DNA is present in the nucleomorph of cryptomonads: Further evidence that the chloroplast evolved from a eukaryotic endosymbiont

Summary The nucleomorph is a unique self-replicating organelle which is invariably present in the periplastidal compartment of cryptomonads. The nucleomorph ofCryptomonas abbreviata is located in a groove on the inner face of the pyrenoid. When JB-4-embedded sections ofC. abbreviata are stained with 4-6-diamidino-2-phenylindole (DAPI), the nucleomorph exhibits a blue fluorescence characteristic of DNA-DAPI complexes. This fluorescence is removed by DNase digestion, but not by RNase. When cells are prepared for electron microscopy by the method of Ryter and Kellenberger (Schreil 1964), a network of fine DNA-like fibrils is observed in the nucleomorph matrix. It is estimated that the nucleomorph contains between 10⁸ and 10⁹ daltons of DNA. The presence of DNA in nucleomorphs strongly supports the hypothesis that the nucleomorph is the vestigial nucleus of a eukaryotic endosymbiont. It is postulated that this eukaryotic symbiont was an ancestral red alga or an organism closely related to red algae. The cryptomonad host cell, on the other hand, is not evolutionarily close to any other group of algae.     

A eukaryotic genome of 660 kb: electrophoretic karyotype of nucleomorph and cell nucleus of the cryptomonad alga, Pyrenomonas salina.

Cryptomonads are unicellular algae with chloroplasts surrounded by four membranes. Between the inner and the outer pairs of membranes is a narrow plasmatic compartment which contains a nucleus-like organelle called the nucleomorph. Using pulsed field gel electrophoresis it is shown that the nucleomorph of the cryptomonad Pyrenomonas salina contains three linear chromosomes of 195 kb, 225 kb and 240 kb all of which encode rRNAs. Thus, this vestigial nucleus has a haploid genome size of 660 kb, harboring the smallest eukaryotic genome known so far. From the cell nucleus of P. salina at least 20 chromosomes ranging from 230 kb to 3.000 kb were fractionated. Here, the rDNA was detected on a single chromosome of about 2.500 kb.     

Jam packed genomes--a preliminary,comparative analysis of nucleomorphs

There are two ways eukaryotic cells can permanently acquire chloroplasts. They can take up a cyanobacterium and turn it into a chloroplast or they can engulf an alga that already has a chloroplast. The second method is far more common and there are at least seven major groups of protists that have obtained their chloroplasts, this way. In most cases little remains of the engulfed alga apart from its chloroplast, but in two groups, the cryptomonads and chlorarachniophytes, a small remnant nucleus of the engulfed alga is still present. These tiny nuclei, called nucleomorphs, are the smallest and most compact eukaryotic genomes known and recently the nucleomorph of the cryptomonad alga Guillardia theta, was completely sequenced (551 kilobases). The nucleomorph of the chlorarachniophyte Bigellowiella natans (380 kilobases), is also being sequenced and is about half complete. We discuss some of the similarities and differences that are emerging between these two nucleomorph genomes. Both genomes contain just three chromosomes that encode mainly housekeeping genes and a few proteins for chloroplast functions. The bulk of nucleomorph gene coding capacity, therefore, appears to be devoted to self perpetuation and creating gene and protein expression machineries to make a small number of essential chloroplast proteins. We discuss reasons why both nucleomorphs are extraordinarily compact and why their gene sequences are evolving rapidly.     

Ancient Gene Duplication and Differential Gene Flow in Plastid Lineages: The GroEL/Cpn60 Example

