메뉴 건너뛰기




Volumn 5, Issue November, 2014, Pages 1-4

The conundrum of discordant protein and mRNA expression. Are plants special?

Author keywords

Alternative splicing; Gene expression; Omics; Post transcriptional regulation; Ribosomes; Systems biology

Indexed keywords


EID: 84910129169     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2014.00619     Document Type: Note
Times cited : (55)

References (31)
  • 1
    • 84866074972 scopus 로고    scopus 로고
    • Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit
    • Baerenfaller, K., Massonnet, C., Walsh, S., Baginsky, S., Bühlmann, P., Hennig, L., et al. (2012). Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol. Syst. Biol. 8, 606. doi: 10.1038/msb.2012.39.
    • (2012) Mol. Syst. Biol , vol.8 , pp. 606
    • Baerenfaller, K.1    Massonnet, C.2    Walsh, S.3    Baginsky, S.4    Bühlmann, P.5    Hennig, L.6
  • 2
    • 72949089708 scopus 로고    scopus 로고
    • Global signatures of protein and mRNA expression levels
    • De Sousa Abreu, R., Penalva, L. O., Marcotte, E. M., and Vogel, C. (2009). Global signatures of protein and mRNA expression levels. Mol. Biosyst. 5, 1512-1526. doi: 10.1039/b908315d.
    • (2009) Mol. Biosyst , vol.5 , pp. 1512-1526
    • De Sousa Abreu, R.1    Penalva, L.O.2    Marcotte, E.M.3    Vogel, C.4
  • 3
    • 74949084336 scopus 로고    scopus 로고
    • Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Filichkin, S. A., Priest, H. D., Givan, S. A., Shen, R., Bryant, D. W., Fox, S. E., et al. (2010). Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20, 45-58. doi: 10.1101/gr.093302.109.
    • (2010) Genome Res , vol.20 , pp. 45-58
    • Filichkin, S.A.1    Priest, H.D.2    Givan, S.A.3    Shen, R.4    Bryant, D.W.5    Fox, S.E.6
  • 4
    • 84859999981 scopus 로고    scopus 로고
    • Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics
    • Hummel, M., Cordewener, J. H., de Groot, J. C., Smeekens, S., America, A. H., and 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, 1024-1038. doi: 10.1002/pmic.201100413.
    • (2012) Proteomics , vol.12 , pp. 1024-1038
    • Hummel, M.1    Cordewener, J.H.2    de Groot, J.C.3    Smeekens, S.4    America, A.H.5    Hanson, J.6
  • 5
    • 84894318608 scopus 로고    scopus 로고
    • Ribosome profiling: New views of translation, from single codons to genome scale
    • Ingolia, N. T. (2014). Ribosome profiling: new views of translation, from single codons to genome scale. Nat. Rev. Genet. 15, 205-213. doi: 10.1038/nrg3645.
    • (2014) Nat. Rev. Genet , vol.15 , pp. 205-213
    • Ingolia, N.T.1
  • 6
    • 84891945795 scopus 로고    scopus 로고
    • Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis
    • Juntawong, P., Girke, T., Bazin, J., and Bailey-Serres, J. (2014). Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 111, E203-E212. doi: 10.1073/pnas.1317811111.
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. E203-E212
    • Juntawong, P.1    Girke, T.2    Bazin, J.3    Bailey-Serres, J.4
  • 7
  • 9
    • 84890795845 scopus 로고    scopus 로고
    • Protein synthesis rate is the predominant regulator of protein expression during differentiation
    • Kristensen, A. R., Gsponer, J., and Foster, L. J. (2013). Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol. Syst. Biol. 9, 689 doi: 10.1038/msb.2013.47.
    • (2013) Mol. Syst. Biol , vol.9 , pp. 689
    • Kristensen, A.R.1    Gsponer, J.2    Foster, L.J.3
  • 10
  • 11
    • 84879222333 scopus 로고    scopus 로고
    • Mapping gene activity of Arabidopsis root hairs
    • Lan, P., Li, W., Lin, W. D., Santi, S., and Schmidt, W. (2013). Mapping gene activity of Arabidopsis root hairs. Genome Biol. 14:R67. doi: 10.1186/gb-2013-14-6-r67.
    • (2013) Genome Biol , vol.14
    • Lan, P.1    Li, W.2    Lin, W.D.3    Santi, S.4    Schmidt, W.5
  • 12
    • 84869236431 scopus 로고    scopus 로고
    • Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation
    • Lan, P., Li, W., and Schmidt, W. (2012). Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. Mol. Cell. Proteomics 11, 1156-1166. doi: 10.1074/mcp.M112.020461.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1156-1166
