Table 3.S1: Strains and primers used in this study.
Bacillus subtilis strains
Name Genotype Source
W168 B. subtilis wild type strain Bacillus Genetic Stock Center Pveg:nll-metRS W168 lacA::Pveg:nll-metRS; ErmR This study
PcomF:nll-metRS W168 lacA::PcomF:nll-metRS; ErmR This study Pveg:mrfp W168 lacA::Pveg:mrfp; ErmR This study PcomF:mrfp W168 lacA::PcomF:mrfp; ErmR This study comK-mWasabi W168 amyE::comK-mWasabi; CmR This study PcomF:nll-metRS_comK-mWasabi W168 amyE::comK-mWasabi; CmR
lacA::PcomF:nll-metRS; ErmR
This study Pveg:nll-metRS_comK-mWasabi W168 amyE::comK-mWasabi; CmR
lacA::Pveg:nll-metRS; ErmR This study
Primers
Name Sequence
YH110 GATCGAATTCGGAGTTCTGAGAATTGGT
YH119 GATCGGTCTCCCACCTTTCTCTAGTAACATTTATTGTACAACACGAGCC YH152 GATCACTAGTTTATTAAGCACCGGTGGAGT
YH235 GATCAAGCTTATCGAATTCGGAACAATTGTGAACGGATAATAAA YH236 GATCGGTCTCTGACTCATATTATGGCCTCCA
YH255 GATCGAATTCTGCGAGCTGCTGTTATCCAC
YH256 GATCGGTCTCTTGAGTTTCAACTGGCACATTCACATAGCAC YH259 GATCGGTCTCACTCAAGTCGCGAAGAAAATTC
YH260 GATCCTCGAGTTTAGAGGCTTCCACCAGTG YH278 GATCGGTCTCCTCCACCATACCGTTCCCCGAGCT
YH279 GATCGGTCTCGTGGAGGAGGATCCGTCAGTAAAGGGGAAGAAAC
proteins identified by LC-MS/MS from the BONCAT-enriched samples are listed. Columns A- E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-M give LC-MS/MS ion intensities for each protein in the wild-type and PpvdF:nll-metRS strains in either iron- depleted or iron-replete conditions. Columns N-U give LC-MS/MS normalized LFQ values for each protein in the wild-type and PpvdF:nll-metRS strains in either iron-depleted or iron-replete conditions.
Data Set A.2 Full proteomic results from P. aeruginosa biofilm labeling experiments. All proteins identified by LC-MS/MS from the BONCAT-enriched samples are listed. Columns A- E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-K give LC-MS/MS iBAQ values for each protein in the PpvdF:nll-metRS (columns F-H) and Ptrc:nll-metRS (columns I-K) strains. Columns L-Q give LC-MS/MS normalized LFQ values for each protein in the PpvdF:nll-metRS (columns L-N) and Ptrc:nll-metRS (columns O-Q) strains. Columns R-T give the log2-transformed LFQ ratios (fold change, PpvdF / Ptrc) for proteins shared between the
two strains, the fold change, and the corresponding FDR adjusted p-values.
Data Set A.3 Full proteomic results from two separate sets of biofilm labeling experiments.
All proteins identified by LC-MS/MS from the BONCAT-enriched samples are listed. Columns A-E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-K give LC- MS/MS iBAQ values for each protein identified in PpvdF:nll-metRS samples prepared from two sets of experiments. Columns L-Q give LC-MS/MS iBAQ values for each protein identified in Ptrc:nll-metRS samples prepared from two sets of experiments. Columns R-W give LC-MS/MS normalized LFQ values for each protein identified in PpvdF:nll-metRS samples prepared from two sets of experiments. Columns X-AC give LC-MS/MS normalized LFQ values for each protein identified in Ptrc:nll-metRS samples prepared from two sets of experiments.
Data Set A.4 Full results from the KEGG Pathway analysis. Each sheet contains LC- MS/MS data from a certain annotated KEGG pathway. Line 1 of each sheet gives the annotation of the KEGG pathway and the Mann-Whitney U test result compared with the control group where all shared proteins were included. Columns A-E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-H give the log2-transformed LFQ ratios (fold change, PpvdF / Ptrc) for proteins shared between the two strains, the fold change, and the corresponding FDR adjusted p-values. Columns I and J show whether a certain protein was
Columns A-E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-H give LC-MS/MS iBAQ values for each protein identified in PpvdF:nll-metRS samples. Columns I-K give LC-MS/MS iBAQ values for each protein identified in PpvdF:nll-metRS samples. Sheet 2 gives the LC-MS/MS results of both the PpvdF:nll-metRS and the Ptrc:nll-metRS samples.
