Dataset Information

Shotgun proteomics (qMS) 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 proteomes of zinc-replete and zinc-limited wild type. Additionally, the study informs how loss of the altRP operon impacts the proteome during zinc limitation by comparing the proteomes 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).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mycobacterium Smegmatis (strain Atcc 700084 / Mc(2)155)

SUBMITTER: Allexa Dow

LAB HEAD: Sladjana Prisic

PROVIDER: PXD029588 | Pride | 2021-11-10

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	Msm_X_SpCs_ALL.csv	Csv
	QEPlus2_12082017_WT_ZLM1.raw	Raw
	QEPlus2_12082017_WT_ZLM2.raw	Raw
	QEPlus2_12082017_WT_ZLM3.raw	Raw
	QEPlus2_12082017_WT_ZRM1.raw	Raw

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Publications

Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis.

Dow Allexa A Burger Andrew A Marcantonio Endrei E Prisic Sladjana S

Frontiers in microbiology 20220210

Zinc ion (Zn2+) is an essential micronutrient and a potent antioxidant. However, Zn2+ is often limited in the environment. Upon Zn2+ limitation, Mycolicibacterium (basonym: Mycobacterium) smegmatis (Msm) undergoes a morphogenesis, which relies on alternative ribosomal proteins (AltRPs); i.e., Zn2+-independent paralogues of Zn2+-dependent ribosomal proteins. However, the underlying physiological changes triggered by Zn<su ...[more]

PMID: 35222334

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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

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

Dataset's files

Publications

Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in <i>Mycobacterium smegmatis</i>.

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