Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

Salas‐Leiva, Dayana E.; Tromer, Eelco C.; Curtis, Bruce A.; Jerlström-Hultqvist, Jon; Kolísko, Martin; Yi, Zhenzhen; Salas‐Leiva, Joan; Gallot-Lavallée, Lucie; Williams, Shelby K.; Kops, Geert J.P.L.; Archibald, John M.; Simpson, Alastair G. B.; Roger, Andrew J.

doi:10.1038/s41467-021-26077-2

Cited by 22 publications

(25 citation statements)

References 99 publications

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“…The conservation of kinetochore proteins varies greatly across organisms (Meraldi et al, 2006;Tromer et al, 2019;van Hooff et al, 2017). Whilst the KMN network is more widely distributed (D'Archivio and Wickstead, 2017;Salas-Leiva et al, 2021), most of the CCAN is not conserved across eukaryotes. In particular, within the phylum of Apicomplexa, most components of the CCAN and SAC as described in animals and fungi, in addition to the majority of the KMN network, are not clearly detected.…”

Section: Introductionmentioning

confidence: 99%

Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation

Brusini

Pacheco

Tromer

et al. 2022

Journal of Cell Biology

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Kinetochores are multiprotein assemblies directing mitotic spindle attachment and chromosome segregation. In apicomplexan parasites, most known kinetochore components and associated regulators are apparently missing, suggesting a minimal structure with limited control over chromosome segregation. In this study, we use interactomics combined with deep homology searches to identify 13 previously unknown components of kinetochores in Apicomplexa. Apicomplexan kinetochores are highly divergent in sequence and composition from animal and fungal models. The nanoscale organization includes at least four discrete compartments, each displaying different biochemical interactions, subkinetochore localizations and evolutionary rates across the phylum. We reveal alignment of kinetochores at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, suggestive of a conserved “hold signal” that prevents precocious entry into anaphase. Finally, we show unexpected plasticity in kinetochore composition and segregation between apicomplexan lifecycle stages, suggestive of diverse requirements to maintain fidelity of chromosome segregation across parasite modes of division.

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Section: Introductionmentioning

confidence: 99%

Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation

Brusini

Pacheco

Tromer

et al. 2022

Journal of Cell Biology

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“…In stark contrast to CHC, the search for bona fide CLC sequences did not retrieve any reliable predictions in available genomes and transcriptomes from species of the Fornicata lineage, including the lineages Hexamitidae, Retortamonas and Carpediemonas-like organisms [ 59 , 75 , 84 – 86 ]. Importantly, this search did not return the putative, highly diverged Gl CLC [ 27 ].…”

Section: Resultsmentioning

confidence: 99%

Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Metamonada

et al. 2022

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Background Giardia lamblia, a parasitic protist of the Metamonada supergroup, has evolved one of the most diverged endocytic compartment systems investigated so far. Peripheral endocytic compartments, currently known as peripheral vesicles or vacuoles (PVs), perform bulk uptake of fluid phase material which is then digested and sorted either to the cell cytosol or back to the extracellular space. Results Here, we present a quantitative morphological characterization of these organelles using volumetric electron microscopy and super-resolution microscopy (SRM). We defined a morphological classification for the heterogenous population of PVs and performed a comparative analysis of PVs and endosome-like organelles in representatives of phylogenetically related taxa, Spironucleus spp. and Tritrichomonas foetus. To investigate the as-yet insufficiently understood connection between PVs and clathrin assemblies in G. lamblia, we further performed an in-depth search for two key elements of the endocytic machinery, clathrin heavy chain (CHC) and clathrin light chain (CLC), across different lineages in Metamonada. Our data point to the loss of a bona fide CLC in the last Fornicata common ancestor (LFCA) with the emergence of a protein analogous to CLC (GlACLC) in the Giardia genus. Finally, the location of clathrin in the various compartments was quantified. Conclusions Taken together, this provides the first comprehensive nanometric view of Giardia’s endocytic system architecture and sheds light on the evolution of GlACLC analogues in the Fornicata supergroup and, specific to Giardia, as a possible adaptation to the formation and maintenance of stable clathrin assemblies at PVs.

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“…Being an early branch of eukaryotes, G. duodenalis is known to lack certain genes involved in processes of DNA repair[ 31 ], possibly resulting in higher chances of replication errors slipping through. Meiosis is never observed in Giardia spp., nevertheless, sequence analysis revealed several homologs of meiosis-specific genes (HMG’s): Hop1, Spo11, Dmc1a, Dmc1b and Mnd1 [ 12 ].…”

Section: Resultsmentioning

confidence: 99%

Variation in haplotypes in single cysts of assemblages C and D, but not of assemblage E of Giardia duodenalis

et al. 2022

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Background Giardia duodenalis, a single-celled intestinal parasite, is divided into eight assemblages (A-H), with differences in host specificity. Giardia duodenalis reproduces asexually and cycles between the binucleated trophozoite (4 N) and the infectious cyst with four nuclei (16 N). Interaction between the nuclei is limited. Therefore, genetic drift causes differences in genetic make-up between the non-daughter nuclei; the allelic sequence heterozygosity (ASH). The ASH is low (0.01%—0.0023%) for the related assemblages A and E, higher (0.43–0.53) for assemblage B and much higher (0.74% -0.89%) for the assemblage C and D at the root of the phylogenetic tree. The heterozygosity in assemblage F, in the same clade as assemblage A and E, was unknown. The heterozygosity in the sequences of the gdh and dis3 genes was used as proxy for the ASH and whole genome amplification of single cysts followed by cloning and Sanger sequencing of dis3 fragment could reveal the genetic variation within the cyst. The aim of the study was to determine the level of heterozygosity within pooled and single cysts of different assemblages. Results The heterozygosity in gdh and dis3 was determined in pooled cysts of the assemblages A to F. Heterozygosity in the isolates of the assemblages C (n = 2) and D (n = 1) ranged from 0.41% to 0.82% for gdh and dis3 and no heterozygosity was found in the isolates of the assemblages A (n = 4), E (n = 3) and F (n = 3). The heterozygosity in assemblage B (n = 7) was intermediate (0% to 0.62%). Next, the number of haplotypes of dis3 was determined for single cysts of assemblages C, D and E. In the assemblages C and D, two to four haplotypes were found per cyst, while in assemblage E only one haplotype was identified. Conclusions Having high heterozygosity is characteristic for the assemblages C and D, while having a low heterozygosity is characteristic for the clade with the assemblages A, E and F. Presence of more than 1 haplotype per cyst in assemblage C and D suggests differences between the non-daughter nuclei, in contrast to the one haplotype in assemblage E.

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Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

Cited by 22 publications

References 99 publications

Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation

Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation

Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Metamonada

Variation in haplotypes in single cysts of assemblages C and D, but not of assemblage E of Giardia duodenalis

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