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1.
Genome Biol Evol ; 11(6): 1618-1629, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-31124562

RESUMO

Nucleomorphs are small nuclei that evolved from the nucleus of former eukaryotic endosymbionts of cryptophytes and chlorarachniophytes. These enigmatic organelles reside in their complex plastids and harbor the smallest and most compacted eukaryotic genomes investigated so far. Although the coding capacity of the nucleomorph genomes is small, a significant percentage of the encoded proteins (predicted nucleomorph-encoded proteins, pNMPs) is still not functionally annotated. We have analyzed pNMPs with unknown functions via Phyre2, a bioinformatic tool for prediction and modeling of protein structure, resulting in a functional annotation of 215 pNMPs out of 826 uncharacterized open reading frames of cryptophytes. The newly annotated proteins are predicted to participate in nucleomorph-specific functions such as chromosome organization and expression, as well as in modification and degradation of nucleomorph-encoded proteins. Additionally, we have functionally assigned nucleomorph-encoded, putatively plastid-targeted proteins among the reinvestigated pNMPs. Hints for a putative function in the periplastid compartment, the cytoplasm surrounding the nucleomorphs, emerge from the identification of pNMPs that might be homologs of endomembrane system-related proteins. These proteins are discussed in respect to their putative functions.


Assuntos
Criptófitas/citologia , Criptófitas/genética , Cromatina , Cromossomos , Fases de Leitura Aberta , Proteoma/genética
2.
Genome Biol Evol ; 11(4): 1117-1134, 2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30949682

RESUMO

The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived "nucleomorph" genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2'-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18-21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.


Assuntos
Criptófitas/genética , RNA Ribossômico/metabolismo , RNA Nucleolar Pequeno , Sequência de Bases , Criptófitas/metabolismo , Evolução Molecular , Humanos , Metilação , Homologia de Sequência do Ácido Nucleico , Spliceossomos
3.
Genome Biol Evol ; 11(4): 1045-1053, 2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30859201

RESUMO

Chlorarachniophyte and cryptophyte algae are unique among plastid-containing species in that they have a nucleomorph genome: a compact, highly reduced nuclear genome from a photosynthetic eukaryotic endosymbiont. Despite their independent origins, the nucleomorph genomes of these two lineages have similar genomic architectures, but little is known about the evolutionary pressures impacting nucleomorph DNA, particularly how their rates of evolution compare to those of the neighboring genetic compartments (the mitochondrion, plastid, and nucleus). Here, we use synonymous substitution rates to estimate relative mutation rates in the four genomes of nucleomorph-bearing algae. We show that the relative mutation rates of the host versus endosymbiont nuclear genomes are similar in both chlorarachniophytes and cryptophytes, despite the fact that nucleomorph gene sequences are notoriously highly divergent. There is some evidence, however, for slightly elevated mutation rates in the nucleomorph DNA of chlorarachniophytes-a feature not observed in that of cryptophytes. For both lineages, relative mutation rates in the plastid appear to be lower than those in the nucleus and nucleomorph (and, in one case, the mitochondrion), which is consistent with studies of other plastid-bearing protists. Given the divergent nature of nucleomorph genes, our finding of relatively low evolutionary rates in these genomes suggests that for both lineages a burst of evolutionary change and/or decreased selection pressures likely occurred early in the integration of the secondary endosymbiont.


Assuntos
Criptófitas/genética , Genoma Mitocondrial , Genomas de Plastídeos , Taxa de Mutação , Evolução Biológica , Simbiose
4.
Genome Biol Evol ; 11(3): 678-687, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30715330

RESUMO

The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved among eukaryotes. Potential exceptions to this are nucleomorphs: Highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here, we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologs. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.


Assuntos
Cercozoários/genética , Criptófitas/genética , Complexo de Proteínas Formadoras de Poros Nucleares/genética , Poro Nuclear , Simbiose
5.
BMC Genomics ; 20(1): 38, 2019 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-30642248

RESUMO

BACKGROUND: The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms. RESULTS: Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life - almost exclusively in phototrophs. CONCLUSION: Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis.


