Cell Biology Monographs – serie

In modern scientific investigation the fields of biochemistry, molecular biology, and morphology comprise an indivisible area of study. The present book results from the cooperation of a bioehernist and morphologists: the revision and unified treatment of available data is the primary object of our work. A comprehensive review of all the available literature is therefore beyond the scope of this volume. lt is intended to be a manual to be used in the laboratory, with convenient guidelines for practical work. Plant microbodies have been treated by B. GERHARDT in Volume 5 of this series. The discovery of fatty acid ß-oxidation in animal peroxisomes has proved once more that plant and animal microbodies are members of the same family of organelles. lt provided new insights into the physiological meaning of these particles; our understanding of these "classical" cell organelies is undergoing continual alteration and development. PETER BöcK Vienna, July 1980 ROBERT KRAMAR MARGIT PAVELKA Acknowledgements We wish to express our gratitude to Prof. Dr. D. H. FAHIMI and Dr. P. KALMBACH (Heidelberg) for kindly providing Figure 14, to Prof. Dr. KARIN GoRGAS (Heidelberg) for allowing the reproduction of Figure 43, to Profs. Dr. L. STOCKINGER and Dr. E. KAISER for helpful criticism, and to all our colleagues in our respective institutes. W e are especially grateful to Drs. H. GoLDENBERG and M. HüTTINGER for continuous discussion, to Mrs. JuTTA SELBMANN for typing the references, and to Mr. P. KAMPFER and Mr. H. WAGNER for carefully drawing some of the figures.

The term cytoskeleton has become firmly established in today's scientific vocabulary. Indeed, it is difficult to believe that only ten years ago, it was virtually non-existent. Since then, the modern field of research on the structural organization of the cytoplasm has turned into one of the most productive and rapidly expanding research areas in Cell Biology today. Considerable progress has been made towards the identification of the various structural components of the cytoskeleton and their interactions with one another and with membranes. The first attempts to understand, in molecular terms, complex cellular processes such as shape changes, locomotion, division, and organelle movements have been made. And it is now apparent that the cytoskeleton has impact on other biological processes such as the control of gene expression, protein synthesis, cell cycle regulation, and development. This monograph outlines the basic properties of the major components of the polymeric filament networks and their interactions and associations. Wherever possible, emphasis is placed on more recent references. Any attempt to cover a research field this complex in an introductory mono­ graph is, by necessity, fragmentary, and oversights or omissions are inevitable. I wish to apologize in advance to all those colleagues who feel that their work is not adequately represented.

A comprehensive review of the Golgi apparatus and its functioning would require a multi-volume publication and not a monograph and it would be so repetitious as to discourage the reader. The requirement at this stage is for a reinterpretation of the character and functioning of this organelle since the last major interpretations have concentrated on its role in secretion and it has now been shown to be a component of essentially all cells whether or not they have been traditionally emphasized as secreting cells. As a conse­ quence the efforts have been placed on the common characteristics of the organelle, a postulate concerning its functioning in cells generally, and the details of variations where these seem important. The major acknowledgment of assistance in compiling the material must go to the investigators whose contributions, sometimes positive and sometimes of a character to spur additional investigations, allowed the development of this postulate. The paper has been prepared with the detailed assistance of Dr. MARIANNE DAUWALDER who, by her own studies and her insight into the significance of other studies, has been a working partner of many years in the development of a general hypothesis and whose knowledge of investiga­ tions of the Golgi apparatus is great enough to let her call attention to instances of support and contention with the general functional hypothesis that has been involved.

Almost twenty years ago DE DuvE discovered the existence in rat liver cells of a novel class of subcellular structures which he termed lysosomes. As the lysosomes are the seat of various hydrolytic enzymes this discovery greatly stimulated the interest in cellular digestive processes. It is now recognized that compartmentation of hydrolases is an outstanding example of the dependence of metabolic functions on cell structure. The important role of lytic processes in plant metabolism made it interesting to correlate the facts on the various phenomena and present them from the point of view of cellular compartmentation. It is not intended to survey in extenso the litera­ ture on the various aspects of localization and function of hydrolases in plant cells as this would be an impossible task. The aim of this monograph is to emphasize the significance of hydrolase compartmentation rather than to strive for complete coverage of work on hydrolases in which other viewpoints have been considered. I thank Miss SONIA TURLER for her great help with the manuscript. I also wish to acknowledge the assistance given by Dr. ELSA HAUSERMANN, Mrs. DORLI FURRER, and Mrs. SILVIA STUNZI. Moreover, I am indebted to my collaborators and particularly to my colleague Dr. A. WIEMKEN for frequent and stimulating discussions on the subject. Zurich (Switzerland), February 1975 PH. MATILE Contents Abbreviations . XIII Introduction: Lysis and the Lytic Compartment. 1 1. Hydrolases and their Localization . . . . . 3 1. 1. Classification and Properties of Hydrolases 3 1. 1. 1. Peptidases . . . . . . . . .

