Evolution of Seed Plants

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Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants A case study of endosymbiotic gene transfer Claus Schnarrenberger 1 and William Martin 2 1 Institut fu È r Biologie, Freie Universita È t Berlin, Germany; 2 Institut fu È r Botanik III, Universita È tDu È sseldorf, Germany The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which p rovides, among other things, electrons for oxidative phosphorylation i n t he inner mitochondrial membrane, intermediates for amin o- acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in g lyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among a-pro- teobacteria, the group of eubacteria as de®ned under rRNA systematics f rom w hich mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previ- ously shown to branch with their homologues from a-pro- teobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories o f all of the enzymes of the tricar- boxylic acid c ycle and the glyoxylate cycle using p rotein maximum likelihood phylogenies, focusing on t he evo lu- tionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryo tic pathway a re most similar t o their a-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not speci®cally a-proteo- bacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and ( b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it i s unrealistic t o expect a ll nuclear genes that were acquired from the a-proteobacterial ancestor of mitochondria to branch speci®cally with their homologues encoded in the genomes o f contemporary a-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly ( which i t does not), then some nuclear-encoded proteins that were acquired from the a-proteobacterial ancestor of mitochondria should, in phylogenetic t rees, branch with homologues that are no longer found in most a-proteobacterial genomes, and some should reside on long branches that reveal anity to eubacterial rather than archaebacterial homologues, but no particular anity for any speci®c eubacterial donor. Keywords: glyoxysomes; microbodies; mitochondria; pathway evolution, pyruvate dehydrogenase. Metabolic pathways are units of biochemical function that encompass a number of su bstrate conversions leading from one chemical intermediate to another. The large amounts of accumulated sequence data from prokaryotic and eukary- otic sources provide novel opportunities to study the molecular evolution not only o f individual enzymes, b ut also of individual pathways consisting of several enzymatic substrate conversions. This opens the door to a number of new and intriguing questions in m olecular e volution, s uch a s the following. Were pathways assembled originally during the early phases of biochemical evolution, and subsequently been passed down through inheritance ever since? Do pathways evolve as coherent entities consisting o f the same group Evolution of Seed Plants Evolution of Seed Plants Bởi: OpenStaxCollege The first plants to colonize land were most likely closely related to modern day mosses (bryophytes) and are thought to have appeared about 500 million years ago They were followed by liverworts (also bryophytes) and primitive vascular plants—the pterophytes—from which modern ferns are derived The lifecycle of bryophytes and pterophytes is characterized by the alternation of generations, like gymnosperms and angiosperms; what sets bryophytes and pterophytes apart from gymnosperms and angiosperms is their reproductive requirement for water The completion of the bryophyte and pterophyte life cycle requires water because the male gametophyte releases sperm, which must swim—propelled by their flagella—to reach and fertilize the female gamete or egg After fertilization, the zygote matures and grows into a sporophyte, which in turn will form sporangia or "spore vessels." In the sporangia, mother cells undergo meiosis and produce the haploid spores Release of spores in a suitable environment will lead to germination and a new generation of gametophytes In seed plants, the evolutionary trend led to a dominant sporophyte generation, and at the same time, a systematic reduction in the size of the gametophyte: from a conspicuous structure to a microscopic cluster of cells enclosed in the tissues of the sporophyte Whereas lower vascular plants, such as club mosses and ferns, are mostly homosporous (produce only one type of spore), all seed plants, or spermatophytes, are heterosporous They form two types of spores: megaspores (female) and microspores (male) Megaspores develop into female gametophytes that produce eggs, and microspores mature into male gametophytes that generate sperm Because the gametophytes mature within the spores, they are not free-living, as are the gametophytes of other seedless vascular plants Heterosporous seedless plants are seen as the evolutionary forerunners of seed plants Seeds and pollen—two critical adaptations to drought, and to reproduction that doesn’t require water—distinguish seed plants from other (seedless) vascular plants Both adaptations were required for the colonization of land begun by the bryophytes and their ancestors Fossils place the earliest distinct seed plants at about 350 million years ago The first reliable record of gymnosperms dates their appearance to the Pennsylvanian period, about 319 million years ago ([link]) Gymnosperms were preceded by progymnosperms, the first naked seed plants, which arose about 