CACO3 OPTICAL DETECTION WITH FLUORESCENT IN SITU HYBRIDIZATION: A NEW METHOD TO IDENTIFY AND QUANTIFY CALCIFYING MICROORGANISMS FROM THE OCEANS1

Open oceanic calcification is mainly driven by unicellular organisms and in particular by eukaryotes such as coccolithophores and foraminifers. Open ocean microcalcifiers, like most planktonic protists, are characterized by extremely fast generation times and occasional sexual reproduction. Populations can alternate between diploid and haploid stages, which often build different kinds of cell covers. In the most important pelagic calcifiers, the coccolithophores, the diploid and haploid stages, which can self‐replicate and grow independently, display radically different morphologies with different modes of calcification or even with the absence of calcification in at least one life cycle stage. Although life cycle strategies seem likely to fundamentally influence the where and when of open ocean calcification, this issue has yet to be seriously addressed in the natural environment. Here, we introduce a new morphogenetic method, “combined CaCO₃ optical detection with fluorescent in situ hybridization,” or COD‐FISH, which is based on a combination of TSA‐FISH and polarized optical microscopy. This technique allows simultaneous assessment of the taxonomic and life cycle status of single coccolithophore cells collected from the ocean. We demonstrate the application of COD‐FISH using both laboratory culture and field samples and discuss its potential value for assessing the ecology, biodiversity, population structure, and life cycles of coccolithophores and other open ocean unicellular calcifiers.     

The cell cycle of Entamoeba histolytica

Entamoeba histolytica, is a microaerophilic protist, which causes amoebic dysentery in humans. This unicellular organism proliferates in the human intestine as the motile trophozoite and survives the hostile environment outside the human host as the dormant quadri-nucleate cyst. Lack of organelles – such as mitochondria and Golgi bodies – and an unequal mode of cell division, led to the popular belief, that this organism preceded other eukaryotes during evolution. However, data from several laboratories have shown that, contrary to this belief, E. histolytica is remarkable in its divergence from other eukaryotes. This uniqueness is witnessed in many aspects of its biochemical pathways, cellular biology and genetic diversity. In this context, I have analysed the cell division cycle of this organism and compared it to that of other eukaryotes. Studies on E. histolytica, suggest that in its proliferative phase, this organism may accumulate polyploid cells. Thus 'checkpoints' regulating alternation of genome duplication and cell division appear to be absent in this unicellular protist. Sequence homologs of several cell cycle regulating proteins have been identified in amoeba, but their structural divergence suggests that they may not have equivalent function in this organism. The regulation of cell proliferation in E. histolytica, may be ideally suited to survival of a parasite in a complex host. Analysis of these molecular details may offer solutions for eradicating the pathogen by hitherto unknown methods.     

Construction of synthetic nucleoli and what it tells us about propagation of sub-nuclear domains through cell division

The cell nucleus is functionally compartmentalized into numerous membraneless and dynamic, yet defined, bodies. The cell cycle inheritance of these nuclear bodies (NBs) is poorly understood at the molecular level. In higher eukaryotes, their propagation is challenged by cell division through an “open” mitosis, where the nuclear envelope disassembles along with most NBs. A deeper understanding of the mechanisms involved can be achieved using the engineering principles of synthetic biology to construct artificial NBs. Successful biogenesis of such synthetic NBs demonstrates knowledge of the basic mechanisms involved. Application of this approach to the nucleolus, a paradigm of nuclear organization, has highlighted a key role for mitotic bookmarking in the cell cycle propagation of NBs.     

LAMMER kinase Kic1 is involved in pre-mRNA processing

The LAMMER kinases are conserved through evolution. They play vital roles in cell growth/differentiation, development, and metabolism. One of the best known functions of the kinases in animal cells is the regulation of pre-mRNA splicing. Kic1 is the LAMMER kinase in fission yeast Schizosaccharomyces pombe. Despite the reported pleiotropic effects of kic1⁺ deletion/overexpression on various cellular processes the involvement of Kic1 in splicing remains elusive. In this study, we demonstrate for the first time that Kic1 not only is required for efficient splicing but also affects mRNA export, providing evidence for the conserved roles of LAMMER kinases in the unicellular context of fission yeast. Consistent with the hypothesis of its direct participation in multiple steps of pre-mRNA processing, Kic1 is predominantly present in the nucleus during interphase. In addition, the kinase activity of Kic1 plays a role in modulating its own cellular partitioning. Interestingly, Kic1 expression oscillates in a cell cycle-dependent manner and the peak level coincides with mitosis and cytokinesis, revealing a potential mechanism for controlling the kinase activity during the cell cycle. The novel information about the in vivo functions and regulation of Kic1 offers insights into the conserved biological roles fundamental to LAMMER kinases in eukaryotes.     

