Unconventional conservation reveals structure-function relationships in the synaptonemal complex
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
Figures
Figure 1 with 3 supplements
The divergence of synaptonemal complex (SC) proteins is driven by neutral evolution.
(A) Left: diagram of the SC. The N- and C-termini of transverse filaments are labeled. SC, pink;axis (scaffold for SC assembly), dark gray; chromosomes, light gray. Right: electron micrographs of …
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Figure 1—source data 1
Syntenic location of Caenorhabditis synaptonemal complex genes.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig1-data1-v1.xlsx
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Figure 1—source data 2
Multiple sequence alignments used in phylogenetic analysis.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig1-data2-v1.txt
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Figure 1—source data 3
Sequences of manually curated genes.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig1-data3-v1.txt
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Figure 1—source data 4
Multiple sequence alignments used in evolutionary analyses.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig1-data4-v1.txt
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Figure 1—source data 5
Sequences of Caenorhabditis synaptonemal complex proteins.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig1-data5-v1.txt
Figure 1—figure supplement 1
Identification of Caenorhabditis synaptonemal complex proteins.
Caenorhabditis species tree including all species investigated in this study. Presence of SC proteins is listed to the right of each species. Filled box, present; unfilled box, no ortholog could be …
Figure 1—figure supplement 2
Maximum likelihood phylogenies of Caenorhabditis synaptonemal complex proteins.
Maximum likelihood phylogenies of SYP-1 (A), SYP-2 (B), SYP-3 (C), SYP-4 (D), and SYP-5 (E). Each phylogeny is rooted on the common ancestor of Caenorhabditis. Bootstrap values above 50 are …
Figure 1—figure supplement 3
Map of sites of under purifying, neutral, or positive selection.
(A) Map of sites under positive (pink), purifying (green), or neutral selection (gray) identified using Fixed Effects Likelihood model from HyPhy for SYP-1–SYP-5 and SMC-1/3. Gene models showing …
Figure 2 with 2 supplements
Protein length and coiled-coil domains are conserved features of synaptonemal complex proteins.
(A) Percent amino acid identity (top), coiled-coil score (middle), and standard deviation of coiled-coil score (bottom) at each aligned position for SYP-1–SYP-5. Sliding window average of percent …
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Figure 2—source data 1
Multiple sequence alignments used in indel analysis.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig2-data1-v1.txt
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Figure 2—source data 2
Phylogenetic trees used in indel analysis.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig2-data2-v1.txt
Figure 2—figure supplement 1
Synaptonemal complex proteins have a significantly higher coiled-coil conservation score than other coiled-coil proteins.
Dot plot comparing the coiled-coil conservation score of SC proteins to all other coiled-coil proteins in Caenorhabditis (CC proteins). See Materials and methods for criteria used for selection of …
Figure 2—figure supplement 2
Synaptonemal complex proteins have limited regions of conserved disorder.
PONDR VL3 score (top) and standard deviation of VL3 score (bottom) at each aligned position for SYP-1–SYP-5. Green and yellow lines, average score at each position; gray lines, scores for each …
Figure 3 with 4 supplements
Synaptonemal complex proteins have an unconventional, but conserved, evolutionary signature.
3D scatter plot comparing amino acid substitutions per site, coefficient of variation of protein length, and coiled-coil conservation score of all proteins in 25 Caenorhabditis species (A), 30 Drosop…
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Figure 3—source data 1
Proteomes used to generate 3D scatter plots.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig3-data1-v1.xlsx
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Figure 3—source data 2
Genomic sequence of L. africana SYCE3 from UCSC Genome Browser.
Note sequence ambiguities.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig3-data2-v1.xlsx
Figure 3—figure supplement 1
Synaptonemal complex proteins have an unconventional evolutionary signature.
(A) 3D scatter plot from Figure 3A reprinted with proteins that cluster with SC proteins based on hierarchical clustering highlighted in blue and green. (B) Hierarchical clustering of all Caenorhabdi…
Figure 3—figure supplement 2
Coiled-coil plots for Drosophila synaptonemal complex proteins.
