribosomal proteins promote leaf adaxial identity. Development 135(7):1325–1334CrossRefPubMedGoogle Scholar
  69. Yu Y, Ji H, Doudna JA, Leary JA (2005) Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes. Protein Sci 14:1438–1446CrossRefPubMedGoogle Scholar
  70. Zanetti ME, Chang IF, Gong F, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138:624–635CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Kathleen Szick-Miranda
    • 1
  • Ammar S. Zanial
    • 1
  • Ali S. Zanial
    • 1
  • Stacey Abidayo
    • 1
  • Karie L. C. Slater
    • 1
  1. 1.Department of BiologyCalifornia State UniversityBakersfieldUSA

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