Fig. 6: YdiP regulates cold shock proteins at low temperature.

a Significant (P = 5.7 e⁻⁷ by Student’s two-sided t-test) differential GIs of ydiP with other TF gene mutants in RM and MM. b, c GI patterns (b) and correlation (c) profile of ydiP in static and differential networks with genes involved in cold shock adaptation. d YdiP interaction with indicated cold shock proteins in different growth and temperature conditions by affinity purification and mass spectrometry (n = 3 biologically independent experiments). e YdiP steady-state level in RM and at different temperatures over time. Band intensities normalized to E. coli Hsp60 loading control (LC; 1:15000 dilution). Immunoblot shown is representative of 2 independent biological experiments. Molecular masses (kDa) of marker proteins are indicated. f Transcript levels of ydiP measured in wild-type (WT) and ydiP mutant strain background in RM and MM at 15 °C are shown as fold change (n = 3 biologically independent experiments; P = 1.1 e⁻³ by Student’s two-sided t-test) after normalizing to respective strains and growth conditions at 37 °C. g Representative cell morphology micrographs of ydiP and csp single and double mutants, as well as overexpression of ydiP (indicated with ‘+’) in ydiP mutant strain in RM at 15 °C are shown along with cell length measurements (n ≥ 25 cells over five biologically independent experiments; P = 1.8 e⁻²⁸ by Student’s two-sided t-test). Scale bar, 10 µm. h Mapped reads from YdiP ChIP-seq is plotted against the position of indicated genes in genomic region, including YdiP binding to its putative cspE target in RM and MM at 15 °C. Positive value indicate plus (or sense) strand, and negative value specify minus (or antisense) strand. Fold enrichment (shown as a zoom-in; n = 3 biologically independent experiments) of YdiP binding site to cspE using a chromosomal YdiP FLAG₃-tagged strain was compared to an untagged strain after normalizing to a negative control (i.e., primers designed away from YdiP binding site of cspE was amplified from YdiP- FLAG₃) in different growth and temperature conditions. Significance (P = 3.4 e⁻⁴ or P = 4.5 e⁻⁵) by Student’s two-sided t-test between the YdiP FLAG₃-tagged strain grown in RM or MM at 15 °C and 37 °C. i Transcript levels of csp genes measured in WT and ydiP mutant in RM and MM at 15 °C are shown as fold change (n = 3 biologically independent experiments) after normalizing to respective strains and growth conditions at 37 °C. Significance (*P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001) by Student’s two-sided t-test. j Model illustrating YdiP as an activator and repressor of various cold shock proteins in RM and MM growth conditions. Data (f–i) are presented as mean ± standard deviation from the indicated number of independent samples. Source data are provided as a Source Data file.