Initiator tRNAs in Bacteria and Eukaryotes

Abstract

A special type of transfer ribonucleic acid (tRNA) is employed in the initiation step of protein synthesis. The differences between the tRNAs involved in initiation and elongation establish the specificity and recognition of the tRNAs by the factors and enzymes involved in the initiation and elongation steps of protein synthesis. The important determinants of the initiator tRNA in bacteria are the absence of a Watson–Crick base pair between positions 1 and 72 in the acceptor stem and the presence of three conserved consecutive G:C base pairs in the anticodon stem. Formylation of the methionine attached to this initiator tRNA is an important feature. Conversely, the eukaryotic initiator tRNA is mainly determined by the presence of a particular A1:U72 Watson–Crick base pair in the acceptor stem as well as the nature of the base pairs 50:64 and 51:63 in the TΨC (T) stem.

Key concepts

  • Initiator tRNA brings methionine to the initiation complex for initiation of protein synthesis.

  • Structural features of initiator tRNAs ensure that they are recognized by translation initiation factors and discriminated against by translation elongation factors.

  • The important determinants of initiator tRNA in bacteria are the absence of a Watson–Crick base pair between positions 1 and 72 in the acceptor stem and the presence of three conserved consecutive G:C base pairs in the anticodon stem.

  • The important determinants of initiator tRNA in eukaryotes are the presence of a particular A1:U72 Watson–Crick base pair in the acceptor stem as well as the nature of the base pairs 50:64 and 51:63 in the T stem.

  • Bacterial initiator tRNA is aminoacylated by methionyl tRNA synthetase, which mainly interacts with the anticodon.

  • The methionine of bacterial initiator tRNA is formylated by methionyl tRNA transformylase, which mainly recognizes the absence of the 1:72 base pair.

  • Initiation factor IF2 ensures recognition and correct binding of bacterial initiator tRNA to the ribosomal P‐site by interacting primarily with the formyl group and the 3′ end of the acceptor arm.

  • Initiation factor IF3 performs proofreading of the 30S initiation complex by verifying base pairing between 5′C of bacterial initiator tRNA anticodon and 3′G of mRNA initiation codon.

  • Bacterial initiator tRNA undergoes several conformational changes during translation initiation to ensure correct positioning in the P‐site of the ribosome.

  • Bacterial initiator tRNA is not a substrate for peptidyl tRNA hydrolase.

Keywords: initiator tRNA; formyl‐methionyl‐tRNA; formylation; translation; initiation

Figure 1.

Cloverleaf structures of initiator and elongator tRNAs. The regions important for initiator and elongator identity are marked with colours and discussed in the text. (a) tRNAf1Met from E. coli (Dube and Marcker, ). (b) tRNAiMet from yeast strain Saccharomyces cerevisiae (Desgrès et al., ). (c) tRNAmMet from E. coli (Cory and Marcker, ). (d) tRNAPhe (major variant) from S. cerevisiae (Keith and Dirheimer, ). tRNA sequences can be obtained from the online database (http://www.staff.uni‐bayreuth.de/∼btc914/search/index.html). C, cytidine; G, guanosine; U, uridine; A, adenosine; s4U, 4thiouridine; D, dihydrouridine; Cm, 2′‐O‐methylcytidine; m7G, 7‐methylguanosine; T, 5‐methyluridine; Ψ, pseudouridine; m1G, 1‐methylguanosine; m2G, N2‐methylguanosine; m22G, N2,N2‐dimethylguanosine; t6A, N6threonylcarbamoyladenosine; m5C, 5‐methylcytidine; m1A, 1‐methyladenosine; Ar(p), 2′‐O‐ribosyladenosine (phosphate); Gm, 2′‐O‐methylguanosine; ac4C, N4‐acetylcytidine; acp3U, 3‐(3‐amino‐3‐carboxypropyl)uridine; yW, wybutosine.

Figure 2.

