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Inorganic Nitrogen Assimilation

Inorganic Nitrogen Assimilation

Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme...

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Identification of Novel Genes Associated with Alginate Production in Pseudomonas aeruginosa Using Mini-himar1 Mariner Transposon-mediated Mutagenesis

Identification of Novel Genes Associated with Alginate Production in Pseudomonas aeruginosa Using Mini-himar1 Mariner Transposon-mediated Mutagenesis

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Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Matthias Schmidt^1,2,3, Allison N Pearson^1,2,4, Matthew R Incha^1,2,4

¹Joint BioEnergy Institute, Emeryville, California, USA.

Applied and Environmental Microbiology

|March 14, 2022

Summary

This summary is machine-generated.

This study identifies hundreds of genes in Pseudomonas putida KT2440 involved in nitrogen compound metabolism. Researchers developed an interactive tool to visualize these findings, aiding metabolic engineering applications.

Keywords:

BarSeq Pseudomonas putida RB-TnSeq amino acid aminotransferase aminotransferases biosensor biosensors lactam metabolism nitrate nitrite nitrogen nitrogen metabolism nucleotide polyamine t-SNE transposon

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Area of Science:

Microbiology
Metabolic Engineering
Systems Biology

Background:

Pseudomonas putida KT2440 is a model organism with extensive metabolic capabilities.
Many genes and proteins responsible for P. putida's metabolic versatility remain uncharacterized.
Understanding nitrogen metabolism is crucial for bioeconomy applications.

Purpose of the Study:

To identify genes and proteins involved in the assimilation of diverse nitrogen-containing compounds.
To characterize key enzymes and regulators for potential synthetic biology applications.
To develop tools for improved data interpretation in microbial systems.

Main Methods:

Pooled mutant fitness assays (BarSeq) across 71 conditions (52 nitrogen compounds, 19 amino acid drop-outs).
In vitro characterization of aminotransferase substrate ranges.
Analysis of transcriptional regulator specificity.
Application of manifold learning for data visualization.

Main Results:

Identified 672 genes with significant fitness phenotypes related to nitrogen assimilation, including 100 transcriptional regulators and 112 transport proteins.
Proposed assimilatory pathways for various nitrogenous compounds based on genetic data.
Characterized substrate specificities of three aminotransferases and five transcriptional regulators.
Developed an interactive visualization tool for BarSeq data.

Conclusions:

This study provides a comprehensive genetic framework for understanding nitrogen metabolism in P. putida KT2440.
Identified enzymes and regulators are valuable targets for metabolic engineering and synthetic biology.
The interactive visualization tool enhances data accessibility and utility for the research community.