Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates
- Stanford University, United States
- University of California, Santa Cruz, United States
- University of California, Los Angeles, United States
- University of California, San Francisco, United States
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
Data availability
Ribosome profiling sequencing data have been deposited in GEO under accession code GSE201845. Other data generated in this study are provided in the supplementary materials and Source Data files. Code used for data analysis is available at https://gitfront.io/r/adelefxu/f94QE89EJwyp/eS27-paralogs/.
-
Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs in vertebratesNCBI Gene Expression Omnibus, GSE201845.
-
MCA DGE DataFigshare, doi:10.6084/m9.figshare.5435866.v8.
-
Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)Figshare, doi:10.6084/m9.figshare.5829687.v8.
-
Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA-sequencingNCBI Gene Expression Omnibus, GSE106273.
Article and author information
Author details
Jonathan K Pritchard
Funding
National Institutes of Health (F30HD100123)
- Adele Francis Xu
Stanford Bio-X
- Adele Francis Xu
National Institutes of Health (5R01HG008140)
- Jonathan K Pritchard
New York Stem Cell Foundation (NYSCF-R-I36)
- Maria Barna
National Institutes of Health (R01HD086634)
- Maria Barna
Alfred P. Sloan Foundation
- Maria Barna
Pew Charitable Trusts
- Maria Barna
National Institutes of Health (R01HD098722)
- Lindsay Hinck
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Shigehiro Kuraku, National Institute of Genetics, Japan
Ethics
Animal experimentation: All animal work was reviewed and approved by the Stanford Administrative Panel on Laboratory Animal Care (APLAC, protocol #27463). The Stanford APLAC is accredited by the American Association for the Accreditation of Laboratory Animal Care. All mice used in the study were housed at Stanford University except where otherwise noted. CRISPR-edited mouse lines were generated at the Gladstone Institute Transgenic Gene Targeting Core (San Francisco, CA). All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of California, San Francisco (protocol #AN180952-01B).
Version history
- Received: March 16, 2022
- Preprint posted: May 4, 2022 (view preprint)
- Accepted: June 9, 2023
- Accepted Manuscript published: June 12, 2023 (version 1)
- Version of Record published: June 30, 2023 (version 2)
Copyright
© 2023, Xu et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,716
- views
-
- 147
- downloads
-
- 3
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates
eLife 12:e78695.
https://doi.org/10.7554/eLife.78695
Further reading
-
- Computational and Systems Biology
- Evolutionary Biology
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
-
- Evolutionary Biology
- Neuroscience
Neuropeptides are ancient signaling molecules in animals but only few peptide receptors are known outside bilaterians. Cnidarians possess a large number of G protein-coupled receptors (GPCRs) – the most common receptors of bilaterian neuropeptides – but most of these remain orphan with no known ligands. We searched for neuropeptides in the sea anemone Nematostella vectensis and created a library of 64 peptides derived from 33 precursors. In a large-scale pharmacological screen with these peptides and 161 N. vectensis GPCRs, we identified 31 receptors specifically activated by 1 to 3 of 14 peptides. Mapping GPCR and neuropeptide expression to single-cell sequencing data revealed how cnidarian tissues are extensively connected by multilayer peptidergic networks. Phylogenetic analysis identified no direct orthology to bilaterian peptidergic systems and supports the independent expansion of neuropeptide signaling in cnidarians from a few ancestral peptide-receptor pairs.