Cryptomonads, small biflagellate algae, contain four different genomes. In addition to the nucleus, mitochondrion, and chloroplast is a fourth DNA-containing organelle the nucleomorph. Nucleomorphs result from the successive reduction of the nucleus of an engulfed phototrophic eukaryotic endosymbiont by a secondary eukaryotic host cell. By sequencing the chloroplast genome and the nucleomorph chromosomes, we identified a groEL homologue in the genome of the chloroplast and a related cpn60 in one of the nucleomorph chromosomes. The nucleomorph-encoded Cpn60 and the chloroplast-encoded GroEL correspond in each case to one of the two divergent GroEL homologues in the cyanobacterium Synechocystis sp. PCC6803. The coexistence of divergent groEL/cpn60 genes in different genomes in one cell offers insights into gene transfer from evolving chloroplasts to cell nuclei and convergent gene evolution in chlorophyll a/b versus chlorophyll a/c/phycobilin eukaryotic lineages. Received: 24 April 1998 / Accepted: 12 June 1998     

The smallest known eukaryotic genomes encode a protein gene: towards an understanding of nucleomorph functions

Cryptomonads are unicellular algae with plastids surrounded by four membranes. Between the two pairs of membranes lies a periplastidal compartment that harbours a DNA-containing organelle, termed the nucleomorph. The nucleomorph is the vestigial nucleus of a phototrophic, eukaryotic endosymbiont. Subcloning of parts of one nucleomorph chromosome revealed a gene coding for an Hsp70 protein. We demonstrate the expression of this nucleomorph protein-coding gene and present a model for protein transport from the host to the endosymbiont compartment.This paper is dedicated to Prof. Dr. Peter Sitte on the occasion of his 65^th birthday     

Molecular, morphological and phylogenetic characterization of six chlorarachniophyte strains

We compare and contrast the morphological and molecular features of six chlorarachniophyte strains, and examine their evolutionary origins. Electron microscopical studies of nucleomorphs and chloroplasts, characterization of nucleomorph karyotypes, and phylogenetic analyses of small subunit ribosomal RNA (srRNA) genes derived from the nucleomorph and host cell genomes have been used to separate the six strains into three distinct groups. One group, dubbed the‘beast group’, contains the strains Chlorarachnion sp. 242, Chlor-arachnion sp. 621, Chlorarachnion sp. 1408 and Chlorarachnion sp. 1481. Members of the beast group have a novel flagellate form and are apparently picoplank-tonic. The other two groups currently contain only one species each: Chlorarachnion reptans and Lotharella sp. 240. All chlorarachniophyte nucleomorphs examined house three small linear chromosomes each furnished with telomeres and srRNA genes.     

CYTOLOGY AND ULTRASTRUCTURE OF CHLORARACHNION REPTANS (CHLORARACHNIOPHYTA DIVISIO NOVA,CHLORARACHNIOPHYCEAE CLASSIS NOVA)1

The green amoeboid cells of Chlorarachnion reptans Geitler are completely naked and each contains a central nucleus, several bilobed chloroplasts each with a central projecting pyrenoid enveloped by a capping vesicle, several Golgi bodies, mitochondria with tubular cristae, extensive rough ER, and a distinct layer of peripheral vesicles. Complex extrusome-like organelles occur rarely in both the amoeboid and flagellate stages. The only organelles entering the reticulopodia are mitochondria, but microtubules are also present. The chloroplasts contain chlorophylls a and b, but histochemical tests suggest that the carbohydrate storage product probably is not a starch. The chloroplast lamellae are composed of one to three thylakoids or form deep stacks. A girdle lamella and interlamellar partitions are absent. Each chloroplast is bounded by either four separate membranes, a pair of membranes with vesicular profiles between them, or three membranes; all three arrangements may occur in the same chloroplast. A periplastidal compartment occurs near the base of the pyrenoid where there are always four surrounding membranes. The compartment has a relatively dense matrix and contains ribosome-like particles and small dense spheres; it extends over and into a deep invagination in the pyrenoid where its contents are enclosed in a double-membraned envelope which is penetrated by wide pores. The zoospores are ovoid and each bears a single laterally inserted flagellum which appears to be wrapped helically around the cell body during swimming. The flagellum lies in a groove in the cell surface and bears fine lateral hairs. Neither a second flagellum or vestige of one, nor an eyespot, is present. A single microtubular root and a larger homogeneous root run from the flagellar base parallel to the emerging flagellum, between the nuclear envelope and the plasmalemma. In the simple flagellar transition region, fine filaments connect adjacent axonemal doublets. A detailed comparison of C. reptans with all other algal taxa results in the conclusion that it must be segregated in the new class Chlorarachniophyceae, the only class in the new division Chlorarachniophyta. The possibility that C. reptans evolved from a symbiosis between a colorless amoeboid cell and a chlorophyll b- containing eukaryote is considered, but the possible affinities of the symbiont remain enigmatic. The implications of the unique chloroplast structure of C. reptans for current hypotheses concerning the origin of chloroplasts are discussed.     

