tRNA Biology
tRNA biology is a complicated and large subject. tRNA molecules interact with many molecules, including aminoacyl-tRNA ligases, initiation factors, EF-Tu, EF-G, mRNA, ribosomes, and peptidylhydrolase. They are also involved in many cellular processes, such as chlorophyll/heme/B12 synthesis, cell division, cell wall biosynthesis, proteolytic degradation, and priming reverse transcriptase in retroviruses. Finally, location matters; the cytosol and mitochondria have a different tRNA population composition. As a result of their complex role, tRNA molecules are heavily modified, and it can be difficult to determine the purpose of each modification.
tRNA modifications occur with the processing of the primary RNA transcript, and the modifying enzymes are position specific (sometimes a given modification will require multiple enzymes).
Increased stability of the mRNA/tRNA complex is determined by several factors: decreased flexibility of the anticodon induced by the anticodon stem, effects of bases outside the anticodon, and modifications within the anticodon loop that enhance stacking.
Known functional roles for modified positions (29 - 44, Yarus extended anticodon hypothesis pg39):
nt32
- modifications can modulate frameshifting (pg43)
nt34
- can be part of the recognition site for aminoacyl-tRNA ligases (pg 31)
- modifications can allow non-specific base pairing (I34 - UAC, cmo5U34 - AUG) (pg 39)
- the modification at this position may depend on the identity of nt2 in the A-site
- modifications result in changes in tRNA binding efficiencies (pg 43)
- modification at this position can affect the frequency of missense errors (pg 54)
- I34 leads to a preference for NNU and NNC codons (R3)(pg 97)
- Q involved in ligase recognition, translation efficiency, fidelity, and codon choice (pg66)
- m5C involved in translation efficiency (pg66)
- ac4C involved in translation efficiency and fidelity (pg66)
- k2C(L) involved in ligase recognition and fidelity (pg66)
- mnm5s2U involved in ligase recognition, translation efficiency, codon context, and codon choice (pg66)
- mcm5U leads to a preference for Lys-AAA when G is at nt1 of the +1 codon, and Lys-AAG when C is at nt1 (R4)(pg97) \\
- mcm5s2U involved in translation efficiency and codon choice (pg 66)
- mnm5Se2U involved in translation efficiency (pg 66)
- cmo5U involved in codon choice (pg66)
- mo5U involved in codon choice (pg66)
nt35
- can be part of the recognition site for aminoacyl-tRNA ligases (pg 32)
- ψ involved in ligase recognition and translation efficiency (pg 66)
nt37
- most not involved in aminoacylation, but some are (pg32)
- spontaneous mutation frequency (pg 38)
- tRNAs that read codons starting with U often have a hydrophobic nucleoside (i6A37), starting with A always have a hydrophilic nucleoside (t6A37)
--- potentially to stabilize weaker A-U bp at position 1
- tRNAs that read codons starting with C/G often have a modified purine or its methylated derivative (m1G37, m1I37, m2A37, m6A37)
- m2A, m6A, i6A, m1G decrease mRNA/tRNA interactions
- ms2i6X37 (stacks with anticodon), t6A37, yW37 stabilize codon-anticodon interactions
- i6A37 and derivatives increase translation efficiences (pg 46), as does t6A (through better stacking of the anticodon), as does yW (pg 48)
- modification at this position can affect the frequency of missense errors (pg 56)
- modifications at this position may be involved in frameshifting errors
--- m1G37 occurs in tRNAs reading CGN codons, and causes G-C base pairing to only have two hydrogen bonds (pg 59)
--- this modification also prevents base pairing of the nucleotide 5' of the codon
- ms2io6A involved in translation efficiency, codon context, and fidelity (pg 66)
- i6A involved in translation efficiency (pg 66)
- t6A involved in translation efficiency and codon context (pg 66)
- ms2t6A involved in fidelity (pg66)
- m1G involved in fidelity (pg66)
- yW involved in codon context and fidelity (pg 66)
nt38,39,40
- modification at these positions can affect the frequency of missense errors (pg 58)
- ψ involved in translation efficiency and fidelity (pg 66)
Codon Bias
E. coli shows a strong context bias around sense codons, particularly for proteins that are expressed in low levels. Proposed mechanisms of tRNA sensitivity to codon context are: the release factor effect for nonsense suppressors, and tRNA-tRNA interactions (like stacking of P-site nt 34 with A-site nt 37) (pg 51). It has also been noted that overrepresented codon pairs are translated more slowly (pg 125).
Separately, in cases where the genetic code is degenerate, more highly expressed genes show a larger codon bias. It is important to note that these highly expressed genes use codons recognized by the most abundant tRNA isoacceptor (R1), and avoid codons from other isoacceptors(pg 96). Codon choice affects both translation fidelity and rate, and codon choice is in part dictated by nt34 modifications. For example U34 is always modified in yeast cytoplasmic tRNAs. In a modification of the chemical type xo5U34, the anticodon rigidity is reduced and the wobble capacity is extended. In contrast, a modification of the chemical type xm5s2U34 (like mcm5s2), the anticodon is more rigid and reading of the third position of the codon is more accurate/restricted (pg 62).
For position 3 of codons, C is preferred over U for codons beginning with AA-, AU-, UA-, and UU (R4)(pg 98). R1-R4 above are together considered to predict optimal codon usage. This has been shown to correlate with increased translation efficiency, especially for more highly translated genes. Interestingly, non-optimal codons have been observed to cluster at the beginning of genes in E. coli, a potential regulatory mechanism. In yeast, genes with higher optimal codon use have a larger percentage of G and C nucleotides at position 3 of codons (pg105-106).
Source: Hatfield, Transfer RNA in Protein Synthesis (2017)