Assuntos
Cercozoários/genética , Criptófitas/genética , Fusão Gênica , Proteínas Mutantes Quiméricas/genética , Ubiquitinas/classificação , Ubiquitinas/genética , Evolução Molecular , Filogenia , Simbiose
6.
Sci Rep ; 8(1): 17189, 2018 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-30464297

RESUMO

Mesodinium spp. are commonly found in marine and brackish waters, and several species are known to contain red, green, or both plastids that originate from cryptophyte prey. We observed the seasonal succession of Mesodinium spp. in a Japanese brackish lake, and we analysed the origin and diversity of the various coloured plastids within the cells of Mesodinium spp. using a newly developed primer set that specifically targets the cryptophyte nuclear 18S rRNA gene. Mesodinium rubrum isolated from the lake contained only red plastids originating from cryptophyte Teleaulax amphioxeia. We identified novel Mesodinium sp. that contained only green plastids or both red and green plastids originating from cryptophytes Hemiselmis sp. and Teleaulax acuta. Although the morphology of the newly identified Mesodinium sp. was indistinguishable from that of M. rubrum under normal light microscopy, phylogenetic analysis placed this species between the M. rubrum/major species complex and a well-supported lineage of M. chamaeleon and M. coatsi. Close associations were observed in cryptophyte species composition within cells of Mesodinium spp. and in ambient water samples. The appearance of suitable cryptophyte prey is probably a trigger for succession of Mesodinium spp., and the subsequent abundance of Mesodinium spp. appears to be influenced by water temperature and dissolved inorganic nutrients.


Assuntos
Cilióforos/crescimento & desenvolvimento , Cilióforos/parasitologia , Criptófitas/classificação , Criptófitas/crescimento & desenvolvimento , Cilióforos/classificação , Cilióforos/genética , Análise por Conglomerados , Criptófitas/genética , DNA de Algas/química , DNA de Algas/genética , DNA de Protozoário/química , DNA de Protozoário/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Japão , Lagos/parasitologia , Filogenia , RNA Ribossômico 18S/genética , Estações do Ano , Análise de Sequência de DNA
7.
BMC Biol ; 16(1): 137, 2018 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-30482201

RESUMO

BACKGROUND: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea-the first for any goniomonad-to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. RESULTS: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is ~ 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. theta appear to operate in the cytoplasm of Go. avonlea, suggesting that metabolic redundancies were generated during the course of secondary plastid integration. Other cytosolic pathways found in Go. avonlea are not found in Gu. theta, suggesting secondary loss in Gu. theta and other plastid-bearing cryptomonads. Phylogenetic analyses revealed no evidence for algal endosymbiont-derived genes in the Go. avonlea genome. Phylogenomic analyses point to a specific relationship between Cryptista (to which cryptomonads belong) and Archaeplastida. CONCLUSION: We found no convincing genomic or phylogenomic evidence that Go. avonlea evolved from a secondary red algal plastid-bearing ancestor, consistent with goniomonads being ancestrally non-photosynthetic eukaryotes. The Go. avonlea genome sheds light on the physiology of heterotrophic cryptomonads and serves as an important reference point for studying the metabolic "rewiring" that took place during secondary plastid integration in the ancestor of modern-day Cryptophyceae.


Assuntos
Criptófitas/genética , Evolução Molecular , Genoma , Plastídeos/genética , Proteínas de Algas/análise , Núcleo Celular/genética , Criptófitas/citologia , Filogenia , Triptofano-tRNA Ligase/análise
8.
Nat Commun ; 9(1): 4125, 2018 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-30297821

RESUMO

Optogenetic silencing allows time-resolved functional interrogation of defined neuronal populations. However, the limitations of inhibitory optogenetic tools impose stringent constraints on experimental paradigms. The high light power requirement of light-driven ion pumps and their effects on intracellular ion homeostasis pose unique challenges, particularly in experiments that demand inhibition of a widespread neuronal population in vivo. Guillardia theta anion-conducting channelrhodopsins (GtACRs) are promising in this regard, due to their high single-channel conductance and favorable photon-ion stoichiometry. However, GtACRs show poor membrane targeting in mammalian cells, and the activity of such channels can cause transient excitation in the axon due to an excitatory chloride reversal potential in this compartment. Here, we address these problems by enhancing membrane targeting and subcellular compartmentalization of GtACRs. The resulting soma-targeted GtACRs show improved photocurrents, reduced axonal excitation and high light sensitivity, allowing highly efficient inhibition of neuronal activity in the mammalian brain.