Changes in structure of isolated chloroplasts ofCodium fragile andCaulerpa filiformis in response to osmotic shock and detergent treatment

Summary The ultrastructure of chloroplasts from two genera of coenocytic green algae,Codium andCaulerpa, were examined after suspension in hypotonic solution and in detergent at various concentrations. The capacity of the suspensions to carry out CO₂-dependent and ferricyanide-dependent O₂ evolution was measured under the same conditions of osmotic strength and detergent concentration.The chloroplasts in the preparations were in the form of cytoplasts and gave rates of O₂ evolution comparable with those expected from undamaged chloroplasts. Suspension in hypotonic solution depressed the rate of CO₂-dependent O₂ evolution in both species, but this was partially restored in theCodium chloroplasts when these were re-suspended in iso-osmotic solutions. Major structural changes were observed only after suspension in buffer when theCodium chloroplasts lost their outer envelope, most of their stroma, and the thylakoids became swollen.Caulerpa chloroplasts were more variable in their response and, even when suspended in buffer only, the proportion of the plastids which had lost all of their stroma and thylakoid swelling was never as common as inCodium chloroplasts. However, once suspended in hyper-osmotic medium below 700 mosmolar,Caulerpa chloroplasts could not regain their capacity for CO₂-dependent O₂ evolution.Detergent treatment removed the cytoplast membrane but not the cytoplasmic material adhering to the chloroplast envelope. High concentrations of detergent were needed to cause loss of the chloroplast envelope, loss of stromal contents and unstacking of the thylakoids.Caulerpa chloroplasts were less sensitive to detergent than those ofCodium. There was no indication that specific structures such as the thylakoid organizing body were resistant to detergent action. The results show that exposure to hypotonic solutions and to detergent results in less damage to these chloroplasts than it would to those of higher plants. It is proposed that the basis of this unusual resistance is not due to the properties of the chloroplast membranes but to the presence of material which coats the organelles during isolation. This material is likely to be identical with the sulphated xylo-mannogalactan isolated from the vacuole contents of these algae and which has the visco-elastic properties essential to allow the organelles to resist disruption by osmotic forces and disintegration by detergents.     

Occurrence and distribution of filipin-sterol complexes in chloroplast envelope membranes of algae and higher plants as visualized by freeze-fracture

Summary The occurrence and planar distribution of 3--hydroxysterols in chloroplast envelope membranes of different algae and higher plants has been studied with the freeze-fracture technique using the polyene antibiotic filipin as cytochemical marker. The inner chloroplast envelope membrane in all organisms studied is devoid of filipin-sterol complexes. The outer chloroplast envelope membranes of isolated higher plant chloroplasts (spinach, pea) and of chloroplasts of the mossPolytrichum piliferum are lacking filipin-sterol complexes, thus indicating a very low concentration of 3--hydroxysterols in chloroplast envelope membranes of higher plants. In contrast filipin-sterol complexes are abundant in the outer chloroplast envelope membrane of the flagellatesChlamydomonas reinhardii, Cryptomonas erosa, andEuglena gracilis. The chloroplast-ER surrounding the plastid ofCryptomonas erosa also exhibits filipin-sterol complexes. Functional and phylogenetic aspects of these observations are discussed.Medizinische Cytobiologie, Westfälische Wilhelms-Universität, Westring 3, D-4400 Münster, Federal Republic of Germany.     

