Deficiency in the Phosphorylated Pathway of Serine Biosynthesis perturbs sulfur assimilation in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA517148 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8488820.fastq.gz | Fastqsanger.gz | |||
| SRR8488821.fastq.gz | Fastqsanger.gz | |||
| SRR8488822.fastq.gz | Fastqsanger.gz | |||
| SRR8488823.fastq.gz | Fastqsanger.gz | |||
| SRR8488824.fastq.gz | Fastqsanger.gz |
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Project description:Although the plant Phosphorylated Pathway of L-serine Biosynthesis (PPSB) is essential for embryo and pollen development, and for root growth, its metabolic implications have not yet been investigated in depth. A transcriptomics analysis of PPSB-deficient mutants at nighttime, where PPSB activity is thought to be more important, pointed the sulfate assimilation process. As sulfate assimilation takes place mainly during the light period, we also investigated this process in PPSB-deficient lines in the daytime. Key genes in the sulfate starvation response, such as the Adenosine 5’phosphosulfate reductase (APR) genes along with sulfate transporters (SULTR), especially those involved in sulfate translocation in the plant, were induced in the PPSB-deficient lines. However, sulfate content did not lower in these lines, and the steady-state level of glutathione (GSH) increased in roots. This scenario suggests that PPSB deficiency perturbs the sulfate assimilation process between tissue/organs. Alteration of thiol distribution in leaves from different developmental stages, and between aerial parts and roots in plants with reduced PPSB activity provided confirmatory support for this idea. Flux analysis indicated that diminished PPSB activity caused an enhanced flux of 35S into thiol biosynthesis especially in roots. GSH turnover also accelerated in the PPSB-deficient lines, which supports the notion that not only biosynthesis, but also transport and allocation of thiols were perturbed in the PPSB mutants. Our results suggest that PPSB is required for sulfide assimilation in specific heterotrophic tissues and that lack of PPSB activity perturbs sulfur homeostasis between photosynthetic and non-photosynthetic tissues.
2019-01-26 | GSE125675 | GEO
Project description:We employed omic data and conducted comparative analysis in Saccharomyces cerevisiae strains with different S-adenosine-L-methionine (SAM) level. This strategy can help us locate the limiting factor for SAM availability. We found sulfur assimilation emerged as the most significantly enriched pathway and further confirmed that sulfur assimilation was the dominant limiting step of SAM biosynthesis in the whole cell system.
2025-07-22 | GSE302904 | GEO
Project description:Sulfur assimilation improves SAM-dependent methylation
| PRJNA1292800 | ENA
Project description:We employed omic data and conducted comparative analysis in Saccharomyces cerevisiae strains with different S-adenosine-L-methionine (SAM) level. This strategy can help us locate the limiting factor for SAM availability. We found sulfur assimilation emerged as the most significantly enriched pathway and further confirmed that sulfur assimilation was the dominant limiting step of SAM biosynthesis in the whole cell system.
2025-07-23 | PXD066499 |
Project description:This study was aimed at elucidating the significance of photorespiratory serine (Ser) production for cysteine (Cys) biosynthesis. For this purpose, sulfur (S) metabolism and its crosstalk with nitrogen (N) and carbon (C) metabolism were analyzed in wildtype Arabidopsis and its photorespiratory bou-2 mutant with impaired glycine decarboxylase (GDC) activity. Foliar glycine and Ser contents were enhanced in the mutant at day and night. The high Ser levels in the mutant cannot be explained by transcript abundances of genes of the photorespiratory pathway or two alternative pathways of Ser biosynthesis. Despite enhanced foliar Ser, reduced GDC activity mediated a decline in sulfur flux into major sulfur pools in the mutant, as a result of deregulation of genes of sulfur reduction and assimilation. Still, foliar Cys and glutathione contents in the mutant were enhanced. The use of Cys for methionine and glucosinolates synthesis was reduced in the mutant. Reduced GDC activity in the mutant downregulated Calvin Cycle and nitrogen assimilation genes, upregulated key enzymes of glycolysis and the tricarboxylic acid (TCA) pathway and modified accumulation of sugars and TCA intermediates. Thus, photorespiratory Ser production can be replaced by other metabolic Ser sources, but this replacement deregulates the cross-talk between S, N, and C metabolism.
2018-11-27 | GSE86380 | GEO
Project description:Investigation of sulfur metabolism in Clostridium thermocellum DSM 1313 ∆hpt, to determine growth and gene expression when the organism is incubated with either the oxidized (i.e., sulfate) or the reduced and assimilated (i.e., cysteine) forms of sulfur. A sulfite reductase (∆hpt ∆SO3R) knockout mutant to limit sulfur assimilation was created to compare the resulting gene expression patterns by RNAseq transciptomics against the parental strain (∆hpt) when both are grown in the presence of sulfate. Additionally, we bypass the sulfate auxotrophy of the mutant by providing assimilated sulfur in the form of cysteine to determine whether growth is restored to normal and whether methionine can be biosynthesized by yet uncharacterized pathways in this organism.
2020-11-01 | GSE100047 | GEO
Project description:The Chlamydomonas reinhardtii transcriptome was characterized from nutrient-replete and sulfur-depleted wild-type and snrk2.1 mutant cells; the mutant is null for the regulatory serine-threonine kinase SNRK2.1, which is required for acclimation to sulfur deprivation. The transcriptome analyses involved microarray hybridization and RNA-seq technology; RT-qPCR evaluation of the data obtained by these techniques showed that RNA-seq is significantly more quantitative than microarray hybridizations. Sulfur-deprivation-responsive transcripts included those encoding proteins involved in sulfur acquisition and assimilation, recycling of sulfur-containing amino acids, synthesis of reduced sulfur metabolites and cofactors, and modification of cellular structures such as the cell wall and complexes associated with the photosynthetic apparatus. Moreover, the data suggest that cells deprived of sulfur favors accumulation of proteins with fewer sulfur-containing amino acids. Most of these sulfur-deprivation responses are controlled by the SNRK2.1 kinase. Furthermore, the snrk2.1 mutant exhibits a set of unique responses during both sulfur-replete and sulfur-depleted conditions that are not observed in wild-type cells. Many of these responses are likely to be elicited by singlet O2 accumulation in the mutant cells. The transcriptome results for the wild-type and mutant cells strongly suggest the occurrence of massive changes in cellular physiology and metabolism as the cells become depleted for sulfur, and reveal aspects of acclimation that are likely critical for cell survival. The three supplementary files GSE17970_supplemental_table_*.xls below include results of the differential expression analysis (expression estimates, fold changes and p-values), and different clusters of functionally related genes.
2010-07-08 | GSE17970 | GEO
Project description:Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2005-07-28 | GSE3015 | GEO
Project description:Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed
2005-07-28 | E-GEOD-3015 | biostudies-arrayexpress
Project description:Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth.
2005-07-22 | E-SMDB-2992 | biostudies-arrayexpress