The regularities detected in the distribution of the aRS classes in the matrix are shown in Table 3. The combinations with the least deviations are: the central A plus the YR quadrant, typical of class I, deviants being only the HisRS class II and the atypical PheRS; the central G plus the YY quadrant, typical of class II, deviants being only the GluRS class I, the LysRS class I of some organisms and the ArgRS expansion. The contribution of synthetase classes to the building of an architecturally integrated network derives also from their specificities for the central purines, which do not distinguish the sectors: class II unites all central G boxes and class I the central A boxes. Further contributions derive from their spreads, which were mostly due to the central Y ambiguity. The spreads become the norm rather than errors or deviations.
A large gap is highlighted between what can be proposed for the constitution of the primeval protein modules, peptides with the predominant aperiodic conformation, composed by the amino acids of the homogeneous sector, and the complex organization of the aRS, that will be difficult to fill. Various changes in the composition and genomic organization of the synthetase sets are being discovered, the majority occurring in the Archaea, which may help in tracing earlier states of the code. An intriguing feature of the collected examples is the high number of occurrences involving members of the families of amino acids derived biosynthetically from the acidics of the NUC box: Glu (Gln and Pro) and Asp (Asn and Lys). Arg also enters the list due to being derived from either one of the acidic amino acids and supposed to have had a predecessor.
Some of the intermediate steps may be called expansions of the aRS specificities. In some organisms, synthetases may accept tRNAs which, in the standard code, are charged by a different enzyme. The paradigmatic cases are of the aRS for the two acidic amino acids: AspRS may accept the tRNAs for Asn to form Asp-tRNAAsn and this will later be transformed into Asn-tRNAAsn by an amidation enzyme; a similar pathway is followed for the formation of Gln-tRNAGln from Glu-tRNAGln. There are many bacterial lineages that still keep the Glu-tRNAGln pathway for obtaining Gln, and it has been proposed that a separate GlnRS arose first in the eukaryotic lineage, later being transfected to some of the bacterial groups (Skouloubris et al., 2003). Another instance of a synthetase with expanded specificity but which remained fixed as such in the standard code is the MetRS that also charges the tRNAiMet. Some archaea lack a separate CysRS and the charging of the tRNACys is achieved by a class II ProRS, which is ambiguous or bi-functional (ProCysRS; Stathopoulos et al., 2000; Yarus 2000). Another form of bi-functionality is the fusion of the ProRS and GluRS into a single polypeptide, in most eukaryotes (Berthonneau and Mirande, 2000).
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