PATHOgenex is a freely available online RNA atlas of 32 human bacterial pathogens exposed to 11 infection relevant stress. The stress exposed bacterial cultures (triplicates) were compared to un-exposed exponentially grown cultures for differential gene expression analysis. The transcriptome data is generated with RNAtag-Seq, which allows multiple library preparation, including rRNA depletion, in one tube.
The data in PATHOgenex atlas can be retrieved either with browsing one/multiple particular strains or searching one/multiple genes by gene name, RefSeq new locus tag or old locus tag, protein ID or gene product name.
Gene expression data:
The relative expression of each gene (annotated CDS) for each strain in the atlas were calculated with TPM and RPKM. The TPM and RPKM values at each stress condition can be visualized on a bar plot and also downloaded as text. The bar plot shows expression values of one selected gene at a time.
Differential gene expression data:
The differential gene expression data was generated with stress exposed bacterial cultures versus un-exposed control cultures. Differentially expressed genes are defined with fold change 1.5 and FDR-corrected p-value < 0.05.
The differential gene expression data can be found under the heatmap tab. Users are able to search one or multiple genes with RefSeq new locus tag, old locus tag, protein ID or gene product name with search function. The results from a search can be visualized with a heatmap (with log2 Fold Change), which allows co-visualization of multiple genes at the same time by selecting desired genes. The default FDR-corrected p-value is set as < 0.05 which could be changed with ‘Set FDR-corrected p-value tool’.
Abbreviations used for stress conditions:
As: Acidic stress
Bs: Bile stress
Li: Low iron
Nd: Nutritional downshift
Ns: Nitrosative stress
Oss: Osmotic stress
Oxs: Oxidative stress
Sp: Stationary phase
Vic: Virulence inducing condition
Clustering genes based on iso-functional homologs in PATRIC database:
The genes of the 32 strains in the atlas were clustered together based on their sequence homology and function with PGfam groups defined in PATRIC database. The clustering was performed with two approaches: first, with clustering all genes from the 32 strains, and second, clustering genes from Gram-negative and -positive strains separately. The PGFam groups associated to each gene can also be seen in the gene table.
PTDEX scores indicate the probability of PGFam groups to be regulated under each stress condition. They are calculated separately according to the two gene clustering approaches named as General PTDEX score and Gram-negative and -positive specific PTDEX scores.
Bacterial strains in PATHOgenex atlas:
|Species||Strain||Genome acc. Num.|
|Burkholderia pseudomallei||K96243||NC_006350, NC_006351|
|Campylobacter jejuni||subsp. jejuni 81-176||NC_008787, NC_008770, NC_08790|
|Escherichia coli EPEC||0127:H6 E2348/69||NC_011601|
|Escherichia coli ETEC||H10407||NC_017633, NC_017721, NC_017722, NC_017723, NC_017724|
|Escherichia coli UPEC||536||NC_008253|
|Francisella tularensis||subsp. holarctica FSC200||C_019551|
|Klebsiella pneumoniae subsp. pneumoniae||MGH 78578||NC_009648, NC_009649, NC_009650,NC_009651, NC_009652, NC_009653|
|Legionella pneumophila subsp. pneumophila||Philadelphia 1||NC_002942|
|Neisseria gonorrhoeae||FA 1090||NC_002946|
|Neisseria meningitidis||serogroup C FAM18||NC_008767|
|Salmonella enterica subsp. enterica serovar Typhimurium||SL1344||NC_016810, NC_017718, NC_017719, NC_017720|
|Shigella flexneri||5a str. M90T||CM001474|
|Staphylococcus aureus||MSSA476||NC_002953, NC_005951|
|Staphylococcus epidermidis||1457||CP020462, CP020463|
|Vibrio cholerae||O1 biovar El Tor str. N16961||NC_002505, NC_002506|
The infection relevant consensus stress conditions:
The bacterial cultures were exposed 10 stresses mimicking different infection-relevant stress conditions expected to be encountered by bacterial pathogens in the human host: acidic stress, bile stress, low iron, hypoxia, nutritional downshift, nitrosative stress, osmotic stress, oxidative stress, high temperature and starvation (stationary phase).
They were also exposed to specific in vitro virulence inducing conditions, such as shifting Yersinia pseudotuberculosis from 26°C to 37°C and depleting extracellular Ca2+, L-lactate supplementation for Neisseria spp., and the presence of charcoal-like resin XAD-4 in the growth medium for Listeria monocytogenes. For some species, such as Mycobacterium tuberculosis and Legionella pneumophila, virulence inducing conditions are unknown and were not performed. As the control for differential expression analyses, we utilized unexposed, exponentially grown bacteria.
The growth temperature and culture medium were adjusted for each specific strain to achieve optimal growth conditions. Similarly, the strength of the stress with the different agents and associated exposure time was designed to be as similar and relevant as possible for each bacterial species. However, minor changes were necessary for certain conditions; for example, the “low pH level” used for Helicobacter pylori strains were lower than for the others, and a significantly higher H2O2 concentration was required to induce a stress response in Acinetobacter baumannii.
|Condition||Growth Medium||Growth Temperature||OD600||Stress||Exposure Time|
|Control (Ctrl)||Ambient Med.||Ambient Temp.||0.1-0.5||-||10 minutes|
|Acidic Stress (As)||Ambient Med.||Ambient Temp.||0.1-0.5||pH: 3-5||10 minutes|
|Bile Stress (Bs)||Ambient Med.||Ambient Temp.||0.1-0.5||0.5% Bile Salts||10 minutes|
|Temperature (Tm)||Ambient Med.||Ambient Temp.||0.1-0.5||41 C||20 minutes|
|Hypoxia (Hp)||Ambient Med.||Ambient Temp.||0.1-0.5||Low oxygen||3-4 hours|
|Low iron (Li)||Ambient Med.||Ambient Temp.||0.1-0.5||250 μM 2,2-dipyridryl||10 minutes|
|Nitrosative Stress (Ns)||Ambient Med.||Ambient Temp.||0.1-0.5||250 μM Spermine NONOate||10 minutes|
|Nutritional downshift (Nd)||Ambient Med.||Ambient Temp.||0.1-0.5||1X M9 salts||30 minutes|
|Osmotic Stress (Oss)||Ambient Med.||Ambient Temp.||0.1-0.5||0.5 M NaCl||10 minutes|
|Oxidative Stress (Oxs)||Ambient Med.||Ambient Temp.||0.1-0.5||0.5-10 mM H2O2||10 minutes|
|Stationary phase (Sp)||Ambient Med.||Ambient Temp.||0.5-2.5||Stationary phase||3-16 hours|
|Vir. Ind. Cond. (Vic)||Ambient Med.||Ambient Temp.||0.1-0.5||Varies||Varies|