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Front Immunol
2022 Jan 01;13:1066510. doi: 10.3389/fimmu.2022.1066510.
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Different sea urchin RAG-like genes were domesticated to carry out different functions.
Yakovenko I
,
Tobi D
,
Ner-Gaon H
,
Oren M
.
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The closely linked recombination activating genes (RAG1 and RAG2) in vertebrates encode the core of the RAG recombinase that mediates the V(D)J recombination of the immunoglobulin and T-cell receptor genes. RAG1 and RAG2 homologues (RAG1L and RAG2L) are present in multiple invertebrate phyla, including mollusks, nemerteans, cnidarians, and sea urchins. However, the function of the invertebrates' RAGL proteins is yet unknown. The sea urchins contain multiple RAGL genes that presumably originated in a common ancestral transposon. In this study, we demonstrated that two different RAG1L genes in the sea urchin Paracentrutus lividus (PlRAG1La and PlRAG1Lb) lost their mobility and, along with PlRAG2L, were fully domesticated to carry out different functions. We found that the examined echinoid RAGL homologues have distinct expression profiles in early developmental stages and in adult tissues. Moreover, the predicted structure of the proteins suggests that while PlRAG1La could maintain its endonuclease activity and create a heterotetramer with PlRAG2L, the PlRAG1Lb adopted a different function that does not include an interaction with DNA nor a collaboration with PlRAG2L. By characterizing the different RAG homologues in the echinoid lineage, we hope to increase the knowledge about the evolution of these genes and shed light on their domestication processes.
Figure 1. Genomic organization and phylogenetic relationships among echinoid RAG1L sequences. (A). annotated RAGL genes in the genomes of P. lividus and S. purpuratus. (B). phylogenetic relationships among echinoid RAG1L sequences. The phylogeny was made using transcribed sequences, based on maximum likelihood with Whelan and Goldman (WAG) model with consensus tree inferred from 500 bootstrap replicates. Drosophila melanogaster Transib autonomous protein was chosen as the outgroup (repbase https://www.girinst.org/server/RepBase/index.php accessed on July 2022). A corresponding guideline phylogeny of species is presented on the right to the phylogenetic relation of RAG1L translated protein sequences.
Figure 2. Relative genomic locations of type I RAGL genes in sea urchin genomes. The relative genomic location of RAG1/2 genomic pairs in S. purpuratus, P. lividus, H. pulcherrimus and L. variegatus is presented. Matching neighboring genes are marked in green. The SpRAG1/2L and HpRAG1/2L loci are similarly neighboring rhodophilin-1 (Rhpn1) gene upstream to the RAG2L sequence. On the other side, upstream to the RAGL1 sequence, the RAG loci are adjacent to 2,4-Dienoyl-CoA Reductase-1 (DECR1) gene. The H. pulcherrimus genome scaffold BEXV01002133.1 is ending in the middle of DECR1 gene but another scaffold - BEXV01001204.1 includes the rest of the DECR1 gene sequence as well as two other genes with similarity to Dolichol-phosphate mannosyltransferase subunit 1 (DPM1) and Retinal Guanylate Cyclase 1-like (GUSY1) similarly to the corresponding neighboring RAG1/2L genes of the S. pupuratus genome.
Figure 3.
SpRAGL genes are immobile in individual sperm and a coelomocyte. The IGV visualized alignment is shown for SpRAG1L type I and II (LOC115920226, LOC105439619, LOC105444038, LOC115920171) genes and their neighboring genes. Red arrows pointing to the RAG1 genes, purple triangles mark the mismatches. Reads with good mapping quality (over 60) are marked in grey, the reads with lower quality mapping are in white.
