Softening-up mannan-rich cell walls

The softening and degradation of the cell wall (CW), often mannan enriched, is involved in several processes during development of higher plants, such as meristematic growth, fruit ripening, programmed cell death, and endosperm rupture upon germination. Mannans are also the predominant hemicellulosic CW polymers in many genera of green algae. The endosperm CWs of dry seeds often contain mannan polymers, sometimes in the form of galactomannans (Gal-mannans). The endo-beta-mannanases (MANs) that catalyse the random hydrolysis of the beta-linkage in the mannan backbone are one of the main hydrolytic enzymes involved in the loosening and remodelling of CWs. In germinating seeds, the softening of the endosperm seed CWs facilitates the emergence of the elongating radicle. Hydrolysis and mobilization of endosperm Gal-mannans by MANs also provides a source of nutrients for early seedling growth, since Gal-mannan, besides its structural role, serves as a storage polysaccharide. Therefore, the role of mannans and of their hydrolytic enzymes is decisive in the life cycle of seeds. This review updates and discusses the significance of mannans and MANs in seeds and explores the increasing biotechnological potential of MAN enzymes.

Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a

Chlorophyll b is an ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. Its biosynthesis plays a key role in the adaptation to various light environments. We isolated six chlorophyll b-less mutants by insertional mutagenesis by using the nitrate reductase or argininosuccinate lyase genes as tags and examined the rearrangement of mutant genomes. We found that an overlapping region of a nuclear genome was deleted in all mutants and that this encodes a protein whose sequence is similar to those of methyl monooxygenases. This coding sequence also contains putative binding domains for a [2Fe-2S] Rieske center and for a mononuclear iron. The results demonstrate that a chlorophyll a oxygenase is involved in chlorophyll b formation. The reaction mechanism of chlorophyll b formation is discussed.

Rapid evolution of sex-related genes in Chlamydomonas

Biological speciation ultimately results in prezygotic isolation—the inability of incipient species to mate with one another–but little is understood about the selection pressures and genetic changes that generate this outcome. The genus Chlamydomonas comprises numerous species of unicellular green algae, including numerous geographic isolates of the species C. reinhardtii. This diverse collection has allowed us to analyze the evolution of two sex-related genes: the mid gene of C. reinhardtii, which determines whether a gamete is mating-type plus or minus, and the fus1 gene, which dictates a cell surface glycoprotein utilized by C. reinhardtii plus gametes to recognize minus gametes. Low stringency Southern analyses failed to detect any fus1 homologs in other Chlamydomonas species and detected only one mid homolog, documenting that both genes have diverged extensively during the evolution of the lineage. The one mid homolog was found in C. incerta, the species in culture that is most closely related to C. reinhardtii. Its mid gene carries numerous nonsynonymous and synonymous codon changes compared with the C. reinhardtii mid gene. In contrast, very high sequence conservation of both the mid and fus1 sequences is found in natural isolates of C. reinhardtii, indicating that the genes are not free to drift within a species but do diverge dramatically between species. Striking divergence of sex determination and mate recognition genes also has been encountered in a number of other eukaryotic phyla, suggesting that unique, and as yet unidentified, selection pressures act on these classes of genes during the speciation process.

Further expansion of the alien seaweed Caulerpa taxifolia var. distichophylla (Sonder) Verlaque, Huisman & Procacini (Ulvophyceae, Bryopsidales) in the Eastern Mediterranean Sea

Date of Acceptance: 27/04/2015 We are grateful to Andreas Antoniou (Dep. of Environment, Ministry of Agriculture, Rural Development & Environment, Cyprus) for his assistance in the preparation of the illustrations. We would also like to thank Dr. Sotiris Orfanidis (NAGREF – Fisheries Research Institute, Kavala, Greece) for his valuable advice and both the DFMR and HSR / HCMR Rhodes crew and George Hatiris for their help in samplings. Special thanks are due to Dinos Leonidou (SeaQuest Divers Cyprus) for accompanying the deep dive for sampling Caulerpa at Cavo Greco. We are grateful to the Total Foundation (Paris) for its funding support to this study within the framework of the project “Brown algal ecology and biodiversity in the eastern Mediterranean Sea” and to the MASTS pooling initiative (Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council and contributing institutions; grant reference HR09011).

Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases

Sequence analysis of chloroplast and mitochondrial large subunit rRNA genes from over 75 green algae disclosed 28 new group I intron-encoded proteins carrying a single LAGLIDADG motif. These putative homing endonucleases form four subfamilies of homologous enzymes, with the members of each subfamily being encoded by introns sharing the same insertion site. We showed that four divergent endonucleases from the I-CreI subfamily cleave the same DNA substrates. Mapping of the 66 amino acids that are conserved among the members of this subfamily on the 3-dimensional structure of I-CreI bound to its recognition sequence revealed that these residues participate in protein folding, homodimerization, DNA recognition and catalysis. Surprisingly, only seven of the 21 I-CreI amino acids interacting with DNA are conserved, suggesting that I-CreI and its homologs use different subsets of residues to recognize the same DNA sequence. Our sequence comparison of all 45 single-LAGLIDADG proteins identified so far suggests that these proteins share related structures and that there is a weak pressure in each subfamily to maintain identical protein–DNA contacts. The high sequence variability we observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into how these proteins evolve new DNA specificity.

PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes

The PLMItRNA database for mitochondrial tRNA molecules and genes in Viridiplantae (green plants) [Volpetti,V., Gallerani,R., DeBenedetto,C., Liuni,S., Licciulli,F. and Ceci,L.R. (2000) Nucleic Acids Res., 28, 159–162] has been enlarged to include algae. The database now contains 436 genes and 16 tRNA entries relative to 25 higher plants, eight green algae, four red algae (Rhodophytae) and two Stramenopiles. The PLMItRNA database is accessible via the WWW at http://bio-www.ba.cnr.it:8000/PLMItRNA.

The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium “Thiodendron latens.” By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This “earliest branching protist” that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

The notion of the Cambrian pananimalia genome.

The toil by photosynthesizing cyanobacteria and blue-green algae of nearly three billion years appeared to have finally resulted in the sufficient accumulation of molecular oxygen. So, the stage was set for the emergence, at the ocean bottom, of diverse animals that were consumers of molecular oxygen. It now appears that this Cambrian explosion, during which nearly all the extant animal phyla have emerged, was of an astonishingly short duration, lasting only 6-10 million years. Inasmuch as only a 1% DNA base sequence change is expected in 10 million years under the standard spontaneous mutation rate, I propose that all those diverse animals of the early Cambrian period, some 550 million years ago, were endowed with nearly identical genomes, with differential usage of the same set of genes accounting for the extreme diversities of body forms. Some of the more pertinent genes that are thought to be included in the Cambrian pananimalia genome are as follows. (i) A gene for lysyloxidase that, in the presence of molecular oxygen, crosslinked collagen triple helices to produce ligaments and tendons, thus contributing to the stout bodies of the Cambrian animals. (ii) Genes for hemoglobin; these internal transporters of molecular oxygen are today seen sporadically in members of diverse animal phyla. (iii) The Pax-6 gene for eye formation; the eyes of a ribbon worm to a human are organized by this gene. In animals without eyes, the same gene organizes other sensory systems and organs. (iv) A series of Hox genes for the anterior-posterior (cranio-caudal) body plans: these genes are also present in all phyla of the kingdom Animalia.

Drosophila melanogaster as a model for basal body research

The fruit fly, Drosophila melanogaster, is one of the most extensively studied organisms in biological research and has centrioles/basal bodies and cilia that can be modelled to investigate their functions in animals generally. Centrioles are nine-fold symmetrical microtubule-based cylindrical structures required to form centrosomes and also to nucleate the formation of cilia and flagella. When they function to template cilia, centrioles transition into basal bodies. The fruit fly has various types of basal bodies and cilia, which are needed for sensory neuron and sperm function. Genetics, cell biology and behaviour studies in the fruit fly have unveiled new basal body components and revealed different modes of assembly and functions of basal bodies that are conserved in many other organisms, including human, green algae and plasmodium. Here we describe the various basal bodies of Drosophila, what is known about their composition, structure and function.