Assuntos
Potenciais de Ação/efeitos da radiação , Channelrhodopsins/metabolismo , Criptófitas/metabolismo , Luz , Optogenética/métodos , Animais , Animais Recém-Nascidos , Ânions/metabolismo , Encéfalo/metabolismo , Encéfalo/fisiologia , Células Cultivadas , Channelrhodopsins/genética , Criptófitas/genética , Feminino , Células HEK293 , Humanos , Masculino , Camundongos Endogâmicos C57BL , Neurônios/citologia , Neurônios/metabolismo , Neurônios/fisiologia , Ratos Sprague-Dawley
9.
Genome Biol Evol ; 10(10): 2834-2852, 2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30247558

RESUMO

Peroxisomes are single-membrane-bound organelles with a huge metabolic versatility, including the degradation of fatty acids (ß-oxidation) and the detoxification of reactive oxygen species as most conserved functions. Although peroxisomes seem to be present in the majority of investigated eukaryotes, where they are responsible for many eclectic and important spatially separated metabolic reactions, knowledge about their existence in the plethora of protists (eukaryotic microorganisms) is scarce. Here, we investigated genomic data of organisms containing complex plastids with red algal ancestry (so-called "chromalveolates") for the presence of genes encoding peroxins-factors specific for the biogenesis, maintenance, and division of peroxisomes in eukaryotic cells. Our focus was on the cryptophyte Guillardia theta, a marine microalga, which possesses two phylogenetically different nuclei of host and endosymbiont origin, respectively, thus being of enormous evolutionary significance. Besides the identification of a complete set of peroxins in G. theta, we heterologously localized selected factors as GFP fusion proteins via confocal and electron microscopy in the model diatom Phaeodactylum tricornutum. Furthermore, we show that peroxins, and thus most likely peroxisomes, are present in haptophytes as well as eustigmatophytes, brown algae, and alveolates including dinoflagellates, chromerids, and noncoccidian apicomplexans. Our results indicate that diatoms are not the only "chromalveolate" group devoid of the PTS2 receptor Pex7, and thus a PTS2-dependent peroxisomal import pathway, which seems to be absent in haptophytes (Emiliania huxleyi) as well. Moreover, important aspects of peroxisomal biosynthesis and protein import in "chromalveolates"are highlighted.


Assuntos
Criptófitas/metabolismo , Biogênese de Organelas , Peroxinas/metabolismo , Peroxissomos/metabolismo , Sequência de Aminoácidos , Sequência Conservada , Criptófitas/genética , Peroxinas/genética , Filogenia , Domínios Proteicos
10.
Protist ; 169(5): 662-681, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30125802

RESUMO

For years the genus Chroomonas was defined as being a cryptophyte with rectangular periplast plates, with a gullet and with biliprotein types PC 630 or 645. In phylogenetic trees the genus proved to be paraphyletic. Moreover, cells with hexagonal periplast plates were found in an SEM preparation from material of the type species C. nordstedtii. In this study, material of Hansgirg's C. nordstedtii was subjected to PCR and to sequencing of two short DNA tags. These tags allowed for an unambiguous identification of the real C. nordstedtii in the phylogeny of the blue-green cryptophytes. The genus Chroomonas corresponds to subclade 1, whereas subclades 3 and 4 do not belong to Chroomonas, if Hemiselmis is maintained. Additional examination by light and scanning electron microscopy and by spectrophotometry demonstrate that subclade 1 comprises only cells with hexagonal periplast plates and PC 630, whereas rectangular periplast plates are found only in subclades 3 and 4. Consequently the genus Chroomonas and its type species, C. nordstedtii, are revised and two novel species, C. debatzensis and C. gentoftensis sp. nov., are described.


