Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres

Navarro-Mendoza, María Isabel; Pérez-Arques, Carlos; Panchal, Shweta; Nicolás, Francisco E.; Mondo, Stephen J.; Ganguly, Promit; Pangilinan, Jasmyn; Grigoriev, Igor V.; Heitman, Joseph; Sanyal, Kaustuv

doi:10.1016/j.cub.2019.09.024

Cited by 83 publications

(85 citation statements)

References 78 publications

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“…In this sense, we characterized the production of siRNAs from Grem-LINE1 transcripts in the pericentric regions of the wild-type strains and the r3b2 Δ and rdrp1 Δ mutants (Fig 5A). The pericentric regions are almost depleted of siRNAs in the ago1 Δ and dcl1 dcl2 Δ mutants, whereas the wild-type strain exhibited an active production of siRNAs aligned to these loci, as previously reported [12]. Interestingly, the r3b2 Δ and rdrp1 Δ mutants displayed an exaggerated production of siRNAs compared to the wild-type strain, especially targeting the second open reading frame (ORF2) and its reverse transcriptase domain (RVT).…”

Section: Resultssupporting

confidence: 76%

“…Because mutants in the machinery of NCRIP also display defects in the production of zygospores during mating, we hypothesized that NCRIP might also contribute in the regulation of genes involved in other stresses such as antifungal agents [4,9] and genomic integrity stress, which could alter complex cell processes involved in mating [10]. A recent study supported this hypothesis, unveiling a direct link between the canonical RNAi pathway and the protection of genome integrity against transposable elements in M. circinelloides [12]. The pericentric regions of M. circinelloides contain a large number of L1-like retrotransposable elements of the Mucoromycotina species called Grem-LINE1s, which are actively silenced by the canonical RNAi machinery.…”

Section: Resultsmentioning

confidence: 99%

“…(B) Heatmap of the differential expression of G enomic retrotransposable e lements of M ucoromycotina LINE1-like (Grem-LINE1s) in the depicted RNAi mutants compared to the RNAi-proficient wild-type strain. Grem-LINE1s are numbered according to Navarro et al classification [12].…”

Section: Resultsmentioning

confidence: 99%

“…DEGs were classified according to Eu k aryotic O rthologous G roups (KOG) and G ene O ntology (GO) terms using EggNOG-mapper v2.0 [28,29] to perform KOG class enrichment analyses with KOGMWU package v.1.2 [30]; statistical significance was assessed with a Fisher’s exact test (p-value ≤0.05). Small RNA reads were obtained from previous studies (see Data Availability) and aligned to the M. circinelloides f. lusitanicus MU402 v1.0 genome (Muccir1_3 [12]) using the B urrows- W heeler A ligner (BWA) v.0.7.8 [31]. This genome was PacBio-sequenced using long reads and thus, exhibit a greater content of repeated elements [12].…”

Section: Methodsmentioning

confidence: 99%

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A non-canonical RNAi pathway controls virulence and genome stability in Mucorales

