Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Gene presence/absence screening

I compiled a list of 67 kinetochore associated genes in the yeast S. cerevisiae by downloading genes annotated with the GO term kinetochore (GO:0000776) in Ensembl release 91. The orthologs of these genes in all twenty yeast species were identified from the Yeast Gene Order Browser (YGOB) (Byrne & Wolfe, 2005). I screened the genomes of all 20 yeast species for the presence of all 67 genes and identified eight genes that are (both copies lost in post-WGD) lost in at least one species (see Supplemental Material S1). Kinetochore genes are known to evolve at a very fast rate, making it hard to identify orthologs of these genes even in closely related species (Van Hooff et al., 2017). It is possible that these genes have evolved at a very fast rate making it unfeasible to establish homology of these genes. Fortunately, the YGOB provides not only the order of the genes but also the intergenic sequences between genes. Based on flanking genes with conserved synteny in other species, I identified the intergenic regions that correspond to the location of the missing genes (see Supplemental Material S2). I checked these intergenic sequences for the presence of open reading frames (ORFs) using the NCBI ORF finder program with default settings. The ORFs that were found in the intergenic regions did not show any homology (inferred using blastn and blastp search against NCBI’s nucleotide collection and non-redundant protein sequences, respectively) to the genes that I have inferred to be lost. Based on the evidence from the identification of syntenic regions using YGOB and additional screening of intergenic regions I am confident of these gene loss events. Nonetheless, the presence of highly diverged copies of these genes in non-syntenic regions and genome assembly errors cannot be ruled out.

Multiple sequence alignments of CENPA/CSE4 gene

The complete open reading frame of the CENPA (CENH3 and CSE4 homolog) gene was used for multiple sequence alignment. To ensure that the results I see are not the result of alignment artifacts, I performed the multiple sequence alignment at the nucleotide sequence level and amino acid residue level using four different programs (Clustal omega (default settings in the webserver), M-coffee (command used and alignment scores are provided in Supplemental Material S3), MUSCLE (default settings in MEGA) and Guidance with PRANK as the aligner (command used is provided in Supplemental Material S3)). All the nucleotide and amino acid sequence alignments are provided as Supplemental Material S3. I investigated the multiple sequence alignments for evidence of lineage-specific patterns of selection in Naumovozyma species using the programs (RELAX, MEME, FEL and BUSTED) available in the HYPHY package (Kosakovsky Pond, Frost & Muse, 2005). The output files of these are also provided in Supplemental Material S3. The presence of additional sequences in the genus Naumovozyma was seen in all of the multiple sequence alignments that I have analyzed. It is possible that longer ORF’s have been incorrectly annotated as the CDS for both Naumovozyma species. However, the second methionine codon in the CDS occurs at the 226th and 40th residue from the currently annotated start codon in N. castellii and N. dairenensis, respectively. If the second methionine is the correct start codon, the N. castellii protein would be just 39 residues. This suggests that the correct ORF is annotated in Naumovozyma species. To further rule out the possibility of erroneous annotation of shorter ORF’s in non-naumovozyma species I extracted the genomic sequence found between genes flanking CENPA (CENH3 and CSE4 homolog) and searched them for ORF’s using the NCBI ORF finder program with default settings (see Supplemental Material S4). I found that the longest ORF that could be identified in this sequence was the currently annotated ORF itself. This further supports the validity of the annotation and multiple sequence alignments generated by me. I used the amino acid alignment generated by MUSCLE aligner to calculate the sequence conservation score using the al2co program (Pei & Grishin, 2001) with default settings along with the-a flag to calculate nine measures of sequence conservation. Per base measures of sequence conservation are provided as Supplemental Material S5.

Calculation of dyad density

Centromere sequences of the two Naumovozyma species were obtained from NCBI and YGOB browser for the remaining 18 species. The intergenic regions in Naumovozyma species orthologous to the old centromeres were extracted from YGOB. All these sequences and their locations are provided in Supplemental Material S6. The program palindrome from the EMBOSS package (Rice, Longden & Bleasby, 2000) was used to identify dyad symmetry (i.e., DNA sequences with base pairs that are inverted repeats of each other). The following settings were used for running the program “-minpallen 5 -maxpallen 100 -gaplimit 20-overlap”. All the palindromes identified for each of the sequences is provided as Supplemental Material S7. The dyad density for each centromere sequence was calculated as the fraction of bases that are part of a dyad. GC content for each sequence was calculated as the fraction of GC bases. GC content and dyad density for each of the centromere sequences are provided in Supplemental Material S8.