Assuntos
Criptófitas/classificação , Criptófitas/genética , Criptófitas/crescimento & desenvolvimento , Criptófitas/ultraestrutura , DNA Ribossômico/genética , Microscopia Eletrônica de Varredura , Filogenia , Análise de Sequência de DNA
11.
Genome Biol Evol ; 10(8): 2061-2071, 2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30085124

RESUMO

Plastids surrounded by four membranes harbor a special compartment between the outer and inner plastid membrane pair, the so-called periplastidal compartment (PPC). This cellular structure is usually presumed to be the reduced cytoplasm of a eukaryotic phototrophic endosymbiont, which was integrated into a host cell and streamlined into a plastid with a complex membrane structure. Up to date, no mitochondrion or mitochondrion-related organelle has been identified in the PPC of any representative. However, two prominent groups, the cryptophytes and the chlorarachniophytes, still harbor a reduced cell nucleus of symbiont origin, the nucleomorph, in their PPCs. Generally, many cytoplasmic and nucleus-located eukaryotic proteins need an iron-sulfur cofactor for their functionality. Beside some exceptions, their synthesis is depending on a so-called iron-sulfur complex (ISC) assembly machinery located in the mitochondrion. This machinery provides the cytoplasm with a still unknown sulfur component, which is then converted into iron-sulfur clusters via a cytosolic iron-sulfur protein assembly (CIA) machinery. Here, we investigated if a CIA machinery is present in mitochondrion-lacking PPCs. By using bioinformatic screens and in vivo-localizations of candidate proteins, we show that the presence of a PPC-specific CIA machinery correlates with the presence of a nucleomorph. Phylogenetic analyses of PPC- and host specific CIA components additionally indicate a complex evolution of the CIA machineries in organisms having plastids surrounded by four membranes.


Assuntos
Criptófitas/metabolismo , Proteínas com Ferro-Enxofre/biossíntese , Plastídeos/metabolismo , Compartimento Celular , Criptófitas/genética , Citosol/metabolismo , Diatomáceas/genética , Genoma , Modelos Biológicos , Filogenia
12.
Genome Biol Evol ; 10(6): 1573-1583, 2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29860351

RESUMO

Eukaryotic genes are interrupted by introns that are removed in a conserved process known as pre-mRNA splicing. Though well-studied in select model organisms, we are only beginning to understand the variation and diversity of this process across the tree of eukaryotes. We explored pre-mRNA splicing and other features of transcription in nucleomorphs, the highly reduced remnant nuclei of secondary endosymbionts. Strand-specific transcriptomes were sequenced from the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, whose plastids are derived from red and green algae, respectively. Both organisms exhibited elevated nucleomorph antisense transcription and gene expression relative to their respective nuclei, suggesting unique properties of gene regulation and transcriptional control in nucleomorphs. Marked differences in splicing were observed between the two nucleomorphs: the few introns of the G. theta nucleomorph were largely retained in mature transcripts, whereas the many short introns of the B. natans nucleomorph are spliced at typical eukaryotic levels (>90%). These differences in splicing levels could be reflecting the ancestries of the respective plastids, the different intron densities due to independent genome reduction events, or a combination of both. In addition to extending our understanding of the diversity of pre-mRNA splicing across eukaryotes, our study also indicates potential links between splicing, antisense transcription, and gene regulation in reduced genomes.


