Identification and transcription of transfer RNA genes in dinoflagellate plastid minicircles

The dinoflagellate chloroplast genome is unique in that the genes are found on small circular DNA molecules carrying from one to three genes. In addition, only 14 of the typical chloroplast-located genes have so far been discovered on minicircles, while a number have been transferred to the nucleus. We have sequenced four new minicircles from the dinoflagellate Heterocapsa triquetra, three of which carry a single protein-coding gene (psbD, psbE, petD) and one that appears to be an "empty" circle. Using the tRNA prediction programs ARAGORN and tRNAscan-SE, tRNA-Met was found in the petD circle immediately downstream of the end of petD, while tRNA-Trp and tRNA-Pro were detected in the psbE and petD circles as well as in several chimeric circles of H. triquetra and the psbA minicircles of Heterocapsa pygmaea. RT-PCR showed that the tRNAs were co-transcribed with the protein-coding genes that preceded them, and cleaved from the precursor before a poly(U) tail was added to the mRNA.     

Molecular cloning and nucleotide sequence analysis of psbA from the dinoflagellates: Origin of the dinoflagellate plastid

Cloning and sequencing of psbA, the gene encoding D1 protein of photosystem II, from six species of dinoflagellates harboring a peridinin type plastid [Prorocentrum micans Ehrenberg, Amphidinium carterae Hulburt, Heterocapsa triquetra Stein, Lingulodinium polyedra (Dodge) Stein, Alexandrium tamarense (Lebour) Balech and Alexandrium catenella (Whedon et Kofoid) Balech] is reported. Using the polymerase chain reaction technique, the psbA gene was detected in a satellite DNA band isolated from total DNA of A. catenella by CsCl-Hoechst 33258 gradient ultracentrifugation. This finding suggests that in dinoflagellates psbA is encoded in the plastid genome. The deduced amino acid sequences of D1 from the dinoflagellates did not reveal a typical ‘C-terminus extension’, which should be removed by proteolytic cleavage from the D1 precursor. Molecular phylogenetic analysis based on the deduced amino acid sequences of D1 revealed that the six species of dinoflagellates are monophyletic and also showed that dinoflagellates cluster with rhodophytes, a cryptophyte and heterokonts. These results support the hypothesis that the peridinin type plastid in dinoflagellates originated from an engulfed red alga.     

Molecular evidence for plastid robbery (Kleptoplastidy) in Dinophysis,a dinoflagellate causing diarrhetic shellfish poisoning

The dinoflagellate genus Dinophysis contains species known to cause diarrhetic shellfish poisoning. Although most photosynthetic dinoflagellates have plastids with peridinin, photosynthetic Dinophysis species have cryptophyte-like plastids containing phycobilin rather than peridinin. We sequenced nuclear- and plastid-encoded SSU rDNA from three photosynthetic species of Dinophysis for phylogenetic analyses. In the tree of nuclear SSU rDNA, Dinophysis was a monophyletic group nested with peridinin-containing dinoflagellates. However, in the tree of plastid SSU rDNA, the Dinophysis plastid lineage was within the radiation of cryptophytes and was closely related to Geminigera cryophila. These analyses indicate that an ancestor of Dinophysis, which may have originally possessed peridinin-type plastid and lost it subsequently, adopted a new plastid from a cryptophyte. Unlike dinoflagellates with fully integrated plastids, the Dinophysis plastid SSU rDNA sequences were identical among the three species examined, while there were species-specific base substitutions in their nuclear SSU rDNA sequences. Queries of the DNA database showed that the plastid SSU rDNA sequence of Dinophysis is almost identical to that of an environmental DNA clone of a <10 pm sized plankter, possibly a cryptophyte and a likely source of the Dinophysis plastid. The present findings suggest that these Dinophysis species engulfed and temporarily retained plastids from a cryptophyte.     

Mono- and digalactosyldiacylglycerol composition of dinoflagellates. VI. Biochemical and genomic comparison of galactolipid biosynthesis between Chromera velia (Chromerida), a photosynthetic alveolate with red algal plastid ancestry,and the dinoflagellate,Lingulodinium polyedrum

