Structural architecture of Galdieria sulphuraria DCN1L.
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ABSTRACT:
SUBMITTER: Sethe Burgie E
PROVIDER: S-EPMC3075430 | biostudies-literature | 2011 Apr
REPOSITORIES: biostudies-literature
Publications
Structural architecture of Galdieria sulphuraria DCN1L.
Sethe Burgie E E Bingman Craig A CA Makino Shin-Ichi S Wesenberg Gary E GE Pan Xiaokang X Fox Brian G BG Phillips George N GN
Proteins 20110118 4
Similar Datasets
Project description:An enzyme with sarcosine dimethylglycine methyltransferase (SDMT) activity has been identified in the thermophilic eukaryote, Galdieria sulphuraria. The crystal structure of the enzyme, solved to a resolution of 1.95 A, revealed a fold highly similar to that of mycolic acid synthases. The kcat and apparent K(M) values were 64.3 min(-1) and 2.0 mM for sarcosine and 85.6 min(-1) and 2.8 mM for dimethylglycine, respectively. Apparent K(M) values of S-adenosylmethionine were 144 and 150 microM for sarcosine and dimethylglycine, respectively, and the enzyme melting temperature was 61.1 degrees C. Modeling of cofactor binding in the active site based on the structure of methoxy mycolic acid synthase 2 revealed a number of conserved interactions within the active site.
| S-EPMC2742680 | biostudies-literature
Project description:BackgroundAs a thermoacidophilic microalga, Galdieria sulphuraria has a unique biological function. MicroRNA (miRNA) plays an important regulating role in plant various stress responses.ObjectiveIn this study, we identified lots of conserved and novel miRNAs in G. sulphuraria (gsu-miRNAs), and predicted their putative targets for the first time.Materials and methodsConserved and novel gsu-miRNAs were predicted via deep sequencing on the Illumina HiSeq 4000 platform combined with bioinformatics analysis with a series of filtration criteria. Characterization of gsu-miRNAs and their targets were searched by different bioinformatics software. Some gsu-miRNAs were validated by Northern blot and RT-PCR analysis. MiRNA target gene function was predicted via GO and KEGG analysis. The interrelationship between gsu-miRNAs and target genes was constructed via Cytoscape networks analysis.ResultsA total of 134 gsu-miRNAs belonging to 124 MIRNA families were identified. Characterization analysis and experimental validation revealed that most of them were credible. A few miRNAs showed conservatism between G. sulphuraria and 20 representative plants. 1,589 putative miRNA targets were predicted. GO analysis revealed that the genes targeted by gsu-miRNAs involved in some important physiological processes of this alga, such as the ETC, and KEGG pathway analysis revealed that RNA transport and the PPP were predicted to be the two most enriched pathways. Cytoscape networks between miRNAs and target genes indicated their various interactions.ConclusionsResearch on gsu-miRNAs, which act as key regulators during gene expression in G. sulphuraria will open a new avenue for further developing this thermoacidophilic alga at the post-transcriptional level.
| S-EPMC8358169 | biostudies-literature
Project description:Nuclear genome sequencing from extremophilic eukaryotes has revealed clues about the mechanisms of adaptation to extreme environments, but the functional consequences of extremophily on organellar genomes are unknown. To address this issue, we assembled the mitochondrial and plastid genomes from a polyextremophilic red alga, Galdieria sulphuraria strain 074 W, and performed a comparative genomic analysis with other red algae and more broadly across eukaryotes. The mitogenome is highly reduced in size and genetic content and exhibits the highest guanine-cytosine skew of any known genome and the fastest substitution rate among all red algae. The plastid genome contains a large number of intergenic stem-loop structures but is otherwise rather typical in size, structure, and content in comparison with other red algae. We suggest that these unique genomic modifications result not only from the harsh conditions in which Galdieria lives but also from its unusual capability to grow heterotrophically, endolithically, and in the dark. These conditions place additional mutational pressures on the mitogenome due to the increased reliance on the mitochondrion for energy production, whereas the decreased reliance on photosynthesis and the presence of numerous stem-loop structures may shield the plastome from similar genomic stress.
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Project description:The ACT domain is a structurally conserved small molecule binding domain which is mostly involved in amino acid and purine metabolism. Here, we report the crystal structure of a tandem ACT domain-containing protein (ACTP) from Galdieria sulphuraria. The two ACTP monomers in the asymmetric unit form a dimer with a non-crystallographic twofold axis in a domain-swapped manner, showing a horseshoe-like structure with a central crevice. This structure contributes to expand our knowledge on the structural diversity of ACT domain-containing proteins.
| S-EPMC4226431 | biostudies-literature
Project description:We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCO) from the red algae Galdieria Sulphuraria. The protein crystallized in two different crystal forms, the I422 crystal form being obtained from high salt and the P21 crystal form being obtained from lower concentration of salt and PEG. We report here the crystallization, preliminary stages of structure determination and the detection of the structural phase transition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzyme belongs to the hexadecameric class (L8S8) with an approximate molecular weight 0.6MDa. The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a single hexadecamer per asymmetric unit. The preservation of diffraction power in a phase transition for such a large macromolecule is rare.
| S-EPMC3871842 | biostudies-literature
Project description:The extremophilic unicellular red microalga Galdieria sulphuraria (Cyanidiophyceae) is able to grow autotrophically, or mixo- and heterotrophically with 1% glycerol as a carbon source. The alga divides by multiple fission into more than two cells within one cell cycle. The optimal conditions of light, temperature and pH (500 µmol photons m-2 s-1, 40 °C, and pH 3; respectively) for the strain Galdieria sulphuraria (Galdieri) Merola 002 were determined as a basis for synchronization experiments. For synchronization, the specific light/dark cycle, 16/8 h was identified as the precondition for investigating the cell cycle. The alga was successfully synchronized and the cell cycle was evaluated. G. sulphuraria attained two commitment points with midpoints at 10 and 13 h of the cell cycle, leading to two nuclear divisions, followed subsequently by division into four daughter cells. The daughter cells stayed in the mother cell wall until the beginning of the next light phase, when they were released. Accumulation of glycogen throughout the cell cycle was also described. The findings presented here bring a new contribution to our general understanding of the cell cycle in cyanidialean red algae, and specifically of the biotechnologically important species G. sulphuraria.
| S-EPMC8301940 | biostudies-literature
Project description:Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis-regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.
| S-EPMC6504705 | biostudies-literature
Project description:Galdieria sulphuraria Raw sRNA sequence reads
| PRJNA315467 | ENA
Project description:Selection for transcript diversity in the extremophile Galdieria sulphuraria results in retention of the splicing machinery
| PRJNA350520 | ENA
Project description:Unicellular red alga found in hot sulphur springs
| PRJNA13024 | ENA