Nitrogen isotope ratios of Cretaceous Atlantic sedimentary sequences

At two locations in the Atlantic Ocean (DSDP Sites 367 and 530) early to middle Cretaceous organic-carbon-rich beds (black shales) were found to have significantly lower delta15N values (lower 15N/14N ratios) than adjacent organic-carbon-poor beds (white limestones or green claystones). While these lithologies are of marine origin, the black strata in particular have delta15N values that are significantly lower than those previously found in the marine sediment record and most contemporary marine nitrogen pools. In contrast, black, organic-carbon-rich beds at a third site (DSDP Site 603) contain predominantly terrestrial organic matter and have C- and N-isotopic compositions similar to organic matter of modern terrestrial origin. The recurring 15N depletion in the marine-derived Cretaceous sequences prove that the nitrogen they contain is the end result of an episodic and atypical biogeochemistry. Existing isotopic and other data indicate that the low 15N relative abundance is the consequence of pelagic rather than post-depositional processes. Reduced ocean circulation, increased denitrification, and, hence, reduced euphoric zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of this sediment 15N-depletion. Lack of parallel isotopic shifts in Cretaceous terrestrially-derived nitrogen (Site 603) argues that the above change in nitrogen cycling during this period did not extend beyond the marine environment.

(Tab. XIII.1) TOC content, carbonate content, carbonate mineralogy, percentage of total carbonate, aragonite, low magnesium calcium, and high magnesium calcium, and grain-size contents from samples from the Golfe d'Arguin and from the Western Sahara

Modern carbonate sedimentation takes place on the northern Mauritanian shelf (20°N), where typical tropical components (e.g. hermatypic reefs, calcareous green algae) are absent. Such deposits are reminiscent of extratropical sediment in the geological record. The tropical open shelf of Mauritania is influenced by large siliciclastic dust input and upwelling, highly fertilizing the ocean, as well as strongly limiting the light penetration. In this context, temperature does not appear to be the steering factor of carbonate production. This thesis describes the depositional system of the Golfe d'Arguin off Mauritania and focuses on environmental conditions that control the depositional pattern, in particular carbonate production. The description of this modern analogue provides a tool for paleoenvironmental interpretation of ancient counterparts. The Golfe d'Arguin is a broad shallow shelf comprising extensive shoals (<10 m water depth; i.e. the Banc d'Arguin) on the inner shelf where waters warm up. The sediments collected in water depths between 4 and 600 m are characterized by mixed carbonate and siliciclastic (dust) deposits. They vary from clean coarse-grained, almost pure carbonate loose sediments to siliciclastic-dominated fine-grained sediments. The carbonate content and sediment grain size show a north-south decreasing pattern through the Golfe d'Arguin and are controlled by the hydraulic regime influenced by wind-driven surface currents, swell, and tidal currents. The carbonate grain association is heterozoan. Components include abundant molluscs, foraminifers, and worm tubes, as well as barnacles and echinoderms, elements that are also abundant in extratropical sediments. The spatial distribution of the sedimentary facies of the Golfe d'Arguin does not display a depth zonation but rather a mosaic (i.e. patchy distribution). The depth and climatic signatures of the different sedimentary facies are determined by taxonomic and ecological investigations of the carbonate-secreting biota (molluscs and foraminifers). While certain planktonic foraminifers and molluscs represent upwelling elements, other components (e.g. mollusc and benthic foraminifer taxa) demonstrate the tropical origin of the sediment. The nutrient-rich (and thus also low light-penetration) conditions are reflected in the fact that symbiotic and photosynthetic carbonate-producing organisms (e.g. hermatypic corals) are absent. The Mauritanian deposits represent an environment that is rare in the modern world but might have been more common in the geological past when global temperatures were higher. Taxonomic and ecological studies allow for distinguishing carbonate sediments formed under either tropical high-nutrient or extratropical conditions, thus improving paleoclimate reconstruction.

Plant species, biomass and environmental characteristics of relevés along the North America Arctic bioclimate gradient

Question: How do interactions between the physical environment and biotic properties of vegetation influence the formation of small patterned-ground features along the Arctic bioclimate gradient? Location: At 68° to 78°N: six locations along the Dalton Highway in arctic Alaska and three in Canada (Banks Island, Prince Patrick Island and Ellef Ringnes Island). Methods: We analysed floristic and structural vegetation, biomass and abiotic data (soil chemical and physical parameters, the n-factor [a soil thermal index] and spectral information [NDVI, LAI]) on 147 microhabitat releves of zonalpatterned-ground features. Using mapping, table analysis (JUICE) and ordination techniques (NMDS). Results: Table analysis using JUICE and the phi-coefficient to identify diagnostic species revealed clear groups of diagnostic plant taxa in four of the five zonal vegetation complexes. Plant communities and zonal complexes were generally well separated in the NMDS ordination. The Alaska and Canada communities were spatially separated in the ordination because of different glacial histories and location in separate floristic provinces, but there was no single controlling environmental gradient. Vegetation structure, particularly that of bryophytes and total biomass, strongly affected thermal properties of the soils. Patterned-ground complexes with the largest thermal differential between the patterned-ground features and the surrounding vegetation exhibited the clearest patterned-ground morphologies.

