Kinetochore size scales with chromosome size in bimodal karyotypes of Agavoideae
Jazyk angličtina Země Anglie, Velká Británie Médium print
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
35576011
PubMed Central
PMC9295917
DOI
10.1093/aob/mcac063
PII: 6586410
Knihovny.cz E-zdroje
- Klíčová slova
- Asparagaceae, cell division, centromere, chromosome size evolution, genome size evolution, intracellular scaling, linear mixed models, structured illumination microscopy,
- MeSH
- buněčné dělení MeSH
- centromera * genetika MeSH
- karyotyp MeSH
- karyotypizace MeSH
- kinetochory * MeSH
- rostliny * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND AND AIMS: In eukaryotes, the total kinetochore size (defined as a chromosomal region containing CENH3-positive nucleosomes) per nucleus strongly correlates with genome size, a relationship that has been hypothesized to stem from general intracellular scaling principles. However, if larger chromosomes within a karyotype required larger kinetochores to move properly, it could also be derived from the mechanics of cell division. METHODS: We selected seven species of the plant subfamily Agavoideae whose karyotypes are characterized by the presence of small and very large chromosomes. We visualized the kinetochore regions and chromosomes by immunolabelling with an anti-CENH3 antibody and DAPI (6'-diamidino-2-phenylindole) staining. We then employed 2D widefield and 3D super-resolution microscopy to measure chromosome and kinetochore areas and volumes, respectively. To assess the scaling relationship of kinetochore size to chromosome size inside a karyotype, we log-transformed the data and analysed them with linear mixed models which allowed us to control for the inherent hierarchical structure of the dataset (metaphases within slides and species). KEY RESULTS: We found a positive intra-karyotype relationship between kinetochore and chromosome size. The slope of the regression line of the observed relationship (0.277 for areas, 0.247 for volumes) was very close to the theoretical slope of 0.25 for chromosome width based on the expected physics of chromosome passage through the cytoplasm during cell division. We obtained similar results by reanalysing available data from human and maize. CONCLUSIONS: Our findings suggest that the total kinetochore size to genome size scaling observed across eukaryotes may also originate from the mechanics of cell division. Moreover, the potential causal link between kinetochore and chromosome size indicates that evolutionary mechanisms capable of leading kinetochore size changes to fixation, such as centromere drive, could promote the size evolution of entire chromosomes and genomes.
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Anjur-Dietrich MI, Kelleher CP, Needleman DJ. 2021. Mechanical mechanisms of chromosome segregation. Cells 10: 465. doi:10.3390/cells10020465 PubMed DOI PMC
Breheny P, Burchett W. 2017. Visualization of regression models using visreg. R Journal 9: 56–71.
Carpenter EJ, Matasci N, Ayyampalayam S, et al. . 2019. Access to RNA-sequencing data from 1,173 plant species: the 1000 Plant transcriptomes initiative (1KP). Gigascience 8: giz126. doi: 10.1093/gigascience/giz126. PubMed DOI PMC
Chang CH, Malik HS. 2021. Putting the brakes on centromere drive in Mimulus. PLoS Genetics 17: e1009494. doi:10.1371/journal.pgen.1009494 PubMed DOI PMC
Cherry LM, Faulkner AJ, Grossberg LA, Balczon R. 1989. Kinetochore size variation in mammalian chromosomes: an image analysis study with evolutionary implications. Journal of Cell Science 92: 281–289. PubMed
Clark J, Hidalgo O, Pellicer J, et al. . 2016. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. New Phytologist 210: 1072–1082. doi: 10.1111/nph.13833. PubMed DOI
Drpic D, Almeida AC, Aguiar P, et al. . 2018. Chromosome segregation is biased by kinetochore size. Current Biology 28: 1344–1356. doi: 10.1016/j.cub.2018.03.023. PubMed DOI PMC
Fujiwara T, Liu H, Meza-Torres EI, et al. . 2021. Evolution of genome space occupation in ferns: linking genome diversity and species richness. Annals of Botany 389. doi: 10.1093/aob/mcab094. PubMed DOI PMC
Glazier DS. 2013. Log-transformation is useful for examining proportional relationships in allometric scaling. Journal of Theoretical Biology 334: 200–203. doi:10.1016/j.jtbi.2013.06.017 PubMed DOI
Granick EB. 1944. A karyosystematic study of the genus Agave. American Journal of Botany 31: 283–298.
