2,456
Views
7
CrossRef citations to date
0
Altmetric
Articles; Agriculture and Environmental Biotechnology

Identification, molecular characterization and expression analysis of RPL24 genes in three Cucurbitaceae family members: cucumber, melon and watermelon

, , , , &
Pages 1024-1034 | Received 28 May 2015, Accepted 30 Jul 2015, Published online: 11 Sep 2015

References

  • Winfield IJ. FAO statistical yearbook 2012: world food and agriculture. J Fish Biol. 2012;81:2095–2096.
  • Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L. Natl Genet. 2009;41:1275–1281.
  • Lough TJ, Lucas WJ. Integrative plant biology: role of phloem long-distance macromolecular trafficking. Annu Rev Plant Biol. 2006;57:203–232.
  • Xoconostle-Cázares B, Xiang Y, Ruiz-Medrano R, et al. Plant paralog to viral movement protein that potentiates transport of mRNA into the phloem. Science. 1999;283:94–98.
  • Garcia-Mas J, Benjak A, Sanseverino W, et al. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA. 2012;109(29):11872–11877.
  • Reyes R, Vazquez D, Ballesta JP. Peptidyl transferase center of rat-liver ribosome cores. Eur J Biochem. 1977;73:25–31.
  • Hartzog GA, Fu J. The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation. Biochim Biophys Acta. 2013;1829(1):105–115.
  • Werner F. A nexus for gene expression-molecular mechanisms of Spt5 and NusG in the three domains of life. J Mol Biol. 2012;417(1–2):13–27.
  • Ben-Shem A, Garreau de Loubresse N, Melnikov S, et al. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science. 2011;334(6062):1524–1529.
  • Klinge S, Voigts-Hoffmann F, Leibundgut M, et al. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science. 2011;334(6058):941–948.
  • Steiner T, Kaiser JT, Marinkovic S, et al. Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities. EMBO J. 2002;21:4641–4653.
  • Kyrpides NC, Woese CR, Ouzounis CA. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci. 1996;21(11):425–426.
  • Zhang Y, Cheng YT, Bi D, et al. MOS2, a Protein containing G-patch and KOW motifs, is essential for innate immunity in arabidopsis thaliana. Curr Biology. 2005;15(21):1936–1942.
  • Wool IG. Extraribosomal functions of ribosomal proteins. Trends Biochem. 1996;21:164–165.
  • Reynaud E, Bolshakov VN, Barajas V, et al. Antisense suppression of the putative ribosomal protein S3A gene disrupts ovarian development in Drosophila melanogaster. Mol Gen Genet. 1997;256:462–467.
  • Qian S, Hongo S, Jacobs-Lorena M. Antisense ribosomal protein gene expression specifically disrupts oogenesis in Drosophila melanogaster. Proc Natl Acad Sci USA. 1988;85:9601–9605.
  • Nishimura T, Wada T, Okada K. A key factor of translation reinitiation, ribosomal protein L24, is involved in gynoecium development in Arabidopsis. Biochem Soc Trans. 2004;32:611–613.
  • Kousteni S, Tura-Kockar FD, Ramji P. Sequence and expression analysis of a novel Xenopus laevis cDNA that encodes a protein similar to bacterial and chloroplast ribosomal protein L24. Gene. 1999;235:13–18.
  • Read LK, Militello KT, Nerantzakis GE. Cloning and characterisation of a cDNA encoding the Trypanosoma brucei ribosomal protein L24p. Int J Parasitol. 1999;29:601–605.
  • Tsutsumi N, Takusagawa S, Suzuki H. Molecular cloning and nucleotide sequencing of nuclear genes coding for the chloroplast ribosomal proteins L13, L24, L28 of rice (Oryza sativa L.) Plant Sci. 1996;121:167–174.
  • Rasmussen SK, Klausen J. Ribosomal protein L24E homologue (accession No. X94296) is expressed in barley endosperms (PGR96-011). Plant Physiol. 1996;110:1047–1048.
  • Estebsan R, Labrador E, Dopico B. Ribosomal protein L24 homologue is expressed in Cicer arietinum L. epicotyls. Plant Physiol. 1998;117:717–718.
  • Baronas-Lowell DM, Warner JR. Ribosomal protein L30 is dispensible in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1990;10:5235–5243.
  • Eng FJ, Warner JR. Structural basis for the regulation of splicing of a yeast messenger RNA. Cell. 1991;65:797–804.
  • Bult CJ, White O, Olsen GJ, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996;273:1058–1073.
  • Kawarabayasi Y, Sawada M, Horikawa H, et al. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 1998;5:55–76.
  • Venter HP, Clayton RA, Tomb JF, et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997;390:364–370.
  • Hoagland DR, Arnon DI. The water-culture method for growing plants without soil. Calif Agric Exp Stn Circ. 1950;347:1–32
  • Baloglu MC, Eldem V, Hajyzadeh M, et al. Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS One. 2014;9:e96014.
  • Livak KJ, Schmittgen TD. Analysis of relative gene expression datausing real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–408.
  • Baloglu MC, Patir MG. Molecular characterization, 3D model analysis, and expression pattern of the CmUBC gene encoding the melon ubiquitin-conjugating enzyme under drought and salt stress conditions. Biochem Gen. 2014;52:90–105.
  • Goodstein DM, Shu S, Howson R, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40:D1178–D1186.
