Book Vol.3

This book concludes our tandem edition on Recombination and Meiosis. Subtitled Models, Means and Evolution, it follows its first-born twin with emphasis on Crossing-Over and Disjunction. In the commissioning of chapter topics we have tried to cover numerous aspects of the meiotic system from many different angles. Both these books are embedded as volumes 2 and 3 in a topical Series devoted to Genome Dynamics and Stability, where DNA transmission and maintenance functions are discussed from experimental and theoretical perspectives. The earlier vol. 1 dealt with Facets and Perspectives of Genome Integrity, focusing on DNA damage repair mechanisms, and an upcoming vol.4 is on transposable elements. These books on meiotic processes, together with other volumes in this Series on genome management in mitotic cells, provide a grass-roots level starting platform—initiating a prospective trajectory superimposable upon the exploding field of molecular cell physiology, or systems biology (see below). The preceding volume preferentially dealt with meiotic processes in multicellular organisms, such as plants and animals including man. Also, basic accomplishments from work on yeasts was presented in a comparative perspective—concerning the decisive roles of Spo11-induced breaks for crossing-over, of sister chromatid cohesion in chromosome disjunction, and cell cycle modulation in the global control of the meiotic program. The present book puts additional focus on yeasts as unicellular model organisms, where progress in revealing the mechanisms of meiotic recombination has taken place most rapidly and systematically. Also, a central aspect of genetic recombination in E. coli is included for its outstanding merits as a universal model. Furthermore, three facets of evolutionary relevance are also discussed. As for the models and means of meiotic recombination, two prominent and comprehensive chapters call for particular attention. Inasmuch as theoretical interpretations of empirical data about the exchange of genetical markers in successive generations has long preceded their biochemical elucidation,James E.Haber gives expert guidance on a veritable tour de force, presenting the Evolution of Recombination Models frompurely genetic crosses into the molecular era. He follows the historical record from simplistic breaking/joining schemes to break-induced replication, from suspected single-strand breaks to partner choice by single-strand annealing, and from the generation of double-strand breaks (DSBs) to their repair by the establishment and resolution of single or double Holliday junctions, and finally to DSB repair in the absence of crossing over accomplished through synthesis-dependent strand annealing that does not involve Holliday junctions. This scenic ride is aptly complemented from the enzymatic perspective, as displayed by Kirk T. Ehmsen and Wolf-Dietrich Heyer on the Biochemistry of Meiotic Recombination: Formation, Processing, and Resolution of Recombination Intermediates. These authors highlight the biochemistry of meiotic recombination, as more and more meiosis-specific enzymes have been added to the basic toolbox, which likewise is at work in mitotic cells (cf. GDS vol. 1, this Series). Overlapping with functions in replication and DSB repair these enzymes comprise topoisomerase, nuclease, recombinase, polymerase, and helicase activities, as well as single-strand stabilizing protein, a protective end-tethering complex and a range of modulating co-factors. The single most remarkable feature about the initiation of meiotic recombination is the deliberate and catalyzed introduction of numerous DSBs in the chromosomal DNA. Notably, the enzyme responsible for this pivotal and conserved activity is derived from a former topoisomerase (Spo11; Keeney, this SERIES), which as such had a cell-intrinsic function essential for the untangling of replication intermediates in every cell cycle. The total number of cuts is even larger than the number of effective crossovers later on2. The important question of how the sites to be cut are chosen in a given cell— among myriads of potentially equivalent sites that are ignored—is still one of the most vigorously pursued aspects of ongoing research. Foremost, the susceptible substrate for meiotic DSBs is not naked DNA, but DNA embedded in chromatin, as highlighted by Michael Lichten, in his chapter on Meiotic Chromatin—the Substrate for Recombination Initiation. The two yeasts compared for this traits how pronounced differences in the distribution of hotspot sites for DSB formation. In Saccharomyces cerevisiae, a fairly promiscuous DSB machinery can be assembled at about every stretch of accessible chromatin that has been opened up for other purposes, especially at activated promoter regions. Michael Lichten coins the term "opportunistic DSBs" for these phenomena, foremost in S. cerevisiae—differentiating meiotic DSBs from both lower

