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Comparative proteomics analysis, Slides of Proteomics

Comparative proteomics analysis of root and nodule mitochondria of soybean

Typology: Slides

2024/2025

Uploaded on 04/14/2025

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Comparative proteomics
analysis of root and nodule
mitochondria of soybean
Sin, wa i - c h i ng & j i n h o n g , liu & z h o ng, jia & l am, hon- m i n g & lim, b o o n .
(2024). C o m p arative proteom i c s a nalysis o f r o o t and no d u l e
mitocho n d r i a of soybea n . P l a nt, cel l & e nvironment.
10.1111 / p c e . 1 5026.
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Comparative proteomics

analysis of root and nodule

mitochondria of soybean

Si n , w a i - ch i ng & j i n ho ng , l i u & z h o ng , j ia & l am , h o n- m i ng & l i m, b o on.

( 20 24). C o mp ara t i v e p ro t e o m ic s a na l ys i s o f ro o t an d n o d ul e

mi t o ch o nd r i a o f s oy b e a n. P la n t , c e l l & e n v i ro nm e n t.

  1. 111 1/ p c e. 1 502 6.

Overview:

The paper investigates a critical aspect of legume biology: the symbiotic relationship between

soybeans and rhizobia, focusing specifically on the metabolic adaptations within soybean root

nodule mitochondria.

The process of nitrogen fixation uses a lot of energy and requires a significant amount of carbon.

To keep this partnership working, legume nodules provide malate to the bacteroids as their main

source of carbon and energy. In return, the bacteroids give the legumes ammonium ions and other

nitrogen compounds.

This paper delves into how the mitochondria within the soybean root nodules adapt their

metabolism to efficiently supply the carbon (as malate) needed for nitrogen fixation.

Overall Principle:

The goal is to identify and quantify the proteins present in the mitochondrial samples.

This is achieved by first digesting the proteins into peptides, separating those peptides using

liquid chromatography, and then identifying and quantifying them using tandem mass

spectrometry.

Mitochondria and protein extraction:

Harvest and Homogenization:

Freeze the tissue,

then grind and

homogenize it.

Isolated

mitochondria were

transferred to 2‐mL

centrifuge tubes in

a 0.7 M sucrose

homogenization

buffer.

Soybean

mitochondria from

uninoculated roots

and nodules were

subsequently

isolated via a

sucrose and Percoll

density gradient.

At 28 days post

inoculation (DPI),

uninoculated root

and nodule tissues

were harvested

separately and

flash‐frozen in

liquid nitrogen.

Peptide

Preparation:

o Protein Digestion : Allows

for the analysis of proteins

at the peptide level, which

is more feasible with mass

spectrometry.

o Desalting : Essential for

maintaining the sensitivity

and accuracy of the mass

spectrometry analysis.

o Drying and Resuspension :

Ensures that the peptides

are in a suitable state for

injection into the mass

spectrometer.