380 million years ago Progymnosperms were a transitional group of plants that superficially resembled 1/10 Evolution of Seed Plants conifers (cone bearers) because they produced wood from the secondary growth of the vascular tissues; however, they still reproduced like ferns, releasing spores into the environment Gymnosperms dominated the landscape in the early (Triassic) and middle (Jurassic) Mesozoic era Angiosperms surpassed gymnosperms by the middle of the Cretaceous (about 100 million years ago) in the late Mesozoic era, and today are the most abundant plant group in most terrestrial biomes Various plant species evolved in different eras (credit: United States Geological Survey) Pollen and seed were innovative structures that allowed seed plants to break their dependence on water for reproduction and development of the embryo, and to conquer dry land The pollen grains are the male gametophytes, which contain the sperm (gametes) of the plant The small haploid (1n) cells are encased in a protective coat that prevents desiccation (drying out) and mechanical damage Pollen grains can travel far from their original sporophyte, spreading the plant’s genes The seed offers the embryo protection, nourishment, and a mechanism to maintain dormancy for tens or even thousands of years, ensuring germination can occur when growth conditions are optimal Seeds therefore allow plants to disperse the next generation through both space and time With such evolutionary advantages, seed plants have become the most successful and familiar group of plants, in part because of their size and striking appearance Evolution of Gymnosperms The fossil plant Elkinsia polymorpha, a "seed fern" from the Devonian period—about 400 million years ago—is considered the earliest seed plant known to date Seed ferns ([link]) produced their seeds along their branches without specialized structures What 2/10 Evolution of Seed Plants makes them the first true seed plants is that they developed structures called cupules to enclose and protect the ovule—the female gametophyte and associated tissues—which develops into a seed upon fertilization Seed plants resembling modern tree ferns became more numerous and diverse in the coal swamps of the Carboniferous period This fossilized leaf is from Glossopteris, a seed fern that thrived during the Permian age (290–240 million years ago) (credit: D.L Schmidt, USGS) Fossil records indicate the first ...Two types of replication protein A in seed plants Characterization of their functions in vitro and in vivo Toyotaka Ishibashi 1 , Asami Koga 1 , Taichi Yamamoto 1 , Yukinobu Uchiyama 1 , Yoko Mori 1 , Junji Hashimoto 2 , Seisuke Kimura 1 and Kengo Sakaguchi 1 1 Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Japan 2 National Institute of Agrobiological Sciences, Ibaraki, Japan Replication protein A (RPA) is a heterotrimeric com- plex composed of 70, 32 and 14-kDa subunits which is involved in various aspects of DNA metabolism [1]. RPA accumulates along stretches of ssDNA generated during DNA replication and DNA repair [2–5]. RPA is known to interact specifically with numerous DNA rep- lication proteins: including T antigen and DNA poly- merase a-primase; the tumor suppressor p53; the transcription factors Gal4 and VP16; the DNA repair proteins XPA, DDB, XPF, XPG, uracil DNA glycosy- lase, Rad52, and Rad51; and the DNA helicases, Bloom’s and Werner’s proteins. RPA was first identified as a factor necessary for simian virus 40 replication in vitro. It is required for activation of the prereplication complex to form the initiation complex, and for the ordered loading of essential initiator functions, such as the DNA poly- merase a-primase complex, to origins of replication [6–9]. Furthermore, during strand elongation, RPA sti- mulates the action of DNA polymerase a¢, d and e. RPA also has essential roles in DNA repair. In nuc- leotide excision repair, RPA interacts with XPA at sites of DNA damage, stimulates XPA–DNA interaction, and recruits the incision proteins ERCC1 ⁄ XPF and XPG to the damaged site [10–12]. In addition, RPA was necessary for the removal of oxidized base lesions from genomic DNA in long-patch base excision repair [13,14]. In the repair of double-strand breaks by homo- logous recombination, RPA greatly stimulates DNA strand exchange by Rad51 protein, provided that RPA is added to a pre-existing complex of Rad51 protein and ssDNA. When double-strand breaks occur in DNA, RPA binds and protects exposed ssDNA ends until they can be coated by Rad51. RPA then catalyzes Keywords Arabidopsis; DNA repair; DNA replication; replication protein A; rice Correspondence K. Sakaguchi, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba-ken 278- 8510, Japan Fax: +81 4 7123 9767 Tel: +81 4 7124 1501 (ext. 3409) E-mail: kengo@rs.noda.tus.ac.jp (Received 20 January 2005, revised 18 March 2005, accepted 15 April 2005) doi:10.1111/j.1742-4658.2005.04719.x Replication protein A (RPA), a heterotrimeric protein composed of 70, 32 and 14-kDa subunits, has been shown to be essential for DNA replication, repair, recombination, and transcription. Previously, we found that, in two seed plants, rice and Arabidopsis, there are two different types of RPA70- kDa subunit. Substantial biochemical and genetic characterization of these two subunits, termed OsRPA70a and OsRPA70b or AtRPA70a and AtRPA70b, respectively, is described in this report. Inactivation of AtRPA70a by transfer DNA insertion or RNA interference