and higher degrees of sequence specificity: on one hand ionizing radiation induced DSBs,which occur with little sequence preference and without regard for chromatin structure, and on the other hand from the site-specific cuts of restriction-type endonucleases—or other nucleic acid transactions, such as transcription promotion, where both chromatinstructure and the recognition of DNA sequence elements contribute to specificity. Such opportunistic usage of promoter-modulated open chromatin can only in part explain the DSB pattern observed in the fission yeast Schizosaccharomyces pombe, where other determinants may play a significant, hotspot-specific role. Also to be determined by meiosis-specific chromatin organization, the assembly of and/or cleavage by the DSB machinery should not be all too promiscuous on a particular issue, in that at most one of two sister chromatids can become susceptible at any given site, whereas the other sister strand needs to be protected around the equivalent site. The molecular basis for this significant restriction still remains to be determined. After the meiosis-specific, Spo11-induced DSBs have been processed to protruding 3 ends, these single strands have to interact with the corresponding sequence on the homologous chromosome, in order to repair and seal the break by homologous recombination. In eukaryotes the crucial strand exchange reaction is catalyzed by RecA-like recombinases of the ubiquitous Rad51 family and/orthemeiosis-specificDmc1protein. As modeled by the most widely studied RecA recombinase of E.coli, Chantal Prévost, in herchapter on Searching for Homology by Filaments of RecA-Like Proteins, discerns their basic functions in the genome-wide search for complementary DNA strands so as to facilitate the initial strand exchange reaction in highly coordinated, helical DNA–protein filaments, which likewise are formed by the eukaryotic RecA homologs. Corresponding studies to the leading work on meiosis in S.cerevisiae have also been pursued in S.pombe,showing striking differences indetail at various levels. The most interesting aspects of this work are pointed out in two chapters specifically devoted to the fission yeast. For one thing, S. pombe belongs to the rather few organisms that have lost the ability to form synaptonemal complexes in meiotic prophase, which usually stands out as the most characteristic structural basis of bivalent synapsis. Instead, another conserved feature of canonical meiosis, the clustering of telomeres in the so-called bouquet arrangement, is vastly exaggerated in a series of nuclear movements, which in S. pombe facilitates a dynamical alignment

