Early diverging fungus Mucor circinelloides lacks centromeric histone CENP-A and displays a mosaic of point and regional centromeres

Abstract

15Centromeres are rapidly evolving across eukaryotes, despite performing a conserved 16 function to ensure high fidelity chromosome segregation. CENP-A chromatin is a hallmark of 17 a functional centromere in most organisms. Due to its critical role in kinetochore architecture, 18 the loss of CENP-A is tolerated in only a few organisms, many of which possess holocentric 19 chromosomes. Here, we characterize the consequence of the loss of CENP-A in the fungal 20 kingdom. Mucor circinelloides, an opportunistic human pathogen, lacks CENP-A along with 21 the evolutionarily conserved CENP-C, but assembles a monocentric chromosome with a 22 localized kinetochore complex throughout the cell cycle. Mis12 and Dsn1, two conserved 23 kinetochore proteins were found to bind nine short overlapping regions, each comprising an 24 2 ~200-bp AT-rich sequence followed by a centromere-specific conserved motif that echoes the 25 structure of budding yeast point centromeres. Resembling fungal regional centromeres, these 26 core centromere regions are embedded in large genomic expanses devoid of genes yet marked 27 by Grem-LINE1s, a novel retrotransposable element silenced by the Dicer-dependent RNAi 28 pathway. Our results suggest that these hybrid features of point and regional centromeres arose 29 from the absence of CENP-A, thus defining novel mosaic centromeres in this early-diverging 30 fungus. 31 Introduction 32Accurate chromosome segregation is crucial to maintain genome integrity during cell 33 division. The timely attachment of microtubules to centromere DNA is essential to achieve 34proper chromosome segregation. This is accomplished by a specialized multilayered protein 35 complex, the kinetochore which links microtubules to centromere DNA. This protein bridge is 36 divided into two layersthe inner and outer kinetochore. The fundamental inner kinetochore 37 protein is the histone H3 variant CENP-A. It binds directly to centromere DNA and lays the 38 foundation to recruit other essential proteins of the kinetochore complex, playing a fundamental 39 role in centromere structure and function, and hence, precise chromosome segregation 1,2 . 40 CENP-A is also found at all identified neocentromeres 3 and at the active centromeres of 41 dicentric chromosomes 4 , acting as an epigenetic determinant of centromeric identity. 42Despite its conserved function, the centromere is one of the most rapidly evolving 43 regions of the genome 5 . This so-called "centromere paradox" has led to centromeres of diverse 44 sizes and content. The first centromeres identified in Saccharomyces cerevisiae were found to 45 be point centromeres -small regions of ~120 bp defined by specific DNA sequences 6,7 . In 46 contrast to point centromeres described in only a few budding yeasts of the phylum 47 Ascomycota, most other fungi and metazoans have regional centromeres that are larger, 48 ranging from a few kilobases to several megabases 8 . Regional centromeres are often 49 3 interspersed with repetitive sequences and are mostly defined by epigenetic fac...

Understanding Mucormycoses in the Age of “omics”

“…Chromatin immunoprecipitation sequencing (ChIP-seq) of M. circinelloides showed that it has a unique "mosaic" centromere structure in Mucoromycotina, with characteristics from point centromeres (seen in Saccharomyces cerevisiae) and regional centromeres (seen in C. albicans, Candida tropicalis, Magnaporthe oryzae, Schizosaccharomyces pombe, and C. neoformans) (Navarro-Mendoza et al, 2019).…”

CenH3 distribution reveals extended centromeres in the model beetle Tribolium castaneum

“…In addition to the highly divergent N-terminal tail, certain changes in the HFD region are declared to be CenH3-specific, so they discriminate CenH3 variants from the canonical H3 and set bioinformatic criteria for identifying putative CenH3 in silico [ 14 ]. Although there have been evidenced species that lack CenH3 [ 6 , 15 , 16 ], CenH3 proteins still represent the most reliable markers of active centromeres. Nevertheless, great interspecies CenH3 varieties, corroborated by extremely divergent underlying DNA sequences, provoke the question of the centromere paradox where the function of the centromere is evolutionarily preserved while its DNA and protein constituents evolve rapidly [ 17 ].…”

CenH3-Independent Kinetochore Assembly in Lepidoptera Requires CCAN, Including CENP-T

“…Finally, our studies of kinetochore composition of CenH3deficient holocentric lepidopteran species, together with the recent finding of a CenH3-deficient monocentric fungus [28,43] that encodes for other CCAN components, including CENP-T, show that CCAN-based CenH3-independent kinetochore assemblies are considerably widespread in diverse eukaryotes.…”

“…Unexpected to its conserved and essential function, CenH3 has been lost in a few select lineages. These include the kinetoplastids [26,27], which have evolved an entirely different kinetochore complex, and an early-diverging fungus with mosaic centromeres characteristic of both regional and point centromeres [28]. In identified the homolog of the a subunit of the ATP synthase (bellwether, GSSPFG00010096001), found previously to localize to kinetochores during Drosophila melanogaster male meiosis [32], indicating that this function might be extended to lepidopteran mitosis.…”