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

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.

Citation
Islas-Morales, P. F., Cárdenas, A., Mosqueira, M. J., Jiménez-García, L. F., & Voolstra, C. R. (2023). Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1075071

Acknowledgements
We want to thank UNAM for its institutional support and KAUST for its institutional and financial support. We further want to thank our colleagues: Silvia Juárez-Chavero from UNAM, Martin Barrios-Llerena, Adriana Valenzuela, Fabia Simona, and Professor Danielle Daffonchio from KAUST for their technical assistance; Professors Jorge Nieto from Instituto de Biología-UNAM and David Romero from Centro de Ciencias Genómicas-UNAM for their critical reading. We also thank Professors Ana María Cetto, Susana Magallón at UNAM, as well as Omar Fayad, Lamán Carranza, and Rosaura Ruiz for their personal support to scientific research in Mexico. Special thanks to the Mexican Embassy in Riyadh and David Yeh at KAUST for supporting science diplomacy between Mexico and Saudi Arabia. Parsifal Fidelio Islas-Morales developed part of this research as doctoral student from the “Programa de Doctorado en Ciencias Biomédicas”, Universidad Nacional Autónoma de Mexico (UNAM) and received a CONACyT fellowship 495217.

Publisher
Frontiers Media SA

Journal
Frontiers in microbiology

DOI
10.3389/fmicb.2023.1075071

PubMed ID
36819014

PubMed Central ID
PMC9932318

Additional Links
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1075071/full

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