L. D. Rumsh

Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia)†

ABSTRACT Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87°C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or α- or β-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.

Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes.

To elucidate the role of amino acid residues adjacent to the catalytic site of pepsin‐like enzymes, we analyzed and compared the crystal structures of these enzymes, their complexes with inhibitors, and zymogens in the active site area (a total of 82 structures). In addition to the water molecule (W1) located between the active carboxyls and playing a role of the nucleophile during catalytic reaction, another water molecule (W2) at the vicinity of the active groups was found to be completely conserved. This water molecule plays an essential role in formation of a chain of hydrogen‐bonded residues between the active site flap and the active carboxyls on ligand binding. These data suggest a new approach to understanding the role of residues around the catalytic site, which can assist the development of the catalytic reaction. The influence of groups adjacent to the active carboxyls is manifested by pepsin activity at pH 1.0. Some features of pepsin‐like enzymes and their mutants are discussed in the framework of the approach.

Mutations in the proteolytic domain of Escherichia coli protease Lon impair the ATPase activity of the enzyme

Conserved residues of the proteolytic domain of Escherichia coli protease Lon, putative members of the classic catalytic triad (H665, H667, D676, and D743) were identified by comparison of amino acid sequences of Lon proteases. Mutant enzymes containing substitutions D676N, D743N, H665Y, and H667Y were obtained by site‐directed mutagenesis. The mutant D743N retained the adenosine triphosphate (ATP)‐dependent proteolytic activity, thereby indicating that D743 does not belong to the catalytic site. Simultaneously, the mutants D676N, H665Y, and H667Y lost the capacity for hydrolysis of protein substrates. The ATPase activity of these three mutants was decreased by more than an order of magnitude, which suggests a close spatial location of the ATPase and proteolytic active sites and their tight interaction in the process of protein degradation.

Post X-ray crystallographic studies of chymosin: the existence of two structural forms and the regulation of activity by the interaction with the histidine-proline cluster of κ-casein

Calf chymosin molecules exist in the two alternative structural forms: the first one has S1 and S3 binding pockets occluded by its own Tyr77 residue (the self‐inhibited form); the second has these pockets free for a substrate binding (the active form). The preliminary incubation of the enzyme with a pentapeptide corresponding to the histidine‐proline cluster of the specific substrate κ‐casein results in a 200‐fold increase of the hydrolysis rate for the enzyme ‘slow substrate’. The result suggests that the cluster is an allosteric effector that promotes the conversion of the enzyme into the active form. These data provide the experimental ground for the explanation of chymosin specificity towards κ‐casein.

The isolated proteolytic domain of Escherichia coli ATP-dependent protease Lon exhibits the peptidase activity

Selective protein degradation is an energy‐dependent process performed by high‐molecular‐weight proteases. The activity of proteolytic components of these enzymes is coupled to the ATPase activity of their regulatory subunits or domains. Here, we obtained the proteolytic domain of Escherichia coli protease Lon by cloning the corresponding fragment of the lon gene in pGEX‐KG, expression of the hybrid protein, and isolation of the proteolytic domain after hydrolysis of the hybrid protein with thrombin. The isolated proteolytic domain exhibited almost no activity toward protein substrates (casein) but hydrolyzed peptide substrates (melittin), thereby confirming the importance of the ATPase component for protein hydrolysis. Protease Lon and its proteolytic domain differed in the efficiency and specificity of melittin hydrolysis.

Autolysis of bovine enteropeptidase heavy chain: evidence of fragment 118^465 involvement in trypsinogen activation

Variations in bovine enteropeptidase (EP) activity were shown to result from autolysis caused by the loss of calcium ions; the cleavage sites were determined. The native enzyme preferred its natural substrate, trypsinogen (K M=2.4 μM), to the peptide and fusion protein substrates (K M=200 and 125 μM, respectively). On the other hand, the truncated enzyme composed of the C‐terminal fragment 466–800 of EP heavy chain and intact light chain did not distinguish these substrates. The results suggest that the N‐terminal fragment 118–465 of the enteropeptidase heavy chain contains a secondary substrate‐binding site that interacts directly with trypsinogen.