Examples of anticodon arm structures of different tRNAs. Bacterial tRNAs: E. coli initiator tRNAf2Met (coordinates obtained from the Brookhaven Protein Data Bank (PDB) entry 3CW5), E. coli initiator tRNAf2Met in complex with MTF (PDB entry 2FMT), E. coli initiator tRNAf1Met in the P‐site of a 70S complex (PDB entry 2J00) and Aquifex aeolicus elongator tRNAmMet in complex with MetRS (PDB entry 2CSX). Eukaryotic tRNAs: initiator tRNAiMet (PDB entry 1YFG) and elongator tRNAPhe (PDB entry 1EHZ) from S. cerevisiae. Colours are used to highlight base pairs or groups of bases. Red, base positions 29, 37 and 41 (involved in the base triple in E. coli initiator tRNAf2Met); orange, base positions 30 and 40; green, base positions 31 and 39; cyan, base positions 32 and 38; blue, base position 33; magenta, base positions 34, 35 and 36 (the anticodon).

Figure 3.

Cloverleaf structure of fMet‐tRNAfMet from E. coli. The important regions for interaction with proteins are coloured. Green, region that initiation factor 3 (IF3) ensures recognition of; red, regions that interact with methionyl tRNA transformylase; black boxes, regions that interact with methionyl tRNA synthetase; grey, regions that interact with IF2; blue, the formyl group which causes recognition by IF2 and rejection by elongation factorEF1A; yellow, the nucleotides 1 and 72 that confer the rejection of peptidyl tRNA hydrolase.

Figure 4.

Structures of tRNAfMet and interacting proteins: (a) methionyl tRNA synthetase (MetRS) and (b) methionyl tRNA transformylase (MTF). (a) Left: tRNAfMet where the sites that interact with MetRS according to footprinting data are coloured red. Right: Monomeric C‐truncated form of MetRS from E. coli, with A. aeolicus tRNAmMet (blue) docked into the tRNA binding site, to indicate the regions of interaction (coordinates are obtained from PDB entry:1QQT for MetRS and 2CSX for tRNAmMet). (b) Left: tRNAfMet where the sites that interact with MTF according to footprinting data are coloured red. Right: complex between MTF and fMet‐tRNAfMet (blue) (PDB entry: 2FMT). C1 and A72 of tRNAfMet are highlighted in magenta.

Figure 5.

Bacterial initiator tRNAfMet in a ribosomal context: (a) 30S initiation complex comprising 30S (orange), IF1 (blue), IF2 (green) and tRNAfMet(red). The location of the four IF2 domains and GTP (yellow) are shown. Modified from Simonetti et al., . (b) 70S pretranslocation complex comprising 30S (cyan), 50S (yellow), mRNA (red), tRNAfMet (blue) in the P‐site, anticodon arm of tRNAPhe (magenta) in the A‐site and a noncognate tRNA (grey) in the E‐site (the E‐site is empty in the pretranslocation complex, and the tRNA is only displayed to show the location of the E‐site). (c) P‐site tRNAfMet (blue) in the 70S pretranslocation complex surrounded by 30S proteins S9 and S13 and helices h24 and h42 of 16S rRNA (cyan), 50S proteins L5, L16 and L27 and helices H69 and P‐loop of 23S rRNA (yellow), mRNA (red), A‐site anticodon arm of tRNAPhe (magenta) and E‐site noncognate tRNA (grey). (d) Details of P‐site tRNAfMet (blue) in the 70S pretranslocation complex. Base pairs G29:C41 and G30:C40 (orange) interact with A1338 and G1339 of 16S rRNA, which together with A790 of 16S rRNA form a gate between the P‐ and E‐sites. The mRNA (red) AUG start codon and the anticodon are shown in magenta. The tRNA is kinked at positions G26 and A44 (lightblue). The 3′end bases C74, C75 and A76 (yellow) interact with G2251, G2252 and A2451 of 23S rRNA. Coordinates are obtained from PDB entries 2J00 and 2J01 for 70S.

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References

Abdi NM and Fredrick K (2005) Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in E. coli. RNA 11: 1624–1632.

Allen GS, Zavialov A, Gursky R, Ehrenberg M and Frank J (2005) The cryo‐EM structure of a translation initiation complex from E. coli. Cell 121: 703–712.

Åstrøm SU, von Pawel‐Rammingen U and Bystrøm AS (1993) The yeast initiator tRNAMet can act as an elongator tRNAMet in vivo. Journal of Molecular Biology 233: 43–58.

Barraud P, Schmitt E, Mechulam Y, Dardel F and Tisné C (2008) A unique conformation of the anticodon stem‐loop is associated with the capacity of tRNAfMet to initiate protein synthesis. Nucleic Acids Research 36: 4894–4901.

