Table 3.
Up-regulated expression of proteins and their biological functions after levulinic acid exposure to Ralstonia eutropha. Results are LC-MS/MS data processed with Mascot search engine and the homology alignments. Uniprot and TIGR classification were used to search cellular roles of identified proteins.
| Protein name | No. of matched peptides | Mascot Score (value P=0.05) | Accession number | Species | Biological function |
|---|---|---|---|---|---|
| Possible proteins involved in PHA production | |||||
| Acetoacetyl-CoA reductase | 1 | 88 (33) | RDALAE or P14697 | Ralstonia eutrophus | PHA metabolism |
| Probable trans-2-enoyl-CoA reductase | 3 | 28 (25) | Q6CBE4 | Yarrowia lipolytica | β-oxidation |
| 3-oxoacyl-(Acyl-carrier-protein) reductase | 2 | 53 (43) | Q8EDH3_SHEON | Shewanella oneidensis | β-oxidation |
| Putative fatty-acid-CoA ligase FadD11 | 5 | 23 (23) | Q10776 | Mycobacterium tuberclosis | Fatty acid biosynthesis |
| Energy metabolism | |||||
| Acetate kinase | 3 | 24 (23) | P37877 | Bacillus subtilis | Acetyl-CoA biosynthesis |
| Amino acid biosynthesis | |||||
| D-isomer specific 2-hydroxyacid dehydrogenase | 9 | 27 (26) | Q5HW94_CAMJR | Campylobacter jejuni | Amino acid (L-serine) biosyntehsis |
| Glutamate synthase | 3 | 30 (21) | P39812 | Bacillus subtilis | Amino acid biosynthesis |
| 5-methyl tetrahydropteroyltriglutamate--homocysteine methyltransferase | 4 | 28 (17) | Q93J59 | Streptomyces coelicolor | Methionine biosynthesis |
| Putative cystathionine gamma-lyase | 2 | 29 (21) | Q59829 | Streptomyces coelicolor | Cysteine biosynthesis |
| Chorismate synthase | 1 | 17 (17) | Q5HSF9 | Campylobacter jejuni | Aromatic amino acid biosynthesis |
| Ketol-acid reductoisomerase (Acetohydroxy-acid isomeroreductase) | 4 | 22 (17) | Q9PHN5 | Campylobacter jejuni | Amino acid biosynthesis |
| Histidinol-phosphate aminotransferase | 2 | 20 (17) | P16246 | Streptomyces coelicolor | |
| Purine and pyrimidine biosynthesis | |||||
| Dihydroorotate dehydrogease | 2 | 27 (25) | Q8NQC0 | Corynebacterium glutamicum | Nucleotide biosynthesis |
| Quinolinate synthetase A | 5 | 22 (17) | Q9F364 | Streptomyces coelicolor | NAD biosynthesis |
| Bifunctional purine biosynthesis protein purH | 4 | 30 (27) | Q8FB68 | Escherichia coli | Nucleotide biosynthesis |
| Nicotinate phosphoribosyltransferase | 2 | 36 (23) | Q5HWN2_CAMJR | Campylobacter jejuni | NAD biosynthesis |
| Cofactor biosynthesis | |||||
| Lipoyl synthase | 4 | 35 (30) | Q8ERL8 | Oceanobacillus iheyensis | Lipoate biosynthesis |
| Lipoyltransferase | 3 | 20 (17) | Q8CK04 | Streptomyces coelicolor | Lipoate metabolism |
| Biotin synthase | 10 | 50 (23) | A81117 | Neisseria meningitidis | Biotin biosynthesis |
| 3-octaprenyl-4-hydroxybenzoate carboxy-lyase | 3 | 20 (19) | Q9JT68 | Neisseria meningitidis | Ubiquinone biosynthesis |
| Stress response proteins | |||||
| 60 kDa chaperonin | 10 | 355 (34) | Q8Y1P8 | Ralstonia solanacearum | Stress |
| Transcription activator of acetoin dehydrogenase operon | 3 | 30 (25) | H69581 | Bacillus subtilis | Transcription |
| Signal recognition particle protein | 6 | 27 (26) | Q5HV72_CAMJR | Campylobacter jejuni | Signal transduction |
| Carboxylate-amine ligase | 2 | 16 (16) | Q9KY07 | Streptomyces coelicolor | Glutathione biosynthesis |
| Superoxide dismutase | 3 | 60 (43) | SODF_PSEPU | Pseudomonas putida | Defense |
| Peroxidase/catalase | 3 | 17 (17) | Q9RJH9 | Streptomyces coelicolor | Response to oxidative stress |
| Thioredoxin reductase | 3 | 31 (29) | O66790 | Aquifex aeolicus | Oxidoreductase |
| Thiol:disulfite interchange protein | 3 | 64 (43) | Q62MY5_BURMA | Burkholderia mallei | Oxidoreductase |
| Formate detoxification proteins | |||||
| Probable formate-tetrahydrofolate ligase | 7 | 29 (27) | Q9JVY8 | Neisseria meningitidis | Methyl cycle |
| Formate dehydrogenase, nitrate inducible | 3 | 29 (27) | P24183 | Escherichia coli | Formate dehydrogenase |
| Others | |||||
| Cation-transporting P-type ATPase B | 3 | 32 (22) | Q10877 | Mycobacterium tuberclosis | Transporter |
| Phosphate transport system protein | 2 | 23 (18) | P0A3Y7 | Streptococcus pneumoniae | Transporter |
| H+/K+-exchanging ATPase | 2 | 37 (25) | A81338 | Campylobacter jejuni | Transporter |
| Hyaluronate lyase precursor | 7 | 25 (19) | Q54873 | Streptococcus pneumoniae | invasive capacity of the pathogen |
| Formamidopyrimidine-DNA glycosylase | 1 | 36 (30) | P42371 | Lactococcus lactis subsp. cremoris | DNA repair |
| BSUB0010 | 12 | 77 (26) | CAD13602 | Bacillus subtilis | |
| SsrA-binding protein | 4 | 41 (25) | Q83N13 | Tropheryma whipplei | Protein biosynthesis |
| Foldase protein | 2 | 24 (21) | P24327 | Bacillus subtilis | Isomerase |
| Carnitine operon protein caiE | 3 | 32 (27) | Q8XA36 | Escherichia coli | Carnitine metabolism |
| Ornitine cabamoyltransferase | 2 | 24 (19) | Q9JTI4 | Neisseria meningitidis | |
| Radical SAM domain protein | 3 | 28 (26) | Q5HTL8_CAMJR | Campylobacter jejuni | |
| Hydrolase, alpha/beta hydrolase fold family | 4 | 26 (26) | Q7D8N4_MYCTU | Mycobacterium tuberclosis | |