Chromera velia is a recently discovered, photosynthetic, free-living alveolate that is the closest free-living relative to non-photosynthetic apicomplexan parasites. Most plastids, regardless of their origin, have membranes composed chiefly of two galactolipids, mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively). Because of the hypothesized shared red algal origin between the plastids of C. velia and dinoflagellates, our primary objectives were to examine how growth temperature affects MGDG and DGDG composition via positive-ion electrospray/mass spectrometry (ESI/MS) and positive ion/electrospray/mass spectrometry/mass spectrometry (ESI/MS/MS), and to examine galactolipid biosynthetic genes to determine if shared ancestry translates into shared MGDG and DGDG composition. When growing at 20°C, C. velia produces eicosapentaenoic acid-rich 20:5(n-3)/20:5(n-3) (sn-1/sn-2) MGDG and 20:5(n-3)/20:5(n-3) DGDG as its primary galactolipids, with relative percentage compositions of approximately 35 and 60%, respectively. At 30°C these are lessened by approximately 5 and 8%, respectively, by the corresponding production of 20:5/20:4 forms of these lipids. The presence of 20:5 at the sn-1 position is similar to what has been observed previously in a cluster of peridinin-containing dinoflagellates, but the presence of 20:5(n-3) at the sn-2 position is extremely rare. Thus, the forms of MGDG and DGDG in C. velia displayed similarities and differences to what has been observed in peridinin-containing dinoflagellates, such as Lingulodinium polyedrum, which produces 20:5/18:5 and 20:5/18:4 as the major forms of MGDG and DGDG. We develop conceptual models from the galactolipids observed and galactolipid-relevant gene annotations to explain the presence of polyunsaturated fatty acid-containing MGDG and DGDG in both L. polyedrum and C. velia.     

Evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles

Dinoflagellate protists harbor a characteristic peridinin-containing plastid that evolved from a red or haptophyte alga. In contrast to typical plastids that have ～100-200 kb circular genomes, the dinoflagellate plastid genome is composed of minicircles that each encode 0-5 genes. It is commonly assumed that dinoflagellate minicircles are derived from a standard plastid genome through drastic reduction and fragmentation. However, we demonstrate that the ycf16 and ycf24 genes (encoded on the Ceratium AF490364 minicircle), as well as rpl28 and rpl33 (encoded on the Pyrocystis AF490367 minicircle), are related to sequences from Algoriphagus and/or Cytophaga bacteria belonging to the Bacteroidetes clade. Moreover, we identified a new open reading frame on the Pyrocystis minicircle encoding a SRP54 N domain, which is typical of FtsY proteins. Because neither of these minicircles share sequence similarity with any other dinoflagellate minicircles, and their genes resemble bacterial operons, we propose that these Ceratium and Pyrocystis minicircles resulted from a horizontal gene transfer (HGT) from a Bacteroidetes donor. Our findings are the first indication of HGT to dinoflagellate minicircles, highlighting yet another peculiar aspect of this plastid genome.     

Selective feeding and foreign plastid retention in an Antarctic dinoflagellate

The peridinin‐containing plastid found in most photosynthetic dinoflagellates is thought to have been replaced in a few lineages by plastids of chlorophyte, diatom, or haptophyte origin. Other distinct lineages of phagotrophic dinoflagellates retain functional plastids obtained from algal prey for different durations and with varying source species specificity. 18S rRNA gene sequence analyses have placed a novel gymnodinoid dinoflagellate isolated from the Ross Sea (RSD) in the Kareniaceae, a family of dinoflagellates with permanent plastids of haptophyte origin. In contrast to other species in this family, the RSD contains kleptoplastids sequestered from its prey, Phaeocystis antarctica. Culture experiments were employed to determine whether the RSD fed selectively on P. antarctica when offered in combination with another polar haptophyte or cryptophyte species, and whether the RSD, isolated from its prey and starved, would take up plastids from P. antarctica or from other polar haptophyte or cryptophyte species. Evidence was obtained for selective feeding on P. antarctica, plastid uptake from P. antarctica, and increased RSD growth in the presence of P. antarctica. The presence of a peduncle‐like structure in the RSD suggests that kleptoplasts are obtained by myzocytosis. RSD cells incubated without P. antarctica were capable of survival for at least 29.5 months. This remarkable longevity of the RSD's kleptoplasts and its species specificity for prey and plastid source is consistent with its prolonged co‐evolution with P. antarctica. It may also reflect the presence of a plastid protein import mechanism and genes transferred to the dinokaryon from a lost permanent haptophyte plastid.     

