TABLE 1.
Genetics and predicted enzymology of amino acid biosynthesis in L. helveticus CNRZ 32
| Amino acid(s) | Gene(s) presenta | Predicted product | Pathway | Essentialb |
|---|---|---|---|---|
| Ala | araT | Aromatic aminotransferase (EC 2.6.1.57) | Completec | No |
| bcaT | Branched-chain aminotransferase (EC 2.6.1.42) | |||
| ataA-C | Aminotransferase (EC 2.6.1.-) | |||
| Arg | argFd* | Ornithine carbamoyltransferase (EC 2.1.3.3) | Incomplete | Yes |
| arcCd* | Carbamate kinase (EC 2.7.2.2) | |||
| arcAd | Arginine deiminase (EC 3.5.3.6) | |||
| carA† | Carbamoyl-phosphate synthase A (EC 6.3.4.16) | |||
| carB† | Carbamoyl-phosphate synthase B (EC 6.3.4.16) | |||
| odcI | Ornithine decarboxylase (EC 4.1.1.17) | |||
| odiC | Ornithine decarboxylase (EC 4.1.1.17) | |||
| Asn, Asp | asnA | Aspartate-ammonia ligase (EC 6.3.1.1) | Incomplete | Asn or Asp |
| asnB | Asparagine synthase (EC 6.3.5.4) | |||
| ans | Asparaginase (EC 3.5.1.1) | |||
| aspC* | Aspartic aminotransferase (EC 2.6.1.1) | |||
| asd* | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | |||
| ppcd | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | |||
| Glu | glnA | Glutamate-ammonia ligase (EC 6.3.1.2) | Incomplete | Yes |
| aspC | Aspartic aminotransferase (EC 2.6.1.1) | |||
| Gln | glnA | Glutamate-ammonia ligase (EC 6.3.1.2) | From Glu | No |
| Cys | cysK* | O-Acetylserine (thiol) lyase (EC 2.5.1.47) | Complete | No |
| cbl* | Cystathionine-beta-lyase (EC 4.4.1.8) | |||
| cysE* | Serine acetyl-transferase (EC 2.3.1.30) | |||
| Met | metA* | Homoserine-O-succinyl transferase (EC 2.3.1.46) | Incomplete | Yes |
| cysK2d* | O-Acetylserine (thiol) lyase (EC 2.5.1.47) | |||
| metE | 5-Methyltetrahydropteroyl(Glu3)-homocysteine | |||
| methyltransferase (EC 2.1.1.14) | ||||
| patCd | Cystathionine-gamma-lyase (EC 4.4.1.1) | |||
| Lys | lysA* | Diaminopimelate decarboxylase (EC 4.1.1.20) | Completec | Yes |
| dapD* | 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) | |||
| dapE* | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | |||
| dapA* | Dihydrodipicolinate synthase (EC 4.2.1.52) | |||
| dapB* | Dihydrodipicolinate reductase (EC 1.3.1.26) | |||
| aspC* | Aspartic aminotransferase (EC 2.6.1.1) | |||
| asd* | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | |||
| lysC† | Aspartate kinase (EC 2.7.2.4) | |||
| dapF† | Diaminopimelate epimerase (EC 5.1.1.7) | |||
| ataA-C | Aminotransferase (EC 2.6.1.-) | |||
| Ile, Leu, Val | bcaT | Branched-chain aminotransferase (EC 2.6.1.42) | Incomplete | Yes |
| ilvB | Acetolactate synthase (EC 2.2.1.6) | |||
| Phe, Tyr, Pro | araT | Aromatic aminotransferase (EC 2.6.1.57) | Incomplete | Yes |
| aspC | Aspartic aminotransferase (EC 2.6.1.1) | |||
| His | none | Incomplete | Yes | |
| Pro | none | Incomplete | Yes | |
| Ser | glyA | Glycine hydroxymethyltransferase (EC 2.1.2.1) | Complete | No |
| glyK | Glycerate kinase (EC 2.7.1.31) | |||
| serC* | Phosphoserine transaminase (EC 2.6.1.52) | |||
| serA* | Phosphoglycerate dehydrogenase (EC 1.1.1.95) | |||
| ycsE | Phosphoserine phosphatase (EC 3.1.3.3) | |||
| sdaBd† | l-Serine ammonia-lyase B (EC 4.3.1.17) | |||
| sdaA† | l-Serine ammonia-lyase A (EC 4.3.1.17) | |||
| Gly | glyA | Glycine hydroxymethyltransferase (EC 2.1.2.1) | From Ser | No |
| Thr | none | Incomplete | Yes |
a
Genes for the same amino acid with a shared symbol (* or †) are adjacent to one another in an operon-like structure in the genome and are listed in predicted order of sequential transcription.
b
As determined by Christensen and Steele (4).
c
Pathway completion assumes activity for one or more transamination reactions is provided by the aromatic-chain (araT), aspartic (aspC), or branched-chain (bcaT) aminotransferase or by one of three other predicted amino acid aminotransferases (ataA-C) whose genes were identified in the L. helveticus CNRZ 32 genome.
d
Probable pseudogene; the product is predicted to lack biological activity.