Columns A-E give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in both the PA14 and PAO1 strains. Columns F-K give LC-MS/MS iBAQ values for each protein in the PpvdF:nll-metRS (columns F-H) and Ptrc:nll- metRS (columns I-K) strains. Columns L-Q give LC-MS/MS normalized LFQ values for each protein in the PpvdF:nll-metRS (columns L-N) and Ptrc:nll-metRS (columns O-Q) strains.
Columns R-T give the log2-transformed LFQ ratios (fold change, PpvdF / Ptrc) for proteins shared between the two strains, the fold change, and the corresponding FDR adjusted p-values.
Data Set A.6 Proteins identified both in the Babin study and in this work, along with the full proteomic results obtained here. Combination of Data Set A.2 with the proteomic data from the Babin study. Columns A-T are the same as those in Data Set A.2. Columns U-W give
the log2-transformed LFQ ratios (fold change, PrpoS / Ptrc) for proteins shared between the two strains, the fold change, and the corresponding FDR adjusted p-values.
Data Set A.7 Proteins identified both in the oxygen limitation study and in this work, along with the full proteomic results obtained here. Combination of Data Set A.2 with the proteomic data from previous oxygen stress study. Columns A-T are the same as those in Data Set A.2. Columns U-W give the log2-transformed LFQ ratios (fold change, anaerobic/aerobic) for proteins shared between the two conditions, the fold change, and the corresponding FDR adjusted p-values.
All proteins identified by LC-MS/MS from the BONCAT-enriched samples are listed. Columns A-D give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in W168 strain. Column E gives LC-MS/MS ion intensities for each protein in the wild-type strain without K-state induction. Columns F-K give LC-MS/MS ion intensities for each protein in the PcomF:nll-metRS strain without (columns F-H) and with (columns I-K) K-state induction. Column L gives LC-MS/MS normalized LFQ values for each protein in the wild-type strain without K-state induction. Columns M-R give LC-MS/MS normalized LFQ values for each protein in the PcomF:nll-metRS strain without (columns M-O) and with (columns P-R) K-state induction.
Data Set B.2 Full proteomic results from B. subtilis K-state labeling experiments. All proteins identified by LC-MS/MS from the BONCAT-enriched samples are listed. Columns A- D give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in W168 strain. Columns E-J give LC-MS/MS iBAQ values for each protein in the PcomF:nll-metRS (columns E-G) and Pveg:nll-metRS (columns H-J) strains.
Columns K-P give LC-MS/MS normalized LFQ values for each protein in the PcomF:nll-metRS
(columns K-M) and Pveg:nll-metRS (columns N-P) strains. Columns Q-S give the log2- transformed LFQ ratios (fold change, PcomF / Pveg) for proteins shared between the two strains, the fold change, and the corresponding FDR adjusted p-values.
Data Set B.3 Full results from the Gene Ontology (GO) analysis. Sheet 1 contains LC- MS/MS data from establishment of competence for transformation (GO: 0030420) pathway;
sheet 2 contains LC-MS/MS data from SOS response (GO: 0009432) pathway. In each sheet, line 1 gives the annotation of the KEGG pathway and the Mann-Whitney U test result compared with the control group where all shared proteins were included. Columns A-D give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in W168 strain. Columns E-G give the log2-transformed LFQ ratios (fold change, PcomF / Pveg) for proteins shared between the two strains, the fold change, and the corresponding FDR adjusted p-values. Columns H and I show whether a certain protein was only identified in at least two replicates of PcomF:nll-metRS and Pveg:nll-metRS samples, respectively.
Data Set B.4 Full results from the KEGG Pathway analysis. Each sheet contains LC- MS/MS data from a certain annotated KEGG pathway. Line 1 of each sheet gives the annotation of the KEGG pathway and the Mann-Whitney U test result compared with the control group where all shared proteins were included. Columns A-D give the Uniprot ID of the protein, the protein description, the corresponding gene name if available, and the locus ID in W168 strain. Columns E-G give the log2-transformed LFQ ratios (fold change, PcomF / Pveg)