Table 5.
Overview of peptidoglycan hydrolase (PGH) genes in complete L. helveticus genomes.
| Strain | LHV_RS00930 N-acetylmuramidase | LHV_RS00935 Amidase | LHV_RS02820 N-acetylmuramidase | LHV_RS03290 Lysozyme | LHV_RS05260 N-acetylmuramidase | LHV_RS06490 M23 family peptidase | LHV_RS07135 Lysin | LHV_RS06550 M23 family peptidase | LHV_RS10160 *1 Lysin |
|---|---|---|---|---|---|---|---|---|---|
| FAM8105 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| FAM22155 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| FAM8627 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| CAUH18 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (ST) | ✓ |
| CNRZ 32 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) | ✓ | P (FS) |
| D76 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| DPC 4571 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| H10 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (ST) | ✓ |
| H9 | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) | ✓ | P (FS) | P (FS) |
| KLDS1.8701 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) |
| MB2-1 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | P (FS) | P (FS) |
| R0052 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| In core genome | Yes | Yes | Yes | Yes | Yes | No | No | No | No |
The locus tags of nine PGH genes of strain DPC 4571 are shown on top along with the annotation of the encoded protein. The nine genes were selected based on a detailed study of PGHs (Jebava et al., 2011). PGHs annotated as functional are marked with a tick mark (✓), pseudogenes are marked with “P”, the reason for the pseudogene annotation is shown in brackets. Five of the nine PGH genes belonged to the core genome and were highly conserved (>98% average pairwise aa identity, using BLSM62 substitution-scoring matrix).
P (ST): Pseudogene with premature stop codon.
P (FS): Pseudogene with frameshift.
*1
Frameshift according to RefSeq annotation.