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Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics

  • Marius MihăşanEmail author
  • Cornelia Babii
  • Roshanak Aslebagh
  • Devika Channaveerappa
  • Emmalyn J. Dupree
  • Costel C. Darie
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1140)

Abstract

Proteomics, or the large-scale study of proteins, is a post-genomics field that, together with transcriptomics and metabolomics, has moved the study of bacteria to a new era based on system-wide understanding of bacterial metabolic and regulatory networks. The study of bacterial proteins or microbial proteomics has found a wide array of applications in many fields of microbiology, from food, clinical, and industrial microbiology to microbial ecology and physiology. The current chapter makes a brief technical introduction into the available approaches for the large-scale study of bacterial proteins using mass-spectrometry. Furthermore, the advantages and disadvantages of using bacteria for proteomics studies are indicated as well as several example studies where MS-based bacterial proteomics had a fundamental role in deciphering the scientific question. Finally, the proteomics study of nicotine catabolism in Paenarthrobacter nicotinovorans pAO1 using nanoLC–MS/MS is given as an in-depth example for possible applications of microbial proteomics.

The nicotine degradation pathway functioning in Paenarthrobacter nicotinovorans is encoded by the catabolic megaplasmid pAO1 that contains about 40 nicotine-related genes making out the nic-gens cluster. Despite the promising biotechnological potential for the production of green-chemicals, only half of the nic-genes have been experimentally linked to nicotine. In an attempt to systematically identify all the proteins involved in nicotine degradation, a gel-based proteomics approach was used to identify a total of 801 proteins when Paenarthrobacter nicotinovorans was grown on three carbon sources: citrate, nicotine and nicotine and citrate. The differences in protein abundance showed that the bacterium is able to switch between deamination and demethylation in the lower nicotine pathway based on the available C source. Several pAO1 putative genes including a hypothetical polyketide cyclase have been shown to have a nicotine-dependent expression and we hypothesize that the polyketide cyclase would hydrolyze the N1-C6 bond from the pyridine ring with the formation of alpha-keto-glutaramate. Two chromosomal proteins, a malate dehydrogenase, and a d-3-phosphoglycerate dehydrogenase were shown to be strongly upregulated when nicotine was the sole carbon source and could be related to the production of the alpha-keto-glutaramate by the polyketide cyclase.

Keywords

Microbial proteomics Mass spectrometry Nicotine metabolism Paenarthrobacter nicotinovorans 

Abbreviations

2D-PAGE

Two-dimensional polyacrylamide gel electrophoresis

ESI-MS/MS

Electrospray ionization tandem mass spectrometry

HPLC

High performance liquid chromatography

IEF

Isoelectric focusing

LC-MS/MS

Liquid chromatography tandem mass spectrometry

MALDI-MS/MS

Matrix-assisted laser desorption/ionization tandem mass spectrometry

MALDI-TOF MS

Matrix-assisted laser desorption/ionization Time-of-flight mass spectrometry

NDM

Nicotine-degrading microorganisms

PMF

Peptide-mass fingerprint

PTMs

Post-translational modifications

SDS-PAGE

Sodium dodecyl sulfate polyacrylamide gel electrophoresis

T4SS

Type IV secretion system

Notes

Acknowledgments

We thank the past and present members of BioActive Group and the Biochemistry & Proteomics Group for the pleasant environment and fruitful discussions. MM was supported by the Fulbright Senior Postdoctoral Fellowship awarded by the Romania-USA Fulbright Commission to MM (guest) and CCD (host).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Marius Mihăşan
    • 1
    • 2
    Email author
  • Cornelia Babii
    • 1
  • Roshanak Aslebagh
    • 2
  • Devika Channaveerappa
    • 2
  • Emmalyn J. Dupree
    • 2
  • Costel C. Darie
    • 2
  1. 1.BioActive Group, Department of BiologyAlexandru Ioan Cuza University of IaşiIasiRomania
  2. 2.Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular ScienceClarkson UniversityPotsdamUSA

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