TABLE 1.
Summary of functional annotation enrichment analyses for the KMC results of the transcriptomic and proteomic data
| Cluster | No. of members | Enriched functional group(s) | DAVID functional annotation clustering result(s) (P value)a | Quantile (%) | Fold change (vs. 0 min) at: |
|||
|---|---|---|---|---|---|---|---|---|
| 10 min | 30 min | 60 min | 120 min | |||||
| Transcriptome | ||||||||
| 1 | 127 | This cluster contains 54 genes previously assigned to the σB-dependent general stress regulon. Of these, 46 show a minimum 8-fold induction 30 min after osmotic upshift. | Stress response (0.035), CBS domain (0.041) | 75 | 10.9 | 19.2 | 6.0 | 7.2 |
| 50 | 5.2 | 10.5 | 3.3 | 3.9 | ||||
| 25 | 3.0 | 4.3 | 2.2 | 2.2 | ||||
| 2 | 104 | This cluster contains 83 genes of unknown function. The remaining 21 genes are functionally very divergent. 47 genes encode IMPs, lipoproteins, or secreted proteins. | Membrane protein (0.026), DNA binding (0.031) | 75 | 2.0 | 6.1 | 1.7 | 1.5 |
| 50 | 1.5 | 3.6 | 1.4 | 1.2 | ||||
| 25 | 1.1 | 2.5 | 1.1 | −1.1 | ||||
| 3 | 109 | This cluster contains 23 σB-dependent genes and 27 genes involved in transport processes (e.g., glnT, gntP, mntACDH, mrpBCDFG, and opu transporters). | Transporter (5.9E−4), lipid-anchored proteins/ABC transporter (0.006), amino/organic acid transport (0.009), tellurium resistance protein (0.013), stress response (0.014) | 75 | 3.2 | 10.5 | 5.0 | 3.8 |
| 50 | 1.9 | 6.1 | 3.3 | 2.5 | ||||
| 25 | 1.6 | 3.9 | 2.3 | 2.0 | ||||
| 4 | 74 | This cluster contains 53 genes of unknown function. The remaining 21 genes are functionally very divergent. This cluster also includes 26 genes encoding IMPs. | Membrane protein (0.046) | 75 | 1.2 | 3.7 | 2.9 | 1.4 |
| 50 | 1.1 | 2.4 | 2.0 | 1.1 | ||||
| 25 | −1.1 | 1.8 | 1.4 | −1.2 | ||||
| 5 | 114 | This cluster shows strong enrichment of genes of primary metabolism (TCA cycle, metabolism of amino acids, nucleotides, lipids, and coenzymes). | Amino acid biosynthesis (1.5E−5), primary metabolism/biosynthesis (1.6E−5), ligase (i.e., aminoacyl-tRNA synthtases), lysine biosynthesis (0.012), arginine biosynthesis (0.013), coenzyme/prosthetic group biosynthesis (0.029), TCA cycle (0.034), nucleotide-binding (0.040) | 75 | 1.0 | −2.2 | −1.3 | 1.0 |
| 50 | −1.2 | −3.0 | −1.7 | −1.2 | ||||
| 25 | −1.5 | −4.6 | −2.2 | −1.6 | ||||
| 6 | 99 | This cluster shows enrichment of genes of the primary metabolism (oxidative phosphorylation, glycolysis, amino acid, nucleotide, lipid, and coenzyme metabolism). | SAM and 4Fe-4S enzymes (0.029), metal binding (0.033), (phospho)transferase (0.048) | 75 | −1.7 | −2.6 | −1.1 | −1.2 |
| 50 | −2.1 | −3.5 | −1.4 | −1.4 | ||||
| 25 | −3.2 | −5.5 | −1.8 | −1.6 | ||||
| 7 | 99 | This cluster comprises 61 genes of unknown function and several small groups with divergent functional annotations. | 2-component system (0.060)* | 75 | −2.1 | −2.6 | −1.9 | −2.0 |
| 50 | −2.6 | −3.5 | −2.5 | −2.4 | ||||
| 25 | −3.4 | −5.2 | −3.1 | −3.1 | ||||
| 8 | 105 | Chemotaxis and motility genes are strongly enriched in this cluster. Moreover, this cluster contains genes involved in a broad range of transport processes and amino acid metabolism. | Motility (7.6E−7), chemotaxis (0.003), membrane protein (0.007), methyl-accepting transducer (0.012), amino acid biosynthesis (0.017) | 75 | −1.1 | −2.9 | −2.8 | −1.9 |
| 50 | −1.4 | −3.7 | −3.9 | −2.5 | ||||
| 25 | −1.8 | −5.8 | −6.2 | −3.5 | ||||
| 9 | 32 | This cluster comprises 18 genes coding for the phage-like element PBSX. | LysM repeat-containing proteins/cell wall (0.016) | 75 | 1.4 | 1.1 | −1.4 | −1.5 |
| 50 | 1.3 | −1.1 | −1.6 | −1.7 | ||||
| 25 | 1.2 | −1.4 | −2.1 | −2.0 | ||||
| 10 | 58 | This cluster contains no prevalent functional gene group(s), but many small groups. Among these are genes for proline biosynthesis and Opu transporters. | Proline/glutamine family biosynthesis (0.055)* | 75 | 1.6 | 3.2 | 4.8 | 3.0 |
