Kirk E. Apt’s research while affiliated with DSM Nutritional Products and other places

Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced dinoflagellate genomic tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR-based contigs. The sequence contains an intron-rich set of five highly-expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice-site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3' splice site are repeated by an identical two to nine base pairs around the 5' splice site. The 5' and 3' splice sites are in the same locations within each repeat so that the repeat is found only once in the mature mRNA. This identically repeated intron boundary (IRIB) sequence might be useful in gene modeling and annotation of genomes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Figure S1. Alignments and mean pairwise identity graphs for the intergenic spacers between alcohol dehydrogenase (ADH) members and the nine introns of the five members of ADH. Length and pairwise identity is displayed to the right of each alignment. Gene sequences are indicated by black bars, and indels are indicated by intervening black lines. Each column of the alignment has a bar graph above it indicating the mean pairwise identity of all pairs in the alignment. The height and color of each bar in the graph is proportional to the mean pairwise identity of all pairs in that column ‐ green at 100%, yellow between 30 and less than 100%, and red when less than 30%.

Schizochytrium produces long chain polyunsaturated fatty acids (PUFAs) via a PUFA synthase. Targeted mutagenesis of one gene of this synthase was conducted to confirm PUFA synthase function and determine its metabolic necessity. The resulting mutants were auxotrophic and required supplementation with PUFAs. In vivo labeling experiments with radioactive fatty acids demonstrated the presence of several elongase and desaturase activities associated with the standard pathway of PUFA synthesis. However, this system was missing a critical Delta12 desaturase activity and was therefore not capable of synthesizing PUFAs from the 16- or 18-carbon saturated fatty acid products of the fatty acid synthase. Because Schizochytrium uses a PUFA synthase system for the production of PUFAs, the existence of a partial desaturase-elongase system (if not a simple vestige) is suggested to be either a scavenging mechanism for intermediate fatty acids prematurely released by the PUFA synthase or for PUFAs found in the organism's native environment.

Filaments of Streblonema sp. isolated from hyperplasia (galls) on Nereocystis luetkeana (Mert.) Post. et Rupr. induced similar gall growths when inoculated on young sporophytes of Nereocystis luetkeana, Macrocystis integrifolia Bory, and Laminaria japonica Aresch. Filaments were irregularly branched and uniseriate with cells 5–8 μm in diameter and 10–30 μm long. Growth under varied cultured conditions produced unilocular sporangia. Zoospores released from the sporangia germinated into identical filaments which also formed unilocular sporangia. Gall tissue originated from the innermost cells of the epidermal meristematic zone. When infected these cells divided in an irregular and unorganized manner. The resulting structure was a pronounced departure from normal morphology.

Diatoms are unicellular brown algae that likely arose from the endocytobiosis of a red alga into a single-celled heterotroph and that constitute an algal class of major importance in phytoplankton communities around the globe. The first whole-genome sequence from a diatom species, Thalassiosira pseudonana Hasle et Heimdal, was recently reported, and features that are central to diatom physiology and ecology, such as silicon and nitrogen metabolism, iron uptake, and carbon concentration mechanisms, were described. Following this initial study, the basic cellular systems controlling cell signaling, gene expression, cytoskeletal structures, and response to stress have been cataloged in an attempt to obtain a global view of the molecular foundations that sustain such an ecologically successful group of organisms. Comparative analysis with several microbial, plant, and metazoan complete genome sequences allowed the identification of putative membrane receptors, signaling proteins, and other components of central interest to diatom ecophysiology and evolution. Thalassiosira pseudonana likely perceives light through a novel phytochrome and several cryptochrome photoreceptors; it may lack the conserved RHO small-GTPase subfamily of cell-polarity regulators, despite undergoing polarized cell-wall synthesis; and it possesses an unusually large number of heat-shock transcription factors, which may indicate the central importance of transcriptional responses to environmental stress. The availability of the complete gene repertoire will permit a detailed biochemical and genetic analysis of how diatoms prosper in aquatic environments and will contribute to the understanding of eukaryotic evolution.

Dinoflagellates are a diverse group of protists, comprising photosynthetic and heterotrophic free-living species, as well as parasitic ones. About half of them are photosynthetic with peridinin-containing plastids being the most common. It is uncertain whether non-photosynthetic dinoflagellates are primitively so, or have lost photosynthesis. Studies of heterotrophic species from this lineage may increase our understanding of plastid evolution. We analyzed an EST project of the early-diverging heterotrophic dinoflagellate Crypthecodinium cohnii looking for evidence of past endosymbiosis. A large number of putative genes of cyanobacterial or algal origin were identified using BLAST, and later screened by metabolic function. Phylogenetic analyses suggest that several proteins could have been acquired from a photosynthetic endosymbiont, arguing for an earlier plastid acquisition in dinoflagellates. In addition, intact N-terminal plastid-targeting peptides were detected, indicating that C. cohnii may contain a reduced plastid and that some of these proteins are imported into this organelle. A number of metabolic pathways, such as heme and isoprenoid biosynthesis, seem to take place in the plastid. Overall, these data indicate that C. cohnii is derived from a photosynthetic ancestor and provide a model for loss of photosynthesis in dinoflagellates and their relatives. This represents the first extensive genomic analysis of a heterotrophic dinoflagellate.

No abstract prepared.

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ∼20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

ABSTRACTA strain of Gracilaria epihippisora Hoyle produces gall-like cell proliferations in culture. These growths can be excised and grown separately, where they retain an undifferentiated morphology and reach 5mm in diameter. The gall tissue consists of a single morphological cell type without any differentiation between surface and internal cells as is characteristic of normal thallus tissue. Gall cells are typically 20–40 μm in diameter and contain the usual complement of organelles and a prominent vacuole, although there are several distinct features. The large multilobed plastids have an extensive proliferation of thylakoid membranes, which form an arrangement of loops and spirals. The thallus outer cell wall layer is highly reduced. The gall growths contain intracellular virus-like particles (ca. 80 nm in diameter) that occur in discrete groups.