Assuntos
Núcleo Celular/genética , Variação Genética/genética , Genoma/genética , Precursores de RNA/genética , Processamento de RNA/genética , Cercozoários/genética , Clorófitas/genética , Criptófitas/genética , Eucariotos/genética , Evolução Molecular , Redes Reguladoras de Genes/genética , Íntrons/genética , Plastídeos/genética , RNA Antissenso/genética , Transcrição Genética/genética , Transcriptoma/genética
13.
BMC Genomics ; 19(1): 275, 2018 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-29678149

RESUMO

BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax. The mitochondrial genomes were similar in terms of their general architecture, gene content and presence of a large repeat region. However, gene order was poorly conserved. Characteristic features of cryptophyte mtDNAs included large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. The cryptophyte mitochondrial genomes retain almost all genes found in many other eukaryotes including the nad, sdh, cox, cob, and atp genes, with the exception of sdh2 and atp3. In addition, gene cluster analysis showed that cryptophytes possess a gene order closely resembling the jakobid flagellates Jakoba and Reclinomonas. Interestingly, the cox1 gene of R. salina, T. amphioxeia, and Storeatula species was found to contain group II introns encoding a reverse transcriptase protein, as did the cob gene of Storeatula species CCMP1868. CONCLUSIONS: These newly sequenced genomes increase the breadth of data available from algae and will aid in the identification of general trends in mitochondrial genome evolution. While most of the genomes were highly conserved, extensive gene arrangements have shuffled gene order, perhaps due to genome rearrangements associated with hairpin-containing mobile genetic elements, tRNAs with palindromic sequences, and tandem repeat sequences. The cox1 and cob gene sequences suggest that introns have recently been acquired during cryptophyte evolution. Comparison of phylogenetic trees based on plastid and mitochondrial genome data sets underscore the different evolutionary histories of the host and endosymbiont components of present-day cryptophytes.


Assuntos
Criptófitas/genética , Genoma Mitocondrial/genética , Genômica , Sequências Repetitivas Dispersas/genética , Rearranjo Gênico , Filogenia
14.
FEMS Microbiol Ecol ; 94(4)2018 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-29360960

RESUMO

Photosynthetic picoeukaryotes (PPEs) play an important role in aquatic ecosystem functioning. There is still a relative lack of information on freshwater PPEs, especially in eutrophic lakes. We used a combination of flow cytometric sorting and pyrosequencing to investigate the PPEs community structure in more than 20 mesotrophic and eutrophic lakes along the middle-lower reaches of the Yangtze River in China. The abundance of PPEs ranged between 2.04 × 103 and 5.92 × 103 cells mL-1. The contribution of PPEs to total picophytoplankton abundance was generally higher in eutrophic lakes than in mesotrophic lakes. The sequencing results indicated that the Shannon diversity of PPEs was significantly higher in mesotrophic lakes than in eutrophic lakes. At the class level, PPEs were mainly dominated by three taxonomic groups, including Cryptophyceae, Coscinodiscophyceae and Chlorophyceae, and 15 additional known phytoplankton classes, including Synurophyceae, Dinophyceae, Chrysophyceae, Trebouxiophyceae and Prymnesiophyceae, were identified. Coscinodiscophyceae dominated in the most eutrophic lakes, while Chrysophyceae, Dinophyceae and other classes of PPEs were more abundant in the mesotrophic lakes. We also observed several PPEs operational taxonomic units, and those affiliated with Cyclotella atomus, Chlamydomonas sp. and Poterioochromonas malhamensis tended to be more prevalent in the eutrophic lakes. The canonical correspondence analysis and Mantel analysis highlighted the importance of environmental parameters as key drivers of PPEs community composition.


Assuntos
Chrysophyta/isolamento & purificação , Criptófitas/isolamento & purificação , Diatomáceas/isolamento & purificação , Dinoflagelados/isolamento & purificação , Haptófitas/isolamento & purificação , Lagos/parasitologia , Fitoplâncton/isolamento & purificação , Rios/parasitologia , Estramenópilas/isolamento & purificação , China , Clorófitas/classificação , Clorófitas/genética , Chrysophyta/classificação , Chrysophyta/genética , Criptófitas/classificação , Criptófitas/genética , Diatomáceas/classificação , Diatomáceas/genética , Dinoflagelados/classificação , Dinoflagelados/genética , Ecossistema , Citometria de Fluxo , Haptófitas/classificação , Haptófitas/genética , Fotossíntese , Fitoplâncton/classificação , Fitoplâncton/genética , Estramenópilas/classificação , Estramenópilas/genética
15.
FEMS Microbiol Ecol ; 94(2)2018 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-29206918