is lethal, so the complex containing RPA70a may be essential for DNA replication. Trans- fer DNA insertion and RNAi lines for AtRPA70b are morphologically nor- mal, albeit hypersensitive to certain mutagens, such as UV-B and methyl methanesulfonate, suggesting that RPA70b Research article Adaptive evolution of centromere proteins in plants and animals Paul B Talbert, Terri D Bryson and Steven Henikoff Address: Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109-1024, USA. Correspondence: Steven Henikoff. E-mail: steveh@fhcrc.org Abstract Background: Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif). Results: Whereas we find no evidence that mammalian CenH3 (CENP-A) has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p) is under negative selection. Conclusions: CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi. BioMed Central Journal of Biology Journal of Biology 2004, 3:18 Open Access Published: 31 August 2004 Journal of Biology 2004, 3:18 The electronic version of this article is the complete one and can be found online at http://jbiol.com/content/3/4/18 Received: 25 May 2004 Revised: 20 July 2004 Accepted: 22 July 2004 © 2004 Talbert et al., licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background Centromeres are the chromosomal loci where kinetochores assemble to serve as attachment sites for the spindle micro- tubules that direct chromosome segregation during mitosis and meiosis. Despite this essential conserved function in all eukaryotes, centromere structure is highly variable, ranging from the simple short centromeres of budding yeast, which have a consensus sequence of approximately 125 base pairs (bp) on each chromosome, to holokinetic cen- tromeres that span the entire length of a chromosome [1]. In plants and animals, centromeres are large and complex, typically comprising megabase-sized arrays of tandemly repeated satellite sequences that are rapidly evolving [2] and may differ significantly between closely related species [3-5]. The failure of conventional cloning and sequencing assem- bly tools to adequately characterize rapidly evolving satellite sequences at centromeres has made them the last regions of most eukaryotic genomes to be well understood [1]. Although there is no discernable conservation of centromeric DNA sequences in disparate eukaryotes, considerable progress has been made in identifying common proteins that form the kinetochore [6]. A universal protein component of centromeric chromatin found in all eukaryotes that have been examined is a centromere-specific e first microRNAs (miRNAs) to be discovered, lin-4 and let-7, were found to be regulators of Caenorhabditis elegans development [1-3], and they established a paradigm for eukaryotic gene regulation in which short hairpins generate RNAs of approximately 22 nucleotides (nt) that repress specific target mRNAs. miRNAs have proved to be pervasive in both animals [4-6] and plants [7,8], acting as sequence-specific guides for target recognition [9,10]. Several thousand miRNAs have now been found in dozens of plants and animals [11]. Moreover, the biogenesis and activity of miRNAs are strongly related to those of small interfering RNAs (siRNAs) that mediate RNA interference, another ancient mechanism for post-transcriptional gene silencing [12]. Although miRNAs mediate diverse aspects of development and physiology in both plants and animals [13,14], there are substantial differences between them. For example, the loci that produce miRNAs have distinct genomic arrangements in each kingdom. Furthermore, miRNAs are excised from precursor transcripts by different pathways in the two kingdoms, and in different subcellular compartments. Once made, plant and animal miRNAs have vastly different suites of direct targets; the number of direct targets of a given animal miRNA generally exceeds that of a given plant miRNA by at least an order of magnitude [15]. Herein, we focus on how these differences contribute to, and are the result of, distinct evolutionary characteristics of miRNAs in the two kingdoms. We also highlight many commonalities between the respective systems that may reflect a shared evolutionary heritage or convergent strategies for handling and metabolizing double-stranded RNAs. Distinct characteristics of miRNA pathways in plants and animals What is a miRNA? Answering this question is not a simple task, as no single definition clearly and specifically encompasses all miRNAs. Although practical guides for miRNA annotation in plants and animals exist [16,17], not all loci reported in the miRBase registry [18] have been annotated to the same degree of confidence. In general, miRNAs are the products of inverted repeat transcripts that are precisely cleaved by RNase III enzyme(s) in the Dicer and/or Drosha protein families to yield small RNAs of approximately 21 to 24 nucleotides that guide Argonaute (AGO) proteins to complementary targets. Analogous, but distinct, core pathways govern the biogenesis of most miRNAs in plants and animals. Although we focus on these canonical miRNA pathways, a plethora of alternative pathways exist. Indeed, the diversity and flexibility of miRNA biogenesis pathways, in concert with related mechanisms that generate siRNAs, have made a significant contribution to miRNA evolution. In addition, while a hallmark of most studied miRNAs is the precise manner in which they are excised from precursor hairpins, there are examples of imprecisely cleaved miRNAs. As