Über Plastidenstapel beiBotrydiopsis alpina sowie Anlage und Vermehrung der Stigmen bei dieser undHeterococcus (Xanthophyceae)

Under certain conditions inBotrydiopsis alpina stacks of chloroplasts are formed. They consist of up to 8 elements. In contrast to what is known from other algae in zoosporangia of this species and ofHeterococcus caespitosus, stigmata are formed in early developmental stages. They are reproduced together with the chloroplasts, in which they occupy a position at the edge and near the existing or future incision. At the side of the old stigma a new one is formed, and partitioning of the chloroplast between these two leads to their distribution to the daughter chloroplasts. Young daughter cells in the zoosporangia ofBotrydiopsis alpina contain one chloroplast which undergoes a last unequal division giving rise to one astigmate and usually somewhat smaller and to one stigmate chloroplast. In both species the capacity for locomotion may be suppressed, the presumptive zoospores thereby becoming aplanospores. Autospores in the proper sense were not observed. Their development quite generally is different from that of aplanospores (and zoospores), and both types of spores should be distinguished.

Herrn Professor Dr.Lothar Geitler zum 80. Geburtstag in Verehrung gewidmet.     

LIGHT AND ELECTRON MICROSCOPIC OBSERVATIONS OF PREFERENTIAL DESTRUCTION OF CHLOROPLAST AND MITOCHONDRIAL DNA AT EARLY MALE GAMETOGENESIS OF THE ANISOGAMOUS GREEN ALGA DERBESIA TENUISSIMA (CHLOROPHYTA)1

Gametogenesis in male and female gametophytes was studied by light microscopy and EM in the dioecious multinucleate green alga Derbesia tenuissima (Moris & De Notaris) P. Crouan & H. Crouan, where male and female gametes differ in size. Gametogenesis was divided into five stages: 32 h (stage 1), 24 h (stage 2), 16 h (stage 3), 8 h (stage 4), and 0.5 h (stage 5) before gamete release. At stage 1, the first sign of gametogenesis observed was the aggregation of gametophyte protoplasm to form putative gametangia. At stage 2, gametangia were separated from the vegetative protoplasm of gametophytes. Morphological changes of nuclei and organelles occurred at this early stage of male gametogenesis, and organelle DNA degenerated. At stage 3, male organelle DNA had completely degenerated, whereas in female gametangia, organelle DNA continued to exist in both chloroplasts and mitochondria. Gametogenesis was almost completed at stage 4 and fully at stage 5. Small male gametes had a DNA‐containing nucleus and a large mitochondrion and one or several degenerated chloroplasts. The mitochondria and plastids were devoid of DNA. The large female gametes had a nucleus and multiple organelles, all of which contained their own DNA. Thus, degeneration of chloroplast DNA along with morphological changes of organelles occurred at male gametogenesis in anisogamous green algae (Bryopsis and D. tenuissima), in contrast with previous studies in isogamous green algae (Chlamydomonas, Acetabularia caliculus, and Dictyosphaeria cavernosa) in which degeneration of chloroplast DNA occurred after zygote formation.     

Nucleomorphs: enslaved algal nuclei

Nucleomorphs of cryptomonad and chlorarachnean algae are the relict, miniaturised nuclei of formerly independent red and green algae enslaved by separate eukaryote hosts over 500 million years ago. The complete 551 kb genome sequence of a cryptomonad nucleomorph confirms that cryptomonads are eukaryote-eukaryote chimeras and greatly illuminates the symbiogenetic event that created the kingdom Chromista and their alveolate protozoan sisters. Nucleomorph membranes may, like plasma membranes, be more enduring after secondary symbiogenesis than are their genomes. Partial sequences of chlorarachnean nucleomorphs indicate that genomic streamlining is limited by the mutational difficulty of removing useless introns. Nucleomorph miniaturisation emphasises that selection can dramatically reduce eukaryote genome size and eliminate most non-functional nuclear non-coding DNA. Given the differential scaling of nuclear and nucleomorph genomes with cell size, it follows that most non-coding nuclear DNA must have a bulk-sequence-independent function related to cell volume.     

