Table 1.
Transcriptional differences in HP compared to the WT strain at the level of biological processes
| Gene sets | HP vs WT | ||||||
|---|---|---|---|---|---|---|---|
| Ontology | Name | Code | Size | t1 | t2 | t3 | t4 |
| KEGG Pathway | Translation | 145 | + | + | |||
| Ribosome | sen03010 | 64 | + | + | |||
| Metabolism of terpenoids and polyketides | 128 | + | + | + | |||
| Biosynthesis of ansamycins | sen01051 | 13 | + | + | + | ||
| Biosynthesis of 12-, 14- and 16-membered macrolides | sen00522 | 8 | + | + | + | ||
| Type I polyketide structures | sen01052 | 9 | + | + | + | ||
| Nitrogen metabolism | sen00910 | 56 | − | ||||
| C5-branched dibasic acid metabolism | sen00660 | 10 | + | ||||
| Valine, leucine and isoleucine biosynthesis | sen00290 | 23 | + | ||||
| Tyrosine metabolism | sen00350 | 38 | − | ||||
| Tryptophan metabolism | sen00380 | 39 | + | + | |||
| Glycolysis/gluconeogenesis | sen00010 | 74 | − | ||||
| Citrate cycle (TCA cycle) | sen00020 | 48 | − | ||||
| Pyruvate metabolism | sen00620 | 73 | − | ||||
| Metabolism of cofactors and vitamins | 192 | + | |||||
| Lipid metabolism | 169 | − | |||||
| Fatty acid biosynthesis | sen00061 | 29 | − | ||||
| Xenobiotics biodegradation and metabolism | 175 | − | |||||
| Styrene degradation | sen00643 | 13 | + | ||||
| Atrazine degradation | sen01052 | 9 | − | − | |||
| Purine metabolism | sen00230 | 88 | − | − | |||
| Nucleotide metabolism | 118 | − | − | − | |||
| Oxidative phosphorylation | sen00190 | 49 | + | ||||
| Inositol phosphate metabolism | sen00562 | 20 | + | ||||
| Membrane transport | 138 | − | |||||
| ABC transporters | sen02010 | 117 | − | ||||
| GO biological process | DNA biosynthetic process | GO:0071897 | 18 | − | − | ||
| DNA replication | GO:0006260 | 29 | − | − | |||
| DNA integration | GO:0015074 | 48 | − | ||||
| DNA recombination | GO:0006310 | 44 | + | − | |||
| DNA repair | GO:0006281 | 45 | − | ||||
| Transposition, DNA-mediated | GO:0006313 | 62 | − | − | − | ||
| DNA-templated transcription, initiation | GO:0006352 | 36 | − | − | − | ||
| Negative regulation of transcription, DNA-templated | GO:0045892 | 19 | − | − | |||
| Translation | GO:0006412 | 68 | + | + | + | ||
| Methylation | GO:0032259 | 126 | + | ||||
| Dephosphorylation | GO:0016311 | 26 | + | ||||
| Biosynthetic process | GO:0009058 | 59 | + | + | |||
| Fatty acid biosynthetic process | GO:0006633 | 23 | − | ||||
| Antibiotic biosynthetic process | GO:0017000 | 16 | + | + | + | ||
| Proteolysis | GO:0006508 | 152 | + | + | + | ||
| Amino acid transmembrane transport | GO:0003333 | 33 | − | ||||
| Carbohydrate transport | GO:0008643 | 25 | − | ||||
For each ontology used, KEGG pathways or GO Biological process, gene set names, codes and sizes (total numbers of S. erythraea genes associated with the gene set) are shown. Significant enrichment (p < 0.01 for KEGG and p < 0.05 for GO) of the individual gene sets in up- or down-regulated genes at individual time points (t1–t4) is represented by ‘+’ or ‘−’, respectively. Pathways with missing codes are the top KEGG ontology terms