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Neumann AJ, Prekeris R. A Rab-bit hole: Rab40 GTPases as new regulators of the actin cytoskeleton and cell migration. Front Cell Dev Biol 2023; 11:1268922. [PMID: 37736498 PMCID: PMC10509765 DOI: 10.3389/fcell.2023.1268922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023] Open
Abstract
The regulation of machinery involved in cell migration is vital to the maintenance of proper organism function. When migration is dysregulated, a variety of phenotypes ranging from developmental disorders to cancer metastasis can occur. One of the primary structures involved in cell migration is the actin cytoskeleton. Actin assembly and disassembly form a variety of dynamic structures which provide the pushing and contractile forces necessary for cells to properly migrate. As such, actin dynamics are tightly regulated. Classically, the Rho family of GTPases are considered the major regulators of the actin cytoskeleton during cell migration. Together, this family establishes polarity in the migrating cell by stimulating the formation of various actin structures in specific cellular locations. However, while the Rho GTPases are acknowledged as the core machinery regulating actin dynamics and cell migration, a variety of other proteins have become established as modulators of actin structures and cell migration. One such group of proteins is the Rab40 family of GTPases, an evolutionarily and functionally unique family of Rabs. Rab40 originated as a single protein in the bilaterians and, through multiple duplication events, expanded to a four-protein family in higher primates. Furthermore, unlike other members of the Rab family, Rab40 proteins contain a C-terminally located suppressor of cytokine signaling (SOCS) box domain. Through the SOCS box, Rab40 proteins interact with Cullin5 to form an E3 ubiquitin ligase complex. As a member of this complex, Rab40 ubiquitinates its effectors, controlling their degradation, localization, and activation. Because substrates of the Rab40/Cullin5 complex can play a role in regulating actin structures and cell migration, the Rab40 family of proteins has recently emerged as unique modulators of cell migration machinery.
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Affiliation(s)
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Prentout D, Stajner N, Cerenak A, Tricou T, Brochier-Armanet C, Jakse J, Käfer J, Marais GAB. Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes. THE NEW PHYTOLOGIST 2021; 231:1599-1611. [PMID: 33978992 DOI: 10.1111/nph.17456] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
We recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants (12-28 Myr old). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus, which is known also to possess XY chromosomes. Here, we used transcriptome sequencing of an F1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. We identified 265 sex-linked genes in H. lupulus, which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex-linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa, Y-linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation. We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21-25 Myr ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes (c. 70%), leading to a degenerated Y chromosome.
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Affiliation(s)
- Djivan Prentout
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Natasa Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, Zalec, SI-3310, Slovenia
| | - Theo Tricou
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Celine Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, 1349-017, Portugal
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Braun M, Lehmbecker A, Eikelberg D, Hellige M, Beineke A, Metzger J, Distl O. De novo ZIC2 frameshift variant associated with frontonasal dysplasia in a Limousin calf. BMC Genomics 2021; 22:1. [PMID: 33388042 PMCID: PMC7777292 DOI: 10.1186/s12864-020-07350-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Background Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examinations and whole genome sequencing on an Illumina NextSeq500 were performed to characterize a stillborn Limousin calf with frontonasal dysplasia. In order to identify private genetic and structural variants, we screened whole genome sequencing data of the affected calf and unaffected relatives including parents, a maternal and paternal halfsibling. Results The stillborn calf exhibited severe craniofacial malformations. Nose and maxilla were absent, mandibles were upwardly curved and a median cleft palate was evident. Eyes, optic nerve and orbital cavities were not developed and the rudimentary orbita showed hypotelorism. A defect centrally in the front skull covered with a membrane extended into the intracranial cavity. Aprosencephaly affected telencephalic and diencephalic structures and cerebellum. In addition, a shortened tail was seen. Filtering whole genome sequencing data revealed a private frameshift variant within the candidate gene ZIC2 in the affected calf. This variant was heterozygous mutant in this case and homozygous wild type in parents, half-siblings and controls. Conclusions We found a novel ZIC2 frameshift mutation in an aprosencephalic Limousin calf. The origin of this variant is most likely due to a de novo mutation in the germline of one parent or during very early embryonic development. To the authors’ best knowledge, this is the first identified mutation in cattle associated with bovine frontonasal dysplasia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07350-y.
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Affiliation(s)
- Marina Braun
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Annika Lehmbecker
- Department for Pathology, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Deborah Eikelberg
- Department for Pathology, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Maren Hellige
- Clinic for Horses, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Andreas Beineke
- Department for Pathology, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany.
