SECOND EDITION
Edited by
David C. Logan
IRHS, Université d’Angers, INRA,
Agrocampus-Ouest, France
This edition first published 2018
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Library of Congress Cataloging‐in‐Publication data applied for
9781118906576
Cover design: Wiley
Cover image: Courtesy of David C. Logan
Annual Plant Reviews
A series for researchers and postgraduates in the plant sciences. Each volume in this series focuses on a theme of topical importance and emphasis is placed on rapid publication.
Editorial Board:
Professor Jeremy A. Roberts (Editor‐in‐Chief), Plant Science Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
Dr David Evans, School of Biological and Molecular Sciences, Oxford Brookes University, Headington, Oxford, OX3 0BP, UK
Professor Hidemasa Imaseki, Obata‐Minami 2419, Moriyama‐ku, Nagoya 463, Japan
Dr Jocelyn K.C. Rose, Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
Titles in the series:
Edited by M. Anderson and J.A. Roberts
Edited by M. Wink
Edited by M. Wink
Edited by M. Dickinson and J. Beynon
Edited by D.G. Robinson and J.C. Rogers
Edited by S.D. O’Neill and J.A. Roberts
Edited by M.T. McManus, W.A. Laing and A.C. Allan
Edited by J.K.C. Rose
Edited by D.G. Robinson
Edited by P.J. Hussey
Edited by N.J. Talbot
Edited by K. Lindsey
Edited by S.G. Moller
Edited by K.M. Davies
Edited by M.R. Blatt
Edited by A.J. Fleming
Edited by C. Turnbull
Edited by K.J. Oparka
Edited by P. Meyer
Edited by C. Ainsworth
Edited by A.J.W. Hall and H.G. McWatters
Edited by W.C. Plaxton and M.T. McManus
Edited by M. Riederer and C. M¨uller
Edited by P. Hedden and S.G. Thomas
Edited by J.A. Roberts and Z. Gonzalez‐Carranza
Edited by S. Gan
Edited by K. Bradford and H. Nonogaki
Edited by C. Finnie
Edited by K.D. Grasser
Edited by G.C. Whitelam and K.J. Halliday
Edited by D.C. Logan
Edited by D. Inzé
Edited by Z. Yang
Edited by J. Parker
Edited by G.M. Coruzzi and R.A. Gutierrez
Edited by C.D. Knight, P.‐F. Perroud and D.J. Cove
Edited by T. Beeckman
Edited by L. Østergaard
Edited by M. Wink
Edited by M. Wink
Edited by P. Ulvskov
Edited by C. Foyer and H. Zhang
Edited by R.D. Hall
Edited by M.T. McManus
Edited by B.A. Ambrose and M.D. Purugganan
Edited by D.E. Evans, K. Graumann and J.A. Bryant
Edited by C. Voelckel and G. Jander
Edited by W.C. Plaxton and H. Lambers
Edited by P. Hedden and S.G. Thomas
Hermann Bauwe
Department of Plant Physiology, University of Rostock, Rostock, Germany
Françoise Budar
Institut Jean‐Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris‐Saclay, 78000 Versailles, Versailles, France
Alan C. Christensen
School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, USA
Néstor Fernández Del‐Saz
Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
Iris Finkemeier
Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany & Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
Marc Hanikenne
InBioS – PhytoSYSTEMS, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
Richard P. Jacoby
ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building M316, University of Western Australia, Crawley, Australia
David C. Logan
IRHS, Université d’Angers, INRA, Agrocampus-Ouest, France
A. Harvey Millar
ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building M316, University of Western Australia, Crawley, Australia
Hakim Mireau
Institut Jean‐Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris‐Saclay, 78000 Versailles, Versailles, France
Oren Ostersetzer‐Biran
Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Gaël Paszkiewicz
IIRHS UMR1345, INRA/Agrocampus‐ouest, Université d’ngers, France
Miquel Ribas‐Carbo
Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
Markus Schwarzländer
Plant Energy Biology Laboratory, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany;Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
Iain Scott
Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, USA
Nicolas L. Taylor
ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building M316, University of Western Australia, Crawley, Australia;Institute of Agriculture, University of Western Australia, Crawley, Australia
Olivier Van Aken
ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia;
Department of Biology, Lund University, 35 Sölvegatan, Lund, Sweden
Gianpiero Vigani
Dipartimenti di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, Università degli studi di Milano, Milano, Italy
Michal Zmudjak
Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Welcome to the second edition of Plant Mitochondria. The first edition was published in 2007, which, perhaps depending on your age, was either a long time ago or almost as if it were yesterday. While we can accept differences in human perception of the passage of time, it becomes more conceptually difficult to understand that time is not an absolute: two people moving through time at different speeds will experience events in that timeline at different relative times. The publication of Albert Einstein’s 1905 paper ‘On the electrodynamics of moving bodies’, which became known as his special relativity paper, was a seminal moment for physics, and science in general (Einstein, 1905). However, at the same time, the organelles fuelling Einstein’s extraordinary thinking did not have an agreed name (Cowdry, 1918), nor, indeed, did we know that the fuelling was even performed by organelles, of whatever name: identification of mitochondria as the site of oxidative metabolism took another 40+ years. Research in physics operates at a pace and scale different to that of biology!