RESUMO

Little is known about how various substances from living and decomposing aquatic macrophytes affect the horizontal patterns of planktonic bacterial communities. Study sites were located within Lake Kolon, which is a freshwater marsh and can be characterised by open-water sites and small ponds with different macrovegetation (Phragmites australis, Nymphea alba and Utricularia vulgaris). Our aim was to reveal the impact of these macrophytes on the composition of the planktonic microbial communities using comparative analysis of environmental parameters, microscopy and pyrosequencing data. Bacterial 16S rRNA gene sequences were dominated by members of phyla Proteobacteria (36%-72%), Bacteroidetes (12%-33%) and Actinobacteria (5%-26%), but in the anoxic sample the ratio of Chlorobi (54%) was also remarkable. In the phytoplankton community, Cryptomonas sp., Dinobryon divergens, Euglena acus and chrysoflagellates had the highest proportion. Despite the similarities in most of the measured environmental parameters, the inner ponds had different bacterial and algal communities, suggesting that the presence and quality of macrophytes directly and indirectly controlled the composition of microbial plankton.


Assuntos
Lagos/microbiologia , Lagos/parasitologia , Fitoplâncton/microbiologia , Fitoplâncton/parasitologia , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Chlorobi/classificação , Chlorobi/genética , Chlorobi/isolamento & purificação , Criptófitas/classificação , Criptófitas/genética , Criptófitas/isolamento & purificação , Euglena/classificação , Euglena/genética , Euglena/isolamento & purificação , Água Doce/microbiologia , Água Doce/parasitologia , Magnoliopsida/crescimento & desenvolvimento , Microbiota , Nymphaea/crescimento & desenvolvimento , Filogenia , Fitoplâncton/classificação , Poaceae/crescimento & desenvolvimento , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
16.
Environ Microbiol ; 20(2): 890-902, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29266690

RESUMO

Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice.


Assuntos
Criptófitas/genética , Dinoflagelados/genética , Haptófitas/genética , Rodopsina/genética , Estramenópilas/genética , Regiões Árticas , Criptófitas/metabolismo , Dinoflagelados/metabolismo , Estuários , Haptófitas/metabolismo , Transporte de Íons/genética , Oceanos e Mares , Fotossíntese/genética , Filogenia , Bombas de Próton/genética , Bombas de Próton/metabolismo , RNA Ribossômico 18S/genética , Rodopsina/biossíntese , Estramenópilas/metabolismo , Svalbard , Transcriptoma/genética
17.
BMC Biol ; 15(1): 103, 2017 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-29100505

RESUMO

BACKGROUND: Optical silencing of activity provides a way to test the necessity of neurons in behaviour. Two light-gated anion channels, GtACR1 and GtACR2, have recently been shown to potently inhibit activity in cultured mammalian neurons and in Drosophila. Here, we test the usefulness of these channels in larval zebrafish, using spontaneous coiling behaviour as the assay. RESULTS: When the GtACRs were expressed in spinal neurons of embryonic zebrafish and actuated with blue or green light, spontaneous movement was inhibited. In GtACR1-expressing fish, only 3 µW/mm2 of light was sufficient to have an effect; GtACR2, which is poorly trafficked, required slightly stronger illumination. No inhibition was seen in non-expressing siblings. After light offset, the movement of GtACR-expressing fish increased, which suggested that termination of light-induced neural inhibition may lead to activation. Consistent with this, two-photon imaging of spinal neurons showed that blue light inhibited spontaneous activity in spinal neurons of GtACR1-expressing fish, and that the level of intracellular calcium increased following light offset. CONCLUSIONS: These results show that GtACR1 and GtACR2 can be used to optically inhibit neurons in larval zebrafish with high efficiency. The activity elicited at light offset needs to be taken into consideration in experimental design, although this property can provide insight into the effects of transiently stimulating a circuit.


