Proteomics

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Optimization of protein extraction methods for root-associated microbes in Arabidopsis

ABSTRACT: The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Variovorax Paradoxus Agrobacterium Arabidopsis Thaliana (mouse-ear Cress) Pseudomonas Arthrobacter

SUBMITTER: Fernanda Salvato  

LAB HEAD: Manuel Kleiner

PROVIDER: PXD026330 | Pride | 2022-09-08

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
Arabidopsis_file_description.txt Txt
FS021b_Arabidopsis_bacmix_4strains.fasta Fasta
Protocol1_A_1500ng_run1.msf Msf
Protocol1_A_1500ng_run1.raw Raw
Protocol1_B_1500ng_run1.msf Msf
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Publications

Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes.

Salvato Fernanda F   Vintila Simina S   Finkel Omri M OM   Dangl Jeffery L JL   Kleiner Manuel M  

Molecular plant-microbe interactions : MPMI 20221031 11

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two  ...[more]

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