Table 2.
Predicted target genes for trans-sRNAs identified during growth of Ruegeria pomeroyi under C- and N-limited conditions.
| ID | Size (nt) | Target Gene Locus Tag | Target Gene Annotation | Functional Category | p-value | RT-qPCR validation |
|---|---|---|---|---|---|---|
| trans6 | 101 | SPO0684 | Glyoxylase family protein | Resistance | 0.000 | |
| SPO1441 | Fatty acid desaturase family protein | Lipid metabolism | 0.000 | |||
| SPO3188 | Hypothetical protein | 0.001 | ||||
| SPO3394 | GDSL-like lipase/acylhydrolase, putative | Lipid metabolism | 0.002 | |||
| SPO2054 | Cytochrome c oxidase assembly protein | Energy production | 0.004 | |||
| SPO2735 | Type I restriction-modification system, R subunit | Nucleic acid metabolism | 0.004 | |||
| SPO0765 | Glutamine synthetase family protein | Amino acid metabolism | 0.005 | |||
| SPO3739 | Hydantoinase/oxoprolinase family protein | Amino acid metabolism | 0.007 | |||
| SPO1134 | NnrU family protein | 0.009 | ||||
| SPO1906 | Hypothetical protein | 0.009 | ||||
| SPO2498 | 2′-deoxycytidine 5′-triphosphate deaminase | Nucleic acid metabolism | 0.009 | |||
| SPO2912 | MerR family transcriptional regulator | Transcriptional regulator | 0.009 | |||
| SPO3245 | Nicotinate-nucleotide pyrophosphorylase | Coenzyme metabolism | 0.009 | |||
| trans11 | 189 | SPO0657 | naaT, metallochaperone, putative | Coenzyme metabolism | 0.003 | |
| SPO1108 | DnaJ-like protein DjlA, putative | Post-translational modification | 0.003 | |||
| SPO3602 | Hypothetical protein | 0.007 | ||||
| trans15 | 225 | SPO0298 | acyl-CoA dehydrogenase family protein | Lipid metabolism | 0.001 | |
| SPO0568 | 2-oxoacid ferredoxin oxidoreductase | Amino acid metabolism | 0.001 | |||
| SPO2180 | Hypothetical protein | 0.002 | ||||
| SPO0940 | Hypothetical protein | 0.005 | ||||
| SPO3617 | Peptidoglycan-binding protein, putative | Cell-cell interaction | 0.005 | |||
| SPO1609 | Polyamine ABC transporter, ATP-binding | Transport | 0.008 | |||
| SPO0831 | Xanthine dehydrogenase family, medium subunit | Nucleic acid metabolism | 0.009 | |||
| SPO0937 | Hypothetical protein | 0.009 | ||||
| trans21 | 264 | SPO1144 | Universal stress protein family protein | 0.003 | ||
| SPO2761 | Pantothenate kinase | Coenzyme metabolism | 0.004 | |||
| SPO0685 | Fumarylacetoacetase | Amino acid metabolism | 0.005 | |||
| SPO2385 | Benzaldehyde lyase, putative | 0.007 | ||||
| trans28 | 161 | SPO0858 | Methylamine utilization protein MauG, putative | 0.000 | ||
| SPO0381 | Protease, putative | Protein degradation | 0.001 | |||
| SPO0129 | T4 family peptidase | Protein degradation | 0.004 | |||
| SPO1697 | Aminotransferase, classes I and II | Amino acid metabolism | 0.006 | |||
| SPO0934 | Hypothetical protein | 0.007 | ||||
| SPO0328 | Hypothetical protein | 0.009 | ||||
| trans30 | 201 | N/A | ||||
| trans33 | 111 | SPO0185 | Hypothetical protein | 0.000 | ||
| SPO2572 | Hypothetical protein | 0.001 | ||||
| SPO2073 | Hypothetical protein | 0.004 | ||||
| SPO0583 | LysR family transcriptional regulator | Transcriptional regulator | 0.005 | |||
