TABLE 2.
L. plantarum genes that are induced during passage through the mouse GI tract as compared to laboratory conditions
| Class | ORF (gene)a | Product or function | Reference(s) |
|---|---|---|---|
| Nutrient acquisition and synthesis | |||
| Sugar | lp_0185a (ptsIBCA) | Sucrose PTS EIIBCA | 27b |
| lp_1164 (pts14C) | Cellobiose PTS, EIIC | 17, 27 | |
| lp_2647c (pts19A) | N-Acetylglucosamine/galactosamine PTS, EIIA | ||
| lp_3473 (ram2) | Alpha-l-rhamnosidase | ||
| lp_3522c (pts32BC) | Sucrose PTS, EIIBC | 27b | |
| lp_3526a (pbg10) | 6-Phospho-beta-glucosidase | ||
| lp_36182,c (pts37A) | Sorbitol PTS EIIA | 22 | |
| lp_36593,d (rbsD) | Ribose transport protein | 11, 31 | |
| lp_36603,d (rbsK3) | Ribokinase | 11, 31 | |
| Nonsugar | lp_0017c (proA) | Glutamate-5-semialdehyde dehydrogenase | 25, 47 |
| lp_0228e (pepD1) | Dipeptidase | ||
| lp_0696 | Cytosine/adenosine deaminase | 43 | |
| lp_0775 (argG) | Argininosuccinate synthase | 7 | |
| lp_0854a,c (birA2) | Biotin (acetyl-coenzyme A-carboxylase) ligase and biotin operon repressor | 10, 26 | |
| lp_1058 (adk) | Adenylate kinase | ||
| lp_1319d (rsuA) | Pseudouridylate synthase | ||
| lp_16027 | Geranyltranstransferase/famesyl di-P-transferase | ||
| lp_2031 (ribC2) | Bifunctional protein: riboflavin kinase and FMN adenylyl- transferase | 34 | |
| Stress | lp_1019 (clpC) | ATP-dependent Clp protease | 24, 32 |
| lp_30554,c (copA) | Copper transporting ATPase | 21, 36 | |
| lp_3288c | Cation efflux protein | ||
| lp_33035 | Putative multidrug transport protein | 25 | |
| Extracellular | |||
| LPQTNE containing | lp_0800 | Cell surface protein precursor | |
| lp_2940c | Cell surface protein precursor | ||
| Other | lp_0141e | Extracellular protein | |
| lp_1403a,d | Cell surface protein | ||
| Regulators | lp_3176c (pkn2) | Serine/threonine protein kinase | |
| lp_3514c (bglG4) | Transcription antitermination | 38 | |
| lp_3646a,d | Transcription regulator | ||
| Other | lp_0237 | Integral membrane protein | |
| lp_0299c | ABC transporter, ATP-binding protein | ||
| lp_0305d (gcsH1) | Glycine cleavage system, H protein | ||
| lp_03931,d (thgA1) | Galactoside O-acetyltransferase | ||
| lp_03941,d | Transport protein | ||
| lp_0419a (plnI) | Immunity protein | ||
| lp_0489 (tktI-N) | Transketolase | ||
| lp_0698a,d (dnaX) | DNA-directed DNA polymerase III, gamma/tau subunit | 27 | |
| lp_07406 (prfB-N) | Peptide chain release factor 2, N-terminal fragment | ||
| lp_07416 (prfB-C) | Peptide chain release factor 2, C-terminal fragment | ||
| lp_16037 (ispA) | Hemolysin homologue | ||
| lp_1847 (codV) | Integrase/recombinase | ||
| lp_3051 (dhaT) | 1,3-Propanediol dehydrogenase | 39 | |
| lp_3082d | Transport protein | ||
| lp_3281d | Transport protein | ||
| lp_3500 | Short-chain dehydrogenase/oxidoreductase | 39 | |
| lp_3505 (est2) | Acetylesterase | ||
| lp_36172,c (tal3) | Transaldolase | ||
| lp_3662c (adhE) | Bifunctional protein: alcohol and acetaldehyde dehydrogenase | 40 | |
| Hypothetical | |||
| Conserved | lp_0026c, lp_0139, lp_0190d, lp_0291a,c, lp_0476∞, lp_0477∞, lp_0907d, lp_1969d, lp_2337c, lp_25079,d, lp_25089,d, lp_2713, lp_2718, lp_30574,c, lp_30584,c and lp_3312c | 52 (for lp_2718, see text) | |
| Not conserved | lp_0118a,d, lp_0292, lp_1788, lp_1872, lp_2112c, lp_2584, lp_3246c, lp_33055 |
Genes with the same superscript number originate from one R-IVET clone. Genes denoted by a superscript “a” were identified twice during the first-round R-IVET screen. After the second-round passage and subsequent sequence analysis, some genes were identified exclusively in the erythromycin sensitive (superscript c) or resistant (superscript e) group. Genes indicated by a superscript “d” were identified in both the erythromycin-resistant and the erythromycin-sensitive groups.
In the original reference, 13 in vivo-induced loci were identified in Streptococcus gordonii. However, these loci were only partially sequenced, and for six loci this was not sufficient to identify a promoter element. At present, with more detailed sequence analysis and the partially available genome sequence, these loci have been assigned a promoter element (Lin Tao, unpublished data).