Project description:The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze both hydrolysis at high water contents and transesterification in quasi-anhydrous conditions. Here, we investigated the Thermomyces lanuginosa lipase structure in solution in the presence of a tributyrin aggregate using 30 ns molecular-dynamics simulations. The water content of the active-site groove was modified between the runs to focus on the protein-water molecule interactions and their implications for protein structure and protein-lipid interactions. The simulations confirmed the high plasticity of the lid fragment and showed that lipid molecules also bind to a secondary pocket beside the lid. Together, these results strongly suggest that the lid plays a role in the anchoring of the protein to the aggregate. The simulations also revealed the existence of a polar channel that connects the active-site groove to the outside solvent. At the inner extremity of this channel, a tyrosine makes hydrogen bonds with residues interacting with the catalytic triad. This system could function as a pipe (polar channel) controlled by a valve (the tyrosine) that could regulate the water content of the active site.

| S-EPMC2712026 | biostudies-literature

Comparative transcriptome analysis of heat stress responses of Clematis lanuginosa and Clematis crassifolia.

Project description:BackgroundClematis species are attractive ornamental plants with a variety of flower colors and patterns. Heat stress is one of the main factors restricting the growth, development, and ornamental value of Clematis. Clematis lanuginosa and Clematis crassifolia are large-flowered and evergreen Clematis species, respectively, that show different tolerance to heat stress. We compared and analyzed the transcriptome of C. lanuginose and C. crassifolia under heat stress to determine the regulatory mechanism(s) of resistance.ResultsA total of 1720 and 6178 differentially expressed genes were identified from C. lanuginose and C. crassifolia, respectively. The photosynthesis and oxidation-reduction processes of C. crassifolia were more sensitive than C. lanuginose under heat stress. Glycine/serine/threonine metabolism, glyoxylic metabolism, and thiamine metabolism were important pathways in response to heat stress in C. lanuginose, and flavonoid biosynthesis, phenylalanine metabolism, and arginine/proline metabolism were the key pathways in C. crassifolia. Six sHSPs (c176964_g1, c200771_g1, c204924_g1, c199407_g2, c201522_g2, c192936_g1), POD1 (c200317_g1), POD3 (c210145_g2), DREB2 (c182557_g1), and HSFA2 (c206233_g2) may be key genes in the response to heat stress in C. lanuginose and C. crassifolia.ConclusionsWe compared important metabolic pathways and differentially expressed genes in response to heat stress between C. lanuginose and C. crassifolia. The results increase our understanding of the response mechanism and candidate genes of Clematis under heat stress. These data may contribute to the development of new Clematis varieties with greater heat tolerance.

| S-EPMC8941805 | biostudies-literature

The complete chloroplast genome sequence of <i>Litsea coreana</i> var<i>. lanuginosa</i> (Lauraceae): genome structure and phylogenetic analysis.

Project description:Litsea coreana var. lanuginose is a perennial, indeciduous, and broad-leaved tree used as an essential medicinal and edible plant. In addition, this species is well-known for its leaves are rich in aromatic oil. In this study, we firstly assembled and characterized the complete chloroplast genome of L. coreana var. lanuginose using Illumina pair-end sequencing and performed a phylogenetic analysis with other 13 species in Lauraceae. The results revealed that its chloroplast genome was 152,859 bp in total length with 39% of GC content, containing a pair of inverted repeats of 20,084 bp (IRA and IRB), separated by a large single-copy (LSC) region of 93,795 bp and a small single-copy (SSC) region of 18,896 bp. The plastid genome of L. coreana var. lanuginose encoded 125 genes, including 81 protein-coding genes, 36 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis suggested that L. coreana var. lanuginose was closely related to the clade of Litsea monopetala, Litsea garrettii, and Litsea elongate in Lauraceae family.

| S-EPMC9467558 | biostudies-literature

Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.

2010-03-09 | GSE17694 | GEO

SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor SoxC in the ascidian early gastrula embryo.

2010-03-09 | GSE17692 | GEO

Snail ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Snail in the ascidian early gastrula embryo.

2010-03-09 | GSE17691 | GEO