| SPO2679 | Short chain oxidoreductase | 0.006 | ||||
| SPO2900 | tRNA 2-selenouridine synthase | Translation and biogenesis | 0.007 | |||
| SPO3172 | Hypothetical protein | 0.007 | ||||
| SPO0759 | Hypothetical protein | 0.008 | ||||
| SPO0872 | Polysaccharide deacetylase family protein | Carbohydrate metabolism | 0.009 | |||
| SPO1845 | Oxidoreductase, molybdopterin-binding | 0.009 | ||||
| trans38 | 311 | SPO1267 | MarR family transcriptional regulator | Transcriptional regulation | 0.001 | |
| SPO2455 | Organic solvent tolerance protein, putative | Membrane protein | 0.002 | |||
| SPO1286 | Hypothetical protein | 0.004 | ||||
| SPO3027 | Histidinol-phosphate aminotransferase | Amino acid metabolism | 0.005 | |||
| SPO1199 | Hypothetical protein | 0.008 | ||||
| SPO3633 | Molybdopterin converting factor, subunit 2 | Coenzyme metabolism | 0.008 | |||
| SPO1311 | Renal dipeptidase family protein | Protein degradation | 0.009 | |||
| SPO2536 | LuxR family transcriptional regulator | Transcriptional regulation | 0.009 | |||
| trans42 | 143§ | SPO3876 | Hypothetical protein | 0.009 | No | |
| trans44 | 265§ | SPO0873 | Ureidoglycolate hydrolase | Nucleic acid metabolism | 0.003 | Yes |
| SPO1532 | Hypothetical protein | 0.005 | ||||
| SPO0005 | Hypothetical protein | 0.008 | ||||
| SPO1350 | Hypothetical protein | 0.009 | ||||
| trans45¶ | 351 | SPO3050 | Hypothetical protein | 0.003 | ||
| SPO2852 | CzcN domain-containing protein | 0.003 | ||||
| SPO2542 | Biotin/lipoate binding domain-containing protein | Coenzyme metabolism | 0.006 | |||
| SPO2703 | Hypothetical protein | 0.008 | ||||
| SPO2977 | Adenylate/guanylate cyclase | Signal transduction | 0.008 | |||
| SPO3862 | Putative lipoprotein | Cell wall/membrane | 0.009 | |||
| trans46 | 141 | SPO3330 | Ribonuclease R | Translation and biogenesis | 0.001 | |
| SPO2342 | Hypothetical protein | 0.004 | ||||
| SPO1399 | AraC family transcriptional regulator | Transcriptional regulation | 0.006 | |||
| SPO3662 | Hypothetical protein | 0.008 | ||||
| SPO2067 | Hypothetical protein | 0.010 | ||||
| SPO2790 | Methylcrotonyl-CoA carboxylase, beta subunit | Lipid metabolism | 0.010 | |||
| SPO3333 | Hypothetical protein | 0.010 | ||||
| trans48¶ | 142 | SPO1762 | 6,7-dimethyl-8-ribityllumazine synthase | Coenzyme metabolism | 0.004 | |
| SPO1508 | Quinoprotein ethanol dehydrogenase | 0.005 | ||||
| SPO3019 | Xanthine dehydrogenase family, large subunit | Nucleic acid metabolism | 0.006 | |||
| SPO1029 | YeeE/YedE family protein | 0.007 | ||||
| trans49 | 124 | SPO1050 | Phage integrase family site specific recombinase | Phage | 0.001 | |
| SPO0323 | Hypothetical protein | 0.001 | ||||
| SPO0526 | Acetylglutamate kinase | Amino acid metabolism | 0.002 | |||
| SPO3390 | Hypothetical protein | 0.003 | ||||
| SPO2630 | C4-dicarboxylate transport sensor protein | Transport | 0.006 | |||
| SPO1884 | Methionine synthase I | Amino acid metabolism | 0.009 | |||
| SPO3077 | TldD/PmbA family protein | 0.009 | ||||
| SPO1050 | Phage integrase family site specific recombinase | Phage | 0.001 | |||
| SPO0323 | Hypothetical protein | 0.001 | ||||