NUCLEOMORPH KARYOTYPE DIVERSITY IN THE FRESHWATER CRYPTOPHYTE GENUS CRYPTOMONAS1

Cryptophytes are unicellular, biflagellate algae with plastids (chloroplasts) derived from the uptake of a red algal endosymbiont. These organisms are unusual in that the nucleus of the engulfed red alga persists in a highly reduced form called a nucleomorph. Nucleomorph genomes are remarkable in their small size (<1,000 kilobase pairs [kbp]) and high degree of compaction (～1 kbp per gene). Here, we investigated the molecular and karyotypic diversity of nucleomorph genomes in members of the genus Cryptomonas. 18S rDNA genes were amplified, sequenced, and analyzed from C. tetrapyrenoidosa Skuja CCAP979/63, C. erosa Ehrenb. emmend. Hoef‐Emden CCAP979/67, Cryptomonas sp. CCAP979/52, C. lundii Hoef‐Emden et Melkonian CCAP979/69, and C. lucens Skuja CCAP979/35 in the context of a large set of publicly available nucleomorph 18S rDNA sequences. Pulsed‐field gel electrophoresis (PFGE) was used to examine the nucleomorph genome karyotype of each of these strains. Individual chromosomes ranged from ～160 to 280 kbp in size, with total genome sizes estimated to be ～600–655 kbp. Unexpectedly, the nucleomorph karyotype of Cryptomonas sp. CCAP979/52 is significantly different from that of C. tetrapyrenoidosa and C. lucens, despite the fact that their 18S rDNA genes are >99% identical to one another. These results suggest that nucleomorph karyotype similarity is not a reliable indicator of evolutionary affinity and provides a starting point for further investigation of the fine‐scale dynamics of nucleomorph genome evolution within members of the genus Cryptomonas.     

Giant chloroplast development in ethylene response1-1 is caused by a second mutation in ACCUMULATION AND REPLICATION OF CHLOROPLAST3 in Arabidopsis

The higher plants of today array a large number of small chloroplasts in their photosynthetic cells. This array of small chloroplasts results from organelle division via prokaryotic binary fission in a eukaryotic plant cell environment. Functional abnormalities of the tightly coordinated biochemical event of chloroplast division lead to abnormal chloroplast development in plants. Here, we described an abnormal chloroplast phenotype in an ethylene insensitive ethylene response1-1 (etr1-1) of Arabidopsis thaliana. Extensive transgenic and genetic analyses revealed that this organelle abnormality was not linked to etr1-1 or ethylene signaling, but linked to a second mutation in ACCUMULATION AND REPLICATION3 (ARC3), which was further verified by genetic complementation analysis. Despite the normal expression of other plastid division-related genes, the loss of ARC3 caused the enlargement of chloroplasts as well as the diminution of a photosynthetic protein Rubisco in etr1-1. Our study has suggested that the increased size of the abnormal chloroplasts may not be able to fully compensate for the loss of a greater array of small chloroplasts in higher plants.     

The chlorarachniophyte: a cell with two different nuclei and two different telomeres

Chlorarachniophyte algae contain a complex chloroplast derived from the endosymbiosis of a eukaryotic alga. The reduced nucleus of the endosymbiont, the nucleomorph, is located between the inner and outer pair of membranes surrounding the chloroplast. The nucleomorph of chlorarachniophytes has previously been demonstrated to contain at least three small linear chromosomes. Here we describe cloning the end of the smallest nucleomorph chromosome which is shown to carry a telomere consisting of a tandemly repeated 7 bp sequence, TCTAGGG. Using the telomere repeat as a probe, we show that nucleomorph telomeres display typical hetero-disperse size distribution. The nucleomorph is shown to contain only three chromosomes with a haploid genome size of just 380kb. All six nucleomorph chromosome termini are identical with an rRNA cistron closely linked to the telomere. The nucleomorph chromosomes thus have relatively large inverted repeats at their ends. Chromosomes from the host nucleus are shown to have a different telomere repeat motif to that of the nucleomorph chromosomes.     

