Partial sequence of the gene for a serine protease from a halophilic archaeum Haloferax mediterranei R4, and nucleotide sequences of 16S rRNA encoding genes from several halophilic archaea

Recent advances in the production, properties and applications of haloextremozymes protease and lipase from haloarchaea

Proteases and lipases are significant groups of enzymes for commercialization at the global level. Earlier, the industries depended on mesophilic proteases and lipases, which remain nonfunctional under extreme conditions. The discovery of extremophilic microorganisms, especially those belonging to haloarchaea, paved a new reserve of industrially competent extremozymes. Haloarchaea or halophilic archaea are polyextremophiles of domain Archaea that grow at high salinity, elevated temperature, pH range (pH 6-12), and low aw. Interestingly, haloarchaeal proteolytic and lipolytic enzymes also perform their catalytic function in the presence of 4-5 M NaCl in vivo and in vitro. Also, they are of great interest to study due to their capacity to function and are active at elevated temperatures, tolerance to pH extremes, and in non-aqueous media. In recent years, advances have been achieved in various aspects of genomic/molecular expression methods involving homologous and heterologous processes for the overproduction of these extremozymes and their characterization from haloarchaea. A few protease and lipase extremozymes have been successfully expressed in prokaryotic systems, especially E.coli, and enzyme modification techniques have improved the catalytic properties of the recombinant enzymes. Further, in-silico methods are currently applied to elucidate the structural and functional features of salt-stable protease and lipase in haloarchaea. In this review, the production and purification methods, catalytic and biochemical properties and biotechnological applications of haloextremozymes proteases and lipases are summarized along with recent advancements in overproduction and characterization of these enzymes, concluding with the directions for further in-depth research on proteases and lipases from haloarchaea.

Halolysin R4 of Haloferax mediterranei confers its host antagonistic and defensive activities

Halolysins, which are subtilisin-like serine proteases of haloarchaea, are usually secreted into the extracellular matrix via the twin-arginine translocation pathway. A small number of activated molecules can greatly affect cell growth owing to their proteolytic activity. It is, however, unclear as to whether this proteolysis-based growth inhibition by halolysins conveys antagonistic or defensive effects against other resident abd potentially competitive microorganisms. Here, we report that halolysin R4 (HlyR4), encoded by the hlyR4 gene, is the key enzyme in the initial steps of extracellular protein utilization in Haloferax mediterranei HlyR4 shows significant antagonistic activity against other haloarchaeal strains. Deletion of hlyR4 completely halts the inhibition activity of Hfx. mediterranei towards other haloarchaea, while correspondingly, complementation of hlyR4 almost completely restores the inhibition activity. Furthermore, Hfx. mediterranei strains containing hlyR4 showed a certain amount of resistance to halocins and halolysins in milieu, and this function of hlyR4 is reproducible in Haloarcula hispanica The versatility of HlyR4 enables its host to outcompete other haloarchaea living in the same hypersaline environment. Intriguingly, unlike the growth phase-dependent halolysins SptA and Nep, it is likely that HlyR4 may be secreted independent of growth phase. This study provides a new peptide antibiotics candidate in haloarchaea, as well as new insight towards a better understanding of the ecological roles of halolysins.Importance: This study shows that halolysin R4 from Haloferax mediterranei provides its host antagonistic and defensive activities against other haloarchaea, which expands our knowledge on the traditional function of haloarchaeal extracellular proteases. Haloarchaeal extracellular serine proteases have been previously discussed as growth-phase-dependent proteins, whereas our study reports constitutive expression of halolysin R4. This work also clearly reveals a hidden diversity of extracellular proteases from haloarchaea. Studies on multifunctional halolysins reveal that they play an important ecological role in shaping microbial community composition and provide a new perspective towards understanding the intricate interactions between haloarchaeal cells in hypersaline environments. HlyR4 can lyse competing cells living in the same environment, and the cell debris may probably be utilized as nutrients, which may constitute an important part of nutrient cycling in extremely hypersaline environments.

Extremophilic proteases as novel and efficient tools in short peptide synthesis

The objective of this review is to outline the crucial role that peptides play in various sectors, including medicine. Different ways of producing these compounds are discussed with an emphasis on the benefits offered by industrial enzyme biotechnology. This paper describes mechanisms of peptide bond formation using a range of proteases with different active site structures. Importantly, these enzymes may be further improved chemically and/or genetically to make them better suited for their various applications and process conditions. The focus is on extremophilic proteases, whose potential does not seem to have been fully appreciated to date. The structure of these proteins is somewhat different from that of the common commercially available enzymes, making them effective at high salinity and high or low temperatures, which are often favorable to peptide synthesis. Examples of such enzymes include halophilic, thermophilic, and psychrophilic proteases; this paper also mentions some promising catalytic proteins which require further study in this respect.

Evaluation of ultrasound velocity measurements for estimating protease activities using casein as substrate

Ultrasonic resonator technology (URT) was compared with the well established UV-Vis/ninhydrin assay to estimate protease activities in defined buffer systems. Hydrolysis of casein was measured using subtilisin, trypsin, halophilic protease from Haloferax mediterranei and Bacillus lentus alkaline protease. Sensitivity, reproducibility, working range as well as the limit of detection and the limit of quantification were comparable for both methods. Salt concentrations (0.5 M NaCl) interfered with the URT method. The quantification of protease activity by URT was possible when the product concentration measured by the UV-Vis/ninhydrin assay was correlated to the corresponding ultrasonic velocity signals.

