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. 2024 Oct 3;12(10):2012.
doi: 10.3390/microorganisms12102012.

Integrating the Transcriptome and Proteome to Postulate That TpiA and Pyk Are Key Enzymes Regulating the Growth of Mycoplasma Bovis

Fei Yang  1   2 , Mengmeng Yang  1   2 , Fan Liu  2 , Yanrong Qi  2 , Yanan Guo  1 , Shenghu He  2
Affiliations

Integrating the Transcriptome and Proteome to Postulate That TpiA and Pyk Are Key Enzymes Regulating the Growth of Mycoplasma Bovis

Fei Yang et al. Microorganisms. .

Abstract

Mycoplasma bovis is a global problem for the cattle industry due to its high infection rates and associated morbidity, although its pathophysiology is poorly understood. In this study, the M. bovis transcriptome and proteome were analyzed to further investigate the biology of clinical isolates of M. bovis. A differential analysis of M. bovis, a clinical isolate (NX114), and an international type strain (PG45) at the logarithmic stage of growth, was carried out using prokaryotic transcriptome and 4D-label-free quantitative non-labeled proteomics. Transcriptomics and proteomics identified 193 DEGs and 158 DEPs, respectively, with significant differences in 49 proteins/34 transcriptomic CDS post-translational protein sequences (15 jointly up-regulated and 21 jointly down-regulated). GO comments indicate membrane, cytoplasmic and ribosome proteins were important components of the total proteins of M. bovis NX114 clinical isolate. KEGG enrichment revealed that M. bovis NX114 is mainly associated with energy metabolism, the biosynthesis of secondary metabolites, and the ABC transporters system. In addition, we annotated a novel adhesion protein that may be closely related to M. bovis infection. Triosephosphate isomerase (TpiA) and Pyruvate kinase (Pyk) genes may be the key enzymes that regulate the growth and maintenance of M. bovis and are involved in the pathogenic process as virulence factors. The results of the study revealed the biology of different isolates of M. bovis and may provide research ideas for the pathogenic mechanism of M. bovis.

Keywords: 4D-label-free quantitative proteomics; Mycoplasma bovis; Pyk; TpiA; prokaryotic transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Organelles of M. bovis NX114 vs. PG45 transmission electron microscopy (12,000×). (A) M. bovis NX114. (B) M. bovis PG45. (black arrow: cytoplasm; blue arrow: soluble protein; red arrow: ribosome).
Figure 2
Figure 2
The general pattern of RNA-seq data and the identification of DEGs for M. bovis NX114 vs. PG45. (A) Genomic gene annotation information. (B) FPKM density distribution. (C) PCA analysis. (D) Volcano map of DEGs.
Figure 3
Figure 3
The annotation of the mRNAs of M. bovis NX114 vs. PG45. (A) Equal scale area Venn diagrams of the annotation information of the two strains of M. bovis together at CARH, VFDB and PHI. (B) Interactive Venn plots of the annotation information of the two strains of M. bovis together at CARH, VFDB and PHI. (C) The annotation information of DEGs of M. bovis NX114 vs. PG45. (D) Up- and down-regulated annotation information for DEGs of M. bovis NX114 vs. PG45.
Figure 4
Figure 4
Functional categorization of DEGs of M. bovis NX114 vs. PG45. (A) GO enrichment analysis of DEGs. (B) KEGG enrichment analysis of DEGs. (C) PPi network analysis of DEGs.
Figure 5
Figure 5
The proteomic analysis of M. bovis NX114 vs. PG45. (A) A Venn diagram of the proteome. (B) A PCA analysis of proteomic profiles. (C) A cluster analysis of DEPs of M. bovis.
Figure 6
Figure 6
Functional categorization of DEPs of M. bovis NX114 vs. PG45. (A) GO annotation of DEPs. (B) KEGG enrichment analysis of DEPs. (C) Network analysis of significantly enriched pathways (p < 0.05) interacting with significantly different proteins, red vertices indicate up-regulated proteins, blue vertices indicate down-regulated proteins, and dotted lines represent key coding proteins. (D) Abundance analysis of key DEPs. ** p < 0.05, *** p < 0.01 and **** p < 0.001.
Figure 7
Figure 7
Results of CC subcellular localization of M. bovis NX114 vs. PG45 histones.
Figure 8
Figure 8
Statistical analysis of DGPs and DEGs of M. bovis (A) Common differential gene/protein differential fold correlation analysis. (B) Venn diagrams of DGPs and DEGs.
Figure 9
Figure 9
Joint analysis of M. bovis DGPs and DEGs. (A) Shared significant difference gene/protein clustering analysis. (B) KEGG comparison Venn diagram. (C) pvalue_heatmap. (D) Significant KEGG comparison bubble plot.
Figure 10
Figure 10
Dynamic Mulberry diagram of the common significant KEGG pathway of M. bovis DGPs and DEGs.
Figure 11
Figure 11
The validation of differentially expressed gene expression levels in M. bovis NX114 vs. PG45. (A) The validation of RNA-seq data for randomly selected genes by real-time PCR. * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0001 ns (no significance) p > 0.05. (B) qRT-PCR was used to detect the relative mRNA expression of TpiA and PyK genes at different growth stages. ## p < 0.01, ### p < 0.001 and #### p < 0.0001, ns (no significance) p > 0.05.
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