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Chong MK, Rosas-Salvans M, Tran V, Dumont S. Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction. J Cell Biol 2024; 223:e202310010. [PMID: 38727808 PMCID: PMC11090132 DOI: 10.1083/jcb.202310010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/15/2024] Open
Abstract
Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.
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Affiliation(s)
- Megan K. Chong
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Miquel Rosas-Salvans
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vanna Tran
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sophie Dumont
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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2
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Kozulin P, Suárez R, Zhao QY, Paolino A, Richards LJ, Fenlon LR. Divergent evolution of developmental timing in the neocortex revealed by marsupial and eutherian transcriptomes. Development 2022; 149:274319. [DOI: 10.1242/dev.200212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Only mammals evolved a neocortex, which integrates sensory-motor and cognitive functions. Significant diversifications in the cellular composition and connectivity of the neocortex occurred between the two main therian groups: marsupials and eutherians. However, the developmental mechanisms underlying these diversifications are largely unknown. Here, we compared the neocortical transcriptomes of Sminthopsis crassicaudata, a mouse-sized marsupial, with those of eutherian mice at two developmentally equivalent time points corresponding to deeper and upper layer neuron generation. Enrichment analyses revealed more mature gene networks in marsupials at the early stage, which reverted at the later stage, suggesting a more precocious but protracted neuronal maturation program relative to birth timing of cortical layers. We ranked genes expressed in different species and identified important differences in gene expression rankings between species. For example, genes known to be enriched in upper-layer cortical projection neuron subtypes, such as Cux1, Lhx2 and Satb2, likely relate to corpus callosum emergence in eutherians. These results show molecular heterochronies of neocortical development in Theria, and highlight changes in gene expression and cell type composition that may underlie neocortical evolution and diversification.
This article has an associated ‘The people behind the papers’ interview.
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Affiliation(s)
- Peter Kozulin
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rodrigo Suárez
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiong-Yi Zhao
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Annalisa Paolino
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Linda J. Richards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura R. Fenlon
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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Begley MA, Solon AL, Davis EM, Sherrill MG, Ohi R, Elting MW. K-fiber bundles in the mitotic spindle are mechanically reinforced by Kif15. Mol Biol Cell 2021; 32:br11. [PMID: 34668719 PMCID: PMC8694074 DOI: 10.1091/mbc.e20-06-0426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mitotic spindle, a self-constructed microtubule-based machine, segregates chromosomes during cell division. In mammalian cells, microtubule bundles called kinetochore fibers (k-fibers) connect chromosomes to the spindle poles. Chromosome segregation thus depends on the mechanical integrity of k-fibers. Here we investigate the physical and molecular basis of k-fiber bundle cohesion. We detach k-fibers from poles by laser ablation-based cutting, thus revealing the contribution of pole-localized forces to k-fiber cohesion. We then measure the physical response of the remaining kinetochore-bound segments of the k-fibers. We observe that microtubules within ablated k-fibers often splay apart from their minus-ends. Furthermore, we find that minus-end clustering forces induced by ablation seem at least partially responsible for k-fiber splaying. We also investigate the role of the k-fiber-binding kinesin-12 Kif15. We find that pharmacological inhibition of Kif15-microtubule binding reduces the mechanical integrity of k-fibers. In contrast, inhibition of its motor activity but not its microtubule binding ability, i.e., locking Kif15 into a rigor state, does not greatly affect splaying. Altogether, the data suggest that forces holding k-fibers together are of similar magnitude to other spindle forces, and that Kif15, acting as a microtubule cross-linker, helps fortify and repair k-fibers. This feature of Kif15 may help support robust k-fiber function and prevent chromosome segregation errors.
