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Abstract
Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.
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Affiliation(s)
- Jérôme Duminil
- DIADE, University of Montpellier, IRD, Montpellier, France.
| | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, EDB, Université Paul Sabatier, Toulouse, France
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2
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Abstract
The phylum of Apicomplexa groups obligate intracellular parasites that exhibit unique classes of unconventional myosin motors. These parasites also encode a limited repertoire of actins, actin-like proteins, actin-binding proteins and nucleators of filamentous actin (F-actin) that display atypical properties. In the last decade, significant progress has been made to visualize F-actin and to unravel the functional contribution of actomyosin systems in the biology of Toxoplasma and Plasmodium, the most genetically-tractable members of the phylum. In addition to assigning specific roles to each myosin, recent biochemical and structural studies have begun to uncover mechanistic insights into myosin function at the atomic level. In several instances, the myosin light chains associated with the myosin heavy chains have been identified, helping to understand the composition of the motor complexes and their mode of regulation. Moreover, the considerable advance in proteomic methodologies and especially in assignment of posttranslational modifications is offering a new dimension to our understanding of the regulation of actin dynamics and myosin function. Remarkably, the actomyosin system contributes to three major processes in Toxoplasma gondii: (i) organelle trafficking, positioning and inheritance, (ii) basal pole constriction and intravacuolar cell-cell communication and (iii) motility, invasion, and egress from infected cells. In this chapter, we summarize how the actomyosin system harnesses these key events to ensure successful completion of the parasite life cycle.
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Affiliation(s)
- Karine Frénal
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, University of Bordeaux and CNRS, Bordeaux Cedex, France. .,Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Choudhry SK, de Boer R, van der Klei IJ. Yeast cells contain a heterogeneous population of peroxisomes that segregate asymmetrically during cell division. J Cell Sci 2018; 131:jcs207522. [PMID: 29361529 DOI: 10.1242/jcs.207522] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/13/2017] [Indexed: 11/20/2022] Open
Abstract
Here, we used fluorescence microscopy and a peroxisome-targeted tandem fluorescent protein timer to determine the relative age of peroxisomes in yeast. Our data indicate that yeast cells contain a heterogeneous population of relatively old and young peroxisomes. During budding, the peroxisome retention factor inheritance of peroxisomes protein 1 (Inp1) selectively associates to the older organelles, which are retained in the mother cells. Inp2, a protein required for transport of peroxisomes to the bud, preferentially associates to younger organelles. Using a microfluidics device, we demonstrate that the selective segregation of younger peroxisomes to the buds is carefully maintained during multiple budding events. The replicative lifespan of mother cells increased upon deletion of INP2, which resulted in the retention of all organelles in mother cells. These data suggest that, in wild-type yeast, transport of aged and deteriorated peroxisomes to the bud is prevented, whereas the young and vital organelles are preferably transported to the newly forming buds.
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Affiliation(s)
- Sanjeev Kumar Choudhry
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 11103, 9700CC, Groningen, The Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 11103, 9700CC, Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 11103, 9700CC, Groningen, The Netherlands
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Hughes L, Borrett S, Towers K, Starborg T, Vaughan S. Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy. J Cell Sci 2017; 130:637-647. [PMID: 28049718 DOI: 10.1242/jcs.198887] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/01/2016] [Indexed: 12/29/2022] Open
Abstract
The major mammalian bloodstream form of the African sleeping sickness parasite Trypanosoma brucei multiplies rapidly, and it is important to understand how these cells divide. Organelle inheritance involves complex spatiotemporal re-arrangements to ensure correct distribution to daughter cells. Here, serial block face scanning electron microscopy (SBF-SEM) was used to reconstruct whole individual cells at different stages of the cell cycle to give an unprecedented temporal, spatial and quantitative view of organelle division, inheritance and abscission in a eukaryotic cell. Extensive mitochondrial branching occurred only along the ventral surface of the parasite, but the mitochondria returned to a tubular form during cytokinesis. Fission of the mitochondrion occurred within the cytoplasmic bridge during the final stage of cell division, correlating with cell abscission. The nuclei were located underneath each flagellum at mitosis and the mitotic spindle was located along the ventral surface, further demonstrating the asymmetric arrangement of cell cleavage in trypanosomes. Finally, measurements demonstrated that multiple Golgi bodies were accurately positioned along the flagellum attachment zone, suggesting a mechanism for determining the location of Golgi bodies along each flagellum during the cell cycle.
