Methanococcoides burtonii
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ABSTRACT:
PROVIDER: PRJNA36685 | ENA |
REPOSITORIES: ENA
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Project description:Methanococcoides burtonii RNA-seq reads
| PRJNA300584 | ENA
Project description:Methanococcoides burtonii is member of the Archaea that is a valuable model for studying cold adaptation. We developed a Agilent microarray for determing which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Agilent 8 x 15K custom gene expression microarrays containing 15128 probes were designed based on the M. burtonii genome sequence. The Microarrays were constructed using 60-mer oligonucleotides covering 2236 genes (86.7% of the total number) on the coding strand (10153 oligonucleotides) and the complementary strand (3671 oligonucleotides), and a large number of intergenic regions (707 oligonucleotides) (Table 1). Each gene and intergenic region was covered by 1 to 6 oligonucleotides (average of 4 per gene). Eight independent replicates were performed using competitive hybridization comparing 8 cultures grown at 4°C vs 8 grown at 23°C. Due to the fact that different ORFs have different numbers of oligonucleotides (ranging from one to six) and that experiments were performed in 8 different replicates, each gene (or intergenic region) has 8 48 measures of fluorescence.
2011-02-01 | E-MEXP-2579 | biostudies-arrayexpress
Project description:The molecular machine that synthesizes RNA in Eucarya and Archaea, RNA polymerase, is composed of 11 or 12 subunits M-^V 9 or 10 that form the core holoenzyme, and a heterodimer formed from subunits E and F that associates with the core.<br><br>In this study we used a recombinant archaeal MbRpoE/F heterodimer to capture cellular mRNA and a custom Agilent microarray to determine which mRNA it binds. Transcripts bound by the heterodimer were identified through competitive hybridization of the total RNA obtained from Methanococcoides burtonii and the RNA obtained through the selection of the transcripts that interact with the MbRpoE/F heterodimer bound to the column.
2011-03-01 | E-MEXP-2625 | biostudies-arrayexpress
Project description:Methanococcoides alaskense overview
| PRJNA917762 | ENA
Project description:Methanococcoides methylutens overview
| PRJNA261087 | ENA
Project description:In photosynthesis Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the often rate limiting CO2-fixation step in the Calvin cycle. This makes Rubisco both the gatekeeper for carbon entry into the biosphere and a target for functional improvement to enhance photosynthesis and plant growth. Encumbering the catalytic performance of Rubisco is its highly conserved, complex catalytic chemistry. Accordingly, traditional efforts to enhance Rubisco catalysis using protracted "trial and error" protein engineering approaches have met with limited success. Here we demonstrate the versatility of high throughput directed (laboratory) protein evolution for improving the carboxylation properties of a non-photosynthetic Rubisco from the archaea Methanococcoides burtonii. Using chloroplast transformation in the model plant Nicotiana tabacum (tobacco) we confirm the improved forms of M. burtonii Rubisco increased photosynthesis and growth relative to tobacco controls producing wild-type M. burtonii Rubisco. Our findings indicate continued directed evolution of archaeal Rubisco offers new potential for enhancing leaf photosynthesis and plant growth.
| S-EPMC4772096 | biostudies-literature
Project description:The pathway for the synthesis of the organic solute glucosylglycerate (GG) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP) from Methanococcoides burtonii. A mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgP) was found in the genome of M. burtonii (http://www.jgi.doe.gov), but an mpgS gene coding for mannosyl-3-phosphoglycerate synthase (MpgS) was absent. The gene upstream of the mpgP homologue encoded a putative glucosyltransferase that was expressed in Escherichia coli. The recombinant product had GpgS activity, catalyzing the synthesis of glucosyl-3-phosphoglycerate (GPG) from GDP-glucose and d-3-phosphoglycerate, with a high substrate specificity. The recombinant MpgP protein dephosphorylated GPG to GG and was also able to dephosphorylate mannosyl-3-phosphoglycerate (MPG) but no other substrate tested. Similar flexibilities in substrate specificity were confirmed in vitro for the MpgPs from Thermus thermophilus, Pyrococcus horikoshii, and "Dehalococcoides ethenogenes." GpgS had maximal activity at 50 degrees C. The maximal activity of GpgP was at 50 degrees C with GPG as the substrate and at 60 degrees C with MPG. Despite the similarity of the sugar donors GDP-glucose and GDP-mannose, the enzymes for the synthesis of GPG or MPG share no amino acid sequence identity, save for short motifs. However, the hydrolysis of GPG and MPG is carried out by phosphatases encoded by homologous genes and capable of using both substrates. To our knowledge, this is the first report of the elucidation of a biosynthetic pathway for glucosylglycerate.
| S-EPMC1347341 | biostudies-literature
Project description:Hyphopichia burtonii has much stronger osmotolerance than model Saccharomyces cerevisiae and other yeast. The transcriptomic changes by RNA-seq analysis in several hyperosmotic stresses and YPD condition as control were investigated, expecting changes in the expression patterns of genes that do not exist or change in other yeast.
2021-12-01 | GSE139920 | GEO
Project description:Hyphopichia burtonii isolate:makgeolli Genome sequencing
| PRJNA417515 | ENA