Coral communities exposed to differential large amplitude internal waves cooling and a severe heat stress in 2010 in the Andaman Sea

Tropical scleractinian corals are particularly vulnerable to global warming as elevated sea surface temperatures (SST) disrupt the delicate balance between the coral host and their algal endosymbionts, leading to symbiont expulsion, mass bleaching and mortality. While satellite sensing of SST has proven a good predictor of coral bleaching at the regional scale, there are large deviations in bleaching severity and mortality on the local scale, which are only poorly understood. Here, we show that internal waves play a major role in explaining local coral bleaching and mortality patterns in the Andaman Sea. In spite of a severe region-wide SST anomaly in May 2010, frequent upslope intrusions of cold sub-pycnocline waters due to breaking large amplitude internal waves (LAIW) alleviated heating and mitigated coral bleaching and mortality in shallow LAIW-exposed waters. In LAIW-sheltered waters, by contrast, bleaching susceptible species suffered severe bleaching and total mortality. These findings suggest that LAIW, which are ubiquitous in tropical stratified waters, benefit coral reefs during thermal stress and provide local refugia for bleaching susceptible corals. The swash zones of LAIW may thus be important, so far overlooked, conservation areas for the maintainance of coral diversity in a warming climate. The consideration of LAIW can significantly improve coral bleaching predictions and can provide a valuable tool for coral reef conservation and management.

Chlorination for degrading saxitoxins (paralytic shellfish poisons) in water

Chlorination was investigated as a treatment option for degrading and thus removing saxitoxins (paralytic shellfish poisons, PSPs) produced by cyanobacteria (blue-green algae) from water. It was found to be effective with the order of ease of degradation of the saxitoxins being GTX5 (B1) similar to dcSTX > STX > GTX3 similar to C2 > C1 > GTX2. However the effectiveness of chlorine was pH dependent. Degradation as a function of pH was not linear with the degree of degradation increasing rapidly at around pH 7.5. At pH 9 > 90% removal was possible provided a residual of 0.5 mg l(-1) free chlorine was present after 30 min contact time. The more effective degradation at higher pH was unexpected as chlorine is known to be a weaker oxidant under these conditions. The more effective degradation, then, must be due to the toxins, which are ionisable molecules, being present in a form at higher pH which is more susceptible to oxidation. The feasibility of using chlorine to remove saxitoxins during water treatment will therefore depend strongly on the pH of the water being chlorinated. Degradation may be improved by pH adjustment but may not be a practical solution. Although saxitoxins were degraded in that the parent compounds were not detected by chemical analysis, there is no indication as to the nature of the degradation products. However, acute toxicity as determined by the mouse bioassay was eliminated.

Disaggregation of Microcystis aeruginosa colonies under turbulent mixing: laboratory experiments in a grid-stirred tank

Samples of the cyanobacterium Microcystis aeruginosa from a small pond were used in laboratory experiments with a grid-stirred tank to quantify the effect of turbulent mixing on colony size. Turbulent dissipation in the tank was varied from 10(-9) m(2) s(-3) to 10(-4) m(2) s(-3), covering the range of turbulence intensities experienced by M. aeruginosa colonies in the field and exceeding the maximum dissipation by two orders of magnitude. Large colonies broke up into smaller colonies during the experiments; the mass fraction of colonies with diameter less than 200 mum increased over time. Colony disaggregation was observed to increase with turbulent dissipation. The maximum stable colony diameter across all experiments was in the range 220-420 mum. The overall change in size distribution during the experiments was relatively small, and the colony size distribution remained very broad throughout the experiments. Since colony size affects migration velocity, susceptibility to grazing and surface area to volume ratios, more work is needed to determine how to best represent this broad size distribution when modelling M. aeruginosa populations.