Origin of the plastid in the anomalously pigmented dinoflagellate Gymnodinium mikimotoi (Gymnodiniales, Dinophyta) as inferred from phylogenetic analysis based on the gene encoding the large subunit of form I-type RuBisCO

The dinoflagellate Gymnodinium mikimotoi Miyake et Kominami ex Oda possesses an anomalously pigmented plastid which contains 19′‐hexanoyloxyfucoxanthin, 19′‐butanoyloxyfucoxanthin and fucoxanthin instead of peridinin as the major carotenoids. Previously, we have shown that the plastid of G. mikimotoi belongs to the rhodoplast lineage as inferred from phylogenetic analyses based on the amino acid sequences deduced from psbA and psaA and the nucleotide sequence of the plastid small subunit ribosomal RNA. Furthermore, in the present study, we cloned and sequenced an additional representative plastid gene, rbcL, encoding the large subunit of ribulose 1–5 bisphosphate carboxylase/oxygenase (RuBisCO LSU) from G. mikimotoi. The amino acid sequence deduced from the rbcL gene of G. mikimotoi apparently revealed the conventional form I RuBisCO LSU, which is present in most photosynthetic organisms, and not the divergent form II existing in typically pigmented dinofl age Nates with plastids containing peridinin as the main carotenoid. This finding supports the hypothesis that the origins of the plastids in G. mikimotoi and peridinin‐type dinoflagellates are not related to each other. Molecular phylogenetic analysis based on the amino acid sequence deduced from the rbcL gene further showed that the plastid of G. mikimotoi belongs to the rhodoplast lineage. In particular, G. mikimotoi clustered with haptophytes in the phylogenetic tree. From this result, two hypotheses with respect to the origin of the plastid in G. mikimotoi can be proposed: G. mikimotoi may have engulfed a haptophyte‐like cell (tertiary symbiosis) or englulfed a rhodophyte‐like cell that was closely related to the origin of the plastid in the haptophyte (secondary symbiosis).     

Identification and expression analysis of MinD gene involved in plastid division in cassava

Cassava is a tropical crop known for its starchy root and excellent properties. Considering that starch biosynthesis in the amyloplast is affected by its division, it appears conceivable that the regulation of plastid division plays an important role in starch accumulation. As a member of the Min system genes, MinD participated in the spatial regulation of the position of the plastid division site.In our studies, sequence analysis and phylogenetic analysis showed that MeMinD has been highly conserved during the evolutionary process. Subcellular localisation indicated that MeMinD carries a chloroplast transit peptide and was localised in the chloroplast. Overexpression of MeMinD resulted in division site misplacement and filamentous formation in E. coli, indicating that MeMinD protein was functional across species. MeMinD exhibited different spatial and temporal expression patterns which was highly expressed in the source compared to that in the sink organ.     

Prorocentrum属涡鞭毛虫核仁的观察

迄今未能在光学显微镜下观察到Prerocentrum属的涡鞭毛虫有核仁。本文作者用伊红的酒精溶液和用甲基缘—派若宁法染色,也未能在Prerocentrum micans和Proro-centrum cassubica的细胞核中显示出核仁来。但是在用专门为显示单细胞生物的核仁组织者区（NOR）而改进了的Ag—1法进行染色时,这两种涡鞭毛虫的核仁都会被染作鲜明的深褐色或深黑色,而身体的所有其他部份,包括染色体,全都不着色。染色适当时可以看出,实际上只是核仁的中央部分被染上色。在电镜下可见,此时所有的银粒全部是集中在核仁的纤维区中。染色的结果表明,Prorocentrum cassbica只有一个扁园形的小核仁,后者是贴附在核膜上,其NOR通常是作O形或C形。与P.cassubica不同,P.micans的核仁的数量变化很大,可以有一个至七个;其核仁的大小与形状同样也变化很大;其NOR的形状也复杂多变。发现P.micans的核仁数量与个体的生活状况有一定的关联:向老的培养液中加入等量的新的培养液一天以后,具有三个核仁的个体是最多的（占三分之一）,具有4—6个核仁的个体占28.5％,只有一个核仁的个体只占8.6％;加入新培养液三天后,具两个核仁的个体变成是最多的（占38.8％）,具4—6个核仁的个体降为占18.4％;加入新培养液一个月以后,只有一个核仁的个体是最多的（占3     

Plastid-derived single gene minicircles of the dinoflagellate Ceratium horridum are localized in the nucleus

Recent reports show that numerous chloroplast-specific proteins of peridinin-containing dinoflagellates are encoded on minicircles-small plasmidlike molecules containing one or two polypeptide genes each. The genes for these polypeptides are chloroplast specific because their homologs from other photosynthetic eukaryotes are exclusively encoded in the chloroplast genome. Here, we report the isolation, sequencing, and subcellular localization of minicircles from the peridinin-containing dinoflagellate Ceratium horridum. The C. horridum minicircles are organized in the same manner as in other peridinin-containing dinoflagellates and encode the same kinds of plastid-specific proteins, as previous studies reported. However, intact plastids isolated from C. horridum do not contain minicircles, nor do they contain DNA that hybridizes to minicircle-specific probes. Rather, C. horridum minicircles are localized in the nucleus as shown by cell fractionation, Southern hybridization, and in situ hybridization with minicircle-specific probes. A high-molecular-weight DNA was detected in purified C. horridum plastids, but it is apparently not minicircular in organization, as hybridization with a cloned probe from the plastid-localized DNA suggests. The distinction between C. horridum and other peridinin-containing dinoflagellates at the level of their minicircle localization is paralleled by C. horridum thylakoid organization, which also differs from that of other peridinin-containing dinoflagellates, indicating that a hitherto underestimated diversity of minicircle DNA localization and thylakoid organization exists across various dinoflagellate groups.     