    • Lan, P.1    Li, W.2    Schmidt, W.3
  • 13
    • 79955639512 scopus 로고    scopus 로고
    • The enigma of eIF5A in the iron deficiency response of Arabidopsis
    • Lan, P., and Schmidt, W. (2011). The enigma of eIF5A in the iron deficiency response of Arabidopsis. Plant Signal. Behav. 6, 528-530. doi: 10.4161/psb.6.4.14747.
    • (2011) Plant Signal. Behav , vol.6 , pp. 528-530
    • Lan, P.1    Schmidt, W.2
  • 14
    • 79960581086 scopus 로고    scopus 로고
    • A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
    • Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., et al. (2011). A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol. 7:514. doi: 10.1038/msb.2011.48.
    • (2011) Mol. Syst. Biol , vol.7 , pp. 514
    • Lee, M.V.1    Topper, S.E.2    Hubler, S.L.3    Hose, J.4    Wenger, C.D.5    Coon, J.J.6
  • 15
    • 84879697865 scopus 로고    scopus 로고
    • Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots
    • Li, W., Lin, W. D., Ray, P., Lan, P., and Schmidt, W. (2013). Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiol. 162, 1750-1763. doi: 10.1104/pp.113.217778.
    • (2013) Plant Physiol , vol.162 , pp. 1750-1763
    • Li, W.1    Lin, W.D.2    Ray, P.3    Lan, P.4    Schmidt, W.5
  • 16
    • 84862908082 scopus 로고    scopus 로고
    • Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis
    • Liu, M. J., Wu, S. H., Chen, H. M., and Wu, S. H. (2012). Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. Mol. Syst. Biol. 8:566. doi: 10.1038/msb.2011.97.
    • (2012) Mol. Syst. Biol , vol.8 , pp. 566
    • Liu, M.J.1    Wu, S.H.2    Chen, H.M.3    Wu, S.H.4
  • 17
    • 84861890038 scopus 로고    scopus 로고
    • Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
    • Marquez, Y., Brown, J. W., Simpson, C., Barta, A., and Kalyna, M. (2012). Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22, 1184-1195. doi: 10.1101/gr.134106.111.
    • (2012) Genome Res , vol.22 , pp. 1184-1195
    • Marquez, Y.1    Brown, J.W.2    Simpson, C.3    Barta, A.4    Kalyna, M.5
  • 18
    • 73249145845 scopus 로고    scopus 로고
    • Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
    • Mustroph, A., Zanettia, M. E., Jang, C. J. H., Holtan, H. E., Repetti, P. P., Galbraith, D. W., et al. (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 106, 18843-18848. doi: 10.1073/pnas.0906131106.
    • (2009) Proc. Natl. Acad. Sci. U.S.A , vol.106 , pp. 18843-18848
    • Mustroph, A.1    Zanettia, M.E.2    Jang, C.J.H.3    Holtan, H.E.4    Repetti, P.P.5    Galbraith, D.W.6
  • 19
    • 84884608076 scopus 로고    scopus 로고
    • The ribosomal protein Rpl22 controls ribosome composition by directly repressing expression of its own paralog, Rpl22l1
    • O'Leary, M. N., Schreiber, K. H., Zhang, Y., Duc, A. C., Rao, S., Hale, J. S., et al. (2013). The ribosomal protein Rpl22 controls ribosome composition by directly repressing expression of its own paralog, Rpl22l1. PLoS Genet. 9:e1003708. doi: 10.1371/journal.pgen.1003708.
    • (2013) PLoS Genet , vol.9
    • O'Leary, M.N.1    Schreiber, K.H.2    Zhang, Y.3    Duc, A.C.4    Rao, S.5    Hale, J.S.6
  • 20
    • 84899649317 scopus 로고    scopus 로고
    • Correlation of mRNA and protein abundance in the developing maize leaf
    • Ponnala, L., Wang, Y., Sun, Q., and van Wijk, K. J. (2014). Correlation of mRNA and protein abundance in the developing maize leaf. Plant J. 78, 424-440. doi: 10.1111/tpj.12482.
    • (2014) Plant J , vol.78 , pp. 424-440
    • Ponnala, L.1    Wang, Y.2    Sun, Q.3    van Wijk, K.J.4
  • 21
    • 0345602742 scopus 로고    scopus 로고
    • Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock
    • Preiss, T., Baron-Benhamou, J., Ansorge, W., and Hentze, M. W. (2003). Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat. Struct. Biol. 10, 1039-1047. doi: 10.1038/nsb1015.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 1039-1047
    • Preiss, T.1    Baron-Benhamou, J.2    Ansorge, W.3    Hentze, M.W.4
  • 23
    • 84870312202 scopus 로고    scopus 로고
    • Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors
    • Rosado, A., Li, R., van de Ven, W., Hsu, E., and Raikhel, N. V. (2012). Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors. Proc. Natl. Acad. Sci. U.S.A. 109, 19537-19544. doi: 10.1073/pnas.1214774109.
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 19537-19544
    • Rosado, A.1    Li, R.2    van de Ven, W.3    Hsu, E.4    Raikhel, N.V.5
  • 24
    • 26944452075 scopus 로고    scopus 로고
    • Identification of cis -elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis
    • Tatematsu, K., Ward, S., Leyser, O., Kamiya, Y., and Nambara, E. (2005). Identification of cis -elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol. 138, 757-766. doi: 10.1104/pp.104.057984.
    • (2005) Plant Physiol , vol.138 , pp. 757-766
    • Tatematsu, K.1    Ward, S.2    Leyser, O.3    Kamiya, Y.4    Nambara, E.5
  • 25
    • 0033389293 scopus 로고    scopus 로고
    • Plant interstitial telomere motifs participate in the control of gene expression in root meristems
    • Tremousaygue, D., Manevski, A., Bardet, C., Lescure, N., and Lescure, B. (1999). Plant interstitial telomere motifs participate in the control of gene expression in root meristems. Plant J. 20, 553-561. doi: 10.1046/j.1365-313X.1999.00627.x.
    • (1999) Plant J , vol.20 , pp. 553-561
    • Tremousaygue, D.1    Manevski, A.2    Bardet, C.3    Lescure, N.4    Lescure, B.5
  • 26
    • 0035868428 scopus 로고    scopus 로고
    • A complete map of the human ribosomal protein genes: Assignment of 80 genes to the cytogenetic map and implications for human disorders
    • Uechi, T., Tanaka, T., and Kenmochi, N. (2001). A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders. Genomics 72, 223-230. doi: 10.1006/geno.2000.6470.
    • (2001) Genomics , vol.72 , pp. 223-230
    • Uechi, T.1    Tanaka, T.2    Kenmochi, N.3
  • 27
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel, C., and Marcotte, E. M. (2012). Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 13, 227-232. doi: 10.1038/nrg3185.
    • (2012) Nat. Rev. Genet , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 28
    • 85047687088 scopus 로고    scopus 로고
    • Reconstruction of protein networks from an atlas of maize seed proteotypes
    • Walley, J. W., Shen, Z., Sartor, R., Wu, K. J., Osborn, J., Smith, L. G., et al. (2013). Reconstruction of protein networks from an atlas of maize seed proteotypes. Proc. Natl. Acad. Sci. U.S.A. 110, E4808-E4817. doi: 10.1073/pnas.1319113110.
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. E4808-E4817
    • Walley, J.W.1    Shen, Z.2    Sartor, R.3    Wu, K.J.4    Osborn, J.5    Smith, L.G.6
  • 29
    • 84887341869 scopus 로고    scopus 로고
    • Expression changes of ribosomal proteins in phosphate-and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition
    • Wang, J. Y., Lan, P., Gao, H. M., Zheng, L., Li, W. F., and Schmidt, W. (2013). Expression changes of ribosomal proteins in phosphate-and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition. BMC Genomics 14:783. doi: 10.1186/1471-2164-14-783.
    • (2013) BMC Genomics , vol.14 , pp. 783
    • Wang, J.Y.1    Lan, P.2    Gao, H.M.3    Zheng, L.4    Li, W.F.5    Schmidt, W.6
  • 30
    • 70349669222 scopus 로고    scopus 로고
    • Transcript profiling provides evidence of functional divergence and expression networks among ribosomal protein gene paralogs in Brassica napus
    • Whittle, C. A., and 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, 2203-2219. doi: 10.1105/tpc.109.068411.
    • (2009) Plant Cell , vol.21 , pp. 2203-2219
    • Whittle, C.A.1    Krochko, J.E.2
  • 31
    • 84893707191 scopus 로고    scopus 로고
    • Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens
    • Wu, H. P., Su, Y. S., Chen, H. C., Chen, Y. R., Wu, C. C., Lin, W. D., et al. (2014). Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol. 15:R10. doi: 10.1186/gb-2014-15-1-r10.
    • (2014) Genome Biol , vol.15
    • Wu, H.P.1    Su, Y.S.2    Chen, H.C.3    Chen, Y.R.4    Wu, C.C.5    Lin, W.D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.