Assuntos
Proteínas de Algas/genética , Channelrhodopsins/genética , Criptófitas/genética , Neurônios/fisiologia , Peixe-Zebra/fisiologia , Proteínas de Algas/metabolismo , Animais , Channelrhodopsins/metabolismo , Criptófitas/metabolismo , Movimento/fisiologia
18.
Genome Biol Evol ; 9(7): 1859-1872, 2017 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-28854597

RESUMO

Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch. placoidea, Cryptomonas curvata, and Storeatula sp. CCMP1868 share a number of features including synteny and gene content with the previously sequenced genomes of Cryptomonas paramecium, Rhodomonas salina, Teleaulax amphioxeia, and Guillardia theta. Our analysis of these plastid genomes reveals examples of gene loss and intron insertion. In particular, the chlB/chlL/chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss and pseudogenization in cryptophytes. Comparison of phylogenetic trees based on plastid and nuclear genome data sets show the introduction, via secondary endosymbiosis, of a red algal derived plastid in a lineage of chlorophyll-c containing algae. This event was followed by additional rounds of eukaryotic endosymbioses that spread the red lineage plastid to diverse groups such as haptophytes and stramenopiles.


Assuntos
Criptófitas/genética , Evolução Molecular , Genomas de Plastídeos , Plastídeos/genética , Simbiose , Criptófitas/fisiologia , Filogenia , Análise de Sequência de DNA/métodos
19.
Sci Rep ; 7(1): 2345, 2017 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-28539635

RESUMO

The chloroplasts of cryptophytes arose through a secondary endosymbiotic event in which a red algal endosymbiont was integrated into a previously nonphotosynthetic eukaryote. The cryptophytes retain a remnant of the endosymbiont nucleus (nucleomorph) that is replicated once in the cell cycle along with the chloroplast. To understand how the chloroplast, nucleomorph and host cell divide in a coordinated manner, we examined the expression of genes/proteins that are related to nucleomorph replication and chloroplast division as well as the timing of nuclear and nucleomorph DNA synthesis in the cryptophyte Guillardia theta. Nucleus-encoded nucleomorph HISTONE H2A mRNA specifically accumulated during the nuclear S phase. In contrast, nucleomorph-encoded genes/proteins that are related to nucleomorph replication and chloroplast division (FtsZ) are constantly expressed throughout the cell cycle. The results of this study and previous studies on chlorarachniophytes suggest that there was a common evolutionary pattern in which an endosymbiont lost its replication cycle-dependent transcription while cell-cycle-dependent transcriptional regulation of host nuclear genes came to restrict the timing of nucleomorph replication and chloroplast division.


Assuntos
Ciclo Celular , Núcleo Celular/metabolismo , Cloroplastos/metabolismo , Criptófitas/metabolismo , Replicação do DNA , Proteínas de Algas/genética , Proteínas de Algas/metabolismo , Sequência de Aminoácidos , Divisão Celular , Núcleo Celular/genética , Cloroplastos/genética , Criptófitas/classificação , Criptófitas/genética , Expressão Gênica , Histonas/genética , Histonas/metabolismo , Filogenia , Homologia de Sequência de Aminoácidos , Simbiose/genética , Fatores de Tempo
20.
PLoS One ; 12(4): e0175808, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28445483

RESUMO

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 µatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.


Assuntos
Código de Barras de DNA Taxonômico , Plâncton/crescimento & desenvolvimento , Alveolados/genética , Alveolados/crescimento & desenvolvimento , Alveolados/metabolismo , Dióxido de Carbono/análise , Clorofila/análise , Clorofila A , Criptófitas/genética , Criptófitas/crescimento & desenvolvimento , Criptófitas/metabolismo , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Fungos/genética , Fungos/crescimento & desenvolvimento , Fungos/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Concentração de Íons de Hidrogênio , Oceanos e Mares , Plâncton/genética , Plâncton/metabolismo , RNA Ribossômico 18S/química , RNA Ribossômico 18S/isolamento & purificação , RNA Ribossômico 18S/metabolismo , Análise de Sequência de DNA , Suécia
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