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RNA-seq of zinc-replete wild type and zinc-limited wild type, altRP operon deletion mutant and its complement strain in Mycolicibacterium (Mycobacterium) smegmatis

ABSTRACT: The study was designed to describe the effects of zinc limitation on gene expression in M. smegmatis by comparing the transcriptomes of zinc-replete and zinc-limited wild type. Additionally, the study informs how loss of the altRP operon impacts the transcriptomic changes during zinc limitation by comparing the transcriptomes of zinc-limited ΔaltRP mutant to the zinc-replete and zinc-limited wild type, and to confirm which changes are complemented in the complement strain (ΔaltRP/c).

ORGANISM(S): Mycolicibacterium smegmatis

PROVIDER: GSE188233 | GEO | 2021/11/10

REPOSITORIES: GEO

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Project description:Zinc is an essential nutrient because of its role in catalysis and in stabilizing protein structure, but excess zinc can also be deleterious. Four nutritional zinc states have been identified in the alga Chlamydomonas reinhardtii: zinc toxic, zinc replete, zinc deficient and zinc limited. Growth is inhibited in zinc-limited and zinc toxic cells relative to zinc-replete cells, while zinc-deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition responsive changes in gene expression. We identified a subset of genes encoding zinc-handling components, including ZIP family transporters and candidate zinc chaperones. In addition, we noted an impact on two other regulatory pathways, the carbon concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc-deficiency, as a likely consequence of reduced carbonic anhydrase activity, which is validated by mass spectrometry and immunoblot analysis of Cah1, Cah3 and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in air in zinc limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. Surprisingly, we noted also that the Crr1 regulon, which responds to Cu limitation, is also turned on in zinc deficiency, and in fact, Crr1 is required for growth in zinc-limiting conditions. Zinc deficient cells are functionally copper deficient, as evidenced by reduced plastocyanin abundance, even though they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester Cu in a bio-unavailable form, perhaps to prevent mis-metallation of critical zinc sites. Zn-limited wild-type cells were generated by transfer of cells from the first round of growth in medium with no supplemental Zn into TAP medium supplemented or not with 2.5 ÂµM Zn-EDTA The control samples for this study are represented in GSE25622

Dataset Information

RNA-seq of zinc-replete wild type and zinc-limited wild type, altRP operon deletion mutant and its complement strain in Mycolicibacterium (Mycobacterium) smegmatis

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