Table 1.
L. casei genes required for intestinal establishment
| Gene tag | Gene name | Operon prediction* |
| Functions lost in establishment | ||
| Housekeeping | ||
| Cellular machinery | ||
| LSEI_0757 | Flavoprotein NrdI | No |
| LSEI_1274 | ATPase for cell division | LSEI_1274-1279 (+) |
| LSEI_1488 | Rad3-related DNA helicase (DinG) | LSEI_1488-1490 (-) |
| LSEI_1539 | Guanosine polyphosphate pyrophosphohydrolase/synthetase | LSEI_1537-1539 (-) |
| LSEI_1600 | RNA-binding protein | LSEI_1600-1601 (-) |
| LSEI_1615 | ATP-dependent DNA helicase RecG | LSEI_1613-1617 (-) |
| LSEI_1656 | tRNA delta (2)-isopentenyl pyrophosphate transferase | No |
| LSEI_1668 | Transcription elongation factor GreA | LSEI_1668-1669 (-) |
| Adaptation to stress and defense mechanisms | ||
| LSEI_1313 | Stress membrane GTPase | No |
| LSEI_1403 | Tyrosine recombinase XerC subunit | LSEI_1402-1403 (+) |
| LSEI_1790 | Predicted Mrr-like endonuclease | No |
| Metabolism | ||
| Carbohydrate metabolism, transport and energy production | ||
| LSEI_0174 | Phosphoketolase | No |
| LSEI_0681 | Lactose transport regulator | LSEI_0676-0681 (-) |
| LSEI_2549 | l-lactate dehydrogenase (LdhL1) | No |
| Amino acid metabolism | ||
| LSEI_0479 | Homoserine transsuccinylase (MetA) | LSEI_0479-0480 (+) |
| LSEI_0480 | Cysteine synthase (CysK) | LSEI_0479-0480 (+) |
| LSEI_1810 | Dipeptidyl aminopeptidase/acylaminoacyl-peptidase | LSEI_1809-1810 (-) |
| LSEI_2162 | Asparagine synthase (AsnB) | LSEI_2161-2162 (-) |
| Transport | ||
| LSEI_0242 | ABC-type Mn/Zn transport system, ATPase component | LSEI_0240-0243 (+) |
| LSEI_1000 | ABC-type Na+ efflux pump, permease component | LSEI_0999-1000 (+) |
| LSEI_1738 | Peptide ABC transporter permease | LSEI_1738-1739 (-) |
| LSEI_1743 | Cation transport ATPase (CopA) | LSEI_1743-1745 (-) |
| LSEI_1759 | Phosphoenolpyruvate-protein phosphotransferase | LSEI_1759-1760 (-) |
| LSEI_2601 | Multidrug ABC transporter ATPase/permease | LSEI_2599-2602 (+) |
| Biogenesis of the cell wall | ||
| LSEI_0221 | d-alanyl-d-alanine carboxypeptidase | LSEI_0219-0221 (+) |
| LSEI_0238 | PST family polysaccharide transporter | LSEI_0238-0240 (+) |
| LSEI_0794 | d-alanine–activating enzyme (DltA) | LSEI_0793-0797 (+) |
| LSEI_0796 | d-alanyl carrier protein (DltC) | LSEI_0793-0797 (+) |
| LSEI_0797 | d-alanyl transfer protein (DltD) | LSEI_0793-0797 (+) |
| LSEI_2546 | Polysaccharide transporter | LSEI_2545-2546 (-) |
| Adaptation to environment | ||
| Regulators | ||
| LSEI_0247 | Transcriptional regulator | No |
| LSEI_0394 | Transcriptional regulator | LSEI_0394-0396 (+) |
| LSEI_2025 | Fe2+/Zn2+ uptake regulation protein | No |
| Two-component systems | ||
| LSEI_0219 | DNA-binding response regulator | LSEI_0219-0221 (+) |
| LSEI_0220 | Signal transduction histidine kinase | LSEI_0219-0221 (+) |
| General functions | ||
| Predicted functions | ||
| LSEI_0135 | Diadenosine tetraphosphatase-like protein | No |
| LSEI_0781 | Phosphoesterase, DHH family protein | LSEI_0780-0783 (+) |
| LSEI_1621 | GTPase | LSEI_1619-1625 (-) |
| No predicted functions | ||
| LSEI_0086 | Hypothetical protein (transmembrane domain) | LSEI_0084-0086 (+) |
| LSEI_0156 | Hypothetical protein | LSEI_0156-0158 (+) |
| LSEI_0806 | Hypothetical protein (transmembrane domain) | LSEI_0805-0807 (+) |
| LSEI_1316 | Hypothetical protein | LSEI_1314-1319 (+) |
| LSEI_1461 | Hypothetical protein (transmembrane domain) | LSEI_1458-1461 (-) |
| LSEI_1710 | Integral membrane domain | LSEI_1710-1712 (-) |
| LSEI_2262 | Hypothetical protein (102aa) | LSEI_2262-2263 (-) |
| LSEI_2553 | Hypothetical protein | LSEI_2551-2553 (+) |
| LSEI_A13 | Hypothetical protein | No |
*
Two consecutive genes were considered to be in the same operon when they were separated by less than 100 bp and no transcription terminator can be predicted. (+) and (−) indicate the orientation of genes, taking the genome sequencing as the (+) orientation.