Psychrophilic trypsin-type protease from Serratia proteamaculans

A preparative method for purification of a novel protease from the psychrotolerant Gram-negative microorganism Serratia proteamaculans (PSP) was developed using affinity chromatography on BPTI-Sepharose. It yielded electrophoretically homogeneous PSP preparation of 60 kD. The PSP properties (temperature and pH stability, high catalytic efficiency) indicate that this enzyme can be defined as a psychrophilic protease. Inhibitory analysis together with substrate specificity indicates that the studied PSP exhibits properties of serine trypsin-like and Zn-dependent protease.

Study of secondary specificity of enteropeptidase in comparison with trypsin.

A comparative study of secondary specificities of enteropeptidase and trypsin was performed using peptide substrates with general formula A-(Asp/Glu)n-Lys(Arg)-↓-B, where n = 1-4. This was the first study to demonstrate that, similar to other serine proteases, enteropeptidase has an extended secondary binding site interacting with 6-7 amino acid residues surrounding the peptide bond to be hydrolyzed. However, in the case of typical enteropeptidase substrates containing four negatively charged Asp/Glu residues at positions P2-P5, electrostatic interaction between these residues and the secondary site Lys99 of the enteropeptidase light chain is the main factor that determines hydrolysis efficiency. The secondary specificity of enteropeptidase differs from the secondary specificity of trypsin. The chromophoric synthetic enteropeptidase substrate G5DK-F(NO2)G (kcat/Km = 2380 mM–1·min–1) is more efficient than the fusion protein PrAD4K-P26 (kcat/Km = 1260 mM–1·min–1).

Gel-immobilized enzymes as promising biocatalysts: Results from Indo-Russian collaborative studies

Chemo-enzymatic methods constitute a promising approach to obtain various biologically active compounds, including enantiomerically pure substances. Entrapment in gels is one of the most convenient methods to stabilize enzymes for their application in water/organic media. Proteases and lipases are widely used for enantioselective transformations of various organic compounds in water-poor media. In this study, chymotrypsin was entrapped into a composite poly(N-vinyl caprolactam)-calcium alginate (PVCL-CaAlg) and covalently attached to poly(vinyl alcohol) (PVA) cryogel beads. Lipase was immobilized by covalently attaching to aldehyde-bearing PVA cryogel beads. The activities of the entrapped biocatalysts were studied. Both entrapped α-chymotrypsin and lipase retained high activity in acetonitrile/water medium (water content 0.5–20 %) and displayed high storage stability for several months. The high operational stability of immobilized α-chymotrypsin and lipase in a cyclic process (up to 912 h in total) was also demonstrated. Gel-immobilized enzymes were successfully used to obtain optically pure L-phenylalanine (ee 98.6 and 83 % in the case of α-chymotrypsin and lipase, respectively) by enantioselective hydrolysis of Schiff’s base of amino acid ethyl ester in an acetonitrile/water system.

Keratinase of an anaerobic thermophilic bacterium Thermoanaerobacter sp. Strain 1004-09 isolated from a hot spring in the Baikal rift zone.

A thermophilic anaerobic bacterial strain 1004-09 belonging to the genus Thermoanaerobacter and capable of growth on protein substrates such as albumin, gelatin, casein, and α- and β-keratins was isolated from the Urinskii hot spring (Barguzin river valley, Republic of Buryatia, Russia). A 150-kDa serine proteinase was revealed in the strain supernatant; it exhibited optimal activity at 60°C and pH 9.3 and was capable of keratin hydrolysis. A number of characteristics for the strain 1004-09 keratinase were established including activation by SDS and NaCl and residual activity (15% to the activity of the intact protein) in the presence of 10% ethanol and acetone.