This brief monograph is intended chiefly for non-specialists and for others interested in a concise introduction to the field. The literature on lysosomes is growing so rapidly that any effort at exhaustive comprehensiveness would be foredoomed to failure. Fortunately, an extensive series of reviews has been published in the past few years (see especially DINGLE and FELL 1969; DINGLE 1972, 1973 a; HERS and VAN HoOF 1973) and the "history" of the organelles is brief enough that major contributors to all stages of that history are still available to provide first-hand discussions (e. g. , DE DUVE and WATTIAUX 1966; DE DUVE 1969; NOVIKOFF 1971, 1973; see also VAN FURTH for work on phago­ cytes and DE REUCK and CAMERON 1963 for useful reviews of early work). New York, N. Y. , September 1975 E. HOLTZMAN Contents I. General Considerations and Background 1. 1. Perspectives 1 1. 2. Definitions . 2 1. 2. 1. General Functional Categories 2 1. 2. 2. Outline of Lysosome Functioning in Phagocytes 3 1. 2. 3. Additional Terms: Heterophagy and Autophagy 4 1. 3. Characterization of Lysosomes . . . . . . . . . . 4 1. 3. 1. Basic Biochemical Characteristics of Lysosomes 5 1. 3. 1. 1. Key Features of Lysosomes 8 1. 3. 1. 2. The Lysosomal Enzymes . 8 1. 3. 1. 3. Digestion in Lysosomes 11 1. 3. 104. Lysosomal "Permeability" 13 1. 3. 2. Some Cytochemical and Morphological Characteristics 15 1. 3. 2. 1. Cytochemical Methods . . . . . . . . . . 16 1. 3. 2. 2. Cytochemical Studies of Exogenous Tracers .

In the past few years, the body of experimental work on the structure, function and assembly processes of mitochondria has expanded rapidly. No one person can believe himself or herself completely in control of the burgeoning literature without possessing serious omissions or blind spots. In the present monograph I have attempted a critical evaluation of the literature. I believe that the common thread of single authorship outweighs the shortcomings of one person presenting many disparate viewpo,ints. It is my hope that the end product represents a comprehensive and coordinated review of the subject matter to the present date. Although the bulk of this monograph was completed by October 1974, I have made some attempts to update several of the sections at later times. Albany, N. Y. , November 1975 H. TEDESCHI Contents A. Structure of Mitochondria 1. General Organization . a) Conventional Thin Section Electron Microscopy b) Negative Staining Techniques . 3 c) Freeze-Cleavage . . . . . . . 4 2. Special Organization and Inclusions 10 a) Prismatic or Atypical Cristae 10 b) Filaments and Tubules . . 11 c) Amorphous Inclusions 12 d) Intramitochondrial Granules 12 e) DNA Containing Fibers 14 3. Topography of the Mitochondrial Transducing Systems 15 B. The Assembly of Mitochondria 18 1. Mitochondrial DNA and Its Genetic Role 19 2. Transcription of the Mitochondrial DNA . 28 a) mRNA . . . . . . . . . . . . . . 30 b) The Machinery for Transcription and Translation 32 c) Turnover of Mitochondrial RNA 36 3. Protein Synthesis . . . . . . . . 37 a) Mitochondrial Protein Synthesis and Its Characteristics 37 b) Role of Mitochondrial Protein Synthesis . .

Mit der vorliegenden monographischen Bearbeitung der Microbodies/ Peroxisomen pflanzlicher Zellen habe ich versucht, eine umfassende Dbersicht uber die - keineswegs widerspruchsfreien - Daten zu geben, die direkt oder indirekt beitragen zur Charakterisierung dieses Zellorganells an sich. In diesen Zusammenhang ist auch ein wesentlicher Teil der tabellarischen Dbersichten einzuordnen, die u. a. verdeutlichen, wie breit z. Zt. die Basis fur generali- sierende Aussagen ist. AuBerdem war es mein Anliegen, die Microbodies/ Peroxisomen unter dem Gesichtspunkt ihrer Integration in die ubergeordnete Einheit "Zelle" kritisch zu behandeln. Vor allem unter diesem Aspekt werden ungeloste Probleme angesprochen werden. In vielen Fallen wird der Benutzer dieser Monographie eher an der Infor- mation uber einen "exemplarischen Fall" interessiert sein - z. B. fur Vor- lesungen - als an einer eingehenden Gesamtdarstellung der Microbodies/ Peroxisomen. Am Anfang der einzelnen Abschnitte werden daher - soweit realisierbar - stets die Befunde behandelt, die fur zwei Standardobjekte der Forschung an Microbodies/Peroxisomen vorliegen.Fur die Glyoxysomen des Endosperms keimender Ricinus-Samen und die Blatt-Peroxisomen des Spinats wird dadurch eine schnelle Zusammenstellung der Forschungsergebnisse ermog- licht. Die Kapitel des Buches sind selbstandige, in sich versrandliche Einheiten. Sie enthalten in der Regel auch eine knappe Zusammenfassung der Befunde, die zur entsprechenden Thematik fur Peroxisomen tierischer Zellen vorliegen. In Kapitel 7.3. wurde allerdings bewuBt auf einen Vergleich der Peroxisomen- enzyme pflanzlicher Zellen mit den Peroxisomenenzymen tierischer Zellen oder mit entsprechenden bakteriellen Enzymen verzichtet. Das abschlieBende Kapitel gibt eine zusammenfassende Beurteilung des derzeitigen Standes der Forschung an Microbodies/Peroxisomen pflanzlicher Zellen.