Coiled-coil plots for C(3)G, Corolla and Corona used to identify conserved coiled-coil domains (gray ovals) displayed in Figure 3. Gray lines, individual species score; magenta and yellow lines, …
Figure 3—figure supplement 3
Coiled-coil plots for mammalian synaptonemal complex proteins.
Coiled-coil plots for SYCP1, SYCE1–3, TEX12, and SIX6S01 used to identify conserved coiled-coil domains (gray ovals) displayed in Figure 3C. Gray lines, individual species score; magenta and yellow …
Figure 3—figure supplement 4
Mammalian synaptonemal complex proteins display a similar, albeit weaker, evolutionary signature.
Dot plot comparing amino acid substitutions per site (A), coiled-coil conservation score (B), and coefficient of variation of protein length (C) of mammalian SC proteins to all other mammalian …
Figure 4 with 4 supplements
Identification of P. pacificus SYP-1.
(A) Flow chart of filtering steps to identify candidate synaptonemal complex proteins in Pristionchus, with the number of remaining proteins after each step shown to the right. See Materials and …
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Figure 4—source data 1
Sequences of CRISPR reagents.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig4-data1-v1.xlsx
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Figure 4—source data 2
Protein sequences of SYP-1 and SYP-2 candidates from C. plicata and C. monodelphis.
- https://cdn.elifesciences.org/articles/72061/elife-72061-fig4-data2-v1.txt
Figure 4—figure supplement 1
Ppa-SYP-1 antibody.
Image of the prophase region of the gonad stained with anti-Ppa-SYP-1 from (A) wild-type P. pacificus and (B) Ppa-syp-1 knockout hermaphrodites. Scale bar = 5 μm.
Figure 4—figure supplement 2
Candidate SYP-1 proteins in C. plicata.
Coiled-coil plots for four candidate SYP-1 proteins in C. plicata (A–D).
Figure 4—figure supplement 3
Candidate SYP-1 proteins in C. monodelphis.
Coiled-coil plots for five candidate SYP-1 proteins in C. monodelphis (A–E). In (A), the position of an ‘STP’ Polo-Box Domain binding motif is labeled. This motif is in a similar position to a …
Figure 4—figure supplement 4
Candidate SYP-2 proteins in C. monodelphis.
Coiled-coil plots for 21 candidate SYP-2 proteins in C. monodelphis (A–U). The large number of candidates is likely due to the relatively short coiled-coil domain in SYP-2 that was used to identify …
Tables
Table 1
Summary table of tests for positive selection on synaptonemal complex proteins and SMC-1 and SMC-3 (controls) in the Elegans group species of Caenorhabditis (Figure 1—figure supplement 1).
p-values from likelihood ratio tests comparing CodeML models M1 vs. M2, M7 vs. M8, and M8a vs. M8 are listed. Each comparison tests the fit of the data to a model that does not allow positive …
| PAML CodeML | HyPhy fixed effects likelihood | |||||
|---|---|---|---|---|---|---|
| Number of species | M1 vs. M2 p-value | M7 vs. M8 p-value | M8a vs. M8 p-value | Sites under positive selection | Sites under negative selection | |
| SYP-1 | 12 | 1.00 | 0.99 | 0.60 | 0/451 | 177/451 (39%) |
| SYP-2 | 12 | 1.00 | 0.90 | 0.56 | 0/203 | 75/202 (37%) |
| SYP-3 | 12 | 0.97 | 0.54 | 0.54 | 2/213 | 109/213 (51%) |
| SYP-4 | 11 | 1.00 | 0.26 | 0.48 | 2/550 | 277/550 (50%) |
| SYP-5 | 10 | 1.00 | 0.99 | 0.59 | 2/554 | 173/554 (31%) |
| SMC-1 | 11 | 1.00 | 0.85 | 0.54 | 1/1300 | 805/1300 (62%) |
| SMC-3 | 12 | 1.00 | 0.51 | 0.41 | 0/1243 | 760/1243 (61%) |
Table 2
Contingency table showing the number of alignment positions containing indels and lacking indels inside versus outside the coiled-coil domain of each synaptonemal complex protein.
