Fig 1.
Cell growth phase sampling strategy at 4°C and 20°C.
Table 1.
Primers used for quantitative PCR validation of RNA-seq data.
Fig 2.
Principle component analysis plot of RNA sequencing biological replicates.
C1 through C5 refer to the L. monocytogenes control cultures grown at 20°C, and T1 through T5 represent the treated cultures grown at 4°C (see Fig 1 for information about the sampling points). Samples marked with * were excluded from our analyses due to an abundance of outlier data points.
Fig 3.
Numbers of L. monocytogenes sense and antisense RNAs differentially expressed at five growth phases in response to cold stress (4°C relative to 20°C).
Differential expression (DE) analyses were performed using DESeq2 and DE was reported as log2 fold changes. Genes with a >2-fold change (> 1 log2) in expression and an adjusted p-value < 0.05 were considered DE. See Fig 1 for information about growth phases.
Fig 4.
Heatmaps showing the number of L. monocytogenes sense and antisense RNA co-upregulated or co-downregulated (>2-fold) between pairs of growth phases at 4°C.
Numbers outside of the pyramids represent the number of genes uniquely upregulated or downregulated at each growth phase. See Fig 1 for information about growth phases.
Table 2.
Core set of genes upregulated (>2-fold) across multiple (≥4) growth phases in L. monocytogenes cells at 4°C vs. 20°C.
Table 3.
Pathways and gene ontology processes significantly (p<0.05*) enriched among genes upregulated (>2-fold) at 4°C vs. 20°C.
Fig 5.
Differential gene expression patterns observed in L. monocytogenes cells grown across five growth phases at 4°C (see Fig 1).
Clusters were formed using fuzzy c-means soft clustering and standardized log2 fold change values for 4°C expression levels vs. 20°C expression levels at each growth phase. Numbers in parentheses denote the number of genes in each cluster core. Represented genes had cluster membership values >0.5. See Fig 1 for information about growth phases.
Table 4.
Pathways and gene ontology processes significantly (p<0.05*) enriched among genes downregulated (>2-fold) at 4°C vs. 20°C.
Table 5.
Top 10 most highly induced genes in L. monocytogenes cells at 4°C vs 20°C at five different growth phases.
Table 6.
Genes commonly associated with the L. monocytogenes CSR.
Table 7.
Transcription regulators significantly (p<0.05*) overrepresented among genes differentially expressed at 4°C vs. 20°C.
Fig 6.
Relative proportions of specific branched-chain fatty acids (FAs) out of total FAs found in L. monocytogenes cells harvested across five growth phases at 4°C and 20°C.
A) anteiso C15:0, B) iso C15:0, and C) anteiso C17:0. Lipids were extracted from cell concentrates and resulting fatty acid methyl esters (FAME) were analyzed by gas chromatography. See Fig 1 for information about growth phases.
Fig 7.
Relative proportion of short chain and unsaturated fatty acids (UFAs) out of total FAs found in L. monocytogenes cells harvested across five growth phases at 4 and 20°C.
A) Proportion of short chain fatty acids containing ≤14 carbons, B) Proportion of C16:1 cis-Δ9 (palmitoleic acid), C18:1 cis-Δ9 (oleic acid), and all remaining UFAs. Lipids were extracted from cell concentrates and resulting fatty acid methyl esters (FAME) were analyzed by gas chromatography. See Fig 1 for information about growth phases.
Fig 8.
Proportions of anteiso C15:0 and the combined sum of the unsaturated fatty acids 16:1 cis-Δ9 and 18:1 cis-Δ9 out of total FAs found in L. monocytogenes cells harvested across five growth phases at 4°C.
Lipids were extracted from cell concentrates and resulting fatty acid methyl esters (FAME) were analyzed by gas chromatography. See Fig 1 for information about growth phases.
Table 8.
Top 20 most highly expressed antisense transcripts in L. monocytogenes at 20°C and 4°C.
Fig 9.
Coverage maps of select highly expressed antisense transcripts in L. monocytogenes cells grown at 20 or 4°C (refer to Table 6).
The coverage maps shown are from stationary phase cultures grown at 4°C. Panels A-F shows individual paired-end, reads while panel G shows overall coverage trends for rRNA (5, 16, and 23S). Reads with the same start and end alignment positions are overlaid and depicted in green. Areas shaded in blue and orange denote sense and antisense transcripts of target genes, respectively.