A genomic “revolving door” in a centromeric gene of nematodes

From the Malik lab, Basic Sciences Division

Essential things tend to endure over time. All cars, from a U-haul truck to a Ferrari, have wheels and brakes. Aspects of the vehicle less critical to its operation are more variable: a minivan boasts spacious seating for additional passengers, while a sports car might eschew backseats altogether. This principle also applies to evolutionary processes. Dogma states that genes with essential functions tend to be conserved, much like the steering wheel, while nonessential genes are more susceptible to significant changes or even complete loss over time. There are, however, always exceptions that prove the rule. A team of researchers co-led by Lews Caro, a PhD candidate at the University of Washington’s Molecular and Cellular Biology Graduate Program, and Dr. Pravrutha Raman, a postdoctoral scholar in Dr. Harmit Malik’s lab in the Fred Hutch Basic Sciences Division, set out to explore one such exception related to the centromeric proteins of Caenorhabditis nematodes in a new study published in Molecular Biology and Evolution.

A fundamental process for organisms is the ability to undergo proper cell division. During eukaryotic cell division, the centromere (the region of the chromosome that links the two sister chromatids) attaches to microtubules via the kinetochore protein complex. The centromeric histone H3 variant, also known as CenH3, packages DNA near the centromere. CenH3 proteins attach chromosomes to microtubules during cell division; without the tension created by this attachment, cells cannot undergo division.

“Mitosis and meiosis are critical processes for development and sexual reproduction in eukaryotes, yet the centromeric histone H3 (CenH3) required for these processes changes dramatically across eukaryotes,” Caro explains. “CenH3 sequences have diversified in sequence and function, duplicated in a handful of eukaryotic lineages, and have even been completely lost in some insects.” The team, which included collaborators Dr. Florian Steiner and Dr. Michael Ailion, was interested in this paradox of the essential CenH3 undergoing rapid evolutionary changes, with a twist. Caro says, “Many studies on CenH3 evolution have looked at species with monocentric chromosomes, where there is only a single centromere per chromosome. However, not all animals or plants are monocentric. Species can be holocentric, where centromeres are distributed along the length of the chromosome. We hypothesized that holocentricity could shape CenH3 evolution in unique and unknown ways.”

The authors examined 32 Caenorhabditis species, and found the retention of the ancestral CenH3 gene (known as hcp-3 in nematodes) and 10 independent CenH3 duplications.
The authors examined 32 Caenorhabditis species, and found the retention of the ancestral CenH3 gene (known as hcp-3 in nematodes) and 10 independent CenH3 duplications. Image taken from article

The authors utilized comparative phylogenomic analyses to look for potential duplications or diversifications of CenH3 genes in 32 Caenorhabditis species. They found retention of the ancestral CenH3 gene in all species, but also 10 additional independent CenH3 duplications. Most of these duplications were only observed in one or two species, expressed regardless of sex, and shared similar histone-fold domains, which play a role in the higher 3D structure of chromatin. “What was surprising is that these nematode centromeric histone duplicates typically arose independently, rarely having a shared paralog between species,” said Caro.” This is unlike monocentric species which are seen to contain evolutionarily long-lived centromeric histone paralogs.”

Additionally, the authors found novel protein motifs that are conserved across the N-terminal domains of Caenorhabditis CenH3. Raman noted that the findings “showcase important motifs and reveal which amino acid residues are changing across Caenorhabditis CenH3.” Raman explained that in subsequent studies, “We can use the well-established model C. elegans to mutate these specific residues and assay functional consequences. The same is true for duplicates – by deleting the duplicates in species, we can assay if the ancestral histone and their duplicates have now acquired different or new functions, or if they have redundant roles as each other.”

Together, these data suggest that centromeric protein duplications are common in Caenorhabditis, but that these duplications are only retained for short periods of time before degenerating or entirely disappearing. This recurrent pattern of gene duplication and loss is called a genomic revolving door, as genes enter and exit the genome much like people through a revolving door. “The holocentric architecture of Caenorhabditis chromosomes may be one factor that contributes to unique selective pressures that lead to this rapid “revolving door” of kinetochore protein paralogs,” said Caro.

This study also highlights the importance of conducting studies on non-traditional model organisms. In evolutionary genetics, researchers are only afforded insight into a snapshot of a species’ evolutionary process. The genomic “revolving-door” discovered in this study would not have been detectable if the authors had focused on one species alone. As the authors conclude, “our study underlines the need for the analysis of non-model organisms and the value of evolutionary comparisons to reveal novelties even in well-studied cellular pathways.”

This work was supported by the National Institutes of Health (NIH) Institutional Traning Grant, the Republic and Canton of Geneva, the Swiss National Science Foundation, the National Science Foundation, the NIH National Institute of Genera Medical Sciences, the Washington Research Foundation, and the Howard Hughes Medical Institute.

The Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium member Dr. Harmit Malik contributed to this work.

Caro L, Raman P, Steiner FA, Ailion M, and Malik HS. 2022. Recurrent but Short-Lived Duplications of Centromeric Proteins in Holocentric Caenorhabditis Species. Molecular Biology and Evolution. 39(10):msac206.