Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395.
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ABSTRACT:
SUBMITTER: Guarnieri MT
PROVIDER: S-EPMC5895722 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Genome Sequence of the Oleaginous Green Alga, <i>Chlorella vulgaris</i> UTEX 395.
Guarnieri Michael T MT Levering Jennifer J Henard Calvin A CA Boore Jeffrey L JL Betenbaugh Michael J MJ Zengler Karsten K Knoshaug Eric P EP
Frontiers in bioengineering and biotechnology 20180405
Similar Datasets
Project description:Chlorella vulgaris strain:UTEX 395 Genome sequencing and assembly
| PRJNA278897 | ENA
Project description:Short Description: Oleaginous microalgae are capable of producing large quantities of fatty acids and triacylglycerides. As such, they are promising feedstocks for the production of biofuels and bioproducts. Genetic strain-engineering strategies offer a means to accelerate the commercialization of algal biofuels by improving the rate and total accumulation of microalgal lipids. However, the industrial potential of these organisms remains to be met, largely due to the incomplete knowledgebase surrounding the mechanisms governing the induction of algal lipid biosynthesis. Such strategies require further elucidation of genes and gene products controlling algal lipid accumulation. In this study, we have set out to examine these mechanisms and identify novel strain-engineering targets in the oleaginous microalga, Chlorella vulgaris. Comparative shotgun proteomic analyses have identified a number of novel targets, including previously unidentified transcription factors and proteins involved in cell signaling and cell cycle regulation. These results lay the foundation for strain-improvement strategies and demonstrate the power of translational proteomic analysis. Experimental: Lysates were diluted 1:300 for quantitation in order to abate interference due to the chlorophyll content of the samples. Quantitation was performed by Qubit fluorometry (Invitrogen) and 20 ug of each sample was solubilized in LDS buffer, heated at 85 C for 5 min and separated on a 4-12% Bis-Tris Novex mini-gel (Invitrogen) using the MOPS buffer system. The gel was stained with coomassie and each lane was excised into 40 equally sized segments. The gel bands were processed using a robot (ProGest, DigiLab) with the following protocol: - Washed with 25mM ammonium bicarbonate followed by acetonitrile. - Reduced with 10mM dithiothreitol at 60 C followed by alkylation with 50mM iodoacetamide at RT. - Digested with trypsin (Promega) at 37 C for 4h. - Quenched with formic acid and the supernatant was analyzed directly without further processing. The gel digests were analyzed by nano LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a ThermoFisher Orbitrap Velos Pro. Peptides were loaded on a trapping column and eluted over a 75um analytical column at 350 nL/min; both columns were packed with Jupiter Proteo resin (Phenomenex).The mass spectrometer was operated in data-dependent mode, with MS performed in the Orbitrap at 60,000 FWHM resolution and MS/MS performed in the LTQ. The fifteen most abundant ions were selected for MS/MS. Mascot DAT files were parsed into the Scaffold software for validation, filtering and to create a non-redundant list per sample. Data were filtered using a minimum protein value of 99%, a minimum peptide value of 50% (Prophet scores) and requiring at least two unique peptides per protein.
2013-06-03 | PXD000250 | Pride
Project description:Toxicity of superparamagnetic iron oxide nanoparticles (SPION) was investigated on Chlorella vulgaris cells exposed during 72 hours to Fe3O4 (SPION-1), Co0.2Zn0.8Fe2O4 (SPION-2), or Co0.5Zn0.5Fe2O4 (SPION-3) to a range of concentrations from 12.5 to 400 μg mL(-1). Under these treatments, toxicity impact was indicated by the deterioration of photochemical activities of photosynthesis, the induction of oxidative stress, and the inhibition of cell division rate. In comparison to SPION-2 and -3, exposure to SPION-1 caused the highest toxic effects on cellular division due to a stronger production of reactive oxygen species and deterioration of photochemical activity of Photosystem II. This study showed the potential source of toxicity for three SPION suspensions, having different chemical compositions, estimated by the change of different biomarkers. In this toxicological investigation, algal model C. vulgaris demonstrated to be a valuable bioindicator of SPION toxicity.
| S-EPMC3867878 | biostudies-literature
Project description:Selenium (Se) is an element with many commercial applications as well as an essential micronutrient. Dietary Se has antioxidant properties and it is known to play a role in cancer prevention. However, the general population often suffers from Se deficiency. Green algae, such as Chlorella vulgaris, cultivated in Se-enriched environment may be used as a food supplement to provide adequate levels of Se. We used Raman microspectroscopy (RS) for fast, reliable, and non-destructive measurement of Se concentration in living algal cells. We employed inductively coupled plasma-mass spectrometry as a reference method to RS and we found a substantial correlation between the Raman signal intensity at 252 cm-1 and total Se concentration in the studied cells. We used RS to assess the uptake of Se by living and inactivated algae and demonstrated the necessity of active cellular transport for Se accumulation. Additionally, we observed the intracellular Se being transformed into an insoluble elemental form, which we further supported by the energy-dispersive X-ray spectroscopy imaging.
