Such an escape can be achieved if we make two assumptions:
1. The organisms use a protease which recognizes “usual” L-amino acids.
2. The oligopeptide bridges of peptidoglycan contain only D-amino acids.
Then L-peptidase cannot digest D-amino acid bridge.
Let’s look at Bacteria cell wall.
Chemical structure of peptidoglycan:
Diversity of peptidoglycan( Brock Biology of Microorganisms, 11th edition, p77):
a. Glycan portion of peptidoglycan is conserved between all types: only N-Acetylglucoseamine (G) and N-acetylmuramic acid build the threads.
b. Tetrapeptide portion shows major variation in only one aminoacid: DAP-Lysine acid variation ( For example, most gram-negative Bacteria have DAP, whereas almost all gram-positive cocci have Lysine ).
Also, G-Glu at position 2 can be hydroxylated in some organisms.
c. Interbridge is responsible for most variation in peptidoglycan – there are more than 100 different peptidoglycan types are known.
Interbridge can have any of amino acids present in the tetrapeptide.
In addition, Glycine, Threonine, Serine and Aspartic acid can be found in interbridge.
However, branched-chain amino acids, aromatic amino acids, sulfur-containing amino acids, and histidine, arginine, and proline are never found in the interbrige.
In any case, L-Lys and D-Ala at positions 3 and 4 accordingly will be seemingly present in any type of glycopeptide representing a site for any kind of peptidase to attack.
Let’s check archaeal cell wall.
There are two types of structures found in archaeal cell wall:
No exact info was found for S-layer.
Chemical structure of pseudopeptidoglycan:
Thus, archaeal cell walls are possibly more attack-prone by any other organism which for sure will have some L-amino acid protease.