The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres

Cisse, O. H.; Curran, S.; Folco, H. D.; Liu, Y.; Bishop, L.; Wang, H.; Fischer, E. R.; Davis, A. S.; Babb-Biernacki, S.; Doyle, V. P.; Richards, J. K.; Hassan, S. A.; Dekker, J. P.; Khil, P. P.; Brenchley, J. M.; Grewal, S.; Cushion, M.; Ma, L.; Kovacs, J. A.

doi:10.1101/2023.05.12.540427

bioRxiv · 10.1101/2023.05.12.540427

The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres

Cisse, O. H.·Curran, S.·Folco, H. D.·Liu, Y.·Bishop, L.·Wang, H.·Fischer, E. R.·Davis, A. S.·Babb-Biernacki, S.·Doyle, V. P.·Richards, J. K.·Hassan, S. A.·Dekker, J. P.·Khil, P. P.·Brenchley, J. M.·Grewal, S.·Cushion, M.·Ma, L.·Kovacs, J. A.

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Abstract

Centromeres are constricted chromosomal regions that are essential for cell division. In eukaryotes, centromeres display a remarkable architectural and genetic diversity. The basis of centromere accelerated evolution remains elusive. Here we focused on Pneumocystis species, a group of Mammalian-specific fungal pathogens that form a sister taxon with that of the Schizosaccharomyces pombe, an important genetic model for centromere biology research. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-Seq, we identified CENP-A bound regions in two Pneumocystis species that diverged [~]35 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. These features suggest an epigenetic specification of centromere function. Analysis of centromeric DNA across multiple Pneumocystis species suggest a vertical transmission at least 100 million years ago. Common ancestry of Pneumocystis and S. pombe centromeres is untraceable at the DNA level but the overall architectural similarity could be the result of functional constraint for successful chromosomal segregation. Significance StatementPneumocystis species offer a suitable genetic system to study centromere evolution in pathogens because of their phylogenetic proximity with the nonpathogenic yeast Schizosaccharomyces pombe, a popular model for cell biology. We used this system to explore how centromeres have evolved after divergence of the two clades [~]460 million years ago. To address this question, we established a protocol combining short-term culture and ChIP-Seq to characterize centromeres in multiple Pneumocystis species. We show that Pneumocystis have short epigenetic centromeres that function differently from those in S. pombe. One sentence summaryInsights into the formation of genic centromeres in fungal pathogens.

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Cisse, O. H., Curran, S., Folco, H. D., Liu, Y., Bishop, L., Wang, H., Fischer, E. R., Davis, A. S., Babb-Biernacki, S., Doyle, V. P., Richards, J. K., Hassan, S. A., Dekker, J. P., Khil, P. P., Brenchley, J. M., Grewal, S., Cushion, M., Ma, L., Kovacs, J. A.. 2023-05-12. The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres. https://doi.org/10.1101/2023.05.12.540427

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