Nuclear Structure and Function Research Group

Resources for CHAPTER 4b: TRANSLATION (an expanded version of Box 1-4)
Updated on 10 March, 2016

Principles
The translation machinery
    tRNAs as adaptors
        Box. tRNA maturation
    Aminoacyl-tRNA synthetase couples an amino acid to the appropriate tRNA
    The ribosome - the translation machine
    The ribosome is a ribozyme
Decoding the message in the ribosome
    Polyribosomes are responsible for protein synthesis
        Box. Initiation in bacteria
    Initiation in eukaryotes
        Box. Internal ribosome entry sites
    Elongation
    Elongation factors
        Box. Inhibitors of protein synthesis
        Box. Translation factors and disease
Fidelity and quality control
    The economics of protein production and degradation
    Protein folding and misfolding
    Molecular chaperones facilitate folding
    Proteasomes and the disposal of misfolded proteins
        Box. Prions, aggresomes
    Nuclear translation


Principles
Reference:
Kapp, L.D., and Lorsch, J.R. (2004). The molecular mechanics of eukaryotic translation. Annu. Rev. Biochem. 73, 657-704. [PubMed]
Merrick, W.C. (2010). Eukaryotic protein synthesis: still a mystery. J. Biol. Chem. 285, 21197-21201. [PubMed]
Moore, P.B., and Steitz, T.A. (2011). The roles of RNA in the synthesis of protein. Cold Spring Harb. Perspect. Biol. 3, a003780. [PubMed]
Web link:
http://learn.genetics.utah.edu/content/begin/dna/ Primer from the University of Utah.

The translation machinery

tRNAs as adaptors
Reference:
Rich, A. (2009). The era of RNA awakening: structural biology of RNA in the early years. Q. Rev. Biophys. 42, 117-137. [PubMed]

Box. tRNA maturation
Reference:
Helm, M. (2006). Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 34, 721-33. [PubMed]
Hopper, A.K., Pai, D.A., and Engelke, D.R. (2010). Cellular dynamics of tRNAs and their genes. FEBS Lett. 584, 310-317. [PubMed]

Aminoacyl-tRNA synthetase couples an amino acid to the appropriate tRNA
Reference:
Chin, J.W. (2012). Reprogramming the genetic code. Science 336, 428-429. [PubMed]
Ling, J., Reynolds, N., and Ibba, M. (2009). Aminoacyl-tRNA synthesis and translational quality control. Annu. Rev. Microbiol. 63, 61-78. [PubMed]

The ribosome - the translation machine
Reference:
Dinman, J.D. (2009). The eukaryotic ribosome: current status and challenges. J. Biol. Chem 284, 11761-11765. [PubMed]
Moore, P.B., and Steitz, T.A. (2011). The roles of RNA in the synthesis of protein. Cold Spring Harb. Perspect. Biol. 3, a003780. [PubMed]
Simonović, M., and Steitz, T.A. (2009). A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Biochim. Biophys. Acta 1789, 612-623. [PubMed]
Thomson, E., Ferreira-Cerca, S., and Hurt, E. (2013). Eukaryotic ribosome biogenesis at a glance. J Cell Sci 126, 4815-4821. [PubMed]

The ribosome is a ribozyme
Reference:
Moore, P.B. (2009). The ribosome returned. J. Biol. 8, 8. [PubMed]
Web link:
http://www.imb-jena.de/RNA.html RNA World site.

Decoding the message in the ribosome
Reference:
Noller, H.F. (2005). RNA structure: reading the ribosome. Science 309, 1508-1514. [PubMed]

Polyribosomes are responsible for protein synthesis
Reference:
Brandt, F., Carlson, L.A., Hartl, F.U., Baumeister, W., and Grünewald, K. (2010). The three-dimensional organization of polyribosomes in intact human cells. Mol. Cell 39, 560-569. [PubMed]
Warner, J.R. and Knopf, P.M. (2002). The discovery of polyribosomes. Trends Biochem Sci. 27, 376-380. [PubMed]

Box. Initiation in bacteria
Reference:
Laursen, B.S., Sorensen, H.P., Mortensen, K.K., and Sperling-Petersen, H.U. (2005). Initiation of protein synthesis in bacteria. Microbiol. Mol. Biol. Rev. 69, 101-123. [PubMed]

Initiation in eukaryotes
Reference:
Hinnebusch, A.G., and Lorsch, J.R. (2012). The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb. Perspect. Biol. 4, doi:pii: a011544. 10.1101/cshperspect.a011544.
Jackson, R.J., Hellen, C.U., and Pestova, T.V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113-127. [PubMed]
Maquat, L.E., Tarn, W.Y., and Isken, O. (2010). The pioneer round of translation: features and functions. Cell 142, 368-374. [PubMed]
Merrick, W.C. (2010). Eukaryotic protein synthesis: still a mystery. J. Biol. Chem. 285, 21197-21201. [PubMed]