Haloarchaeal proteases and proteolytic systems

Proteases play key roles in many biological processes and have numerous applications in biotechnology and industry. Recent advances in the genetics, genomics and biochemistry of the halophilic Archaea provide a tremendous opportunity for understanding proteases and their function in the context of an archaeal cell. This review summarizes our current knowledge of haloarchaeal proteases and provides a reference for future research.

Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences

Twenty-two extremely halophilic aerobic archaeal strains were isolated from enrichments prepared from Dead Sea water samples collected 57 years ago. The isolates were phenotypically clustered into five different groups, and a representative from each group was chosen for further study. Almost the entire sequences of the 16S rRNA genes of these representatives, and of Haloarcula hispanica ATCC 33960, were determined to establish their phylogenetic positions. The sequences of these strains were compared to previously published sequences of 27 reference halophilic archaea (members of the family Halobacteriaceae) and two other archaea, Methanobacterium formicicum DSM 1312 and Methanospirillum hungatei DSM 864. Phylogenetic analysis using approximately 1,400 base comparisons of 16S rRNA-encoding gene sequences demonstrated that the five isolates clustered closely to species belonging to three different genera--Haloferax, Halobacterium, and Haloarcula. Strains E1 and E8 were closely related and identified as members of the species Haloferax volcanii, and strain E12 was closely related and identified as a member of the species Halobacterium salinarum. However, strains E2 and E11 clustered in the Haloarcula branch with Haloarcula hispanica as the closest relative at 98.9 and 98.8% similarity, respectively. Strains E2 and E11 could represent two new species of the genus Haloarcula. However, because strains of these two new species were isolated from a single source, they will not be named until additional strains are isolated from other sources and fully characterized.

Halolysin R4, a serine proteinase from the halophilic archaeon Haloferax mediterranei; gene cloning, expression and structural studies

A gene encoding a halophilic serine proteinase, halolysin R4, from a halophilic archaeon Haloferax mediterranei strain R4 was cloned, its nucleotide sequence determined, and expressed in Haloferax volcanii WFD11. The deduced amino-acid sequence (403 aa in length) showed the highest similarity to halolysin 172P1, produced by another halophilic archaeon, strain 172P1 (now designated as Natrialba asiatica). Both halolysins belong to the thermitase branch of class I subtilases, but show long C-terminal extensions of 117 and 123 amino acids, respectively. Removal of this "tail' region from halolysin R4 abolished proteinase activity, indicating it provides an essential (but as yet unknown) function. Substitution of the two cysteine residues in the C-terminal extension with serine decreased enzyme stability in hypotonic solutions, possibly owing to disruption of potential disulfide bonds or perturbation of calcium binding site(s).

Polar lipids of a non-alkaliphilic extremely halophilic archaebacterium strain 172: a novel bis-sulfated glycolipid

Extremely halophilic archaebacteria which require high salt concentrations for growth and survival contain glycerol diether analogues of phospholipids and sulfated glycolipids as major membrane polar lipids. A non-alkaliphilic, non-pigmented rod-shaped extreme halophile, isolated from sea sand in Japan and designated 'strain 172', was found to contain two phospholipids, phosphatidylglycerol (PG) and phosphatidylglyceromethylphosphate (PGP-Me), derived from both C20-C20- and C20-C25-glycerol diethers, and a novel major glycolipid (designated SGL-X). This glycolipid has been identified as a bis-sulfated diglycosyl C20-C20- or C20-C25-glycerol diether, on the basis of its TLC mobility, positive-staining behavior with sugar and sulfate-staining reagents, its mole ratio sulfate/glycolipid = 2.2, and by spectrometric analysis (IR and FAB-MS) of the intact and the desulfated SGL-X. The sugars were identified as mannose and glucose, after acid hydrolysis of SGL-X, by paper chromatography of the free sugars and GC-MS of the derivatized sugars (alditol acetates). Permethylation analysis and 1H- and 13C-NMR analysis established the position and configuration of the sugar linkages and the positions of the sulfate groups. The final structure of SGL-X (now designated S2-DGD-1) is proposed to be: 2,3-diphytanyl- or phytanyl-sesterterpenyl-1-[2,6-(HSO3)2-alpha-Manp-1--> 2- Glcp]-sn-glycerol. This lipid is the first bis-sulfated glycolipid to be reported in extremely halophilic archaebacteria, and is the first in the biosphere that possesses two sulfate groups attached to the same monosaccaride.

Comparative studies on ion pumps of the bacterial rhodopsin family

Bacteriorhodopsin (proton pump), halorhodopsin (anion pump), sensory rhodopsin and phoborhodopsin (photosensors) are found in Halobacterium salinarium (halobium). In some other strains, other sets of rhodopsin pumps and sensors have been found. Here, these bacterial rhodopsins are classified according to their amino acid sequence homologies, and their host genera are assigned on the basis of 16S rRNA sequence comparison. Haloarcula is the host for cruxrhodopsins and a new genus (temporarily "Halorubra") is the host for archaerhodopsins. Difference in the all-trans:13-cis ratios of retinal in two proton pumps (bacteriorhodopsin and archaerhodopsin-2) at equilibrium states in the dark was ascribed to only one amino acid residue in the retinal pocket. This predicted methionine-145 in bacteriorhodopsin was point-mutated to phenylalanine as in archaerhodopsin-2. The mutated bacteriorhodopsin (M145F) became to show the same dark-adapted isomer ratio that archaerhodopsin-2 shows. Chimeric proton pumps were made by exchanging genes of one or more helix regions of two similar pumps (archaerhodopsin-1 and -2) in order to know structural delicacy of the inter-helix space. Preliminary results show that some photochemical properties depend on one helix or one distinct amino acid residue on the helix. Such new lines initiated by our archaerhodopsins are discussed for studying structure and function of these unique bacterial rhodopsins.