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The Ribosomal Protein Cluster Organization In Asgard Archaea -- An Analysis
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  • Madhan R. Tirumalai,
  • George E. Fox,
  • Raghavan V. Sivaraman Jr,
  • Layla A. Kutty,
  • Eric L. Song
Madhan R. Tirumalai
University of Houston, University of Houston

Corresponding Author:mrtirum2@central.uh.edu

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George E. Fox
University of Houston, University of Houston
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Raghavan V. Sivaraman Jr
Harvard Medical School, Harvard Medical School, Wyss Institute Boston MA, USA
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Layla A. Kutty
University of Texas at Austin, University of Texas at Austin, Austin, TX, USA
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Eric L. Song
University of Texas at Austin, Austin, TX, USA, University of Texas at Austin, Austin, TX, USA
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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.