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Affiliation(s)
- Marcus A Begley
- Department of Physics, North Carolina State University, Raleigh, NC 27607
| | - April L Solon
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | | | | | - Ryoma Ohi
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Mary Williard Elting
- Department of Physics, North Carolina State University, Raleigh, NC 27607.,Quantitative and Computational Developmental Biology Cluster, North Carolina State University, Raleigh, NC 27695
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Jin W, Zucker M, Pralle A. Membrane nanodomains homeostasis during propofol anesthesia as function of dosage and temperature. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183511. [PMID: 33245892 DOI: 10.1016/j.bbamem.2020.183511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/01/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022]
Abstract
Some anesthetics bind and potentiate γ-aminobutyric-acid-type receptors, but no universal mechanism for general anesthesia is known. Furthermore, often encountered complications such as anesthesia induced amnesia are not understood. General anesthetics are hydrophobic molecules easily dissolving into lipid bilayers. Recently, it was shown that general anesthetics perturb phase separation in vesicles extracted from fixed cells. Unclear is whether under physiological conditions general anesthetics induce perturbation of the lipid bilayer, and whether this contributes to the transient loss of consciousness or anesthesia side effects. Here we show that propofol perturbs lipid nanodomains in the outer and inner leaflet of the plasma membrane in intact cells, affecting membrane nanodomains in a concentration dependent manner: 1 μM to 5 μM propofol destabilize nanodomains; however, propofol concentrations higher than 5 μM stabilize nanodomains with time. Stabilization occurs only at physiological temperature and in intact cells. This process requires ARP2/3 mediated actin nucleation and Myosin II activity. The rate of nanodomain stabilization is potentiated by GABAA receptor activity. Our results show that active nanodomain homeostasis counteracts the initial disruption causing large changes in cortical actin. SIGNIFICANCE STATEMENT: General anesthesia is a routine medical procedure with few complications, yet a small number of patients experience side-effects that persist for weeks and months. Very young children are at risk for effects on brain development. Elderly patients often exhibit subsequent amnesia. Here, we show that the general anesthetic propofol perturbs the ultrastructure of the lipid bilayer of the cell membrane in intact cells. Initially propofol destabilized lipid nanodomains. However, with increasing incubation time and propofol concentration, the effect is reversed and nanodomains are further stabilized. We show that this stabilization is caused by the activation of the actin cortex under the membrane. These perturbations of membrane bilayer and cortical actin may explain how propofol affects neuronal plasticity at synapses.
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Affiliation(s)
- Weixiang Jin
- Dept. of Physics, University at Buffalo, SUNY, Buffalo, NY 14260-1500, USA
| | - Michael Zucker
- Dept. of Physics, University at Buffalo, SUNY, Buffalo, NY 14260-1500, USA
| | - Arnd Pralle
- Dept. of Physics, University at Buffalo, SUNY, Buffalo, NY 14260-1500, USA.
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Long AF, Suresh P, Dumont S. Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure. J Cell Biol 2020; 219:e201911090. [PMID: 32435797 PMCID: PMC7401803 DOI: 10.1083/jcb.201911090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/16/2020] [Accepted: 04/27/2020] [Indexed: 01/16/2023] Open
Abstract
At cell division, the mammalian kinetochore binds many spindle microtubules that make up the kinetochore-fiber. To segregate chromosomes, the kinetochore-fiber must be dynamic and generate and respond to force. Yet, how it remodels under force remains poorly understood. Kinetochore-fibers cannot be reconstituted in vitro, and exerting controlled forces in vivo remains challenging. Here, we use microneedles to pull on mammalian kinetochore-fibers and probe how sustained force regulates their dynamics and structure. We show that force lengthens kinetochore-fibers by persistently favoring plus-end polymerization, not by increasing polymerization rate. We demonstrate that force suppresses depolymerization at both plus and minus ends, rather than sliding microtubules within the kinetochore-fiber. Finally, we observe that kinetochore-fibers break but do not detach from kinetochores or poles. Together, this work suggests an engineering principle for spindle structural homeostasis: different physical mechanisms of local force dissipation by the k-fiber limit force transmission to preserve robust spindle structure. These findings may inform how other dynamic, force-generating cellular machines achieve mechanical robustness.
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Affiliation(s)
- Alexandra F. Long
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA
| | - Pooja Suresh
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA
| | - Sophie Dumont
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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6
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Hurst-Kennedy J, Saum M, Achat-Mendes C, D’Costa A, Javazon E, Katzman S, Ricks E, Barrera A. The Impact of a Semester-Long, Cell Culture and Fluorescence Microscopy CURE on Learning and Attitudes in an Underrepresented STEM Student Population. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2020; 21:jmbe-21-25. [PMID: 32341731 PMCID: PMC7173631 DOI: 10.1128/jmbe.v21i1.2001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/27/2020] [Indexed: 06/11/2023]
Abstract
Georgia Gwinnett College (GGC) is an access institution with a diverse student body, located in metro Atlanta. To strengthen research skills, teach employer-valued cell biology laboratory techniques, and increase student engagement, a semester-long, inquiry-based CURE was developed and implemented in Cell Biology with Laboratory (BIOL3400K), a sophomore-level course, which serves as a "gateway" to all upper-level biology courses. This CURE centers on the investigation of a student-chosen experimental factor on the viability of cultured, mammalian cells. Through participation in this CURE, students gain experience in cell culture, fluorescence microscopy, and viability assays, and strengthen important research skills, such as literature searches, graphing, and data analyses. The impact of this CURE on student learning gains and attitudes was assessed using pre-/post-content exams and the Colorado Learning Attitudes about Science Survey (CLASS). Our data show that all students made significant content gains. Female students made larger learning gains than male students. Additionally, minority students performed better than majority students in some content areas. Student attitudes did not change, or in some cases were slightly more negative after the CURE. Overall, this CURE had a positive impact on students by engaging them in an inquiry-based laboratory experience.
