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Comparative proteomics analysis of root and nodule mitochondria of soybean
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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.
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.
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.
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.