Figure 4. Expression patterns of PlRAGL1a, PlRAGL2, PlRAGL1b, PlArtemisL and PlTdTL genes in adult tissues and early developmental stages of P. lividus
(A). Relative gene expression in of the tested genes in adult sea urchin tissues and organs by qPCR. Ax - axial organ, Coe - coelomocytes, Es - esophagus, Gon - gonads, Gut, Tf - tubefeet. (B). Relative gene expression of PlRAG1a and PlRAG1b in the early developmental stages by qPCR. The PlRAG2L expression is showed according to the PRJNA264358, PRJNA376650 and PRJEB10269 RNA-seq databases. (C). PlRAG1b expression in the developmental stages visualized by the in-situ hybridization. Gene accession numbers in octopus database (http://octopus.obs-vlfr.fr/): PlRAG1a - Pliv25095.1 (type I), PlRAG1b- Pliv07077.1 (type II), PlRAG2L- Pliv25741.1, PlArtemisL - Pliv23693.1, PlTdTL - Pliv29804.1.
Figure 5. Predicted protein structure of PlRAGLs. (A). sequences alignment of SpRAG1L, PlRAG1a and PlRAG1b with domains (Martin, Vicari et al., 2020). blue stars – contacting residues with RAG2 (RAG1 for RAG2), purple crosses - RAG1 dimerization contacts, green dots - contacting residues of RAG1 with DNA. Grey areas - places that are aligned to the ZDD and NBD domains of Mus musculus RAG1 with low similarity. Boxed section - missing sequence in the catalytic RNH domain in the RAG1Lb protein sequence. (B). SpRAG2L and PlRAG2L sequence alighnment. (C). Model structure of P. lividus Rag1L-Rag2L-nicked DNA complex. (i) The P. lividus Rag1/2L_DNA dimeric structure is shown using cartoon representation. One PlRag1L/PlRag2L complex is colored skyblue/hotpink and the other cyan/salmon, with the DNA colored orange. (ii) Monomeric half of the PlRAGL complex with the exposed DNA nick (marked with ‘N’). The region colored in yellow is missing in the PlRAG1b predicted protein. The region colored in white is missing in the PlRAG2L compared to SpRAG2L (iii) Magnification of the missing DNA binding (in RNAse H domain) region in PlRAG1b (shown in yellow spheres) and its interaction with the nicked DNA helix (shown in orange) (IV) Magnification of the missing region in PlRAG2L (white spheres) as compared with the SpRAG2L. The figure was prepared using the PyMol software 3.
Agrawal,
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system.
1998, Pubmed
Agrawal,
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system.
1998,
Pubmed
Arbuckle,
Elucidating the domain architecture and functions of non-core RAG1: the capacity of a non-core zinc-binding domain to function in nuclear import and nucleic acid binding.
2011,
Pubmed
Avgan,
Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control.
2019,
Pubmed
Ben-Tabou de-Leon,
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown.
2013,
Pubmed
,
Echinobase
Callebaut,
The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis.
1998,
Pubmed
Carmona,
Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination.
2016,
Pubmed
,
Echinobase
Cortes,
RAG-1 interacts with the repeated amino acid motif of the human homologue of the yeast protein SRP1.
1994,
Pubmed
Danecek,
Twelve years of SAMtools and BCFtools.
2021,
Pubmed
Fiser,
Template-based protein structure modeling.
2010,
Pubmed
Flajnik,
Origin and evolution of the adaptive immune system: genetic events and selective pressures.
2010,
Pubmed
Foster,
Single cell RNA-seq in the sea urchin embryo show marked cell-type specificity in the Delta/Notch pathway.
2019,
Pubmed
,
Echinobase
Foster,
A single cell RNA sequencing resource for early sea urchin development.
2020,
Pubmed
,
Echinobase
Fugmann,
An ancient evolutionary origin of the Rag1/2 gene locus.
2006,
Pubmed
,
Echinobase
Fugmann,
The origins of the Rag genes--from transposition to V(D)J recombination.
2010,
Pubmed
Gwyn,
A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity.
2009,
Pubmed
Hiom,
DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations.
1998,
Pubmed
Huang,
Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination.
2016,
Pubmed
Jones,
Autoubiquitylation of the V(D)J recombinase protein RAG1.