  • Guo S, Zhang J, Sun H, et al. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Natl Genet. 2012;45:51–58.
  • Letunic I, Doerks T, Bork P. Smart 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2012;40:D302–D305.
  • Punta M, Coggill PC, Eberhardt RY, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290–D301.
  • Guo AY, Zhu QH, Chen X, et al. GSDS: a gene structure display server. Yi Chuan. 2007;29:1023–1026.
  • Tamura K, Peterson D, Peterson N, et al. Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–2739.
  • Thompson JD, Gibson TJ, Plewniak F, et al. The Clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–4882.
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–425.
  • Letunic I, Bork P. Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475–478.
  • Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Paper presented at: Intelligent Systems for Molecular Biology. Proceedings of the Second International Conference. August 14–17, 1994; Menlo Park, CA.
  • Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33:W116–W120.
  • Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28:235–242.
  • Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Natl Protoc. 2009;4(3):363–371.
  • Pateraki I, Sanmartin M, Kalamaki MS, et al. Molecular characterization and expression studies during melon fruit development and ripening of L-galactono-1,4-lactone dehydrogenase. J Exp Bot. 2004;55(403):1623–1633.
  • Hu LF, Liu SQ. Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers. Genet Mol Biol. 2011;34:624–633.
  • Marchler-Bauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015;43(Database issue):D222–D226.
  • Puranik S, Sahu PP, Srivastava PS, et al. NAC proteins: regulation and role in stress tolerance. Trends Plant Sci. 2012;17:1360–1385.
  • Söding J. Protein homology detection by HMM–HMM comparison. Bioinform. 2005;21:951–60.
  • Jefferys BR, Kelley LA, Sternberg MJ. Protein folding requires crowd control in a simulated cell. J Mol Biol. 2010;397:1329–1338.
  • Mukhopadhyay P, Reddy MK, Singla-Pareek SL, et al. Transcriptional downregulation of rice rpL32 gene under abiotic stress is associated with removal of transcription factors within the promoter region. PLoS ONE. 2011;6(11):e28058.
  • Kim KY, Park SW, Chung YS, et al. Molecular cloning of low-temperature-inducible ribosomal proteins from soybean. J Exp Bot. 2004;55:1153–1155.
  • Ludwig A, Tenhaken R. Suppression of the ribosomal L2 gene reveals a novel mechanism for stress adaptation in soybean. Planta. 2001;212:792–798.
  • Saez-Vasquez J, Gallois P, Delseny M. Accumulation and nuclear targeting of BnC24: a Brassica napus ribosomal protein corresponding to a mRNA accumulating in response to cold treatment. Plant Sci. 2000;156:35–46.
  • Brosché M, Strid A. The mRNA-binding ribosomal protein S26 as a molecular marker in plants: molecular cloning, sequencing and differential gene expression during environmental stress. Biochim Biophys Acta. 1999;1445:342–344.
  • Gao J, Kim SR, Chung YY, et al. Developmental and environmental regulation of two ribosomal protein genes in tobacco. Plant Mol Biol. 1994;25:761–770.
  • Rogalski M, Schöttler MA, Thiele W, et al. Rpl33: a nonessential plastid-encoded ribosomal protein in tobacco is required under cold stress conditions. Plant Cell. 2008;20:2221–2237.
  • Mukhopadhyay P, Singla-Pareek SL, Reddy MK, et al. Stress-mediated alterations in chromatin architecture correlate with down-regulation of a gene encoding 60S rpL32 in rice. Plant Cell Physiol. 2013;54(4):528–540.
  • Mahfouz MM, Kim S, Delauney AJ, Verma DP. Arabidopsis target of rapamycin interacts with raptor, which regulates the activity of S6 kinase in response to osmotic stress signals. Plant Cell. 2006;18:477–490.
  • Tatematsu K, Ward S, Leyser O, et al. Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol. 2005;138:757–766.
  • Wullschleger S, Loewith R, Oppliger W, et al. Molecular organization of target of rapamycin complex 2. J Biol Chem. 2005;280:30697–30704.
  • Kawaguchi R, Girke T, Bray EA, et al. Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J. 2004;38:823–839.
  • Turck F, Zilbermann F, Kozma SC, et al. Phytohormones participate in an S6 kinase signal transduction pathway in Arabidopsis. Plant Physiol. 2004;134:1527–1535.
  • Trémousaygue D, Garnier L, Bardet C, et al. Internal telomeric repeats and ‘TCP domain’ protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J. 2003;33:957–966.
  • Liu X, Baird WV. The ribosomal small-subunit protein S28 gene from Helianthus annuus (Asteraceae) is down-regulated in response to drought, high salinity, and abscisic acid. Am J Botany. 2003;90:526–531.
  • Giannino D, Frugis G, Ticconi C, et al. Isolation and molecular characterisation of the gene encoding the cytoplasmic ribosomal protein S28 in Prunus persica [L.] Batsch. Mol Gen Genet. 2000;263:201–212.
  • Beltrán-Peña E, Ortíz-López A, de Jiménez ES. Synthesis of ribosomal proteins from stored mRNAs early in seed germination. Plant Mol Biol. 1995;28:327–336.