Bell SD and Jackson SP (1998) Transcription and translation in archaea: a mosaic of eukaryal and bacterial features. Trends in Microbiology 6: 222–228.

Cory S and Marcker KA (1970) The nucleotide sequence of methionine transfer RNA‐M. European Journal of Biochemistry 12: 177–194.

Cory S, Dube SK, Clark BFC and Marcker KA (1968) Separation of two initiator transfer RNAs from E. coli. FEBS Letters 1: 259–261.

Das G, Thotala DK, Kapoor S et al. (2008) Role of 16S ribosomal RNA methylations in translation initiation in E. coli. EMBO Journal 27: 840–851.

Desgrès J, Keith G, Kuo KC and Gehrke CW (1989) Presence of phosphorylated O‐ribosyl‐adenosine in T‐psi‐stem of yeast methionine initiator tRNA. Nucleic Acids Research 17: 865–882.

Drabkin HJ, Estrella M and Rajbhandary UL (1998) Initiator–elongator discrimination in vertebrate tRNAs for protein synthesis. Molecular and Cellular Biology 18: 1459–1466.

Dube SK and Marcker KA (1969) The nucleotide sequence of N‐formyl‐methionyl‐transfer RNA. Partial digestion with pancreatic and T‐1 ribonuclease and derivation of the total primary structure. European Journal of Biochemistry 8: 256–262.

Dutka S, Meinnel T, Lazennec C, Mechulam Y and Blanquet S (1993) Role of the 1‐72 base pair in tRNAs for the activity of E. coli peptidyl‐tRNA hydrolase. Nucleic Acids Research 21: 4025–4030.

Guillon JM, Mechulam Y, Schmitter JM, Blanquet S and Fayat G (1992) Disruption of the Gene for Met‐tRNAfMet Formyltransferase Severely Impairs Growth of E. coli. Journal of Bacteriology 174: 4294–4301.

Hansen PK, Wikman F, Clark BFC, Hershey JWB and Petersen HU (1986) Interaction between initiator Met‐tRNAfMet and elongation factor EF‐Tu from E. coli. Biochimie 68: 697–703.

Kapp LD, Kolitz SE and Lorsch JR (2006) Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation. RNA 12: 751–764.

Keith G and Dirheimer G (1987) Evidence for the existence of an expressed minor variant of tRNAPhe in yeast. Biochemical and Biophysical Research Communications 142: 183–187.

Korostelev A, Trakhanov S, Laurberg M and Noller HF (2006) Crystal structure of a 70S ribosome‐tRNA complex reveals functional interactions and rearrangements. Cell 126: 1065–1077.

Lancaster L and Noller HF (2005) Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNA. Molecular Cell 20: 623–632.

Marck C and Grosjean H (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon‐sparing strategies and domain‐specific features. RNA 8: 1189–1232.

Mechulam Y, Schmitt E, Maveyraud L et al. (1999) Crystal structure of E. coli methionyl‐tRNA synthetase highlights: species‐specific features. Journal of Molecular Biology 294: 1287–1297.

Mortensen KK, Kildsgaard J, Moreno JMPM et al. (1998) A six‐domain structural model for E. coli translation initiation factor IF2: characterisation of twelve surface epitopes. Biochemistry and Molecular Biology International 46: 1027–1041.

Myasnikov AG, Marzi S, Simonetti A et al. (2005) Conformational transition of initiation factor 2 from the GTP‐ to GDP‐bound state visualized on the ribosome. Nature Structural and Molecular Biology 12: 1145–1149.

Nakanishi K, Ogiso Y, Nakama T, Fukai S and Nureki O (2005) Structural basis for anticodon recognition by methionyl‐tRNA synthetase. Nature Structural & Molecular Biology 12: 931–932.

Newton DT, Creuzenet C and Mangroo D (1999) Formylation is not essential for initiation of protein synthesis in all eubacteria. Journal of Biological Chemistry 274: 22143–22146.

Pestova TV and Hellen CUT (2001) Preparation and activity of synthetic unmodified mammalian tRNAiMet in initiation of translation in vitro. RNA 7: 1496–1505.