of homologous chromosomes from nuclear fusion throughout the entire prophase of meiosis (D.Q. Dingand Y. Hiraoka, this BOOK). Furthermore, the crossover mechanism itself is peculiar as well. Whilst many organisms including S. cerevisiae actually employ two partly overlapping crossover pathways, one of these pathways is entirely missing in S. pombe. Characteristically, the main recombinational intermediate in S.pombe consists of single Holliday junctions (G. Cromie and G.R.Smith, this BOOK), whilst earlier results on S. cerevisiae had suggested double Holliday junctions as the canonical model. The species-oriented chapter by Gareth Cromie and Gerald R. Smith, on Meiotic Recombination in S. pombe: A Paradigm for Genetic and Molecular Analysis,was published Online FirstinJune2007. At thatrelatively early date, most of their extensive data on DSB hotspot distribution in S. pombe were mentioned in brief as unpublished results. These significant data are now more fully discussed, as mentioned above, in Michael Lichten’s comparative chapter—with due reference to their recent publication in the mean time (Cromie et al. 2007). Unfortunate as such asynchrony appears to be, this is a price to pay for the advantages of Online First publication for the individual chapters as they are being completed—with a spread of Online First dates up to a year per book in such a series. Three evolutionary topics relating to meiosis have been selected to conclude this book: the putative origin of the meiotic system, the confinement of meiosis to the germline in animals, and the abandonment of meiosis in relatively few eukaryotic lineages, some of which are remarkably persistent on the evolutionary time scale—capable of lasting for millions of years. At the dawn of genetics, crossing-over and meiosis had been considered very much the same, but the early view of apparent congruence between the two phenomena has long since been abandoned. Instead, genetic recombination as such has proved to have much earlier and more fundamental roles than the complex and highly integrated pattern of mainstream meiosis, of which crossing-over has become the most characteristic ingredient. In short, homologous DNA recombination has directly co-evolved with faithful replication (see R. Egel and D.Penny, thisBOOK), clearing physical damageand/or broken replication forks as they arise (C. Rudolph, K.A. Schürer, and W. Kramer, GDS vol. 1, this Series)—potentially in each cell cycle of prokaryotes and eukaryotes alike. Of more sporadic occurrence, on the other hand, meiosis only happens once per generation,or life cycle—whatever meaning may be attached to these derived terms for unicellular organisms (see below). N.B., bacteria and archaea are proficient in recombinational repair of DSB damage to their DNA, but meiosis is missing altogether. In multicellular organisms, the meanings of generation and lifecycle are evident, and the complex inter-relationship of germline development and maintaining sexuality in animals and plants was already recognized by Charles Darwin and August Weissmann by the end of the 19th century. In his chapter on The Legacy of the Germ Line—Maintaining Sex and Life in Metazoans: Cognitive Roots of the Concept of Hierarchical Selection, Dirk-Henner Lankenau follows the germline concept to its historical roots, and he addresses the multiple levels of selective evolution related to this concept. Also, he fathoms Weismann’s prescient usage of germ plasm in its original meaning that nowadays has been replaced by genes and genomes—and he sketches a tie to modern frontiers, discussing the so-called nuage as a germline-specific germplasm organelle of multiple RNA processing, where a suspended term is thus revived in new guises. A hallmark of meiosis is the production of recombinant offspring, efficiently scrambling the parental genotypes. The overwhelming majority of taxonomic groups throughout eukaryotes show proficiency of meiosis, at least to begin with. Higher plants and animals would probably never have originated without the evolutionary thrust empowered by meiosis. Yet, sexual propagation including meiosis has been lost repeatedly in evolution, although major evolutionary innovations have never sprung from such secondarily asexual lineages. Hence, asexual lineages of relatively ancient origins can serve as virtual mirrors to reflect the evolutionary importance of meiosis in the remaining majority of animals and plants, as thoroughly discussed by Isa Schön, Dunja K.Lamatsch,

