Introduction: It has been proposed that the recently discovered superphylum of Asgard archaea may represent a historical link/bridge between the Archaea and Eukarya. The arrangement of genes in genomes is a window to understand how organisms are related. In particular, the translation machinery and the genes that encode the same have a long evolutionary history. In order to gain further insight into the evolutionary position of the Asgard archaea, the genome order of ribosomal protein coding genes was analyzed. The Asgard archaea were compared with non-Asgard archaeal and bacterial genomes. Results: A core of co-occurring 15 genes belonging to the segment of the S10 and spc cluster (which are characterized and established as operons in Bacteria), was identified as conserved in gene order, arrangement and genome location in Asgard archaea, non-Asgard archaea and Bacteria. This core occurs as a complete set in the genomes of Lokiarchaeota MK-D1 (Candidatus Prometheoarchaeum syntrophicum), and Candidatus Odinarchaeota archaeon LCB_4. The genome assemblies of the other Asgard genomes are incomplete and occur in multiple contigs (>50) and hence this cluster is found in sections across contigs, with a section often either ending or beginning a contig. The cluster organization is indicative of co-occurrence, if the genome was complete. A second smaller cluster comprising the homologs of the most conserved genes of the bacterial S10 operon/cluster namely, uS10-uL3-uL4-uL23-uL2 occurs independently on the Asgard genomes, separate from the rest, a feature shared by many non-Asgard archaea as well. Other clusters. A new cluster L7ae-infB was identified to co-occur with the minor S24e-S27ae cluster in the two complete Asgard genomes. The L7ae-infB cluster co-occurs with the S24e-S27ae cluster in some (non-Asgard) Crenarchaeota (Desulfurococcacea) and Euryarchaeota (Methanobacteriaceae), while it co-occurs with the (Alpha operon) L18e cluster in some (non-Asgard) Euryarchaeota (Halobacteriaceae). Overall, the organization of the most universal and highly conserved S10 and spc cluster in Asgard archaea resembles that of the non-Asgard Thaumarchaeota and the DPANN group. References: Wang J et al (2009) Archaea, 2(4), 241–251. Da Cunha V et al (2017) Plos Genetics 13(6), e1006810. Bowman J. C. et al. (2020) Chem Rev, 120(11), 4848-4878.

The ribosome is a universal molecular machine (comprised of RNA and proteins) which translates the message from the genome into proteins (polymers of amino acids) in biology. Similar to how Flight and Cockpit voice recorders record and preserve an aircraft’s flight history, the ribosome has recorded signatures of its evolution. Tapping this resource is important for understanding the origins of life. The electrostatic properties/net positive charge(s) of ribosomal proteins (RPs) stabilize interactions with the negatively charged ribosomal RNA (rRNA) and influence the assembly and folding of ribosomes. A high percentage of RPs from extremely halophilic archaea are known to be acidic/negatively charged. Recently the net charges (at pH 7.4) of the RPs from a highly conserved cluster of RPs were found to have an inverse relationship with the halophilicity/halotolerance (ability to survive under salt conditions) levels in bacteria and archaea. In non-halophilic bacteria, these RPs are generally basic, contrasting with the acidic proteomes of the extreme halophiles. We explore the use of a new mathematical modeling technique based on interaction graphs to provide a systematic understanding of the structural differences in the Large Subunit (LSU) of the bacterium Escherichia coli and that of the extremely halophilic archaeon Haloarcula marismortui.