Dataset Information

Quantitative proteome analysis of biological nitrogen fixation and phosphorous mobilization in Azotobacter chroococcum NCIMB 8003

ABSTRACT: Quantitative proteomic analysis of Azotobacter chroococcum NCIMB 8003 under diazotrophic and/or phosphorous mobilization conditions.

INSTRUMENT(S):

ORGANISM(S): Arachis Hypogaea (peanut)

SUBMITTER: Alfonso Olaya Abril

LAB HEAD: Conrado Moreno Vivián

PROVIDER: PXD034112 | Pride | 2025-10-06

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 16

Publications

Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.

Biełło Karolina A KA Die José V JV Amil Francisco F Fuentes-Almagro Carlos C Pérez-Rodríguez Javier J Olaya-Abril Alfonso A

International journal of molecular sciences 20250921 18

Quantitative proteomics relies on robust statistical methods for differential expression, critically impacting downstream functional enrichment. This meta-analysis systematically investigated how statistical hypothesis testing approaches and criteria for defining biological relevance influence functional enrichment concordance. We reanalyzed five independent label-free quantitative proteomics datasets using diverse frequentist (<i>t</i>-test, Limma, DEqMS, MSstats) and Bayesian (rstanarm) approa ...[more]

PMID: 41009792

Similar Datasets

Project description:A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium, Azotobacter vinelandii (A. vinelandii). Here, we report the first CRISPR interference (CRISPRi) system for targeted gene silencing in A. vinelandii that integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ~60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system fills an important gap for engineering microbial nitrogen fixation for desired purposes.IMPORTANCEAll life on Earth requires nitrogen to survive. About 78% of the atmosphere alone is nitrogen, yet humans cannot use it directly. Instead, we obtain the nitrogen we need for our survival through the food we eat. For more than 100 years, a substantial portion of agricultural productivity has relied on industrial methods for nitrogen fertilizer synthesis, which consumes significant amounts of nonrenewable energy resources and exacerbates environmental degradation and human-induced climate change. Promising alternatives to these industrial methods rely on engineering the only biological pathway for generating bioaccessible nitrogen: microbial nitrogen fixation. Bioengineering strategies require an extensive understanding of underlying genetics in nitrogen-fixing microbes, but genetic tools for this critical goal remain lacking. The CRISPRi gene silencing system that we report, developed in the broadly utilized nitrogen-fixing bacterial model, Azotobacter vinelandii, is an important step toward elucidating the complexity of nitrogen fixation genetics and enabling their manipulation.

			Action	DRS
	FBN_PM_C1.raw	Raw
	FBN_PM_C2.raw	Raw
	FBN_PM_C3.raw	Raw
	FBN_PM_FBN1.raw	Raw
	FBN_PM_FBN2.raw	Raw