Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth
Fig 5
Genetic background shapes adaptive trajectories.
A) Principal component analysis (PCA) of variance stabilizing transformed expression counts from ancestral and evolved biofilm populations. Arrows are drawn between corresponding ancestral and evolved populations, indicating the trajectory of evolution across passaging. Points are colored by sub-lineage of the ancestral population. B) PCA of variance stabilizing transformed expression counts from ancestral and evolved populations grown under planktonic conditions. Like panel A, arrows are drawn between corresponding ancestral and evolved populations and are colored by sub-lineage. Biofilm passaging reduced transcriptome diversity, with populations converging on a sub-lineage-specific signature (A); this pattern was not observed under planktonic growth conditions (B). N.B. While the positions of ancestral and evolved states are known (dots on the PCA), the trajectories between them are not, and connecting lines shown here are schematic. C) Bar plot of DEGs comparing evolved and ancestral biofilm populations broken down by sub-lineage. There are 680 DEGs shared between sub-lineages, and 405 and 200 DEGs unique to L4.4 and L4.9, respectively. Opacity of the bar indicates the subset of DEGs that are either up (dark) or downregulated (light) after passaging. The pellicle biofilm transcriptome is characterized by broad scale downregulation of gene expression with a smaller complement of genes that are upregulated in a sub-lineage specific manner. D) Differential expression of DEGs unique to each sub-lineage, from the comparison of evolved to ancestral biofilm populations. Log transformed adjusted p-values plotted against the log2 fold change for each gene. Genes that did not have significant differential expression are shown in grey. Lineage 4.9 evolved a larger complement of upregulated genes in response to biofilm passaging.