PMC

Clustering of biofilm and planktonic samples based on transcriptomic data. Data represent results of principal-component analysis (PCA) of log₂ FPKM expression values from each sample. The PCA plot represents 1,781 genes for which expression values were available. Biological triplicates are shown by matching symbols.

Correlation between transcriptome and proteome. Expression values within each time point were normalized by z-scoring, and the Pearson correlation coefficient was calculated for all genes with corresponding proteins identified in either the cellular proteome (A) or the cell wall proteome (B). The graphical representation of the full correlation between the indicated time points is available in the supplemental material.

Clustering of biofilm and planktonic samples based on proteomic data. Data represent results of principal-component analysis (PCA) of log₂ LFQ intensity values from each sample in either the cellular proteome (A) or the cell wall proteome (B). The PCA plot represents 532 proteins (cellular proteome) or 489 proteins (cell wall proteome) for which expression values were available. Technical triplicates are shown by matching symbols and colors. Biological duplicates are shown by matching symbols.

Expression profiles of GAS virulence factors during planktonic and biofilm growth. (A) z-scored expression values for 54 characterized and putative GAS virulence factor genes. The putative phage hyaluronidase genes are denoted with the symbol “hyl” followed by the predicted molecular mass. (B) z-scored expression values for the 14 of the 54 GAS virulence factors with corresponding proteomic data in the cellular fraction. (C) z-scored expression values for the 12 of the 54 GAS virulence factors with corresponding proteomic data in the cell wall fraction.

Characterization of differentially expressed genes based on their COG classification. Genes that were determined to have a significant 2-fold difference in expression between at least one biofilm time point and one planktonic time point were categorized based on their COG classification. The numbers of genes in each COG classification are shown for the 1,039 genes with differential expression based on transcriptome data. Letter designations refer to the standard COG abbreviations. Numbers sum to greater than 1,039 due to some genes fitting in two or more COG classifications. The “Poorly Characterized” group includes COG classifications R (general function prediction only) and S (unknown function) in addition to unclassified genes.

Characterization of differentially expressed proteins based on their COG classification. Proteins that were determined to have a significant 2-fold difference in expression between at least one biofilm time point and one planktonic time point were categorized based on their COG classification. The numbers of proteins in each COG classification are shown for the 320 proteins with differential expression based on cellular proteome data (A) and for the 376 proteins with differential expression based on cell wall proteome data (B). Letter designations refer to the standard COG abbreviations. Numbers sum to greater than 320 or 376 due to some proteins fitting in two or more COG classifications. The “Poorly Characterized” group includes COG classifications R (general function prediction only) and S (unknown function) in addition to unclassified proteins.