| trans54 | 207 | N/A | ||||
| trans56 | 146 | SPO0201 | Hypothetical protein | 0.001 | ||
| SPO1217 | DNA-binding protein, putative | Transcriptional regulation | 0.001 | |||
| SPO0547 | Hypothetical protein | 0.002 | ||||
| SPO1032 | Hypothetical protein | 0.006 | ||||
| SPO2286 | Autoinducer-binding regulator LuxR | Transcriptional regulation | 0.007 | |||
| SPO0201 | Hypothetical protein | 0.001 | ||||
| trans58 | 141 | SPO3492 | Hypothetical protein | 0.000 | ||
| SPO2182 | Permease, putative | Transport | 0.001 | |||
| SPO0236 | Glycerophosphoryl diester phosphodiesterase putative | Lipid metabolism | 0.001 | |||
| SPO0950 | Uracil-DNA glycosylase, putative | Nucleic acid metabolism | 0.001 | |||
| SPO3756 | OmpA domain-containing protein | Cell wall/membrane | 0.004 | |||
| SPO1732 | Single-stranded-DNA-specific exonuclease RecJ | Recombination and repair | 0.005 | |||
| SPO0965 | Acetyltransferase | 0.006 | ||||
| SPO1596 | Hypothetical protein | 0.006 | ||||
| SPO0846 | Phosphopantetheinyl transferase PptA, putative | Coenzyme metabolism | 0.008 | |||
| SPO1099 | Hypothetical protein | 0.010 | ||||
| trans59¶ | 124 | N/A | ||||
| trans62¶ | 225§ | SPO0491 | Hypothetical protein | 0.001 | Yes | |
| SPO2176 | Hypothetical protein | 0.003 | ||||
| SPO2943 | Alpha/beta fold family hydrolase | 0.004 | ||||
| SPO2635 | Phosphoadenosine phosphosulfate reductase | Sulfur metabolism | 0.004 | |||
| SPO2397 | Carbon monoxide dehydrogenase, large subunit | 0.005 | ||||
| SPO2759 | NUDIX family hydrolase | Nucleic acid metabolism | 0.005 | |||
| SPO0294 | NUDIX family hydrolase | Nucleic acid metabolism | 0.007 | |||
| SPO0571 | PKD domain-containing protein | 0.007 | ||||
| SPO1376 | Glycosyl transferase, group 2 family protein | Carbohydrate metabolism | 0.008 | |||
| SPO2218 | Excinuclease ABC subunit A | Recombination and repair | 0.008 | |||
| SPO2718 | Hypothetical protein | 0.008 | ||||
| SPO2640 | XdhC/CoxI family protein | Nucleic acid metabolism | 0.009 | |||
| SPO3493 | Transporter, putative | Transport | 0.009 | |||
| trans63¶ | 488 | SPO0331 | Thiol:disulfide interchange protein, putative | 0.000 | ||
| SPO0965 | Acetyltransferase | 0.002 | ||||
| SPO3587 | Hypothetical protein | 0.004 | ||||
| SPO1527 | Hypothetical protein | 0.005 | ||||
| SPO2008 | Polyamine ABC transporter, permease protein | Transport | 0.009 | |||
| SPO0305 | AzlC family protein | Amino acid metabolism | 0.010 | |||
| SPO0773 | Acetyl-CoA acyltransferase/thiolase family | Lipid metabolism | 0.010 | |||
| SPO2147 | Hypothetical protein | 0.010 | ||||
| trans65 | 295 | SPO1043 | Hypothetical protein | 0.000 | ||
| SPO3750 | Hypothetical protein | 0.001 | ||||
| SPO2911 | Thioesterase family protein | 0.003 | ||||
| SPO2543 | GntR family transcriptional regulator | Transcriptional regulation | 0.004 | |||
| SPO2551 | Peptide/opine/nickel uptake ATP-binding protein | Transport | 0.008 | |||
| SPO0919 | MarR family transcriptional regulator | Transcriptional regulation | 0.009 | |||
| trans66 | 130 | SPO0164 | Oxidoreductase, FMN nucleotide-disulfide | 0.003 | ||
| SPO1125 | Hypothetical protein | 0.006 | ||||