| S-EPMC8069876 | biostudies-literature
Project description:The complete nucleotide sequence of the chloroplast genome (150,613 bp) from the unicellular green alga Chlorella vulgaris C-27 has been determined. The genome contains no large inverted repeat and has one copy of rRNA gene cluster consisting of 16S, 23S, and 5S rRNA genes. It contains 31 tRNA genes, of which the tRNALeu(GAG) gene has not been found in land plant chloroplast DNAs analyzed so far. Sixty-nine protein genes and eight ORFs conserved with those found in land plant chloroplasts have also been found. The most striking is the existence of two adjacent genes homologous to bacterial genes involved in cell division, minD and minE, which are arranged in the same order in Escherichia coli. This finding suggests that the mechanism of chloroplast division is similar to bacterial division. Other than minD and minE homologues, genes encoding ribosomal proteins L5, L12, L19, and S9 (rpl5, rpl12, rpl19, and rps9); a chlorophyll biosynthesis Mg chelating subunit (chlI); and elongation factor EF-Tu (tufA), which have not been reported from land plant chloroplast DNAs, are present in this genome. However, many of the new chloroplast genes recently found in red and brown algae have not been found in C. vulgaris. Furthermore, this algal species possesses two long ORFs related to ycf1 and ycf2 that are exclusively found in land plants. These observations suggest that C. vulgaris is closer to land plants than to red and brown algae.
| S-EPMC20890 | biostudies-literature
Project description:Micractinium conductrix SAG 241.80 secretes sugars (especially maltose) at pH 5.7 while very little sugar is found at pH 7.6. Another algae, Chlorella sorokiniana does not secrete sugars at either pH. We evaluated the transcriptional profiles of both species of algae at pH 5.7 and 7.6 to make comparisons in the regulation of potential genes involved in these pathways.
2017-12-27 | GSE98781 | GEO
Project description:A contig covering the entire region of Chlorella vulgaris chromosome I (980 kb long), consisting of 33 cosmid clones has been constructed. By cross-hybridization with other chromosomal DNAs, universal structural elements were detected and localized on the contig. They were composed of at least three different elements: short interspersed DNA elements (SINE)-like elements, long interspersed DNA elements (LINE)-like elements and a putative centromere-like element. At least 36 copies of SINE-like elements were distributed over chromosome I with preferential locations on the right half of the chromosome. DNA fragments containing a SINE-like sequence showed a bent or curved DNA nature on polyacrylamide gel electrophoresis. LINE-like elements were clustered at the left terminus of chromosome I where they formed a tandem array of six copies immediately adjacent to the telomeric repeats. A long sequence element localized at a unique region of chromosome I also existed in a single copy on each chromosome and contained a sequence related to the reverse transcriptase domain of retrotransposons. This feature was compared with the reported centromere-associated elements of higher plants. With its comparative simplicity, the organization of Chlorella chromosome I genomic elements may serve as a prototypic experimental system for deciphering the complexity of huge plant chromosomes.
| S-EPMC147790 | biostudies-other
Project description:In a recent study, it has been shown that biosynthesis of triacylglycerol (TAG) in the oleaginous green alga Chlorella desiccata is preceded by a large increase in acetyl-coenzyme A (Ac-CoA) levels and by upregulation of plastidic pyruvate dehydrogenase (ptPDH). It was proposed that the capacity to accumulate high TAG critically depends on enhanced production of Ac-CoA. In this study, two alternative Ac-CoA producers-plastidic Ac-CoA synthase (ptACS) and ATP citrate lyase (ACL)-are shown to be upregulated prior to TAG accumulation under nitrogen deprivation in the oleaginous species C. desiccata, but not in the moderate TAG accumulators Dunaliella tertiolecta and Chlamydomonas reinhardtii. Measurements of endogenous acetate production and of radiolabelled acetate incorporation into lipids are consistent with the upregulation of ptACS, but suggest that its contribution to the overall TAG biosynthesis is negligible. Induction of ACS and production of endogenous acetate are correlated with activation of alcohol dehydrogenase, suggesting that the upregulation of ptACS is associated with activation of PDH-bypass in C. desiccata. It is proposed that activation of the PDH-bypass in C. desiccata is needed to enable a high rate of lipid biosynthesis under nitrogen deprivation by controlling the level of pyruvate reaching ptPHD and/or mtPDH. This may be an important parameter for massive TAG accumulation in microalgae.
| S-EPMC4765794 | biostudies-literature
Project description:The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.
| S-EPMC3293424 | biostudies-literature
Project description:The complete mitochondrial genome of Chloroidium sp. UTEX 3077 was determined in this study. The circular genome was 90,774 bp in length with the GC content of 38.8%. It contained 30 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and 2 ribosome RNA (rRNA) genes. A phylogenetic analysis based on the 8 mitochondrial genomes of Trebouxiophyceae indicated that Chloroidium sp. UTEX 3077 grouped with Chlorellales.
| S-EPMC7748729 | biostudies-literature