Two tailed p-value from Fisher’s exact test is shown in the last column. Total number of insertions and deletions is depleted in the coiled-coil domains of SYP-1, SYP-4, and SYP-5.
| Inside coiled-coil | Outside coiled-coil | ||||
|---|---|---|---|---|---|
| Protein | Alignment positions with indels | Total alignment positions | Alignment positions with indels | Total alignment positions | p-value |
| SYP-1 | 30 | 407 | 54 | 157 | <0.0001 |
| SYP-2 | 4 | 104 | 3 | 92 | N.A. |
| SYP-3 | 8 | 251 | 0 | 33 | N.A. |
| SYP-4 | 3 | 237 | 31 | 161 | <0.0001 |
| SYP-5 | 14 | 372 | 14 | 131 | 0.0063 |
| Total | 59 | 1371 | 102 | 574 | <0.0001 |
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Pristionchus pacificus) | PPA16075; Ppa-syp-1 | El Paco genome reference, V2 | ||
| Gene (P. pacificus) | PPA10754 | El Paco genome reference, V2 | ||
| Gene (P. pacificus) | PPA35551 | El Paco genome reference, V2 | ||
| Gene (Caenorhabditis elegans) | syp-1 | https://wormbase.org/#012-34-5, WS279 | F26D2.2 | See Figure 1—source data 5 |
| Gene (C. elegans) | syp-2 | https://wormbase.org/#012-34-5, WS279 | C24G6.1 | See Figure 1—source data 5 |
| Gene (C. elegans) | syp-3 | https://wormbase.org/#012-34-5, WS279 | F39H2.4 | See Figure 1—source data 5 |
| Gene (C. elegans) | syp-4 | https://wormbase.org/#012-34-5, WS279 | H27M09.3 | See Figure 1—source data 5 |
| Gene (C. elegans) | syp-5 | https://wormbase.org/#012-34-5, WS279 | Y54E10A.12 | See Figure 1—source data 5 |
| Gene (C. elegans) | spd-5 | https://wormbase.org/#012-34-5, WS279 | F56A3.4 | |
| Strain, strain background (P. pacificus) | PS312 | Caenorhabditis Genetics Center | PS312 | |
| Genetic reagent (P. pacificus) | Ppa-syp-1 | This paper | Null allele, available by request from the Rog lab | |
| Genetic reagent (P. pacificus) | HA::Ppa-syp-1 | This paper | In-frame insertion of HA tag, available by request from the Rog lab | |
| Genetic reagent (P. pacificus) | Ppa-syp-1::OLLAS | This paper | In-frame insertion of OLLAS tag, available by request from the Rog lab | |
| Antibody | Anti-Ppa-SYP-1 (rabbit polyclonal) | This paper, Pocono Rabbit Farm and Laboratory | Antibody targeting GSKSNKRQTRARGKKRTK in Ppa-SYP-1Available by request from the Rog lab(1:1000) | |
| Antibody | Anti-HA (mouse monoclonal) | Roche | 12CA5 | (1:500) |
| Antibody | Anti-OLLAS (rat monoclonal) | Invitrogen | MA5-16125 | (1:200) |
| Sequence-based reagent | Guide RNAs, DNA repair templates, and genotyping primers | This paper | See Figure 4—source data 1 | |
| Sequence-based reagent | Alt-R CRISPR-Cas9 tracrRNA | Integrated DNA Technologies | Cat # 1072532 | |
| Peptide, recombinant protein | Antigen for anti-Ppa-SYP-1 antibody | This paper | Peptide sequence: GSKSNKRQTRARGKK | |
| Peptide, recombinant protein | Alt-R S.p. Cas9 Nuclease V3 | Integrated DNA Technologies | Cat # 1081058 |