Rajbhandary UL (2000) More surprises in translation: initiation without the initiator tRNA. Proceedings of the National Academy of Sciences of the USA 97: 1325–1327.

Rajbhandary UL and Chow CM (1995) Initiator tRNAs and initiation of protein synthesis. In: Söll D (ed) tRNA: Structure, Biosynthesis, and Function, pp. 511–528. Washington, DC: ASM Press.

Schmitt E, Guillon JM, Meinnel T, Darddel F and Blanquet S (1996) Molecular recognition governing the initiation of translation in E. coli: a review. Biochimie 78: 543–554.

Schmitt E, Panvert M, Blanquet S and Mechulam Y (1998) Crystal structure of methionyl‐tRNA‐fMet transformylase complexed with initiator formyl‐methionyl‐tRNAfMet. EMBO Journal 17: 6819–6826.

Schmitt E, Takeuchi N, Vial L et al. (2000) Mitochondrial methionyl‐tRNA transformylases. 18th tRNA Workshop ‘tRNA 2000’, Session 6a‐101, Cambridge, UK.

Selmer M, Dunham CM, Murphy FV IV et al. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935–1942.

Seong BL and Rajbhandary UL (1987) E. coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proceedings of the National Academy of Sciences of the USA 84: 334–338.

Simonetti A, Marzi S, Myasnikov AG et al. (2008) Structure of the 30S translation initiation complex. Nature 455: 416–420.

Spurio R, Brandi L, Caserta E et al. (2000) The C‐terminal subdomain (IF2 C‐2) contains the entire fMet‐tRNA binding site of initiation factor IF2. Journal of Biological Chemistry 275: 2447–2454.

Stortchevoi A, Varshney U and Rajbhandary UL (2003) Common location of determinants in initiator transfer RNAs for initiator‐elongator discrimination in bacteria and in eukaryotes. Journal of Biological Chemistry 278: 17672–17679.

Thanedar S, Vinay N and Varshney U (2000) Fate of the initiator tRNAs is sensitive to the critical balance between interacting proteins. Journal of Biological Chemistry 275: 20361–20367.

Varshney U and Rajbhandary UL (1992) Role of methionine and formylation of initiator tRNA in initiation of protein synthesis in E. coli. Journal of Bacteriology 174: 7819–7826.

Varshney U, Lee CP and Rajbhandary UL (1993) From elongator tRNA to initiator tRNA. Proceedings of the National Academy of Sciences of the USA 90: 2305–2309.

Varshney U, Lee CP, Seong BL and Rajbhandary UL (1991) Mutants of initiator tRNA that function both as initiators and elongators. Journal of Biological Chemistry 266: 18018–18024.

Further Reading

Cusack S (1999) RNA–protein complexes. Current Opinion in Structural Biology 9: 66–73.

Laursen BS, Sørensen HP, Mortensen KK and Sperling‐Petersen HU (2005) Initiation of protein synthesis in bacteria. Microbiology and Molecular Biology Reviews 69: 101–123.

Mangroo D, Wu X and Rajbhandary UL (1995) E. coli initiator tRNA: structure–function relationships and interactions with the translational machinery. Biochemistry and Cell Biology 73: 1023–1031.

Mayer C, Stortchevoi A, Köhrer C, Varshney U and Rajbhandary UL (2001) Initiator tRNA and its role in initiation of protein synthesis. Cold Spring Harbor Symposia on Quantitative Biology 66: 195–206.

Meinnel TM, Mechulam Y and Blanquet S (1993) Methionine as translation start signal: a review of the enzymes of the pathway in E. coli. Biochimie 75: 1061–1075.

Rajbhandary UL (1994) Minireview: initiator transfer RNAs. Journal of Bacteriology 176: 547–552.

Schmitt E, Panvert M, Mechulam Y and Blanquet S (1997) General structure/function properties of microbial methionyl‐tRNA synthetases. European Journal of Biochemistry 246: 539–547.

Simonetti A, Marzi S, Jenner L et al. (2009) A structural view of translation initiation in bacteria. Cellular and Molecular Life Sciences. 66: 423–436.

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Rasmussen, Louise CV, Laursen, Brian S, Mortensen, Kim K, and Sperling‐Petersen, Hans U(Sep 2009) Initiator tRNAs in Bacteria and Eukaryotes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000543.pub2]