we shall see, this phenomenon might have implications for miRNA evolution, but it also poses challenges for the accurate distinction of bona fide miRNAs from fortuitous hairpins associated with short RNAs not generated by a specific biogenesis machinery. Canonical miRNA biogenesis in plants versus animals e biogenesis of plant miRNAs has been documented most thoroughly in Arabidopsis thaliana (Figure 1a). Primary miRNA (pri-miRNA) transcripts are products of RNA polymerase II that contain a hairpin RNA secondary structure [19]. e length of plant pri-miRNA Abstract MicroRNAs are pervasive in both plants and animals, but many aspects of their biogenesis, function and evolution dier. We reveal how these dierences contribute to characteristic features of microRNA evolution in the two kingdoms. © 2010 BioMed Central Ltd Vive la diérence: biogenesis and evolution of microRNAs in plants and animals Michael J Axtell* 1 , Jakub O Westholm 2 and Eric C Lai* 2 R EVI E W *Correspondence: Michael J Axtell, The Role of PowerChapter 8 OutlineRole of PowerRules for Using Power Role of PowerPower defined: •Ability or official capacity to exercise control; authority•Ability to influence or control othersSources of Power•Information•Status•Social networks•Physical appearance Rules for Using PowerThe text describes 16 rules for using power in negotiation.  Each will be discussed in the following slides. Rule #1: Establish CredibilityIntroduction by othersBiographical sketchTake notesBe a good listener Demonstrate recall & understanding of informationSuggest an agenda Rule #2: Do Your ResearchSmart talk – sounding confident, articulate or eloquentStay abreast of content areas and read a broad range of materialsKnowledge leads to confidencePresent information constructively and with intent to help Rule #3: Don’t Have All the AnswersDon’t flaunt your expertiseHelp the other side remain confident (face issues)Utilize esteem­reviving comments•Useful when other side takes offense or negatively reacts to statements•“If you don’t mind, let’s back up here to see if I’ve misstated my intentions.”•“If I seemed to be abrasive a few moments ago…”•“I may have spoken too quickly” Rule #4: Don’t Sweat the Small StuffDon’t push too hard for minor gainsQuibbling over small stuff creates bad willBundle small items with others into one package•Example – Negotiating relocation expenses as part of a salary negotiation Rule #5: Create DependenceCreate relianceIdentify what you have the other side might wantRelationship between power & dependence•Power A, B = Dependence B, A•Power of person A over B is equal to the dependence of person B on A Rule #6: Power of Who You KnowIt’s not what you know but who you knowIdentify how your negotiation counterpart might perceive your references or connections•Utilize when they are highly regarded and perceived as credible sources•Make a subtle reference [...]... Landscape  Types of Political Environments • Minimally Politicized Arena – power possessed by those  who are truthful and demonstrate regard for their own  outcomes and those of others • Moderately Politicized Area – greater acceptance of behind­ the scenes tactics so long as the goals of the group are  achieved • Highly Politicized Arena – conflict is frequent and often  pervasive – who you know more important that what you  know • Pathologically Politicized Arena – characterized by  frequent, often long­lasting conflict; high levels of distrust Rule #14: Don’t Negotiate Alone  Have support of others – either present  or whom you can mention during the negotiation process  “Friends in high places” are an  important part of evidentiary support ... Power The text describes 16 rules for using  power in negotiation.  Each will be  discussed in the following slides. Rule #8: Use Time Strategically  Pace proposals so it fits the circumstances and the other side’s  expectations  Mirror your counterpart’s style to pace  appropriately  Be flexible Rule #5: Create Dependence  Create reliance  Identify what you have the other side  might want  Relationship between power &  dependence • Power A, B = Dependence B, A • Power of person A over B is equal to the dependence of person B on A ... Dependence  Create reliance  Identify what you have the other side  might want  Relationship between power &  dependence • Power A, B = Dependence B, A • Power of person A over B is equal to the dependence of person B on A Rule #12: Remain Flexible  Constantly reevaluate the effectiveness  of your choices  Be prepared for anything  Utilize creative thinking and  experimentation Rule #9: Carefully Choose Context  The environment of The Role of Seed Plants The Role of Seed Plants Bởi: OpenStaxCollege Without seed plants, life as we know it would not be possible Plants play a key role in the maintenance of terrestrial ecosystems through stabilization of soils, cycling of carbon, ... earliest seed plant known to date Seed ferns ([link]) produced their seeds along their branches without specialized structures What 2/10 Evolution of Seed Plants makes them the first true seed plants. .. dry growth conditions 3/10 Evolution of Seed Plants This boreal forest (taiga) has low-lying plants and conifer trees (credit: L.B Brubaker, NOAA) Seeds and Pollen as an Evolutionary Adaptation... a species, separates into two or more species 7/10 Evolution of Seed Plants This phylogenetic tree shows the evolutionary relationships of plants Phylogenetic trees have been built to describe