The a single tRNA species that contains modifications

The ribosome allows the
best possible spatial arrangement of the various partners and ensures catalysis
but the adaptor molecule which acts as a link between codes
of mRNA and amino acids of polypeptide is the tRNA. For play this major role, tRNAs have two distinct
characteristics corresponding to two different genetic codes, the anticodon and
the operational codes. The latter which is mainly embodied in the acceptor-stem
allows to bind covalently and with a high specificity an amino acid to a tRNA,
a reaction catalyzed by a specific aminoacyl-tRNA synthetase (aaRS). The
operational code might have actually predated the “classic” code
associated with anticodons (Schimmel
et al., 1993) . Moreover, the
tRNAs exhibit diversity in uniqueness, all of them
must be similar for entering the ribosome machinery; so, they generally look
structurally homogeneous, especially in their secondary and tertiary structures
even if “non-classical” tRNAs are known. Moreover, cloverleaf
structure and especially the tertiary interaction network governing the
L-shaped tRNA architecture imply conserved and semi-conserved bps and nts. On
the other side, each type of tRNA structures must interact specifically with aaRSs
and post-transcriptional modification enzymes which implies that parts of their
sequences and of their structures (as the V-R size) allow to distinguish them.

Reduced bacterial and most organelle
genomes do not encode the full set of 32 tRNA species required to read all
triplets of the standard genetic code according to the conventional wobble
rules. Superwobbling, in which a single tRNA species that contains modifications
of the anticodon loop, such as an hypermodified uridine in the wobble position 34
of the anticodon, allows to read all 4 nts in the third codon position, has
been suggested as a possible mechanism for how reduced tRNA sets may be functional
(Agris et al., 2007)
, e.g., in several metazoan mtDNAs only a total of 22 tRNAs are
sufficient to recognize all codons (two tRNAs each for serine and
leucine and one tRNA for each of the other 18 amino acids). However, superwobbling induces a
reduced translational efficiency, which could explain why most organisms have
adopted pairs of isoaccepting tRNAs over the superwobbling mechanism (Rogalski et al., 2008) . As,
e.g., in Cnidaria (sea anemones, corals, etc…) or
Chaetognatha (marine invertebrates), current mtDNAs have lost several of their trn genes and the absence of an
apparently full set of mt-trn genes
has also been mentioned (Huot et al., 2014) . Studies have investigated the fate of missing
tRNAs and their corresponding aaRSs (Haen et al. 2010) and in
many cases, the lost tRNAs are functionally replaced by imported of nucleus-encoded tRNAs (Huot
et al., 2014) . However, a recent
strategy strongly suggests that efficient reanalyzes allow to found several
tRNA-like structures (TLS) which can be efficient tRNAs (Barthélémy and Seligmann, 2016)

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