As biologists, we use time, in our experiments, all the time. We are interested in the rate of change of an activity or behaviour. And central to all biology is evolution, which is change over time. As Theodosius Dobzhansky famously wrote in his essay of the same title, ‘Nothing in biology makes sense except in the light of evolution’ (Dobzhansky, 1973). A true statement cannot be more true, just as a falsehood is a lie, but in the case of mitochondria, we can say the statement is particularly apt; indeed, perhaps the corollary is valid, and nothing in the evolution of life on earth makes sense without considering mitochondria?
The world at the time of publication of the first edition of this book was very different from the world of 2017. The first iPhone was released in 2007, cloud computing took off in 2007 (for example, Dropbox was started in 2007), Google introduced Android, and Amazon introduced the Kindle. These advances changed the way many of us interact with the world around us, with parallel developments in social media: Facebook had only opened up to individuals with private email addresses in September 2006, and Twitter, launched in July 2006, was showing traffic of 400 000 tweets per quarter in 2007, rising to 50 million per day in February 2010, and now stands at 500 million tweets per day! Social media has revolutionized the way many people communicate science. However, 2007 also marked the end of a period of economic growth and optimism that culminated in a massive loss of optimism and a global financial crash from which the world still reels. This led to ‘austerity’, budget cuts and drastic reductions in the funding of basic scientific research, as the reduced funds available are earmarked to support research some believe is more likely to lead to economic recovery.
Despite years of austerity for fundamental plant biology research funding, we have seen major breakthroughs in our understanding of plant mitochondria, and thus a new edition of this book was timely. The evolving story of the mitochondrion, the story of the evolving mitochondrion, is the longest in the history of the eukaryotic cell. To paraphrase Roy Batty, the mitochondrion has seen things other organelles wouldn’t believe. But, in what ways has our understanding of plant mitochondria advanced in 10 years?
We have seen dramatic advances in next‐generation sequencing since 2007, and use of this technology has had a profound influence on our understanding of the evolution of mitochondrial genomes. The availability of sequence data and bioinformatic advances were also critical to the discovery of PPR proteins as editing factors, and subsequently, the amino acid code they use for RNA recognition (Barkan et al., 2012). And, more recently, advances in genome sequencing led to the discovery of the first mitochondriate eukaryote, amongst over 300 mitogenomes analysed, to lack complex I (Skippington et al., 2015).
We have seen fresh views on the photorespiratory pathway, which enables continued operation of the Calvin–Benson cycle, rather than being a wasteful process. And interactions between the two processes apparently include regulatory feedback between glycine decarboxylation in the mitochondrion and CO2 fixation in the chloroplast (Hagemann & Bauwe, 2016).
Our understanding of other signalling processes between mitochondria and other cell components, and how these signals regulate mitochondrial activity, has increased apace in the past 10 years. We have also seen advances in our understanding of retrograde signalling, for example via NAC transcription factors (de Clercq et al., 2013; Ng et al., 2013), and there is growing evidence for retrograde signalling as a means to regulate nutrition, with a potential role for mitochondria as nutrient sensors (Vigani and Briat, 2015).
Signals induce changes in activity and one means to alter protein activity is by protein modification, but until recently we knew little about modification to mitochondrial proteins. However, lysine acetylation has now been identified as a common modification of mitochondrial proteins, and Arabidopsis sirtuin 2 was identified as the first plant mitochondrial lysine deacytylase (Finkemeier et al., 2011; König et al., 2014).
Finally, I end this preface with microscopy, the scientific tool first used to investigate mitochondria in the late 19th century. Our knowledge of mitochondrial cell biology has advanced dramatically since 2007, aided by the development of better imaging systems and the relatively massive computing power at our disposal to drive image analysis. These have allowed precise quantitative analysis of changes in the dynamics and, even more excitingly, the physiology of each individual mitochondrion, in real time. These advances have underpinned work identifying energy transients in individual mitochondria within living plant cells, in situ, and components of mitochondrial calcium regulation (Schwarzländer and Finkemeier, 2013; Schwarzländer et al., 2012a, b, 2014; Wagner et al., 2015).
Advances in our understanding of plant mitochondria are made through the actions of research scientists, and communicating those advances is a vital part of their job. The purpose of this book is to communicate to you some of the most important aspects of plant mitochondrial biology, and who better to serve as the conduit for that communication than the researchers responsible for those very advances? The chapter authors are experts in their field – many of the advances in plant mitochondrial biology over the past 10 years arise from the primary research output of these authors or members of their teams. I would like to thank them all for their excellent contributions to plant mitochondrial biology, for staying with this project through its long gestation and, in many cases, for being great friends to have within the community.
David C. Logan
June 2017
Tusson, France