A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis

Figures & data

Figure 1. Overview of the study and experiment design.

Figure 2. Consistent differential gene expression in H112 across 7H9 (nutrient-rich) and NR (stress) medium conditions relative to H54.

The number of differentially expressed genes in each growth condition and the intersections (number of common genes) between them are illustrated. For example, in the right panel, 221 genes showed consistent differential expression (downregulated) at RNA levels across both 7H9 and NR conditions, whereas 121 genes were upregulated at RNA levels under the conditions. Consistent differential gene expression at both RNA levels across conditions is highlighted in blue. Similarly, 20 and 5 genes were downregulated and upregulated, respectively, at both RNA and protein levels (highlighted in maroon) across the conditions. The direction of expression change is indicated as in H112 relative to H54.

Figure 3. An integrated analysis of genomic, transcriptomic, and proteomic differences between hyper-virulent strain H112 and phylogenetically related low-virulent strain H54.

A and B depict gene expression changes in H112 relative to H54. The up- and down-regulated genes are presented with red and blue color, respectively, where the intensity of the color is proportional to the expression fold difference (p-value <0.05).

Table 1. Associations between genetic mutations in the hyper-virulent strain and differential gene expression.

Gene	Mutation in the hyper virulent strain (M. tuberculosis H112 and others)		Differential transcript abundance under stress		Differential transcript abundance under exponential growth		Differential protein abundance under exponential growth
	Nucleotide-change	Amino acid change	log2 FC	adjusted p-value^1	log2 FC	adjusted p-value^1	log2 FC	p-value^1
rv0178	209387T>G	D150E	−0.053	0. 945135842	0.088	0. 66248835	0.001231521	0. 997765
rv0209	249350 G>A	A105T	−0.489	0. 49130674	−0.164	0. 523453133	ND	ND
fadE5 (Rv0244c)	295746C> T	Intergenic	−3.712	1.43E-22	−4.406	3.6477E-288	−0. 316649866	0.019496
mkl (Rv0655)	752134C>T	Synonymous	−0.473	0. 326913082	−0.718	1.12108E-07	−0.032799587	0. 894773
rv1443c (Rv1443c)	1622580C>A	R38 L	0.079	0. 933935313	−0.089	0. 75301824	−1. 15916957	0.045304
higB (Rv1955)	2201808C>G	D30E	1.256	0.006633891	1.405	2.24982E-24	ND	ND
rv2696c	3012950 G>T	A220E	−0.132	0. 845216821	−0.087	0. 655654126	0. 377485595	0. 238744
fadD29 (Rv2950c)	3301648T>G	M270 L	−1.407	0. 180054358	−1.548	5.24449E-30	1. 290589217	0.014501
agpS (Rv3107c)	3476350 G>A	Synonymous	−0.202	0. 783781504	−0.251	0. 256871347	−5.18E-01	0.001954
uvrD2 (Rv3198c)	3569220 G>A	Synonymous	−0.41	0. 442191072	−0.224	0. 189296005	ND	ND
rv3371	3785898 G>A	A323T	−2.597	2.34E-07	−2.315	1.08152E-64	ND	ND
eccC4 (Rv3447c)	3865243 G>T	A999D	−0.102	0. 938408558	0.527	0. 142335432	ND	ND
rv0633c	9bp Deletion at 730085	Within coding-sequence	0.473	0. 453204256	0.317	0.07937841	ND	ND
phoP (Rv0757)	2bp Deletion at 854259	Intergenic	1.253	0.003101432	0.844	3.74101E-11	−9.67E-02	0. 297817
pip (Rv0840c)	1358bp Insertion at 937115	Within coding-sequence	−1.257	0.004845373	−0.656	0.000120335	ND	ND
rv2168c	1bp Deletion at 2431514	Intergenic					ND	ND
rv2286c	1358bp Insertion at 2559504	Within coding-sequence	−0.445	0. 48226638	−0.852	0.000356763	ND	ND

^ap-value <0.05 are highlighted in orange. Log2 FC refers to fold-change in H112 relative to H54. ND refers to proteins that were not detected.

Figure 4. Proposed mechanisms of hyper-virulence in the clinical strain H112 compared to low-virulent strain H54.

Data availability statement

The raw data of RNA seq and LC-MS/MS and the expression differences for each gene between hyper-virulent strain H112 and ordinary virulent strain H54 can be accessed through https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203662 (RNA) and https://doi.org/10.1080/21505594.2022.2087304 (Protein).