Composition of galactolipids,betaine lipids and triglyceride-associated fatty acids of the symbiotic dinoflagellate Zooxanthella (Brandtodinium) nutricula: A glimpse into polyunsaturated fatty acids available to its polycystine radiolarian host

Zooxanthella nutricula is a photosynthetic dinoflagellate symbiont of polycystine radiolarians. As such, it is hypothesized to provide fixed organic carbon, including in the form of acylglycerolipids and sterols, to its non-photosynthetic host. We have previously characterized the sterols of Z. nutricula that may be transferred to its host and, in the present study, have turned our attention to three classes of fatty acid-containing lipids, chloroplast-associated galactolipids, betaine lipids, which are non-phosphorylated phospholipid analogs present in many eukaryotes, and triglycerides. Zooxanthella nutricula was observed using positive-ion electrospray/mass spectrometry (ESI/MS) and ESI/MS/MS to produce the galactolipids mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively) enriched in octadecapentaenoic (18:5(n-3)) and octadecatetraenoic (18:4(n-3)) acid to place it within a group of peridinin-containing dinoflagellates in a C₁₈/C₁₈ (sn-1/sn-2 fatty acid regiochemistry) cluster, as opposed to another cluster with C₂₀/C₁₈ MGDG and DGDG, where the C₂₀ fatty acid is eicosapentaenoic acid (20:5(n-3)) and the C₁₈ fatty acid is either 18:5(n-3) or 18:4(n-3). Zooxanthella nutricula was also observed to produce 38:10 (total number of fatty acid carbons:total number of double bonds), 38:6, and 44:7 diacylglycerylcarboxyhydroxymethylcholine (DGCC) as the sole type of betaine lipid. Although it is more difficult to determine which fatty acids are present in the sn-1 and sn-2 positions on the glycerol backbone of DGCC using ESI/MS/MS, gas chromatography/mass spectrometry (GC/MS)-based examination indicated the putatively DGCC-associated polyunsaturated fatty acid (PUFA) docosahexaenoic acid (22:6(n-3)). Coupled with the C₁₈ PUFAs of MGDG and DGDG, and fatty acids associated with triglycerides (also examined via GC/MS), Z. nutricula could serve as a rich source of PUFAs for its radiolarian host. These data demonstrate that Z. nutricula produces a similar set of PUFA-containing lipids as Symbiodinium microadriaticum, a photosynthetic dinoflagellate symbiont of cnidarians, indicating a metabolic commonality in these phylogenetically discrete dinoflagellate symbionts with unrelated host organisms.     

Bubble stimulation efficiency of dinoflagellate bioluminescence

Dinoflagellate bioluminescence , a common source of bioluminescence in coastal waters , is stimulated by flow agitation . Although bubbles are anecdotally known to be stimulatory , the process has never been experimentally investigated . This study quantified the flash response of the bioluminescent dinoflagellate Lingulodinium polyedrum to stimulation by bubbles rising through still seawater . Cells were stimulated by isolated bubbles of 0 . 3–3 mm radii rising at their terminal velocity , and also by bubble clouds containing bubbles of 0 . 06–10 mm radii for different air flow rates . Stimulation efficiency , the proportion of cells producing a flash within the volume of water swept out by a rising bubble , decreased with decreasing bubble radius for radii less than approximately 1 mm . Bubbles smaller than a critical radius in the range 0 . 275–0 . 325 mm did not stimulate a flash response . The fraction of cells stimulated by bubble clouds was proportional to the volume of air in the bubble cloud , with lower stimulation levels observed for clouds with smaller bubbles . An empirical model for bubble cloud stimulation based on the isolated bubble observations successfully reproduced the observed stimulation by bubble clouds for low air flow rates . High air flow rates stimulated more light emission than expected , presumably because of additional fluid shear stress associated with collective buoyancy effects generated by the high air fraction bubble cloud . These results are relevant to bioluminescence stimulation by bubbles in two‐phase flows , such as in ship wakes , breaking waves , and sparged bioreactors . Copyright © 2015 John Wiley & Sons, Ltd.