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Affiliation(s)
- Jennifer Hurst-Kennedy
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Michael Saum
- School of Science and Technology, Mathematics, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Cindy Achat-Mendes
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Allison D’Costa
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Elisabeth Javazon
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Shoshana Katzman
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Ernest Ricks
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Alessandra Barrera
- School of Science and Technology, Biology, Georgia Gwinnett College, Lawrenceville, GA 30043
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7
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Suresh P, Long AF, Dumont S. Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes. eLife 2020; 9:e53807. [PMID: 32191206 PMCID: PMC7117910 DOI: 10.7554/elife.53807] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/18/2020] [Indexed: 12/21/2022] Open
Abstract
The spindle generates force to segregate chromosomes at cell division. In mammalian cells, kinetochore-fibers connect chromosomes to the spindle. The dynamic spindle anchors kinetochore-fibers in space and time to move chromosomes. Yet, how it does so remains poorly understood as we lack tools to directly challenge this anchorage. Here, we adapt microneedle manipulation to exert local forces on the spindle with spatiotemporal control. Pulling on kinetochore-fibers reveals the preservation of local architecture in the spindle-center over seconds. Sister, but not neighbor, kinetochore-fibers remain tightly coupled, restricting chromosome stretching. Further, pulled kinetochore-fibers pivot around poles but not chromosomes, retaining their orientation within 3 μm of chromosomes. This local reinforcement has a 20 s lifetime, and requires the microtubule crosslinker PRC1. Together, these observations indicate short-lived, specialized reinforcement in the spindle center. This could help protect chromosome attachments from transient forces while allowing spindle remodeling, and chromosome movements, over longer timescales.
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Affiliation(s)
- Pooja Suresh
- Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Alexandra F Long
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Sophie Dumont
- Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
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O'Toole E, Morphew M, McIntosh JR. Electron tomography reveals aspects of spindle structure important for mechanical stability at metaphase. Mol Biol Cell 2019; 31:184-195. [PMID: 31825721 PMCID: PMC7001478 DOI: 10.1091/mbc.e19-07-0405] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Metaphase spindles exert pole-directed forces on still-connected sister kinetochores. The spindle must counter these forces with extensive forces to prevent spindle collapse. In small spindles, kinetochore microtubules (KMTs) connect directly with the poles, and countering forces are supplied either by interdigitating MTs that form interpolar bundles or by astral MTs connected to the cell cortex. In bigger spindles, particularly those without structured poles, the origin of extensive forces is less obvious. We have used electron tomography of well-preserved metaphase cells to obtain structural evidence about interactions among different classes of MTs in metaphase spindles from Chlamydomonas rheinhardti and two strains of cultured mammalian cells. In all these spindles, KMTs approach close to and cross-bridge with the minus ends of non-KMTs, which form a framework that interdigitates near the spindle equator. Although this structure is not pole-connected, its organization suggests that it can support kinetochore tension. Analogous arrangements of MTs have been seen in even bigger spindles, such as metaphase spindles in Haemanthus endosperm and frog egg extracts. We present and discuss a hypothesis that rationalizes changes in spindle design with spindle size based on the negative exponential distribution of MT lengths in dynamically unstable populations of tubulin polymers.
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Affiliation(s)
- Eileen O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309
| | - Mary Morphew
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309
| | - J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309
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dos Santos ÍGD, de Oliveira Mendes TA, Silva GAB, Reis AMS, Monteiro-Vitorello CB, Schaker PDC, Herai RH, Fabotti ABC, Coutinho LL, Jorge EC. Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum. BMC Genomics 2019; 20:866. [PMID: 31730444 PMCID: PMC6858782 DOI: 10.1186/s12864-019-6240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development. RESULTS The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development. CONCLUSIONS The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.