| SPO1226 | Putative lipoprotein | Lipid metabolism | 0.006 | |||
| SPO1510 | Efflux ABC transporter, permease protein | Transport | 0.007 | |||
| SPO3172 | Hypothetical protein | 0.009 | ||||
| trans69 | 160§ | SPO0934 | Hypothetical protein | 0.007 | Yes | |
| SPO3650 | Adenylate/guanylate cyclase | Signal transduction | 0.009 | |||
| trans79 | 436 | SPO3223 | Response regulator | Transcriptional regulation | 0.002 | |
| SPO1656 | Oligopeptide/dipeptide ABC, ATP-binding | Transport | 0.003 | |||
| SPO0310 | Molybdopterin biosynthesis protein MoeA | Coenzyme metabolism | 0.004 | |||
| SPO1432 | Rhodanese domain-containing protein | 0.006 | ||||
| SPO0078 | Ribosomal subunit interface protein, putative | Translation and biogenesis | 0.007 | |||
| SPO2314 | DsbE periplasmic thiol:disulfide oxidoreductase | Post-translational modification | 0.007 | |||
| trans83 | 121 | SPO1889 | Alcohol dehydrogenase, zinc-containing | 0.002 | ||
| SPO0829 | Hypothetical protein | 0.002 | ||||
| SPO2580 | Hypothetical protein | 0.003 | ||||
| SPO1905 | Fumarate hydratase | Energy production | 0.004 | |||
| SPO2296 | Hypo#thetical protein | 0.006 | ||||
| SPO0451 | D-alanyl-D-alanine carboxypeptidase | Amino acid metabolism | 0.007 | |||
| SPO1189 | Hypothetical protein | 0.007 | ||||
| SPO1273 | FAD-dependent thymidylate synthase | Nucleic acid metabolism | 0.007 | |||
| SPO2196 | Diaminopropionate ammonia-lyase | Amino acid metabolism | 0.007 | |||
| SPO2407 | ISSpo6, transposase orfB | Recombination and repair | 0.007 | |||
| trans85¶ | 116 | SPO0295 | Hypothetical protein | 0.003 | ||
| SPO2757 | EF hand domain-containing protein | 0.007 | ||||
| trans87¶ | 150 | SPO1856 | ribonuclease BN, putative | Translation and biogenesis | 0.009 | |
| SPO3851 | HemY domain-containing protein | Coenzyme metabolism | 0.009 | |||
| trans91¶ | 201 | SPO0387 | Hypothetical protein | 0.002 | ||
| SPO2407 | ISSpo6, transposase orfB | Recombination and repair | 0.009 | |||
| trans98 | 337 | SPO0220 | rRNA large subunit methyltransferase | 0.001 | ||
| SPO3402 | Amino acid transporter LysE | Transport | 0.002 | |||
| SPO1802 | Hypothetical protein | 0.003 | ||||
| SPO1481 | Hypothetical protein | 0.003 | ||||
| SPO2249 | Hypothetical protein | 0.005 | ||||
| SPO0879 | acyl-CoA dehydrogenase family protein | Lipid metabolism | 0.005 | |||
| SPO3823 | 50S ribosomal protein L23 | Translation and biogenesis | 0.005 | |||
| SPO3600 | Pyruvate kinase | Carbohydrate metabolism | 0.007 | |||
| SPO1395 | AraC family transcriptional regulator | Transcriptional regulation | 0.010 | |||
| trans100 | 201 | SPO0259 | Hypothetical protein | 0.000 | ||
| SPO1198 | Hypothetical protein | 0.006 |
Target genes were predicted with a p < 0.01 using TargetRNA2. sRNAs found previously in R. pomeroyi transcriptomes are indicated by ¶ (Burns, unpublished data). Trans-sRNAs for which Northern blotting was carried out to confirm size predicted by transcriptome analysis are indicated by §. See Table S1 for Northern Blotting size data and genome coordinates. N/A, no significant target genes were predicted.