Impaired cell-cell communication in multicellular cyanobacteria affects carbon uptake, photosynthesis and the cell wall
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ABSTRACT:
PROVIDER: PRJNA675510 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13010317.fastq.gz | Fastqsanger.gz | |||
| SRR13010318.fastq.gz | Fastqsanger.gz | |||
| SRR13010319.fastq.gz | Fastqsanger.gz | |||
| SRR13010320.fastq.gz | Fastqsanger.gz | |||
| SRR13010321.fastq.gz | Fastqsanger.gz |
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Project description:Cell-cell communication is an essential attribute of multicellular organisms. We studied the effects of perturbed communication in multicellular filaments of mutant derivatives of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, in which septal proteins were deleted. Filaments of sepJ and sepJ/fraC/fraD deleted strains showed marked differences in growth, pigment absorption spectra and spatial patterns of expression of the hetR gene encoding a master regulator of heterocyst differentiation. To understand the global changes in gene expression that take place as a result of impaired cell-cell molecular transfer, we mapped the transcriptional landscape of wild-type and mutant filaments using RNA-seq, both under nitrogen-replete and nitrogen-poor conditions. Our results show that the effects of sepJ and fraC/fraD deletions are not additive, and that far from affecting only passive transport between cells, perturbations to cell-cell communication in this model organism lead to significant changes in gene expression. Most significant effects include increased expression of genes encoding carbon uptake systems and some components of the photosynthetic apparatus, and decreased expression of genes encoding cell wall components related to heterocyst differentiation and to polysaccharide export. Thus, impairment of intercellular communication strongly affects specific aspects, notably related to carbon metabolism, of the biology of Anabaena.
2021-01-19 | GSE161085 | GEO
Project description:Cell-cell communication is an essential attribute of multicellular organisms. The effects of perturbed communication were studied in septal protein mutants of the heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120 model organism. Strains bearing sepJ and sepJ/fraC/fraD deletions showed differences in growth, pigment absorption spectra, and spatial patterns of expression of the hetR gene encoding a heterocyst differentiation master regulator. Global changes in gene expression resulting from deletion of those genes were mapped by RNA sequencing analysis of wild-type and mutant strains, both under nitrogen-replete and nitrogen-poor conditions. The effects of sepJ and fraC/fraD deletions were non-additive, and perturbed cell-cell communication led to significant changes in global gene expression. Most significant effects, related to carbon metabolism, included increased expression of genes encoding carbon uptake systems and components of the photosynthetic apparatus, as well as decreased expression of genes encoding cell wall components related to heterocyst differentiation and to polysaccharide export.
| S-EPMC7797909 | biostudies-literature
Project description:Protein interaction network reveals the biofunctional difference between vegetative cell and heterocyst in multicellular cyanobacteria
2022-04-26 | PXD025312 |
Project description:In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. In both species a conserved cistrome was identified for each cell type and initiation of photosynthesis gene expression was conditioned by cell identity. Photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C3 guard cells. We conclude C4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C3 plants.
2023-12-05 | GSE248919 | GEO
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Project description:Improving photosynthesis is a major approach to increase crop yield potential. Here we report a negative transcription factor of photosynthesis, which can be manipulated to increase rice photosynthesis and plant biomass in the field. This transcription factor named negative regulator of photosynthesis 1 (NRP1) (Os07g0471900) which was identified through a co-expression analysis using rice leaf RNA sequencing (RNA-seq) data. The NRP1 showed significantly negative correlation with the expression of many genes involved in photosynthesis. Knocking out NPR1 led to greater photosynthesis and increased biomass in the field, while overexpression of NRP1 decreased photosynthesis and biomass. Transcriptomic data analysis shows that NRP1 can negatively regulate the expression of photosynthetic genes. Protein transactivation experiments show that NRP1 is a transcription activator, implying that NRP1 may indirectly regulate photosynthesis gene expression through an unknown regulator. This study shows that combination of bioinformatics analysis with transgenic testing can be used to identify new regulators to improve photosynthetic efficiency in crops.
2019-10-15 | GSE136918 | GEO
Project description:Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
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Project description:Macrophage containing multicellular lung organoids
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Project description:Oxygenic photosynthesis contains multiple proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Accordingly, its composition is heavily re-organized when iron becomes limiting as a nutrient factor, a situation that is frequently encountered in nature. However, the molecular mechanisms controlling the reorganization of the photosynthetic system upon iron deprivation have remained enigmatic. Here we show that the small regulatory RNA IsaR1 (Iron-stress activated RNA 1) plays a pivotal role in acclimation to low iron conditions. The transcription factor Fur cannot facilitate iron starvation dependent repression of it’s targets because it requires iron for DNA binding. We show that the Fur repressed sRNA IsaR1 fulfills this repressor function in iron homeostasis. The IsaR1 regulon consists of at least 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, the detoxification of anion radicals, citrate cycle, and in tetrapyrrole biogenesis. We demonstrate that IsaR1 is absolutely necessary to maintain physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (i) directly, via posttranscriptional repression of gene expression and indirectly, (ii) via the suppression of Fe/S cluster co-factor and (iii) pigment biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a riboregulator of central importance. These findings provide a new perspective for studies of the regulation of iron homeostasis in photosynthetic organisms.
2016-10-01 | GSE87496 | GEO
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased. Whole plants in Col, C24, and their F1 hybrids with two replications
2012-03-06 | E-GEOD-36273 | biostudies-arrayexpress