2003,
Pubmed
Kallenbach,
Three lymphoid-specific factors account for all junctional diversity characteristic of somatic assembly of T-cell receptor and immunoglobulin genes.
1992,
Pubmed
Kapitonov,
Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon.
2015,
Pubmed
,
Echinobase
Kapitonov,
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.
2005,
Pubmed
,
Echinobase
Kim,
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
2019,
Pubmed
Kim,
Crystal structure of the V(D)J recombinase RAG1-RAG2.
2015,
Pubmed
Kim,
Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase.
1999,
Pubmed
Kumar,
TimeTree 5: An Expanded Resource for Species Divergence Times.
2022,
Pubmed
Lee,
Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida.
2003,
Pubmed
,
Echinobase
Li,
Minimap2: pairwise alignment for nucleotide sequences.
2018,
Pubmed
Lott,
The importin β binding domain as a master regulator of nucleocytoplasmic transport.
2011,
Pubmed
Maezawa,
Double-strand break repair based on short-homology regions is suppressed under terminal deoxynucleotidyltransferase expression, as revealed by a novel vector system for analysing DNA repair by nonhomologous end joining.
2016,
Pubmed
Martin,
Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin.
2020,
Pubmed
Matthews,
RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination.
2007,
Pubmed
Minokawa,
Expression patterns of four different regulatory genes that function during sea urchin development.
2004,
Pubmed
,
Echinobase
Morales Poole,
The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates.
2017,
Pubmed
Nair,
Macroarray analysis of coelomocyte gene expression in response to LPS in the sea urchin. Identification of unexpected immune diversity in an invertebrate.
2005,
Pubmed
,
Echinobase
Oettinger,
RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination.
1990,
Pubmed
Oren,
Individual Sea Urchin Coelomocytes Undergo Somatic Immune Gene Diversification.
2019,
Pubmed
,
Echinobase
Oren,
Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family.
2016,
Pubmed
,
Echinobase
Rodgers,
A zinc-binding domain involved in the dimerization of RAG1.
1996,
Pubmed
Ru,
Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.
2015,
Pubmed
Sakano,
Sequences at the somatic recombination sites of immunoglobulin light-chain genes.
1979,
Pubmed
Sali,
Comparative protein modelling by satisfaction of spatial restraints.
1993,
Pubmed
Schatz,
Antigen receptor genes and the evolution of a recombinase.
2004,
Pubmed
Terwilliger,
Distinctive expression patterns of 185/333 genes in the purple sea urchin, Strongylocentrotus purpuratus: an unexpectedly diverse family of transcripts in response to LPS, beta-1,3-glucan, and dsRNA.
2007,
Pubmed
,
Echinobase
Thompson,
New insights into V(D)J recombination and its role in the evolution of the immune system.
1995,
Pubmed
Thorvaldsdóttir,
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
2013,
Pubmed
Tonegawa,
Somatic generation of antibody diversity.
1983,
Pubmed
Tu,
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
2012,
Pubmed
,
Echinobase
Tu,
Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus.
2014,
Pubmed
,
Echinobase
van Gent,
The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination.
1996,
Pubmed
Wang,
Recombination-activating gene 1 and 2 (RAG1 and RAG2) in flounder (Paralichthys olivaceus).
2014,
Pubmed
Whelan,
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
2001,
Pubmed
Wick,
Completing bacterial genome assemblies with multiplex MinION sequencing.
2017,
Pubmed
Wilson,
The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails.
2008,
Pubmed
,
Echinobase
Yakovenko,
Guardian of the Genome: An Alternative RAG/Transib Co-Evolution Hypothesis for the Origin of V(D)J Recombination.
2021,
Pubmed
Yakovenko,
The Diverse Transformer (Trf) Protein Family in the Sea Urchin Paracentrotus lividus Acts through a Collaboration between Cellular and Humoral Immune Effector Arms.
2021,
Pubmed
,
Echinobase
Yanagi,
A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains.
NULL,
Pubmed
Zhang,
Transposon molecular domestication and the evolution of the RAG recombinase.
2019,
Pubmed
