Dataset Information

A conserved nucleotide-dependent metal chaperone for managing the cellular zinc economy during zinc limitation

ABSTRACT: How cells safeguard essential zinc-dependent functions during zinc deficiency is poorly understood. A long-debated strategy is whether soluble metal-trafficking chaperones exist to prioritize specific zinc-dependent proteins. We identified a eukaryotic family of metallochaperones that physically interacts with zinc-dependent methionine aminopeptidase type I (MAP1) in human and yeast. Deletion of the yeast metallochaperone-encoding gene NMC1 (formerly YNR029c) leads to a zinc-deficiency growth defect and defective initiator methionine cleavage caused by loss of Map1p activity. To better understand the observed fitness defects due to the lack of NMC1 under zinc deficiency, we used proteomics with Tandem Mass Tag (TMT) quantitation derived from WT, nmc1Delta, and map2Delta nmc1Delta strains grown in zinc-limited (1 uM) or zinc-replete (100 uM) conditions. Proteomics reveal global impacts due to the loss of NMC1 and Map1p function, including mis-regulation of the Zap1p regulon, and suggests that Nmc1p is required to avoid a compounding effect of Map1p dysfunction on cell survival during zinc deficiency.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Crysten Blaby-Haas

PROVIDER: MSV000088135 | MassIVE |

SECONDARY ACCESSION(S): PXD028687

REPOSITORIES: MassIVE

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Publications

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.

Pasquini Miriam M Grosjean Nicolas N Hixson Kim K KK Nicora Carrie D CD Yee Estella F EF Lipton Mary M Blaby Ian K IK Blaby Ian K IK Haley John D JD Blaby-Haas Crysten E CE

Cell reports 20220501 7

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p ...[more]

PMID: 35584675

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Project description:Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified. Experiment Overall Design: Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.

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