Vesicle-like biomechanics governs important aspects of nuclear geometry in fission yeast

It has long been known that during the closed mitosis of many unicellular eukaryotes, including the fission yeast (Schizosaccharomyces pombe), the nuclear envelope remains intact while the nucleus undergoes a remarkable sequence of shape transformations driven by elongation of an intranuclear mitotic spindle whose ends are capped by spindle pole bodies embedded in the nuclear envelope. However, the mechanical basis of these normal cell cycle transformations, and abnormal nuclear shapes caused by intranuclear elongation of microtubules lacking spindle pole bodies, remain unknown. Although there are models describing the shapes of lipid vesicles deformed by elongation of microtubule bundles, there are no models describing normal or abnormal shape changes in the nucleus. We describe here a novel biophysical model of interphase nuclear geometry in fission yeast that accounts for critical aspects of the mechanics of the fission yeast nucleus, including the biophysical properties of lipid bilayers, forces exerted on the nuclear envelope by elongating microtubules, and access to a lipid reservoir, essential for the large increase in nuclear surface area during the cell cycle. We present experimental confirmation of the novel and non-trivial geometries predicted by our model, which has no free parameters. We also use the model to provide insight into the mechanical basis of previously described defects in nuclear division, including abnormal nuclear shapes and loss of nuclear envelope integrity. The model predicts that (i) despite differences in structure and composition, fission yeast nuclei and vesicles with fluid lipid bilayers have common mechanical properties; (ii) the S. pombe nucleus is not lined with any structure with shear resistance, comparable to the nuclear lamina of higher eukaryotes. We validate the model and its predictions by analyzing wild type cells in which ned1 gene overexpression causes elongation of an intranuclear microtubule bundle that deforms the nucleus of interphase cells.     

The function of the ocelloid and piston in the dinoflagellate Erythropsidinium (Gymnodiniales,Dinophyceae)

The marine dinoflagellate Erythropsidinium possesses an ocelloid, the most elaborate photoreceptor organelle known in a unicellular organism, and a piston, a fast contractile appendage unknown in any other organism. The ocelloid is able to rotate, often before the cell swims. The ocelloid contains lenses that function to concentrate light. The flagellar propulsion is atrophied, and the piston is responsible for locomotion through successive extensions and contractions. During the “locomotion mode”, the contraction is ~4 times faster than the extension. The piston attained up to 50 mm · s^?1 and the cell jumps backwards at ?4 mm · s^?1, while during the piston extension the cell moves forwards. The net speed of ~?1 mm · s^?1 is faster than other dinoflagellates. The piston usually moved in the “static mode” without significant cell swimming. This study suggests that the piston is also a tactile organelle that scans the surrounding waters for prey. Erythropsidinium feeds on copepod eggs by engulfing. The end of the piston possesses a “suction cup” able to attach the prey and place it into the posterior cavity for engulfing. The cylindrical shape of Erythropsidinium, and the anterior position of the ocelloid and nucleus, are morphological adaptations that leave space for the large vacuole. Observations are provided on morphological development during cell division. Most of the described species of Erythropsidinium apparently correspond to distinct life stages of known species, and the genus Greuetodinium (=Leucopsis) corresponds to an earlier division stage.     

Multicellularity arose several times in the evolution of eukaryotes (Response to DOI 10.1002/bies.201100187)

The cellular slime mold Dictyostelium has cell‐cell connections similar in structure, function, and underlying molecular mechanisms to animal epithelial cells. These similarities form the basis for the proposal that multicellularity is ancestral to the clade containing animals, fungi, and Amoebozoa (including Dictyostelium): Amorphea (formerly “unikonts”). This hypothesis is intriguing and if true could precipitate a paradigm shift. However, phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell‐cell connections.     

