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Molecular-Level Architecture of Chlamydomonas reinhardtii’s Glycoprotein-Rich Cell Wall

ABSTRACT: Microalgae are a renewable and promising biomass for large-20 scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii. Using in situ solid-state and sensitivity-enhanced nuclear magnetic 25 resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The 30 structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Adnan Halim

LAB HEAD: Adnan Halim

PROVIDER: PXD048024 | Pride | 2024-01-09

REPOSITORIES: Pride

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Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

Project description:A transcriptome analysis of P. alba cambial zone was performed with the aim to unravel the gene network underlying the response to water deficit within the cambium and the differentiating derivatives cambial cells. Water stress was induced on one-year-old plant of Populus alba by withholding water for 9 days. At that time, leaf Ψpd fell down to -0,8 MPa resulting in a significant reduction of the stomatal conductance, CO2 assimilation, consistent increment of stem shrinkage and cessation of the radial growth. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected a few functional categories as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.

2009-12-22 | GSE18675 | GEO

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

Project description:A transcriptome analysis of P. alba cambial zone was performed with the aim to unravel the gene network underlying the response to water deficit within the cambium and the differentiating derivatives cambial cells. Water stress was induced on one-year-old plant of Populus alba by withholding water for 9 days. At that time, leaf Î¨pd fell down to -0,8 MPa resulting in a significant reduction of the stomatal conductance, CO2 assimilation, consistent increment of stem shrinkage and cessation of the radial growth. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected a few functional categories as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit. Three-condition experiment, Stress vs. Control, Re-hydrated vs. Stress and Re-hydrated vs Control. Each sample consists of a pool of two plants independently grown and harvested. Two technical replicates are performed for each of the three treatments. One swap replicate per array.

2010-05-16 | E-GEOD-18675 | biostudies-arrayexpress

RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts

Project description:The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. The genome-wide comparative study of the transcript profiles of these isolines revealed 364 differentially expressed genes in common between the two varieties that were further divided into different broad functional categories. Genes related to cell wall processes accounted for 19% of the differentially expressed genes in the middle developmental stage of 100-200 mg seed weight. Within this class, the cell wall proline-rich and glycine-rich protein genes were highly differentially expressed in both genetic backgrounds. Other genes that showed significant expression changes in each of the isoline pairs at the 100-200 mg seed weight stage were xylem serine proteinase, fasciclin-related genes, auxin and stress response related genes, TRANSPARENT TESTA 1 (TT1) and other transcription factors. The mutant appears to shift the timing of either the increase or decrease in the levels of some of the transcripts. The analysis of these data sets reveals the physiological changes that the seed coat undergoes during the formation of the breaks in the cell wall. Examination of soybean isolines in two different genetic background at three different seed weight stages: Seed coats of Clark standard (CS, wild type) & Clark defective (CD, seed coat mutant), Harosoy Standard (HS) & Harosoy defective (HD) at 50-100mg, 100-200mg and 400-500mg.

2014-05-16 | E-GEOD-54903 | biostudies-arrayexpress

Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides thetaiotaomicron)

Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization. Growth of Bacteroides thetaiotaomicron in vitro in minimal medium plus different purified complex glycans. Observation of increased gene expression was used to determine genes that are involved in metabolism of each glycan. Two biological replicates each.

2011-05-01 | E-GEOD-25572 | biostudies-arrayexpress

Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides ovatus)

2011-05-01 | GSE25575 | GEO

Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides thetaiotaomicron)

2011-05-01 | GSE25572 | GEO

Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides ovatus)

Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization. Bacteroides ovatus bacteria were grown either in vitro on defined complex glycan sources, or in vivo in the intestinal tract of gnotobiotic mice fed variable diets. Increased in vitro gene expression was used to indicate the genes required for metabolism of complex glycans and compared to in vivo transcriptional activity to determine expression in the mouse gut.

2011-05-01 | E-GEOD-25575 | biostudies-arrayexpress

RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts

2014-05-16 | GSE54903 | GEO

RNA-seq, G pallida population D383 batch 1-2A cyst and hatched J2 samples, exposed for 8h, 24h, 48h to 2nM Solanoeclepin A (dissolved in 1% EtOH), potato root diffusate from wild accession PNT 777-2 (diluted to 0,1x with tap water) or tap water with 1% EtOH (spontaneous hatching control)

Project description:In this experiment we evaluate the transcriptional responses of G pallida D383 1-2A to diverse hatching stimulations by pure Solanoeclepin A or by potato root exudate. We used cysts hydrated for 7 days in tap water for the experiment. Water for hydration was changed every day. After hydration approximately 13mg of cysts (50-100 cysts) were placed over Netwell inserts (Corning) with 74um mesh size. For this experiment we used 5 “technical” replicates, all performed in the same experiment. Worms underwent the treatment at the Laboratory of Nematology (WUR)(Spit lab) and RNA was extracted in the same lab using the Qiagen RNeasy Micro kit. RNA samples were measured by Nanodrop and Qubit and were sent to the Wageningen BioInformatics business unit. (Wageningen, The Netherlands, Dr. Sara Diaz Trivino’s team) on dry ice. Sequencing was performed by the DLO in Wageningen.

2023-04-01 | E-MTAB-11228 | biostudies-arrayexpress

Nucleocytoplasmic O-Man glycoproteome

Project description:Dynamic cycling of N-Acetylglucosamine (GlcNAc) on serine (Ser) and threonine (Thr) residues (O-GlcNAcylation) is an essential process in all eukaryotic cells except yeast, e.g Saccharomyces cerevisiae. O-GlcNAcylation modulates signaling and cellular processes in an intricate interplay with protein phosphorylation, and serves as a key sensor of nutrients by linking the hexosamine biosynthetic pathway (HBP) to cellular signaling. A longstanding conundrum has been how yeast survives without O-GlcNAcylation in light of its similar phosphorylation signaling system. We previously developed a sensitive lectin enrichment and mass spectrometry workflow for identification of the human O-Mannose (O-Man) glycoproteome, and used this to identify a pleothora of O-linked mannose glycoproteins in human cell lines including the large family of cadherins and protocadherins. Here, we applied the workflow to yeast with the aim to characterize the yeast O-Man glycoproteome, and doing so we discovered hitherto unknown O-Man glycosites on nuclear, cytoplasmic and mitochondrial proteins in Saccharomyces cerevisiae. The type of nucleocytoplasmic proteins and the localization of identified O-Man residues mirrors that of the O-GlcNAc glycoproteome in other eukaryotic cells, indicating that the two different types of O-glycosylations serve the same important biological functions. The discovery opens for exploration of the enzyme machinery that is predicted to regulate the discovered nucleocytoplasmic O-Man glycosylation. It is likely that manipulation of this type of O-Man glycosylation will have wide applications for yeast bioprocessing.

2015-12-08 | PXD002924 | Pride

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