Patterns of kinetochore gene loss

My study system consists of eight Pre-WGD and twelve Post-WGD yeast species at varying evolutionary distances (see Fig. 1, phylogeny based on (Gordon, Byrne & Wolfe, 2011; Feng et al., 2017)). Based on screening of twenty yeast genomes for the presence of kinetochore genes I identified that eight genes (NKP1, NKP2, CENPL/IML3, CENPN/CHL4, CENPT/CNN1, CENPW/WIP1, FIN1 and BIR1) are lost at least once (see Fig. 1 and Supplemental Material S1). Intriguingly, five of the eight genes (i.e., NKP1, NKP2, CENPL/IML3, BIR1 and WIP1) that have lost both their copies in the Post-WGD species are also the ones that are lost in the Pre-WGD species (see Fig. 1). This hints at the dispensability of these genes over the course of evolution. In this study, I focus on the set of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) that are lost in Naumovozyma (a genus known to have novel point centromeres). As the name suggests, the Non-essential Kinetochore Protein genes NKP1 and NKP2 produce proteins that localize to kinetochores and when deleted produce viable single gene mutants (Cheeseman et al., 2002). However, both single gene mutants are known to show elevated rates of chromosome loss (Fernius & Marston, 2009). Knockout of both NKP1 and NKP2 only shows a moderate increase in chromosome loss (Tirupataiah et al., 2014). Despite being non-essential genes, at least one copy of both of these genes is found in 15 of the 20 yeast species screened in this study. A broader phylogenetic search for homologs of these genes has shown the repeated loss of these two genes in various taxa (Tromer, 2017). While it was known that NKP1 and NKP2 bind to COMA complex (Hornung et al., 2014), recent work has shown that NKP1 and NKP2 are positioned at the bottom of the CTF19 complex and form a four-chain helical coil along with OKP1 and AME1 at their c-terminus (Hinshaw & Harrison, 2019). The main function of the NKP1 and NKP2 heterodimer is thought to be the stabilization of the COMA complex (Schmitzberger et al., 2017). The COMA complex is known to interact directly with the CENPA/CSE4 protein (Fischböck-Halwachs et al., 2019).

The CENPN/CHL4 (CHromosome Loss 4) single-gene knockouts are also viable but are known to show increased levels of chromosome loss, miss-segregation, and abnormal kinetochores (Roy et al., 1997). However, based on the chromatin state CENPN/CHL4 mutant cells are known to show two distinct (high and low) levels of mitotic mobility (Roy & Sanyal, 2011). This suggests that CENPN/CHL4 mutants can be compensated through changes in the chromatin state. CENPL/IML3 (Increased Minichromosome Loss) protein forms a stable heterodimer with CENPN/CHL4 protein (Hinshaw & Harrison, 2013). Although CENPL/IML3 and CENPN/CHL4 are known interactors, the phylogenetic distribution of CENPL/IML3 seems to be more restricted than that of CENPN/CHL4. The association of cohesin with the pericentromeric regions is ensured by the action of CENPL/IML3 and CENPN/CHL4. The lack of these two genes leads to reduced cohesin binding at the pericentromere that results in the miss-segregation of chromosomes (Fernius & Marston, 2009).

The function of the genes lost in Naumovozyma may be performed by genes that are found in Naumovozyma but are absent in S. cerevisiae. Naumovozyma species have 46 genes that are absent in the other 18 species analyzed in this study. To evaluate whether any of these genus specific genes could have taken over the role performed by the four missing genes, I identified homologs of each of these genes by performing blastp search against the non-redundant protein database with an e-value cut-off of 10⁻³. None of the identified homologs had a characterized role related to the kinetochore machinery. However, profile-versus-profile search based comparisons have identified that NKP1 and NKP2 are extremely similar to Mis12 and Nnf1 (Tromer et al., 2019). Since, one copy (NCAS0H00450 and NDAI0K02740) of the Nnf1 gene is present in each of the Naumovozyma species; it is possible that the functions of NKP1/2 are compensated.