Autophagy in unicellular eukaryotes

Cells need a constant supply of precursors to enable the production of macromolecules to sustain growth and survival. Unlike metazoans, unicellular eukaryotes depend exclusively on the extracellular medium for this supply. When environmental nutrients become depleted, existing cytoplasmic components will be catabolized by (macro)autophagy in order to re-use building blocks and to support ATP production. In many cases, autophagy takes care of cellular housekeeping to sustain cellular viability. Autophagy encompasses a multitude of related and often highly specific processes that are implicated in both biogenetic and catabolic processes. Recent data indicate that in some unicellular eukaryotes that undergo profound differentiation during their life cycle (e.g. kinetoplastid parasites and amoebes), autophagy is essential for the developmental change that allows the cell to adapt to a new host or form spores. This review summarizes the knowledge on the molecular mechanisms of autophagy as well as the cytoplasm-to-vacuole-targeting pathway, pexophagy, mitophagy, ER-phagy, ribophagy and piecemeal microautophagy of the nucleus, all highly selective forms of autophagy that have first been uncovered in yeast species. Additionally, a detailed analysis will be presented on the state of knowledge on autophagy in non-yeast unicellular eukaryotes with emphasis on the role of this process in differentiation.     

Primary and secondary structure of the nuclear small subunit ribosomal RNA of the cryptomonadPyrenomonas salina as inferred from the gene sequence: Evolutionary implications

Summary The cryptomonadPyrenomonas salina presumably has arisen from a symbiotic event involving a flagellated phagotrophic host cell and a photosynthetic eukaryote as the symbiont. Correspondingly, in this unicellular alga there are four different genomes, e.g., the nuclear and the mitochondrial genomes of the host cell as well as the plastid genome and the genome contained in the vestigial nucleus of the endocytobiont (nucleomorph). To analyze the orgin of one of the symbiotic partners the small subunit rRNA gene sequence of the host cell nucleus was determined, and a secondary structure model has been constructed. This sequence is compared to those of 40 other eukaryotes. A phylogenetic tree constructed using the neighborliness method revealed a close relationship between the host cell ofP. salina and the chlorophytes, whereas the rhodophytes diverge more deeply in the tree.     

Programmed nuclear destruction in yeast

Studies of the budding yeast Saccharomyces cerevisiae have provided many of the most important insights into the mechanisms of autophagy, which are common to all eukaryotes. However, investigation of yeast self-destruction pathways, including autophagy and programmed cell death, has been almost exclusively restricted to cells undergoing vegetative growth, leaving very little exploration of their functions during developmental transitions in the yeast life cycle. We have recently discovered that whole nuclei are subject to programmed destruction during yeast gametogenesis. Programmed nuclear destruction (PND) possesses characteristics of apoptosis in the form of DNA cleavage by endonuclease G, and involves bulk protein turnover through an unusual autophagic pathway involving lysis of the vacuole rather than delivery of components to it through macroautophagy. We thus illuminate an example of developmentally programmed cellular “self-eating” in yeast, which is associated with the rupture of a lytic organelle, reminiscent of programmed cell death mechanisms in plants and animals.     

A mathematical model for the batch reactor kinetics of algae growth

A mathematical model based on the Einstein law of photochemical equivalence is proposed to describe the batch growth of unicellular algae. The model was applied in an integrated form to cell concentration versus growth time data taken over an extended range of cell concentrations which include both the regions of “exponential” and “linear” growth. It is shown that a certain function of cell concentration contained in the integrated form of the model is linearly dependent on the growth time over both the “exponential” and “linear” growth regions.     