Box. Internal ribosome entry sites
Reference:
Filbin, M.E., and Kieft, J.S. (2009). Toward a structural understanding of IRES RNA function. Curr. Opin. Struct. Biol. 19, 267-276. [PubMed]

Elongation
Reference:
Groppo, R., and Richter, J.D. (2009). Translational control from head to tail. Curr. Opin. Cell Biol. 21, 444-451. [PubMed]

Elongation factors
Reference:
Nilsson, J., and Nissen, P. (2005). Elongation factors on the ribosome. Curr. Opin. Struct. Biol. 15, 349-354. [PubMed]

Box. Inhibitors of protein synthesis
Reference:
Tenson, T., and Mankin, A. (2006). Antibiotics and the ribosome. Mol. Microbiol. 59, 1664-1677. [PubMed]
Web link:
Sohmen, D., Harms, J.M., Schlünzen, F., and Wilson, D.N. (2009). SnapShot: Antibiotic inhibition of protein synthesis I. Cell 138, 1248. [PubMed]
Sohmen, D., Harms, J,M., Schlünzen, F., and Wilson, D.N. (2009). Enhanced SnapShot: Antibiotic inhibition of protein synthesis II. Cell 139, 212-212. [PubMed]

Box. Translation factors and disease
Reference:
Scheper, G.C., van der Knaap, M.S., and Proud, C.G. (2007). Translation matters: protein synthesis defects in inherited disease. Nat. Rev. Genet. 8, 711-723. [PubMed]

Fidelity and quality control
Reference:
Francklyn, C.S. (2008). DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression. Biochemistry 47, 11695-11703. [PubMed]
Hershey, J.W., Sonenberg, N., and Mathews, M.B. (2012). Principles of translational control: an overview. Cold Spring Harb. Perspect. Biol. doi: 10.1101/cshperspect.a011528.
Kurosaki, T., and Maquat, L.E. (2016). Nonsense-mediated mRNA decay in humans at a glance. J. Cell Sci. 129, 461-467. [PubMed]
Pechmann, S., Willmund, F., and Frydman, J. (2013). The ribosome as a hub for protein quality control. Mol. Cell 49, 411-421. [PubMed]

The economics of protein production and degradation
Reference:
Yewdell, J.W. (2001). Not such a dismal science: the economics of proteins synthesis, folding, degradation and antigen processing. Trends Cell Biol. 11, 294-297. [PubMed]
Schubert, U., Antón, L.C., Gibbs, J., Norbury, C.C., Yewdell, J.W. and Bennink, J.R. (2001). Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404, 770-774. [PubMed]

Protein folding and misfolding
Reference:
Fersht, A.R. (2008). From the first protein structures to our current knowledge of protein folding: delights and scepticisms. Nat. Rev. Mol. Cell Biol. 9, 650-654. [PubMed]
Hartl, F.U., and Hayer-Hartl, M. (2009). Converging concepts of protein folding in vitro and in vivo. Nat. Struct. Mol. Biol. 16, 574-581. [PubMed]
Winklhofer, K.F., Tatzelt, J., and Haass, C. (2008). The two faces of protein misfolding: gain- and loss-of-function in neurodegenerative diseases. EMBO J. 27, 336-349. [PubMed]

Molecular chaperones facilitate folding
Reference:
Hartl, F.U., and Hayer-Hartl, M. (2009). Converging concepts of protein folding in vitro and in vivo. Nat. Struct. Mol. Biol. 16, 574-581. [PubMed]
Liberek, K., Lewandowska, A., and Zietkiewicz, S. (2008). Chaperones in control of protein disaggregation. EMBO J. 27, 328-335. [PubMed]

Proteasomes and the disposal of misfolded proteins
Reference:
Navon, A., and Ciechanover, A. (2009). The 26S proteasome - from basic mechanisms to drug targeting. J. Biol. Chem. [PubMed]

Box. Prions, aggresomes
Reference:
Cobb, N.J., and Surewicz, W.K. (2009). Prion diseases and their biochemical mechanisms. Biochemistry 48, 2574-2585. [PubMed]
Halfmann, R., Jarosz, D.F., Jones, S.K., Chang, A., Lancaster, A.K., and Lindquist, S. (2012). Prions are a common mechanism for phenotypic inheritance in wild yeasts. Nature 482, 363-368. [PubMed]
Soto, C. (2012). Transmissible proteins: expanding the prion heresy. Cell 149, 968-977. [PubMed]
Tuite, M.F., and Cox, B.S. (2009). Prions remodel gene expression in yeast. Nat. Cell Biol. 11, 241-243. [PubMed]
Web link:
http://learn.genetics.utah.edu/content/begin/dna/prions/ Primer from the University of Utah.

Nuclear translation
See 'Nuclear translation' in Chapter 4: Transcription.

 

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