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High-density CRISPRi screens reveal adaptive transcriptional gradients in cyanobacteria

ABSTRACT: Cyanobacteria are the oldest form of photosynthetic life and contribute to primary production in nearly every habitat, from permafrost to hot springs. Despite longstanding interest in the biochemical basis of environmental adaptation in these microbes, it remains poorly understood. Here we used a high-density, genome-wide CRISPRi screen to examine the influence of gene-specific transcriptional variation on the growth of Synechococcus sp. PCC 7002 under environmental extrema. Surprisingly, many partial knockdowns enhanced fitness under cold monochromatic conditions. Notably, transcriptional repression of a gene for a core subunit of the NDH-1 complex, which is important for photosynthesis and carbon uptake, improved growth rates under both red and blue light but at distinct, color-specific optima. Multi-target transcriptional repression produced nonadditive effects. Findings reveal diverse mechanisms of environmental adaptation in cyanobacteria and provide a new approach for using gradients in sgRNA activity to pinpoint biochemically influential transcriptional changes in cells.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Synechococcus Sp. Pcc 7002 (ncbitaxon:32049)

SUBMITTER: Paul Abraham

PROVIDER: MSV000094564 | MassIVE | Thu Apr 18 08:01:00 BST 2024

SECONDARY ACCESSION(S): PXD051561

REPOSITORIES: MassIVE

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CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate.

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| S-EPMC7874482 | biostudies-literature

RNA-seq of a Streptococcus agalactiae A909 mutant strain deleted for the pleiotropic transcriptional regulator CcpA

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2022-07-12 | E-MTAB-11639 | biostudies-arrayexpress

Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]

Project description:We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions

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Gain-of-function genetic screens in human cells identify SLC transporters overcoming environmental nutrient restrictions

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2022-09-20 | MTBLS4268 | MetaboLights

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2008-09-20 | E-GEOD-12832 | biostudies-arrayexpress

Proteomic changes in liver of Channa striatus in response to high temperature stress

Project description:Climate change and resulting global warming are challenging environmental problems. Understanding the thermal adaptation mechanisms and survival strategies are of paramount importance. Fish has served as excellent animal model for understanding many biological processes. The present study was undertaken to investigate the proteomic changes in liver of murrel Channa striatus exposed to high temperature stress. Fishes were exposed to 36 °C for 4 days and liver proteome changes were analyzed using gel- based proteomics i.e. 2D gel electrophoresis, MALDI-TOF-MS and validation by transcript analysis. The study showed, besides others, up regulation of two sets of proteins, the antioxidant enzymes SOD, ferritin, GST and chaperones HSP60, PDI which was validated by transcript analysis. Further, gene expression analysis was also carried out in the fishes exposed to thermal stress for longer duration (30 days, in the laboratory and beyond, taking Channa collected from a hot spring runoff at a water temperature 36-38 °C); hsp60, sod and gst were found to continue to remain up regulated at 11, 8 and 3 folds, respectively in the hot spring runoff fish. Thus the study showed that SOD, GST and HSP60 play important role in thermal adaptation and survival under chronic heat stress.

2016-04-12 | PXD002608 | Pride

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CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer.

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