N-terminus divergence of CENPA/CSE4 gene in Naumovozyma

The detailed study of the interactions between kinetochore proteins in S. cerevisiae has led to a better understanding of their roles (Measday et al., 2005; Baetz, Measday & Andrews, 2006). However, the evolution of the kinetochore network across Eukaryotes has been shown to be a complex process that requires further investigation (Van Hooff et al., 2017). In the current study, I have focussed on well-studied genetic interactions of the selected genes that have lost both copies in Post-WGD yeast species. Chromatin Immuno-Precipitation (ChIP) of CENPA/CSE4 protein followed by sequencing of DNA fragments was used by Kobayashi et al. (2015) to identify all the CENPA/CSE4 binding sites in the N. castellii genome. Based on this experimental data for CENPA/CSE4 along with similar ChIP-seq data for the NDC10, NDC80, and CEP3 proteins the locations of the new centromeres in N. castellii have been validated (Kobayashi et al., 2015). The multiple sequence alignment of amino-acid sequences across the study species (see Supplemental Material S3) shows that the CENPA/CSE4 genes of N. castellii and N. dairenensis have a stretch of approximately ten amino acid residues at the very beginning of the CENPA/CSE4 gene that is absent in other species. It is known that the C-terminus of the CENPA/CSE4 protein binds to the centromeric DNA sequence, and the N-terminus interacts with the CCAN/CTF19 complex (Chen et al., 2000). The N-terminus region has overall reduced sequence conservation across all species compared to the C-terminus region (see Fig. 2). I also find evidence of significant relaxed selection in the N. castellii and N. dairenensis lineages using the hypothesis testing framework available in the RELAX program (version 2.1) on the multiple sequence alignments generated by MUSCLE. However, when the alignments generated using guidance with PRANK as aligner was used, the relaxed selection in the N. castellii lineage was not found to be statistically significant (see Supplemental Material S3). These differences in the inferences based on the multiple sequence aligner used are known to occur when the sequences are highly diverged (Blackburne & Whelan, 2013). I have shown earlier that genes can experience relaxed selection when the c-terminal end is increased in length due to change in the position of the stop codon (Shinde et al., 2019). Hence, the relaxed selection detected in the CENPA/CSE4 gene could simply be a result of drastic change in the length of the n-terminal sequence.

The N-terminus of the CENPA/CSE4 protein has been shown to play a role in the ubiquitin-mediated proteolysis of the CENPA/CSE4 protein (Au et al., 2013). More recently, sumoylation and ubiquitination of the N-terminus have been shown to be required to prevent the mislocalization of CENPA/CSE4 to non-centromeric chromatin (Ohkuni et al., 2018). The lysine 65 residue (K65) in the CENPA/CSE4 gene has been identified as the residue important for proper localization. Changes in the N-terminus region of CENPA/CSE4 gene could have led to changes in the post-translational modifications resulting in changes in the localization patterns and subsequent movement of centromeres in Naumovozyma.

Dyad density at point centromeres

Dyad symmetry refers to the presence of inverted repeats or palindromes in the sequence. The inverted repeats identified on the centromere of S. cerevisiae are provided in Fig. 3 as an example. It has been shown that centromere regions are defined by the presence of Non-B-form DNA structures resulting from the presence of dyad symmetry in the nucleotide sequence (Kasinathan & Henikoff, 2018). While the new Naumovozyma centromeres are enriched for dyad symmetries and non-B-form DNA, the dyad symmetry was less and the SIST DNA melting and cruciform extrusion scores were lower in Naumovozyma (sensu lato, demarcated by a red box in Fig. 1) compared to sensu strictu species (demarcated by a blue box in Fig. 1 (Pulvirenti et al., 2000)). However, they utilized the contrast of sensu stricto vs sensu lato and ignore other species that have been phylogenetically placed closer to the sensu strictu species. Using a larger sample size (centromeres from various budding yeast species) I show that the GC content shows a significant negative correlation (Kendall’s rank correlation coefficient tau of −0.59, p-value < 2.2E−16) with dyad density (see Fig. 4A). This correlation is reflective of the genome-wide pattern seen in S. cerevisiae (Lisnić et al., 2005).

The unconventional centromeres in the yeast species N. castellii and N. dairenensis are in most cases located at a different genomic locus compared to the point centromeres found in other budding yeast species such as S. cerevisiae (Kobayashi et al., 2015). This movement of centromeres has partly been attributed to chromosomal re-arrangements. I show that the GC content of the intergenic regions corresponding to the older (S. cerevisiae like) centromeres is very high and dyad density is low (see Fig. 4A; red colored circles). On the other hand the new unconventional centromeres that have been identified in Naumovozyma (see Fig. 4A; blue colored circles) are having higher dyad densities and lower GC content. I note that the pattern is the same for both Naumovozyma species (see Fig. 4A; filled circles for N. castellii and unfilled circles for N. dairenensis). The new (mean: 25.80, median: 24.77, min: 20.00 and max: 35.16) centromeres in N. dairenensis have a lower GC content than the older regions (mean: 31.58, median: 32.90, min: 22.03 and max: 37.32). Similarly, the new (mean: 21.36, median: 20.91, min: 18.18 and max: 24.55) centromeres in N. castellii have a lower GC content than the older regions (mean: 30.15, median: 30.35, min: 21.82 and max: 36.47). I used a pair-wise wilcoxon test with holm multiple testing correction (also see Fig. 4B) to compare the GC content of the old and new centromere regions and find a difference in both N. castellii (q-value: 0.0067) and N. dairenensis (q-value: 0.0778). This change in dyad density and GC content probably reflects a divergence that occurred after the change in the location of the centromere.