Pérez-Arques

Navarro-Mendoza

Murcia

et al. 2020

Preprint

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8Epimutations in fungal pathogens are emerging as novel phenomena that could 9 explain the fast-developing resistance to antifungal drugs and other stresses. These 10 epimutations are generated by RNA interference (RNAi) mechanisms that transiently 11 silence specific genes to overcome stressful stimuli. The early-diverging fungus Mucor 12 circinelloides exercises a fine control over two interacting RNAi pathways to produce 13 epimutants: the canonical RNAi pathway and a new RNAi degradative pathway. The 14 latter is considered a non-canonical RNAi pathway (NCRIP) because it relies on RNA-15 dependent RNA polymerases (RdRPs) and a novel ribonuclease III-like named R3B2 to 16 degrade target transcripts. Here in this work, we uncovered the role of NCRIP in 17regulating virulence processes and transposon movements through key components of the 18 pathway, RdRP1, and R3B2. Mutants in these genes are unable to launch a proper 19 virulence response to macrophage phagocytosis, resulting in a decreased virulence 20 potential. The transcriptomic profile of rdrp1Δ and r3b2Δ mutants revealed a pre-21 exposure adaptation to the stressful phagosomal environment even when the strains are 22 not confronted by macrophages. These results suggest that NCRIP represses key targets 23 during regular growth and release its control when the fungus is challenged by a stressful 24 environment. NCRIP interacts with the RNAi canonical core to protect genome stability 25 by controlling the expression of centromeric retrotransposable elements. In the absence 2 26 of NCRIP, these retrotransposons are robustly repressed by the canonical RNAi 27 machinery; thus, supporting the antagonistic role of NCRIP in containing the 28 epimutational pathway. Both interacting RNAi pathways might be essential to govern 29 host-pathogen interactions through transient adaptations, contributing to the unique traits 30 of the emerging infection mucormycosis. 31 Author summary 32 Mucormycosis is an emergent and lethal infectious disease caused by Mucorales, a fungal 33 group resistant to most antifungal drugs. Mucor circinelloides, a genetic model to 34 characterize this infection, can develop drug resistance via RNAi epimutations. This 35 epimutational RNAi mechanism interacts with a novel non-canonical RNAi pathway36 (NCRIP), where the ribonuclease III-like R3B2 and the RNA-dependent RNA 37 polymerase RdRP1 are essential. The analysis of the transcriptomic response to 38 phagocytosis by macrophage in rdrp1Δ and r3b2Δ mutants revealed that NCRIP might 39 control virulence in M. circinelloides. These mutants showed constitutive activation of 40 the response to phagocytosis and a reduction in virulence in a mouse model, probably 41 caused by a disorganized execution of the genetic program to overcome host defense 42 mechanisms. The antagonistic role of the NCRIP and the RNAi canonical core is evident 43 during post-transcriptional regulation of centromeric retrotransposons. These44 retrotransposons are silenced by the canonical RNAi pathway, but this regulation is...

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Section: Resultssupporting

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales

Pérez-Arques

Navarro-Mendoza

Murcia

et al. 2020

Preprint

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“…Emerging long-read sequencing technologies, such as Pacific Bioscience (PacBio) and Oxford Nanopore Technology (ONT), have led to substantial advances in resolution of chromosomal structures including highly repetitive sequences such as centromeres. Using these technologies, centromeres that were difficult to resolve using short-read sequencing, were defined in various organisms, from fungi (12, 19, 20) to insects (21), plants (22) and humans (23).…”

Section: Introductionmentioning

confidence: 99%

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

Fang

Coelho

Shu

et al. 2019

Preprint

Self Cite

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26Centromeres are chromosomal regions that serve as platforms for kinetochore assembly 27 and spindle attachments, ensuring accurate chromosome segregation during cell division. 28Despite functional conservation, centromere DNA sequences are diverse and often repetitive, 29 making them challenging to assemble and identify. Here, we describe centromeres in an 30 oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and 31 chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput 32 sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and 33 during nuclear division. We report an improved genome assembly of the P. sojae reference strain, 34 which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. 35By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are 36 regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, 37 and lack the histone modification H3K4me2 but are embedded within regions with the 38 heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like 39 transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements 40 are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction 41 of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes 42 as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup 43 including diatoms and Plasmodium falciparum that have relatively short and simple regional 44 centromeres. Identification of P. sojae centromeres in turn also augments the genome assembly. 45 46 Significance Statement 49Oomycetes are fungal-like microorganisms that belong to the stramenopiles within the 50 Stramenopila-Alveolata-Rhizaria (SAR) supergroup. The Phytophthora oomycetes are infamous 51 as plant killers, threatening crop production worldwide. Because of the highly repetitive nature of 52 their genomes, assembly of oomycete genomes presents challenges that impede identification of 53 centromeres, which are chromosomal sites mediating faithful chromosome segregation. We 54 report long-read sequencing-based genome assembly of the Phytophthora sojae reference strain, 55 which facilitated the discovery of centromeres. P. sojae harbors large regional centromeres 56 enriched for a Copia-like transposon that is also found in discrete clusters in other oomycetes. 57This study provides insight into the oomycete genome organization, and broadens our knowledge 58 of the centromere structure, function and evolution in eukaryotes. 59 60 Accurate segregation of chromosomes during mitosis and meiosis is critical for the 61 development and reproduction of all eukaryotic organisms. Centromeres are specialized regions 62 of chromosomes that mediate kinetochore formation, spindle attachment, and sister chromatid 63 segregation during cell division (1, 2). T...

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Insights Into the Evolutionary Diversity of Centromeres

CORTES‐SILVA,

SENARATNE,

DRINNENBERG

2023

Function and Evolution of Repeated DNA Sequences

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Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres

Cited by 83 publications

References 78 publications

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

Insights Into the Evolutionary Diversity of Centromeres

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