and Koen Martens in their chapter on Lessons to Learn from Ancient Asexuals. To single out a particular highlight, the purging of deleterious mutations by a meiotic recombination appears to be remarkably effective—readily compensating for the low mutation rates observed. As for the inferred origin of the meiotic system, this does not only far predate the emergence of multicellular animals, fungi and plants—it even dates back before the last common ancestor of all the eukaryotic phyla known today (LECA). As canonical meiosis, therefore, is a common heritage to all eukaryotes, there are no comparative cues among different lineages living today from which by parsimony to deduce a likely order of step-wise additions to the basic toolbox of meiotic mechanisms. On the other hand, the meiotic system is so complex in its widely conserved pattern, that its instantaneous invention from scratch appears unlikely. Against this rather uninformative backdrop, Richard Egel and David Penny, in their chapter On the Origin of Meiosis in Eukaryotic Evolution, propose a possible series of incremental steps towards meiosis, each of which could have added some selective advantage on its own. This series may well have started before the mitotic division system had been perfected to its present fidelity, e.g. when telomere-directed chromosome movements may have preceded the establishment of centromeres. Hence their hypothesis is subtitled Coevolution of Meiosis and Mitosis from Feeble Beginnings. A likely driving force to establish a proto-meiotic system—alternating with proto-mitotic nuclear division—is seen in maintaining a periodically needed dormancy program, so as to protect it against the accumulation of dormancy-deficient mutations at the higher error load presumed in early evolution. This is in line with the common correlation between meiosis and the formation of dormant spores or cysts in extant microbial eukaryotes. In a certain sense, therefore, a single generation in the life cycle of unicellular eukaryotes would last from one stage of encystment or sporulation to the next. With the commissioning and presentation of the various chapter topics on the genomic aspects of the meiotic system we hope to have served a salient need for integrating basic knowledge gained from studying diverse genetic model organisms. Research on meiotic exchange and segregation mechanisms may appear more esoteric than the vast resources spent on understanding metabolism and growth in mitotic cells. While emphasis on the latter area is motivated by the numerical predominance of mitotic divisions, as well as the direct connection of mitotic cell divisions to the immense problems of cancerous growth in human disease, meiosis in its paucity is more secluded and its medical aspects are limited to less pressing problems, such as impaired fertility or Down-like syndromes (H.Kokotas,M.Grigoriadou,andM.B.Petersen, this Series). Also, a certain twist of hierarchy is undeniable: whilst endless perpetuation of mitotic divisions can be viable as an evolutionarily stable strategy, a contiguous series of several meioses is certainly not. In this sense meiosis will always be the subordinate companion of mitosis. At the conceptual level, however, the complexity of molecular mechanisms applying to meiosis far exceeds that of its mitotic counterpart. And for the continuity of generations in most eukaryotic forms of life, both meiosis and mitosis are complementary features of general and essential interest. Traditionally, the largest share of meiotic research has been focused on DNA exchange and related features, whereas the immense field of protein–protein interactions in the rewiring of the meiotic cell out of and back into the mitotic cell cycle stood in second place. The concluding chapter of the preceding volume specifically deals with these meiotic aspects of molecular cell physiology (L. Pérez-Hidalgo, S. Moreno, and C. Martin-Castellanos, this Series). As pioneered with yeasts, genome-wide expression studies have started with identifying all the genes upregulated in meiotic cells and sorting them into functional categories. This is a long way off fromknowing all their particular functions. To illustrate the scope of the barely charted field: of 4,824 annotated genes in S. pombe, 955 proteins contain coiled-coil motifs4; of these, 180 are upregulated before, during or after meiosis—21 exclusively so, but not expressed during mitosis (Ohtaka et al. 2007). The interactive potential of so many proteins is enormous, and the systemsbiology of meiosis has merely just begun. To form a link between both books on Recombination and Meiosis, the list of chapter titles in the preceding volume is included after the Contents table of this book. In fact, as some of the individual chapters already had been published Online First, before the editorial decision to divide the printed edition into two books, the preliminary cross references had not yet accounted for the split. We apologize for any inconvenience this may cause, but the listing of all the chapter titles in both books should hopefully direct the reader to the proper destination. We would also like to point out that the missing chapter numbers are no neglect but reflect an obligatory compromise necessitated by publishing all manuscripts OnlineFirst immediately

after they have been peer-reviewed, revised, accepted and copy-edited (see, www.springerlink.com/content/119766/). We most cordially thank all the chapter authors for contributing to this topical edition of two accompanying books focusing on meiotic recombination. Without their expertise and dedicated work this comprehensive treatise would not have been possible. Receiving the incoming drafts as editors, we had the great privilege of being the first to read so many up-to-date reviews on the various aspects of meiotic recombination and model studies elucidating this ever-captivating field. Also, we greatly appreciate the productive input of numerous referees, who have assisted us in thriving for the highest level of expertship, comprehensiveness, and readability. We are again deeply indebted to the editorial staff at Springer. We would especially like to mention the editor Sabine Schwarz at Springer Life Sciences(Heidelberg), the deskeditor Ursula Gramm (Springer,Heidelberg),and the production editor Martin Weissgerber (le-tex publishing services oHG, Leipzig).

April 2008

Copenhagen, Richard Egel

Ladenburg, Dirk-Henner Lankenau

 

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