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Affiliation(s)
- Íria Gabriela Dias dos Santos
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | | | - Gerluza Aparecida Borges Silva
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | - Amanda Maria Sena Reis
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
| | | | - Patricia Dayane Carvalho Schaker
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo Brazil
| | - Roberto Hirochi Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | | | - Luiz Lehmann Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo Brazil
| | - Erika Cristina Jorge
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais Brazil
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Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A. Speciation Generates Mosaic Genomes in Kangaroos. Genome Biol Evol 2018; 10:33-44. [PMID: 29182740 PMCID: PMC5758907 DOI: 10.1093/gbe/evx245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 12/22/2022] Open
Abstract
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.
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Affiliation(s)
- Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Yichen Zheng
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
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11
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Elting MW, Prakash M, Udy DB, Dumont S. Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and Redundancy. Curr Biol 2017; 27:2112-2122.e5. [PMID: 28690110 DOI: 10.1016/j.cub.2017.06.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/04/2017] [Accepted: 06/08/2017] [Indexed: 11/25/2022]
Abstract
Active forces generated at kinetochores move chromosomes, and the dynamic spindle must robustly anchor kinetochore fibers (k-fibers) to bear this load. The mammalian spindle bears the load of chromosome movement far from poles, but we do not know where and how-physically and molecularly-this load distributes across the spindle. In part, this is because probing spindle mechanics in live cells is difficult. Yet answering this question is key to understanding how the spindle generates and responds to force and performs its diverse mechanical functions. Here, we map load-bearing across the mammalian spindle in space-time and dissect local anchorage mechanics and mechanism. To do so, we laser-ablate single k-fibers at different spindle locations and in different molecular backgrounds and quantify the immediate relaxation of chromosomes, k-fibers, and microtubule speckles. We find that load redistribution is locally confined in all directions: along the first 3-4 μm from kinetochores, scaling with k-fiber length, and laterally within ∼2 μm of k-fiber sides, without detectable load sharing between neighboring k-fibers. A phenomenological model suggests that dense, transient crosslinks to the spindle along k-fibers bear the load of chromosome movement but that these connections do not limit the timescale of spindle reorganization. The microtubule crosslinker NuMA is needed for the local load-bearing observed, whereas Eg5 and PRC1 are not detectably required, suggesting specialization in mechanical function. Together, the data and model suggest that NuMA-mediated crosslinks locally bear load, providing mechanical isolation and redundancy while allowing spindle fluidity. These features are well suited to support robust chromosome segregation.
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Affiliation(s)
- Mary Williard Elting
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Manu Prakash
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dylan B Udy
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sophie Dumont
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
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12
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Long AF, Udy DB, Dumont S. Hec1 Tail Phosphorylation Differentially Regulates Mammalian Kinetochore Coupling to Polymerizing and Depolymerizing Microtubules. Curr Biol 2017; 27:1692-1699.e3. [PMID: 28552353 DOI: 10.1016/j.cub.2017.04.058] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/22/2017] [Accepted: 04/27/2017] [Indexed: 02/02/2023]
Abstract
The kinetochore links chromosomes to dynamic spindle microtubules and drives both chromosome congression and segregation. To do so, the kinetochore must hold on to depolymerizing and polymerizing microtubules. At metaphase, one sister kinetochore couples to depolymerizing microtubules, pulling its sister along polymerizing microtubules [1, 2]. Distinct kinetochore-microtubule interfaces mediate these behaviors: active interfaces transduce microtubule depolymerization into mechanical work, and passive interfaces generate friction as the kinetochore moves along microtubules [3, 4]. Despite a growing understanding of the molecular components that mediate kinetochore binding [5-7], we do not know how kinetochores physically interact with polymerizing versus depolymerizing microtubule bundles, and whether they use the same mechanisms and regulation to do so. To address this question, we focus on the mechanical role of the essential load-bearing protein Hec1 [8-11] in mammalian cells. Hec1's affinity for microtubules is regulated by Aurora B phosphorylation on its N-terminal tail [12-15], but its role at the interface with polymerizing versus depolymerizing microtubules remains unclear. Here we use laser ablation to trigger cellular pulling on mutant kinetochores and decouple sisters in vivo, and thereby separately probe Hec1's role on polymerizing versus depolymerizing microtubules. We show that Hec1 tail phosphorylation tunes friction along polymerizing microtubules and yet does not compromise the kinetochore's ability to grip depolymerizing microtubules. Together, the data suggest that kinetochore regulation has differential effects on engagement with growing and shrinking microtubules. Through this mechanism, the kinetochore can modulate its grip on microtubules over mitosis and yet retain its ability to couple to microtubules powering chromosome movement.