GENETIC EXCHANGES OF INTEINS BETWEEN PRASINOVIRUSES (PHYCODNAVIRIDAE)

Phylogenetic diversity in the Phycodnaviridae (double‐stranded DNA viruses infecting photosynthetic eukaryotes) is most often studied using their DNA polymerase gene (PolB). This gene and its translated protein product can harbor a selfish genetic element called an “intein” that disrupts the sequence of the host gene without affecting its activity. After translation, the intein peptide sequence self‐excises precisely, producing a functional ligated host protein. In addition, inteins can encode homing endonuclease (HEN) domains that permit the possibility of lateral transfers to intein‐free alleles. However, no clear evidence for their transfer between viruses has previously been shown. The objective of this paper was to determine whether recent transfers of inteins have occurred between prasinoviruses (Phycodnaviridae) that infect the Mamiellophyceae, an abundant and widespread class of unicellular green algae, by using DNA sequence analyses and cophylogenetic methods. Our results suggest that transfer among prasinoviruses is a dynamic ongoing process and, for the first time in the Phycodnaviridae family, we showed a recombination event within an intein.     

New insights into cyclins, CDKs, and cell cycle control

Since their initial discovery in yeast, cyclin-dependent kinases have proven to be universal regulators of the cell cycle in all eukaryotes. In unicellular eukaryotes, cell cycle progression is principally governed by one catalytic subunit (cyclin-dependent kinase) that pairs with cell cycle-specific regulatory subunits known as cyclins. Progression through a specific phase of the cell cycle is under the control of a specific class of cyclin. Cell cycle control in multicellular eukaryotes has an additional layer of complexity, as multiple CDKs and cyclins are required. In this review, we will discuss recent advances in the area of cyclins and CDKs, with emphasis on the role of the mammalian proteins in cell cycle control at the cellular and at the organismal level. Many recent surprises have come to light recently as a result of genetic manipulation of cells and mice, and these findings suggest that our understanding of the intricacies of the cell cycle is still rudimentary at best.     

Cellular Dynamics of Small RNAs

ABSTRACT

This review highlights the unexpectedly complicated nuclear egress and nuclear import of small RNAs. Although nucleus/cytoplasm trafficking was thought to be restricted to snRNAs of many, but not all, eukaryotes, recent data indicate that such traffic may be more common than previously appreciated. First, in conflict with numerous previous reports, new information indicates that Saccharomyces cerevisiae snRNAs may cycle between the nucleus and the cytoplasm. Second, recent studies also provide evidence that other small RNAs that function exclusively in the nucleus—the budding yeast telomerase RNA and possibly small nucleolar RNAs—may exit to the cytoplasm, only to return to the nucleus. Third, nucleus/cytoplasm cycling of RNAs also occurs for RNAs that function solely in the cytoplasm, as it has been discovered that cytoplasmic tRNAs of budding yeast travel “retrograde” to the nucleus and, perhaps, back again to the cytoplasm to function in protein synthesis. Fourth, there is at least one example in ciliates of small double-stranded RNAs traveling multiple cycles between the cytoplasm and distinct nuclei to direct genome structure. This report discusses data that support or argue against nucleus/cytoplasm bidirectional movement for each category of small RNA and the possible roles that such movement may serve.     

Effects of Actinomycin D on Generation Time and Morphogenesis in Paramecium*

SYNOPSIS. The sensitivity of Paramecium tetraurelia (=P. aurelia syngen 4) cells to pulse treatments with various doses of Actinomycin D (AMD) was estimated by comparing the generation times of treated and untreated sister cells. It was found that the delay of division in treated cells depended on the concentration of AMD, on their “age” at the time of the pulse treatment, and on their individual sensitivity. Sensitivity of Paramecium to AMD changes during the cell cycle in a predictable way. About 3 1/2 hr before the normally expected cell fission (total generation time ～ 5 1/2 hr) there is a decrease of sensitivity. Thereafter, the cell enters a new stage with a progressive increase of sensitivity. This 2nd phase ends at the “transition point” (～ 2 hr before cell division), when sensitivity drops abruptly. The division process itself may be altered and slowed down by high concentrations of AMD, even if the drug is applied after the transition point, but this process can never be completely annulled. The impairment of the division mechanism may lead to morphologic anomalies in the offspring. Resorption of oral anlagen in P. tetraurelia probably never occurs during the cell cycle after AMD treatment. The reason for individual variability of the cells, mechanisms controlling development, and the question of an obligate sequence of gene action in each cell cycle are discussed.     

