Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics data reveal the effects of the non-natural cofactor nicotinamide cytosine dinucleotide on Escherichia coli

ABSTRACT: Nicotinamide adenine dinucleotide is an ubiquitous cofactor in cells. Non-natural cofactor or biomimetic cofactors have attracted great attention on account of their low cost, high stability and the application of efficient synthesis. Nicotinamide cytosine dinucleotide is reported as a non-natural cofactor that can be synthesized in vivo, and metabolic systems have been built using NCD as the cofactor. In this study, we investigated the biological effects of this non-natural cofactor by conducting proteomics analysis.

ORGANISM(S): Escherichia Coli

SUBMITTER: Zongbao Zhao

PROVIDER: PXD064813 | iProX | Tue Jun 10 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Diazirine photo-immobilisation for target profiling of natural products and co-factors: pulldown data

Project description:Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contribute to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens help to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilisation of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that amongst 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilised. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated <100 µM targets of 9 molecules. Among them, immobilisation of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilisation of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.

2022-10-06 | PXD033292 | Pride

Bacteria boost mammalian host NAD metabolism by engaging the deamidated biosynthesis pathway

Project description:Nicotinamide adenine dinucleotide (NAD), a cofactor for hundreds of metabolic reactions in all cell types, plays an essential role in diverse cellular processes including metabolism, DNA repair, and aging. NAD metabolism is critical to maintain cellular homeostasis in response to environmental signals, however, how it is impacted by the environment remains unclear. Here, we report an unexpected trans-kingdom cooperation between bacteria and mammalian cells wherein bacteria contribute to host NAD biosynthesis. Bacteria confer mammalian cells with the resistance to inhibitors of NAMPT, the rate limiting enzyme in the main vertebrate NAD salvage pathway. Mechanistically, a microbial nicotinamidase (PncA) that converts nicotinamide to nicotinic acid, a key precursor in the alternative deamidated NAD salvage pathway, is necessary and sufficient for this protective effect. This bacteria-enabled bypass of the pharmacologically induced metabolic block in mammalian cells represents a novel paradigm in drug resistance. This host-microbe metabolic interaction also dramatically enhances the hepatic NAD-boosting efficiency of nicotinamide and nicotinamide riboside supplementation, demonstrating a crucial role of microbes, gut microbiota in particular, in systemic NAD metabolism.

2020-03-03 | GSE127750 | GEO

Nicotinamide enhances natural killer cell function and yields remissions in patients with non-Hodgkin lymphoma

Project description:Nicotinamide enhances natural killer cell function and yields remissions in patients with non-Hodgkin lymphoma

| PRJNA920515 | ENA

Nanopore RNA-seq of human cell lines treated with or without nicotinamide adenine dinucleotide (NAD+)

Project description:Investigation of transcriptome changes in four human cell lines (BJ, BJ-5ta, U2OS and HeLa) after treatment for 24 hours with nicotinamide adenine dinucleotide (NAD+). Cells were untreated as the control condition. Nanopore sequencing of cDNA was performed after library preparation with the ONT SQK-PCB109 kit.

2023-09-20 | E-MTAB-13187 | biostudies-arrayexpress

NAD capping of mRNAs is abundant but strongly guarded against in yeast

Project description:The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5'-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG motif for this purpose. Most NAD-RNAs are 3'-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

2020-09-02 | PXD017893 | Pride

GNPS - Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

Project description:Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

2022-02-12 | MSV000088828 | GNPS

Natural variation in Arabidopsis thaliana transcriptomes

Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.

2012-03-12 | GSE24669 | GEO

Natural variation in Arabidopsis thaliana transcriptomes

2012-05-22 | GSE38109 | GEO

ALDH7A1 inhibits the intracellular transport pathways during hypoxia and starvation to promote cellular energy homeostasis

Project description:Aldehyde dehydrogenase 7A1 (ALDH7A1) is a metabolic enzyme that converts aldehydes to carboxylates. Here, we find that the reductive consequence of this catalytic activity, which generates NADH (nicotinamide adenine dinucleotide, reduced form) from NAD (nicotinamide adenine dinucleotide), underlies how ALDH7A1 coordinates a broad inhibition of the intracellular transport pathways. Studying vesicle formation by the Coat Protein I (COPI) complex, we elucidate that NADH generated by ALDH7A1 targets Brefeldin-A ADP-Ribosylated Substrate (BARS) to inhibit the fission stage. Moreover, defining a physiologic role for the broad transport inhibition exerted by ALDH7A1, we find that it acts to reduce energy consumption during hypoxia and starvation to promote cellular energy homeostasis. These findings uncover a non-canonical function of ALDH7A1, and also an unexpected way that NADH acts in cellular energetics. Moreover, the findings advance the understanding of intracellular transport by elucidating how multiple pathways can be coordinated, as well as defining physiologic circumstances in which this coordination occurs.

2019-09-12 | PXD014645 | Pride

Nuclear IMPDH2 controls the DNA damage response by modulating PARP1 activity

Project description:Nuclear metabolism and DNA damage response are intertwined processes, but the precise molecular connections remain elusive. Here, we delve into this crosstalk using as a model triple-negative breast cancer (TNBC), a subtype often prone to DNA damage accumulation. We reveal that the de novo purine synthesis enzyme Inosine monophosphate dehydrogenase 2 (IMPDH2) is enriched on chromatin in TNBC when compared to other subtypes. IMPDH2 chromatin localization is DNA damage dependent and IMPDH2 repression leads to DNA damage accumulation. On chromatin, IMPDH2 interacts and modulates Poly [ADP-ribose] polymerase 1 (PARP1) activity by controlling nuclear availability of nicotinamide adenine dinucleotide (NAD+) -a shared metabolic cofactor- to fine-tune the DNA damage response. However, when IMPDH2 is restricted to the nucleus, it depletes nuclear NAD+, leading to PARP1 cleavage and cell death. Our study identifies a non-canonical nuclear role for IMPDH2 that act as convergence point of nuclear metabolism and DNA damage response. # Contributed equally *Corresponding authors: sara.sdelci@crg.eu; marta.garciacao@crg.eu

2024-09-16 | GSE271269 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data