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Affiliation(s)
- Alexandra F Long
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dylan B Udy
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; MCB Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Sophie Dumont
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cell and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Walczak CE, Zong H, Jain S, Stout JR. Spatial regulation of astral microtubule dynamics by Kif18B in PtK cells. Mol Biol Cell 2016; 27:3021-3030. [PMID: 27559136 PMCID: PMC5063611 DOI: 10.1091/mbc.e16-04-0254] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/19/2016] [Indexed: 01/07/2023] Open
Abstract
The spatial and temporal control of microtubule dynamics is fundamentally important for proper spindle assembly and chromosome segregation. This is achieved, in part, by the multitude of proteins that bind to and regulate spindle microtubules, including kinesin superfamily members, which act as microtubule-destabilizing enzymes. These fall into two general classes: the kinesin-13 proteins, which directly depolymerize microtubules, and the kinesin-8 proteins, which are plus end-directed motors that either destabilize microtubules or cap the microtubule plus ends. Here we analyze the contribution of a PtK kinesin-8 protein, Kif18B, in the control of mitotic microtubule dynamics. Knockdown of Kif18B causes defects in spindle microtubule organization and a dramatic increase in astral microtubules. Kif18B-knockdown cells had defects in chromosome alignment, but there were no defects in chromosome segregation. The long astral microtubules that occur in the absence of Kif18B are limited in length by the cell cortex. Using EB1 tracking, we show that Kif18B activity is spatially controlled, as loss of Kif18B has the most dramatic effect on the lifetimes of astral microtubules that extend toward the cell cortex. Together our studies provide new insight into how diverse kinesins contribute to spatial microtubule organization in the spindle.
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Affiliation(s)
| | - Hailing Zong
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Sachin Jain
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Jane R Stout
- Medical Sciences, Indiana University, Bloomington, IN 47405
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Bain PA, Papanicolaou A, Kumar A. Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PLoS One 2015; 10:e0142636. [PMID: 26599404 PMCID: PMC4658143 DOI: 10.1371/journal.pone.0142636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Murray-Darling rainbowfish (Melanotaenia fluviatilis [Castelnau, 1878]; Atheriniformes: Melanotaeniidae) is a small-bodied teleost currently under development in Australasia as a test species for aquatic toxicological studies. To date, efforts towards the development of molecular biomarkers of contaminant exposure have been hindered by the lack of available sequence data. To address this, we sequenced messenger RNA from brain, liver and gonads of mature male and female fish and generated a high-quality draft transcriptome using a de novo assembly approach. 149,742 clusters of putative transcripts were obtained, encompassing 43,841 non-redundant protein-coding regions. Deduced amino acid sequences were annotated by functional inference based on similarity with sequences from manually curated protein sequence databases. The draft assembly contained protein-coding regions homologous to 95.7% of the complete cohort of predicted proteins from the taxonomically related species, Oryzias latipes (Japanese medaka). The mean length of rainbowfish protein-coding sequences relative to their medaka homologues was 92.1%, indicating that despite the limited number of tissues sampled a large proportion of the total expected number of protein-coding genes was captured in the study. Because of our interest in the effects of environmental contaminants on endocrine pathways, we manually curated subsets of coding regions for putative nuclear receptors and steroidogenic enzymes in the rainbowfish transcriptome, revealing 61 candidate nuclear receptors encompassing all known subfamilies, and 41 putative steroidogenic enzymes representing all major steroidogenic enzymes occurring in teleosts. The transcriptome presented here will be a valuable resource for researchers interested in biomarker development, protein structure and function, and contaminant-response genomics in Murray-Darling rainbowfish.
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Affiliation(s)
- Peter A. Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Urrbrae, South Australia, Australia
- * E-mail:
| | - Alexie Papanicolaou
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Black Mountain, Australian Capital Territory, Australia
| | - Anupama Kumar
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Urrbrae, South Australia, Australia
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