The subject of this book has not been treated comprehensively before. For many years I have hesitated to attempt a monographic presentation because I felt uneasy about the idea of delineating something I am not sure about myself, and I felt it might be rash to try to integrate what seemed-and largely still seems-to consist of a heap of tessera not fitting together. The conviction won over, however, that the many details accumulated thus far call for some order now, and that an appraisal of where we stand would be appropriate. This book, I hope, can fill a gap barring the way to further progress in the field. It is not only a compilation of details but also an attempt to delineate the first outlines of a picture-blurry, obscure, and controversial as it must appear. The imagination of the research worker will be aroused, I hope, and stimulate further progress. In addition to data widely dispersed in the literature much unpublished material has been included. The limited space available prevented me from giving all the details known. The subject is also linked to many neighboring fields of study, but these relationships and their ramifications could not be discussed at length. This is a minor shortcoming, however, compared with our great ignorance of the subject in general.

In 1958 E. BUNNING published a book in the former series "Proto­ plasmatologia" entitled "Polaritat und inaquale Teilung des pflanzlichen Protoplasten" (polarity and unequal division of the plant protoplast) in which for the first time results of experimental plant cytomorphogenesis were re­ viewed. This book was based completely on light microscopic observations and rather simple experimental techniques. Since then our knowledge of basic cytomorphogenetic mechanisms has greatly increased, especially with the introduction of modern ultrastructural, biochemical and sophisticated experi­ mental methods so that the field of cytomorphogenesis in our days should be considered a separate discipline within the general field of cell biology. This book, "Cytomorphogenesis in Plants", represents a necessary attempt to bring together current knowledge in this field of research on a comparable basis. Unfortunately enormous gaps in our understanding of the underlying principles of cytomorphogenetic events still exist. Therefore it seemed reason­ able to present a book composed of individual chapters, each written by experts for a defined experimental system. Each chapter represent a separate treatise with its own references, hence it was not possible to avoid some overlap both in the text and in the literature of the chapters without destroying the uni­ formity of the respective article.

Rapid progress in the field of sialic acids has made it desirable to collect the new data about these unique sugars and to continue the series of books on this topic. In 1960, A. GOTTSCHALK wrote "The Chemistry and Biology of Sialic Acids and Related Substances" (Cambridge University Press) and in 1976, A. ROSENBERG and C. -L. SCHENGRUND published "Biological Roles of Sialic Acids" (Plenum Press). In this book emphasis is given to various modern methods used in the isolation and analysis of sialic acids. New approaches to the synthesis of free and bound sialic acids are described and the vast field of occurrence and metabolism of these substances is reviewed. Sialidoses are dealt with in one of the chapters, because sialidases have been recognized as factors of pathophysiological im­ portance. As knowledge is increasing about the involvement of sialic acids in many aspects of cell biology, another chapter is devoted to these phenomena. With this book I intend to demonstrate modern trends in sialic acid chemistry and biochemistry, and I hope that it will be of practical use and find its place in laboratories rather than in libraries. This publication offers an opportunity to thank all colleagues in many countries, including my coworkers at the universities of Bochum and Kiel, for their cooperation, stimulating discussions and, very important, useful criticism. The continuous cooperation with J. F. G. VLIEGENTHART and his coworkers, Utrecht, has been rewarding in many respects.

In 1977 I wrote a grant proposal in which I applied to study developmental patterns in enzymatic methylation of DNA in eukaryotes. One part of the proposal was to assay cells at different embryonic developmental stages for maintenance and de novo type methylase activity. With one exception the referees, probably developmental biologists, recommended that the work not be supported because there was no evidence that methylation plays any role in eukaryotic gene regulation. Aside from proving that innovative ideas can seldom be used to successfully compete for grant funds, the skepticism of biologists toward methylation as a regulatory mechanism was, and still is, widespread even among some of those who investigate the problem. That is a healthy situation for all points of view should be brought to bear on a problem of such importance. However, to deny funds to investigate a problem because one has already formed an opinion without evidence is hardly commendable. The great skepticism about the significance of DNA methylation is based in part on the evidence that it is absent or very little used in Drosophila, a favorite organism for genetic and developmental studies. There now remains little doubt that methylation of cytosine in certain CpG sites can strikingly affect the transcription of sequences 3' to the methylated doublet. How this inhibition operates and to what extent it is utilized in cells is still debatable.