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Ruzzenenti P, Asperti M, Mitola S, Crescini E, Maccarinelli F, Gryzik M, Regoni M, Finazzi D, Arosio P, Poli M. The Ferritin-Heavy-Polypeptide-Like-17 (FTHL17) gene encodes a ferritin with low stability and no ferroxidase activity and with a partial nuclear localization. Biochim Biophys Acta Gen Subj 2015; 1850:1267-73. [DOI: 10.1016/j.bbagen.2015.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 02/13/2015] [Accepted: 02/26/2015] [Indexed: 12/12/2022]
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Lee JH, Pooley NJ, Mohd-Adnan A, Martin SAM. Cloning and characterisation of multiple ferritin isoforms in the Atlantic salmon (Salmo salar). PLoS One 2014; 9:e103729. [PMID: 25078784 PMCID: PMC4117605 DOI: 10.1371/journal.pone.0103729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/06/2014] [Indexed: 12/21/2022] Open
Abstract
Ferritin is a highly-conserved iron-storage protein that has also been identified as an acute phase protein within the innate immune system. The iron-storage function is mediated through complementary roles played by heavy (H)-chain subunit as well as the light (L) in mammals or middle (M)-chain in teleosts, respectively. In this study, we report the identification of five ferritin subunits (H1, H2, M1, M2, M3) in the Atlantic salmon that were supported by the presence of iron-regulatory regions, gene structure, conserved domains and phylogenetic analysis. Tissue distribution analysis across eight different tissues showed that each of these isoforms is differentially expressed. We also examined the expression of the ferritin isoforms in the liver and kidney of juvenile Atlantic salmon that was challenged with Aeromonas salmonicida as well as in muscle cell culture stimulated with interleukin-1β. We found that each isoform displayed unique expression profiles, and in certain conditions the expressions between the isoforms were completely diametrical to each other. Our study is the first report of multiple ferritin isoforms from both the H- and M-chains in a vertebrate species, as well as ferritin isoforms that showed decreased expression in response to infection. Taken together, the results of our study suggest the possibility of functional differences between the H- and M-chain isoforms in terms of tissue localisation, transcriptional response to bacterial exposure and stimulation by specific immune factors.
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Affiliation(s)
- Jun-Hoe Lee
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
- School of Biosciences and Biotechnology, Faculty of Science & Technology, University of Kebangsaan, Selangor, Malaysia
| | - Nicholas J. Pooley
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Adura Mohd-Adnan
- School of Biosciences and Biotechnology, Faculty of Science & Technology, University of Kebangsaan, Selangor, Malaysia
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Selangor, Malaysia
| | - Samuel A. M. Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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Karn RC, Laukaitis CM. The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family. PLoS One 2012; 7:e47697. [PMID: 23094077 PMCID: PMC3477143 DOI: 10.1371/journal.pone.0047697] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/18/2012] [Indexed: 11/22/2022] Open
Abstract
Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although not in all of them. Our studies of selection identified at least two amino acid sites in β-sheets as having evolved under positive selection in the mouse Class A and Class B MUPs and in rat MUPs. We show that selection may have acted on the ESPs by determining K(a)/K(s) for Exon 3 sequences with and without the converted sequence segment. While it appears that purifying selection acted on the ESP signal peptides, the secreted portions of the ESPs probably have undergone much more rapid evolution. When the inner gene converted fragment sequences were removed, eleven Esp paralogs were present in two or more pairs with K(a)/K(s) >1.0 and thus we propose that positive selection is detectable by this means in at least some mouse Esp paralogs. We compare and contrast the evolutionary histories of all three mouse pheromone gene families in light of their proposed functions in mouse communication.
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Affiliation(s)
- Robert C Karn
- Department of Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America.
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Woodcock MR. Nested Hierarchal Organization of Conservation for MicroRNAs and Their Putative Targets to Drosophila melanogaster. Chem Biodivers 2012; 9:945-64. [DOI: 10.1002/cbdv.201100358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Salemi M, Barone C, Romano C, Ridolfo F, Salluzzo R, Scillato F, Scavuzzo C, Caraci F, Calogero AE, Romano C, Bosco P. Expression of LDOC1 mRNA in leucocytes of patients with Down's syndrome. J Genet 2012; 91:95-98. [PMID: 22546831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Michele Salemi
- Laboratory of Cytogenetics, Oasi Institute for Research on Mental Retardation and Brain Aging, Troina, Italy
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Sun S, Evans BJ, Golding GB. "Patchy-tachy" leads to false positives for recombination. Mol Biol Evol 2011; 28:2549-59. [PMID: 21498600 DOI: 10.1093/molbev/msr076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call "patchy-tachy" (PT), where different partitions of sequences evolve at different rates, that leads to an excess of false positives for recombination inferred by indirect tests. To explore this phenomena, we characterized the false positive rates of six widely used indirect tests for recombination using simulations of general models for mtDNA evolution with PT but without recombination. All tests produced 30-99% false positives for recombination, although the conditions that produced the maximal level of false positives differed between the tests. To evaluate the degree to which conditions that exacerbate false positives are found in published sequence data, we turned to 20 animal mtDNA data sets in which recombination is suggested by indirect tests. Using a model where different regions of the sequences were free to evolve at different rates in different lineages, we demonstrated that PT is prevalent in many data sets in which recombination was previously inferred using indirect tests. Taken together, our results argue that PT without recombination is a viable alternative explanation for detection of widespread recombination in animal mtDNA using indirect tests.
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Affiliation(s)
- Stephanie Sun
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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