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Affiliation(s)
- Louise Hughes
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Samantha Borrett
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Katie Towers
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Tobias Starborg
- Wellcome Centre for Cell Matrix Research, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford OX3 0BP, UK
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Knoblach B, Rachubinski RA. Sharing with your children: Mechanisms of peroxisome inheritance. Biochim Biophys Acta 2015; 1863:1014-8. [PMID: 26620799 DOI: 10.1016/j.bbamcr.2015.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
Abstract
Organelle inheritance is the process by which eukaryotic cells actively replicate and equitably partition their organelles between mother cell and daughter cell at cytokinesis to maintain the benefits of subcellular compartmentalization. The budding yeast Saccharomyces cerevisiae has proven invaluable in helping to define the factors involved in the inheritance of different organelles and in understanding how these factors act and interact to maintain balance in the organelle populations of actively dividing cells. Inheritance factors can be classified as motors that transport organelles, tethers that retain organelles, and connectors (receptors) that mediate the attachment of organelles to motors and anchors. This article will review how peroxisomes are inherited by cells, with a focus on budding yeast, and will discuss common themes and mechanisms of action that underlie the inheritance of all membrane-enclosed organelles.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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Abstract
Eukaryotic cells replicate and partition their organelles between the mother cell and the daughter cell at cytokinesis. Polarized cells, notably the budding yeast Saccharomyces cerevisiae, are well suited for the study of organelle inheritance, as they facilitate an experimental dissection of organelle transport and retention processes. Much progress has been made in defining the molecular players involved in organelle partitioning in yeast. Each organelle uses a distinct set of factors - motor, anchor and adaptor proteins - that ensures its inheritance by future generations of cells. We propose that all organelles, regardless of origin or copy number, are partitioned by the same fundamental mechanism involving division and segregation. Thus, the mother cell keeps, and the daughter cell receives, their fair and equitable share of organelles. This mechanism of partitioning moreover facilitates the segregation of organelle fragments that are not functionally equivalent. In this Commentary, we describe how this principle of organelle population control affects peroxisomes and other organelles, and outline its implications for yeast life span and rejuvenation.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, AL T6G 2H7, Canada
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Kinkhabwala A, Khmelinskii A, Knop M. Analytical model for macromolecular partitioning during yeast cell division. BMC Biophys 2014; 7:10. [PMID: 25737777 PMCID: PMC4347614 DOI: 10.1186/s13628-014-0010-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell - which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles - can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. RESULTS Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. CONCLUSIONS In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning.
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Affiliation(s)
- Ali Kinkhabwala
- Abteilung Systemische Zellbiologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, Dortmund 44227, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) and Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH-Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
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Abstract
Mitochondria are the site of oxidative phosphorylation, play a key role in cellular energy metabolism, and are critical for cell survival and proliferation. The propagation of mitochondria during cell division depends on replication and partitioning of mitochondrial DNA, cytoskeleton-dependent mitochondrial transport, intracellular positioning of the organelle, and activities coordinating these processes. Budding yeast Saccharomyces cerevisiae has proven to be a valuable model organism to study the mechanisms that drive segregation of the mitochondrial genome and determine mitochondrial partitioning and behavior in an asymmetrically dividing cell. Here, I review past and recent advances that identified key components and cellular pathways contributing to mitochondrial inheritance in yeast. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference. Guest Editors: Manuela Pereira and Miguel Teixeira.
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