3.5 Multi-omics identification of key miRNAs, genes, proteins,
and metabolites
The hierarchical clustering of the DEP, DEMI, DEG and DEM based on the
fold change’ Z score of M4a/(M4b, M4c, M0a, M0b, M0c), six samples’
log10 (Norm), six samples’ Z score of TPM and 20 samples’ Z score of
Norm were showed that all samples can be divided into two different
groups according to control and hypoxia treatment (Fig. S1) . In
general, environmental hypoxia had a significant effect on the overall
gene /miRNA/ protein/metabolite expression profile of P. vachellimuscle.
In this study, the transcriptome, miRNAome, proteome and metabolome ofP. vachelli muscle under hypoxia stress were integrated by
investigating whether changes in “genes/proteins” levels correlated
with changes in the corresponding “negative miRNAs”, and coupled with
mutual KEGG pathways for DEM. This was based on 145 negative
miRNA-mRNA-protein pairs and 33 unique DEM, 16 DEMI, 23 co-DEG/DEP and
17 DEM were involved in the 19
mutual KEGG pathways (Fig.
4B ).
These mutual pathways contained carbohydrate metabolism (i.e., TCA
cycle, pentose phosphate pathway, starch, sucrose, pyruvate, butanoate,
glyoxylate and dicarboxylate metabolism), amino acid metabolism (i.e.,
valine, leucine, isoleucine, cysteine, methionine, alanine, aspartate,
glutamate, D-Glutamine and D-glutamate metabolism), other metabolic
processes (i.e., purine and nitrogen metabolism, biosynthesis of
aminoacyl-tRNA, unsaturated fatty acids, butirosin and neomycin),
membrane transport (i.e., ABC transporters), signal transduction (i.e.,
mTOR signaling pathway), and cellular community (i.e., gap junction).
Genes produce proteins through complex transcription and translation
processes to regulate the metabolism of organisms (Table S5 ).
In our case, downregulated
miR-193b/457a/15b-OGDH, miR-210/338-SDHb, and miR-457a/214-MDH1 led to
suppression of aerobic metabolism (e.g., “Pyruvate metabolism” and
“TCA cycle”), thus making intermediate products rise (e.g., citric
acid and S-lactoylglutathione). “Aminoacyl-tRNA biosynthesis” was
regulated by downregulated miR-15b/338/457a-Aars/mars and
miR-133b/18a/PC-7236-hars to accumulate intermediates (proline,
isoleucine, and methionine).