# Emergence of a \"Cyclosome\" in a Primitive Network Capable of Building \"Infinite\" Proteins +
## 4 Nucleo-Nucleic and Nucleo-Peptide Mechanisms
### Ribzymes  
An RNA catalytic domain has been found within the sequence of the 359 base long negative-strand satellite RNA of tobacco ringspot virus [73]. The catalytic domain contains 2 minimal sequences of satellite RNA, a 14-base substrate RNA, and a 50-base catalytic RNA containing 2 AL-pentamers:  
5'-AAACAGAGAAGUCAACCAGAGAACACACAGUUGGAUAUUACCUGGAU-3'  
A minimal RNA hairpin ribozyme discovered 18 years later [74] shows an interesting catalytic activity due to its chain D with 3 AL-pentamers present in its 19 bases: 5'-UCG  
Table 4 and Figure 6 show the values of the AL-proximity (for the 9 most frequent AL pentamers) for the tRNA synthetases of the different microorganisms studied in [86; 87; 88; 89; 90; 91; 92; 93], especially Bacteria, Archaea, and one Fungus. We observe that Archaea have the maximal values of this proximity and by comparing the sequences of these synthetases [93], we see that the clustering tree based on the sequence resemblance (for the Hamming distance) described as narrow are synthetases having similar values of their AL-proximity (except the pair Haloferax larsenii / Helicobacter pylori).  
The Table 5 gives the values of the AL-proximity for different tRNA synthetases (called also tRNA ligases) and ribosomal or transfer RNAs, showing that the 40S ribosomal RNAs; tRNA synthetases; and 60S, 18S, and 16S ribosomal RNAs have, in this order, decreasing proximities to the AL. The high values of the AL-proximity for the synthetases are consistent with a very early role in a protein-synthesizing machine, by increasing the efficacy of amino acid binding to an RNA-oligopeptide complex such as the AL ring coupled with ligases.  
\begin{table}
\begin{tabular}{|p{341.4 pt}|} \hline Homo sapiens mRNA for glycyl-tRNA synthetase, complete cds GenBank: D30658.1 36 \(\times\) 100/2279 = 1.58 Helicobacter pylori B38 complete genome, strain B38 NCBI Reference Sequence: NC\_012973.1: c941829-940933 \\ glycyl–tRNA ligase subunit alpha 15x100/893 = 1.68 \\ \hline Methanococcus marijuana, strain DSM 2067 chromosome, complete genome NCBI Reference Sequence: NZ\_CP026606.1:782166-783890 glycyl-tRNA synthetase 32x100/1721 = 1.86 \\ \hline Fusarium oxysporum f. sp. melonis 26406 unplaced genomic scaffold supercontt1.3, whole genome shotgun sequence GenBank: JH659331.1: c2101550-2098309 glycyl-tRNA synthetase 68x100/3238 = 2.10 \\ \hline Prochlorococcus marinus str. NATL1A, complete genome GenBank: CP000553.1: 728949-731111 glycyl-tRNA synthetase 50x100/2155 = 2.32 \\ \hline Methanocoldococcus jannaschili DSM 2661, complete genome GenBank: L77117.1: 219104-220837 glycyl-tRNA synthetase 41x100/1730 = 2.37 \\ \hline Archaea Methanococcus methylutens MM1, complete genome GenBank: CP009518.1: 1554853-1556598 glycyl-tRNA synthetase 43x100/1738 = 2.47 \\ \hline Archaea Candidatus Nanosalinarum sp. J07 AB56 genomic scaffold scf\_7180000039101, whole genome shotgun sequence GenBank: GL982569.1 571934-572506 prolyl-tRNA synthetase 32x100/1286 = 2.49 \\ \hline Methanococcus marijuana C5, complete genome GenBank: CP000609.1: c1395811-1394084 glycylyl-tRNA synthetase 43x100/1720 = 2.50 \\ \hline Methanobacterium formiccium strain BRM9, complete genome GenBank: CP006933.1 556622-558343 glycyl-tRNA synthetase 44x100/1718 = 2.56 \\ \hline Rickettsía prowazekii strain Naples-lchromosome, complete genome GenBank: CP014865.1: c1072366-1071497 glycine-tRNA ligase subunit alpha 25x100/866 = 2.89 \\ \hline \end{tabular}
\end{table}
Table 4: Gly-tRNA synthetases of different microorganisms [69] with (in red) their AL-proximity.  
Figure 6: Clustering tree of the synthetases of certain microorganisms based on their sequence resemblance (for the Hamming distance) (after [93]) with indication (in red) of AL-proximity.