Guadalupe P, Martínez J, Méndez I. 2008. Karyotype studies in cultivars of Agave tequilana Weber. Caryologia 61: 144–153. doi: 10.1080/00087114.2008.10589622. DOI
Henikoff S, Ahmad K, Malik HS. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293: 1098–1102. doi:10.1126/science.1062939 PubMed DOI
Heslop-Harrison JS, Schwarzacher T. 1993. Molecular cytogenetics – biology and applications in plant breeding. In: Sumner AT, Chandley AC, eds. Chromosomes today. Dordrecht: Springer, 191–198.
Houben A, Schroeder-Reiter E, Nagaki K, et al. . 2007. CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116: 275–283. doi:10.1007/s00412-007-0102-z PubMed DOI
Houchmandzadeh B, Marko JF, Chatenay D, Libchaber A. 1997. Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration. Journal of Cell Biology 139: 1–12. doi: 10.1083/jcb.139.1.1 PubMed DOI PMC
Irvine DV, Amor DJ, Perry J, Sirvent N, Pedeutour F, Choo KHA, Saffery R. 2004. Chromosome size and origin as determinants of the level of CENP-A incorporation into human centromeres. Chromosome Research 12: 805–815. doi: 10.1007/s10577-005-5377-4. PubMed DOI
Kaneko K. 1966. Cytological studies on some species of Hosta I. Karyotypes of H. montana, H. lancifolia, H. chibai and H. capitate. Botanical Magazine Tokyo 79: 131– 137. doi: 10.15281/jplantres1887.79.131. DOI
Kramer EM, Tayjasanant PA, Cordone B. 2021. Scaling laws for mitotic chromosomes. Frontiers in Cell and Developmental Biology 9: 684278. doi:10.3389/fcell.2021.684278 PubMed DOI PMC
Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. 2021a. Comparing super-resolution microscopy techniques to analyze chromosomes. International Journal of Molecular Sciences 22: 1903. doi: 10.3390/ijms22041903 PubMed DOI PMC
Kubalová I, Câmara AS, Cápal P, et al. . 2021. b. Helical metaphase chromatid coiling is conserved. bioRxiv doi: 10.1101/2021.09.16.460607. Preprint. DOI
Kursel LE, Malik HS. 2018. The cellular mechanisms and consequences of centromere drive. Current Opinion in Cell Biology 52: 58–65. doi: 10.1016/j.ceb.2018.01.011. PubMed DOI PMC
Levy DL, Heald R. 2012. Mechanisms of intracellular scaling. Annual Review of Cell and Developmental Biology 28: 113–135. doi: 10.1146/annurev-cellbio-092910-154158. PubMed DOI
Malik HS. 2009. The centromere-drive hypothesis: a simple basis for centromere complexity. Progress in Molecular and Subcellular Biology 48: 33–52. doi: 10.1007/978-3-642-00182-6_2 PubMed DOI
McEwen BF, Ding Y, Heagle AB. 1998. Relevance of kinetochore size and microtubule-binding capacity for stable chromosome attachment during mitosis in PtK1 cells. Chromosome Research 6: 123–132. doi: 10.1023/a:1009239013215. PubMed DOI
McKelvey SD, Sax K. 1933. Taxonomic and cytological relationships of Yucca and Agave. Journal of the Arnold Arboretum 14: 76–81.