Comparative rates of evolution in endosymbiotic nuclear genomes

Background  

The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded.     

Characterization of genes encoding the light-harvesting proteins in diatoms: biogenesis of the fucoxanthin chlorophylla/c protein complex

In chromophytic algae the major light-harvesting complex is the fucoxanthin chlorophylla/c protein complex. Recently, we have cloned several highly related cDNA and genomic sequences encoding the fucoxanthin chlorophylla/c proteins from the diatomPhaeodactylum tricornutum. These genes are clustered on the nuclear genome. The sequences of the fucoxanthin chlorophylla/c proteins as deduced from the gene sequences have some similarity to the chlorophylla/b proteins associated with light-harvesting complexes of higher plants and green algae. Like the chlorophylla/b proteins of higher plants, the fucoxanthin chlorophylla/c proteins are synthesized as higher-molecular weight precursors in the cytoplasm of the cell and are transported into the plastids. However, the mode of transport into diatom plastids is very different from the mechanism involved in transporting proteins into the chloroplasts of higher plants and green algae. We focus here on the characteristics of the fucoxanthin chlorophylla/c proteins, the mode of transport of these proteins into plastids, the arrangement of the genes encoding these proteins, and efforts to utilize these genes to develop a DNA transformation system for diatoms.     

ENDOMEMBRANE ULTRASTRUCTURE AND POSSIBLE CHLOROPLAST PROTEIN IMPORT PATHWAY IN HETEROSIGMA AKASHIWO (RAPHIDOPHYCEAE)

Chloroplasts in heterokont algae probably originated from a red algal endosymbiont which was engulfed and retained by a eukaryotic host, and are surrounded by four envelope membranes. The outermost of these membranes is called chloroplast ER (CER) and usually connects with the nuclear envelope. This information, however, is based mainly on studies on single‐plastid heterokont algae. In multi‐plastid heterokont algae, it is still unclear whether CER is continuous with the nuclear envelope. Since nuclear‐encoded chloroplast proteins are synthesized by ribosomes on the ER membrane, clarifying the ER‐CER structure in the heterokont algae is important in order to know the targeting pathway of those proteins. We did a detailed ultrastructural observation of endomembrane systems in a multi‐plastid heterokont alga: Heterosigma akashiwo, and confirmed that the CER membrane was continuous with the ER membrane. However, unlike the CER membranes in other heterokont algae, it seemed to have very few ribosome attached. We also performed experiments for protein targeting into canine microsomes using a precursor for a nuclear‐encoded chloroplast protein, a fucoxanthin‐chlorophyll protein (FCP), of H. akashiwo, to see if the protein is targeted to the ER. It demonstrated that the precursor has a functional signal sequence for ER targeting, and is co‐translationally translocated into the microsomes. Based on these data, we propose a hypothesis that, in H. akashiwo, nuclear‐encoded chloroplast protein precursors that have been co‐translationally inserted into the ER lumen are sorted in the ER and transported to the chloroplasts through the ER.     

Actin-mediated chloroplast movement in Griffithsia pacifica (Ceramiales, Rhodophyta)

Chloroplast banding occurs in Griffithsia pacifies Kylin in a daily rhythm. At the start of the light period, chloroplasts have a uniform distribution. During the light period chloroplasts move away from the ends of the cell leaving two chloroplast-free regions by mid-afternoon. Later in the light period these bands disperse as chloroplasts return to the ends of cell where they remain throughout the dark period. After enzyme treatment with β-glucuronidase to permeabilize cell walls, non-banded plants did not form bands after the addition of 5 μg ml^?1 cytochalasin B in dimethyl sulfoxide (DMSO). When enzyme-grown plants with chloroplast bands were treated with cytochalasin B, bands were retained for at least three days. Plants grown in media supplemented with β-glucuronidase or DMSO alone gave banding consistent with untreated controls. Staining of microfilaments with rhodamine-phalloidin before and after treatment with cytochalasin B gave results consistent with chloroplast movement studies. This is the first report of actin-mediated organelle movement in red algae.