| 50 | 1.3 | 2.3 | 3.1 | 2.1 | ||||
| 25 | 1.1 | 1.8 | 2.3 | 1.6 | ||||
| 11 | 28 | This cluster contains no prevalent functional gene group(s). One small group is related to sporulation and germination (5 genes). | Sporulation/germination (0.083)* | 75 | 1.3 | 1.5 | 1.9 | 4.0 |
| 50 | 1.1 | 0.0 | 1.5 | 2.5 | ||||
| 25 | −1.1 | −1.2 | 1.3 | 2.3 | ||||
| Proteome | ||||||||
| 1 | 10 | All proteins are non-membrane proteins of the primary metabolism detected in the membrane fraction. | Biosynthetic process (0.182)†, ATP binding (0.184)† | 75 | 2.3 | 2.2 | 1.9 | 1.9 |
| 50 | 2.0 | 1.9 | 1.6 | 1.6 | ||||
| 25 | 1.9 | 1.7 | 1.5 | 1.5 | ||||
| 2 | 15 | Peripheral membrane proteins as well as ribosomal proteins dominate this cluster. In addition, three (putative) detoxification proteins (SodA, YaaN, YceC) grouped in this cluster were detected in the membrane fraction. | Ribosomal proteins (0.080) | 75 | 2.1 | 2.6 | 2.9 | 2.7 |
| 50 | 1.9 | 2.3 | 2.3 | 2.1 | ||||
| 25 | 1.6 | 2.2 | 1.9 | 1.9 | ||||
| 3 | 12 | Membrane proteins involved in osmostress resistance (Opu proteins, YtxH, and YuaG) are enriched in this cluster. | Glycine betaine/proline transport (0.036) | 75 | 1.2 | 1.9 | 2.8 | 3.1 |
| 50 | 1.1 | 1.6 | 2.1 | 2.4 | ||||
| 25 | −1.0 | 1.3 | 1.7 | 2.0 | ||||
| 4 | 8 | Cytosolic proteins with only very weak significant changes are comprised in this cluster. The assignment of any biological significance to this cluster is therefore difficult or questionable. | Oxidoreductase (0.020) | 75 | 1.1 | −1.0 | 1.1 | 1.4 |
| 50 | 0.0 | −1.1 | 1.1 | 1.3 | ||||
| 25 | −1.0 | −1.1 | −1.0 | 1.2 | ||||
| 5 | 13 | 12 proteins of this cluster are known/predicted to be IMPs, lipoproteins, or secreted proteins. All proteins of this cluster were detected in the membrane fraction. | Membrane protein (0.038) | 75 | −1.4 | −1.3 | −1.2 | −1.2 |
| 50 | −1.6 | −1.5 | −1.2 | −1.3 | ||||
| 25 | −1.7 | −1.6 | −1.4 | −1.4 | ||||
| 6 | 10 | 7 proteins of this cluster are known to be IMPs or lipoproteins. These proteins were detected in the membrane fraction. | Membrane protein (0.402)† | 75 | −1.3 | −1.3 | 1.0 | 0.5 |
| 50 | −1.9 | −1.6 | −1.1 | −1.1 | ||||
| 25 | −2.7 | −3.3 | −1.1 | −1.3 | ||||
| 7 | 9 | 8 proteins of this cluster are IMPs, lipoproteins, or known to be cell surface associated, mostly detected in the membrane fraction. Two cell wall proteins, PonA and PbpC, also fall within this group. | Cell envelope biogenesis/developmental process (0.192)† | 75 | −1.3 | −1.3 | −1.4 | −1.3 |
| 50 | −1.6 | −1.5 | −1.8 | −1.8 | ||||
| 25 | −1.6 | −1.9 | −2.2 | −2.0 | ||||
| 8 | 7 | All proteins are of cytosolic origin and show only very weak significant changes. The inference of biological significance is therefore difficult or questionable. | Primary metabolic process (0.206)† | 75 | 1.1 | 1.2 | 1.1 | −1.1 |
| 50 | 1.0 | 1.1 | 1.0 | −1.1 | ||||
| 25 | 0.0 | 1.1 | 1.0 | −1.1 | ||||
| 9 | 4 | 2 proteins of this very small cluster are involved in motility (Hag and FlgG), show a ≥2-fold downregulation, and were detected in the membrane fraction. | No terms clustered | 75 | 1.2 | −0.4 | −1.5 | −1.2 |
| 50 | 0.0 | −1.1 | −1.8 | −1.6 | ||||
| 25 | −1.1 | −1.2 | −2.1 | −2.1 | ||||
a
Different significance thresholds for the DAVID Functional Annotation Clustering approach were applied for the transcriptomic data and the proteomic data. Since the number of genes per cluster is reasonably high for the transcriptomic data, a P value of ≤0.05 was applied. Because the number of proteins per cluster is, with a few exceptions, rather low, a less stringent P value (≤0.1) was chosen as a significance threshold. The P value is given in parentheses. *, no significant (P ≤ 0.05) functional annotation cluster (the next best hit is displayed); †, no significant (P ≤ 0.1) functional annotation cluster (the next best hit is displayed).