Moens PB. 1979. Kinetochore microtubule numbers of different sized chromosomes. Journal of Cell Biology 83: 556–561. doi: 10.1083/jcb.83.3.556. PubMed DOI PMC
Murillo-Pineda M, Jansen LET. 2020. Genetics, epigenetics and back again: lessons learned from neocentromeres. Experimental Cell Research 389: 111909. doi: 10.1016/j.yexcr.2020.111909. PubMed DOI
Nakazato T, Barker MS, Rieseberg LH, Gastony GJ. 2008. Evolution of the nuclear genome of ferns and lycophytes. In: Ranker TA, Haufler CH, eds. Biology and evolution of ferns and lycophytes. Cambridge: Cambridge University Press, 175–198.
NCBI Resource Coordinators. 2018. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 46: D8–D13. doi: 10.1093/nar/gkx1095. PubMed DOI PMC
Nicklas RB. 1965. Chromosome velocity during mitosis as a function of chromosome size and position. Journal of Cell Biology 25: 119– 135. PubMed PMC
Nicklas RB. 1983. Measurements of the force produced by the mitotic spindle in anaphase. Journal of Cell Biology 97: 542–548. doi: 10.1083/jcb.97.2.542. PubMed DOI PMC
One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679–685. doi: 10.1038/s41586-019-1693-2. PubMed DOI PMC
Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team. 2021. nlme: linear and nonlinear mixed effects models. R package version 3.1-152. https://cran.r-project.org/web/packages/nlme/.
Plačková K, Bureš P, Zedek F. 2021. Centromere size scales with genome size across Eukaryotes. Scientific Reports 11: 19811. doi:10.1038/s41598-021-99386-7 PubMed DOI PMC
R Core Team. 2020. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/.
Schubert I, Oud JL. 1997. There is an upper limit of chromosome size for normal development of an organism. Cell 88: 515–520. doi:10.1016/s0092-8674(00)81891-7 PubMed DOI
Schwarzacher T, Heslop-Harrison JS, Anamthawat-Jonsson K, Finch RA, Bennett MD. 1992. Parental genome separation in reconstructions of somatic and premeiotic metaphases of Hordeum vulgare × H. bulbosum. Journal of Cell Science 101: 13–24.
Shimamoto Y, Maeda YT, Ishiwata S, Libchaber AJ, Kapoor TM. 2011. Insights into the micromechanical properties of the metaphase spindle. Cell 145: 1062–1074. doi: 10.1016/j.cell.2011.05.038 PubMed DOI PMC
Talbert PB, Henikoff S. 2020. What makes a centromere? Experimental Cell Research 389: 111895. doi: 10.1016/j.yexcr.2020.111895. PubMed DOI
Taylor EW. 1965. Brownian and saltatory movements of cytoplasmic granules and the movement of anaphase chromosomes. Proceedings of the International Congress on Rheology 4: 175–191.
Ui TJ, Hussey RG, Roger RP. 1984. Stokes drag on a cylinder in axial motion. Physics of Fluids 27: 787–795. doi: 10.1063/1.864706. DOI
Wang N, Dawe RK. 2018. Centromere size and its relationship to haploid formation in plants. Molecular Plant 11: 398–406. doi:10.1016/j.molp.2017.12.009 PubMed DOI
Wang N, Liu J, Ricci WA, Gent JI, Dawe RK. 2021. Maize centromeric chromatin scales with changes in genome size. Genetics 217: iyab020. doi: 10.1093/genetics/iyab020. PubMed DOI PMC
Watkins GM. 1936. Chromosome numbers and species characters in Yucca. American Journal of Botany 23: 328–333.
Weisshart K, Fuchs J, Schubert V. 2016. Structured illumination microscopy (SIM) and photoactivated localization microscopy (PALM) to analyze the abundance and distribution of RNA polymerase II molecules in flow-sorted Arabidopsis nuclei. Bio-protocol 6: e1725. http://www.bio-protocol.org/e1725
Zedek F, Bureš P. 2016. CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model. Scientific Reports 6: 33308. doi:10.1038/srep33308 PubMed DOI PMC
Zhang H, Dawe RK. 2012. Total centromere size and genome size are strongly correlated in ten grass species. Chromosome Research 20: 403–412. doi: 10.1007/s10577-012-9284-1. PubMed DOI PMC
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