The small ubiquitin-like modifier (SUMO) is essential in cell cycle regulation in Trypanosoma brucei

SUMO, a reversible post-translational protein modifier, plays important roles in many processes of higher eukaryotic cell life. Although SUMO has been identified in many eukaryotes, SUMO and SUMO system are still unknown in some eukaryotic unicellular organisms, such as Trypanosoma brucei (T. brucei). In this study, only one SUMO homologue (TbSUMO) was identified in T. brucei. Expression of TbSUMO was knocked down by using RNA interference technique in procyclic-form T. brucei. The growth of TbSUMO-deficient cells was significantly inhibited. TbSUMO-deficient cells were arrested in G₂/M phase accompanied with an obvious increase of 0N1K cells (zoids), and failed in chromosome segregation. These results indicate that TbSUMO is essential in cell cycle regulation, with one important role in mitosis. Meanwhile, the enrichment of zoids suggests the inhibition of mitosis does not prevent the cell division in procyclic-form T. brucei. HA-tagged TbSUMO was overexpressed in T. brucei and was shown to be localized to the nucleus through the whole cell cycle, further revealing its distinguished functions in nucleus. All these accumulated data imply that a SUMO system essential for regulating cell cycle progression might exist in the procyclic-form T. brucei.     

In Vitro Cellular Division of Trypanosoma abeli Reveals Two Pathways for Organelle Replication

Since the observation of the great pleomorphism of fish trypanosomes, in vitro culture has become an important tool to support taxonomic studies investigating the biology of cultured parasites, such as their structure, growth dynamics, and cellular cycle. Relative to their biology, ex vivo and in vitro studies have shown that these parasites, during the multiplication process, duplicate and segregate the kinetoplast before nucleus replication and division. However, the inverse sequence (the nucleus divides before the kinetoplast) has only been documented for a species of marine fish trypanosomes on a single occasion. Now, this previously rare event was observed in Trypanosoma abeli, a freshwater fish trypanosome. Specifically, from 376 cultured parasites in the multiplication process, we determined the sequence of organelle division for 111 forms; 39% exhibited nucleus duplication prior to kinetoplast replication. Thus, our results suggest that nucleus division before the kinetoplast may not represent an accidental or erroneous event occurring in the main pathway of parasite reproduction, but instead could be a species‐specific process of cell biology in trypanosomes, such as previously noticed for Leishmania. This “alternative” pathway for organelle replication is a new field to be explored concerning the biology of marine and freshwater fish trypanosomes.     

DIATOM MINERALIZATION OF SILICIC ACID. II. REGULATION OF Si (OH)4 TRANSPORT RATES DURING THE CELL CYCLE OF NAVICULA PELLICULOSA1

Synchronized populations of Navicula pelliculosa (Bréb.) Hilse show a 10-fold increase in Si(OH)₄ transport rate during traverse through the cell division cycle. The transport activity pattern is similar to a “peak enzyme.” Kinetic analysis showed there was a significant change in K_s values, indicating increased “affinity” for Si(OH)₄ as cells neared maximal uptake rates. However, the dramatic changes in transport rate at various cell cycle stages were also reflected by alterations in the V_max, values of the transport process, suggesting a change in the number of functional transport “sites” in the plasma membrane. Cells in the wall forming stage, arrested from further development by Si(OH)₄ deprivation, maintained high transport rates for as long as 7 h. The rates decreased rapidly if protein synthesis were blocked or if Si(OH)₄ was added, the latter allowing the cells to traverse the rest of the cycle. The half-life of the transport activity ranged from 1.0 to 2.2 h when protein synthesis was inhibited at various cell cycle stages and during the natural decline of activity late in the cycle. The transport system appears to be metabolically unstable as is typical for a “peak protein.” The rise in transport rate through the cell cycle did not depend on the presence of Si(OH)₄ in the medium; therefore, the transport system does not appear to be induced by its substrate. The rise in transport is also observed in L:D synchronized cells developing in the presence of Si(OH)₄; neither does the transport system appear to be derepressed. The transport rate was strongly cell cycle-stage dependent; the data appeared to fit the “dependent pathway” model proposed by Hart-well to explain oscillations in enzyme synthesis during the cell cycle.