Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon

Parsifal F Islas-Morales; Anny Cárdenas; María J Mosqueira; Luis Felipe Jiménez-García; Christian R Voolstra

doi:10.3389/fmicb.2023.1075071

Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon

Front Microbiol. 2023 Feb 2:14:1075071. doi: 10.3389/fmicb.2023.1075071. eCollection 2023.

Authors

Parsifal F Islas-Morales^{1

2

3}, Anny Cárdenas^{3

4

5}, María J Mosqueira^{3

6}, Luis Felipe Jiménez-García^{1

7}, Christian R Voolstra^{3

4}

Affiliations

¹ Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico.
² UNESCO Chair on Science Diplomacy and Scientific Heritage, Instituto de Biología, UNAM, Mexico City, Mexico.
³ Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
⁴ Department of Biology, University of Konstanz, Konstanz, Germany.
⁵ Department of Biology, American University, Washington, DC, United States.
⁶ NEOM, Saudi Arabia.
⁷ Department of Cell Biology, Faculty of Sciences, UNAM, Mexico City, Mexico.

Abstract

Nucleoli are subcellular compartments where transcription and maturation of pre-ribosomal RNAs occur. While the transcription of ribosomal RNAs is common to all living cells, the presence and ultrastructure of nucleoli has been only documented in eukaryotes. Asgard-Archaea, the closest prokaryotic relatives of eukaryotes, and their near relatives TACK-Archaea have homologs of nucleolar proteins and RNAs in their genome, but the cellular organization of both is largely unexplored. Here we provide ultrastructural and molecular evidence for the presence of putative nucleolus-like subcellular domains in the TACK crenarchaeon Saccharolobus solfataricus (formerly known as Sulfolobus solfataricus). Transmission electron microscopy (TEM) revealed consistent electron-dense fibro-granular compartments, also positive to the specific silver staining for nucleolar organizer regions (AgNOR). TEM also confirmed that ribosomal DNA (rDNA) is spatially distributed in non-random, clustered arrays underlying fine structures, as observed by ultrastructural in situ hybridization (UISH). To further explore these observations, proteomic sequencing of isolated bands from AgNOR-stained protein gels was conducted and compared against a compiled inventory of putative nucleolar homologs from the S. solfataricus P1 genome. Sequenced AgNOR-sensitive peptides encoded homologs of eukaryotic nucleoli proteins, enriched for nucleolus-related functions. Our results provide first evidence that subcellular domains of nucleolar-like nature are not exclusive to eukaryotes. Based on our data, we propose a model for a putative nucleolus in S. solfataricus. Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.

Keywords: AgNOR; Archaea; Saccharolobus; TACK; evolution; microscopy; nucleolus; proteomics.