Asparaginyl-N-acetylgalactosamine. Linkage unit of halobacterial glycosaminoglycan

The cell surface glycoprotein of Halobacteria contains two different types of sulfated saccharides: hexuronic acid-containing oligosaccharides linked to the protein via asparaginylglucose, and a serially repeated saccharide unit containing amino sugars that resembles the animal glycosaminoglycans. Here we report that 1) the sulfated repeating unit saccharide is linked to the cell surface glycoprotein via asparaginyl-N-acetylgalactosamine, 2) the amino acid sequence surrounding this linkage region is -Asn-Ala-Ser-, and thus in agreement with the acceptor sequence ASN-X-Thr(Ser) common to all eucaryotic N-glycosidically bound saccharides determined so far; 3) in addition to galactose, galacturonic acid, N-acetylglucosamine, and N-acetylgalactosamine, the methylated hexuronic acid 3-O-methylgalacturonic acid occurs as a stoichiometric constituent of the sulfated building block of the glycosaminoglycan chain.     

Sequence and expression of a halobacterial beta-galactosidase gene

Studies of gene expression in haloarchaea have been greatly hindered by the lack of a convenient reporter gene. In a previous study, a beta-galactosidase from Haloferax alicantei was purified and several peptide sequences determined. The peptide sequences have now been used to clone the entire beta-galactosidase gene (designated bgaH) along with some flanking chromosomal DNA. The deduced amino acid sequence of BgaH was 665 amino acids (74 kDa) and showed greatest amino acid similarity to members of glycosyl hydrolase family 42 [classification of Henrissat, B., and Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 293: 781-788]. Within this family, BgaH was most similar (42-43% aa identity) to enzymes from extremely thermophilic bacteria such as Thermotoga and Thermus. Family 42 enzymes are only distantly related to the Sulfolobus LacS and Escherichia coli LacZ enzymes (families one and two respectively). Three open reading frames (ORFs) upstream of bgaH were readily identified by database searches as glucose-fructose oxidoreductase, 2-dehydro-3-deoxyphosphogluconate aldolase and 2-keto-3-deoxygluconate kinase, enzymes that are also involved in carbohydrate metabolism. Downstream of bgaH there was an ORF which contained a putative fibronectin III motif. The bgaH gene was engineered into a halobacterial plasmid vector and introduced into Haloferax volcanii, a widely used strain that lacks detectable beta-galactosidase activity. Transformants were shown to express the enzyme; colonies turned blue when sprayed with Xgal and enzyme activity could be easily quantitated using a standard ONPG assay. In an accompanying publication, Patenge et al. (2000) have demonstrated the utility of bgaH as a promoter reporter in Halobacterium salinarum.     

A family of halobacterial transducer proteins

Abstract A DNA probe to the signaling domain of a halobacterial transducer for phototaxis (HtrI) was used to clone and sequence four members of a new family of transducer proteins (Htps) in Halobacterium salinarium potentially involved in chemo- or phototactic signal transduction. The signaling domains in these proteins have 31–43% identity when compared with each other or with their bacterial analogs, the methyl-accepting chemotaxis proteins. An additional region of homology found in three of the Htps has 31–43% identity with Htrl. The Htps contain from 0 to 3 transmembrane helices and Western blotting showed that HtpIII is soluble. The arrangement of the domains in these Htps suggests a modular architecture in their construction.     

Phosphorylation in halobacterial signal transduction.

Regulated phosphorylation of proteins has been shown to be a hallmark of signal transduction mechanisms in both Eubacteria and Eukarya. Here we demonstrate that phosphorylation and dephosphorylation are also the underlying mechanism of chemo- and phototactic signal transduction in Archaea, the third branch of the living world. Cloning and sequencing of the region upstream of the cheA gene, known to be required for chemo- and phototaxis in Halobacterium salinarium, has identified cheY and cheB analogs which appear to form part of an operon which also includes cheA and the following open reading frame of 585 nucleotides. The CheY and CheB proteins have 31.3 and 37.5% sequence identity compared with the known signal transduction proteins CheY and CheB from Escherichia coli, respectively. The biochemical activities of both CheA and CheY were investigated following their expression in E.coli, isolation and renaturation. Wild-type CheA could be phosphorylated in a time-dependent manner in the presence of [gamma-32P]ATP and Mg2+, whereas the mutant CheA(H44Q) remained unlabeled. Phosphorylated CheA was dephosphorylated rapidly by the addition of wild-type CheY. The mutant CheY(D53A) had no effect on phosphorylated CheA. The mechanism of chemo- and phototactic signal transduction in the Archaeon H.salinarium, therefore, is similar to the two-component signaling system known from chemotaxis in the eubacterium E.coli.     

ATP-synthesis in archaea: Structure-function relations of the halobacterial A-ATPase

The archaeal (A)-ATPase has been described as a chimeric energy converter with close relationship to both the vacuolar ATPase class in higher eukaryotes and the coupling factor (F)-ATPase class in eubacteria, mitochondria and chloroplasts. With respect to their structure and some inhibitor responses, A-ATPases are more closely related to the vacuolar ATPase type than to F-ATPase. Their function, ATP synthesis at the expense of an ion gradient, however, is a typical attribute of the F-ATPase class. V-type ATPases serve as generators of a proton gradient driving the accumulation of solutes within vesicles such as the vacuoles of plant cells. The three catalytic subunits (A) of the archaeal ATPases are the largest subunits of the A1-part and, like in V-ATPases, closer related to the F-ATPase -subunits, whereas B corresponds to F-ATPase . The catalytic subunits A of archaeal ATPases contain an insert of about 80 amino acids in their primary structures that may be aligned to comparable structures in V-ATPases. The location of this additional peptide in Haloferax volcanii is shown using the 2.8 Å X-ray resolution of the bovine mitochondrial F-ATPase [Abrahams et al. (1994) Nature 370: 621-628]. A three dimensional structure for the catalytic subunit of Haloferax volcanii ATPase is proposed using the Swiss-Model Automated Protein Modelling Server. The halobacterial ATPase is a halophilic protein; it contains about 20% negatively charged amino acid residues. A large portion of acidic residues is located on the outer surface of the protein as well as in the insert of subunit A. This result is discussed in terms of protein stability under high salt stress conditions.     

Morphology, function and isolation of halobacterial flagella

Halobacterium halobium has right-handed helical flagella. During the logarithmic phase of growth, cells are predominantly monopolar, whereas in the stationary phase they are mostly bipolarly flagellated. The flagellar bundle consists of several filaments. Halobacteria swim forward by clockwise and backwards by counterclockwise rotation of their flagella. The flagellar bundle does not fly apart when the sense of rotation changes. In addition to the flagella attached to the cells, large amounts of loose flagella, which aggregate into thick super-flagella, can be observed at all phases of growth. During stationary phase, the production of these super-flagella, which are generally 10 to 20 times longer than the cell body, is significantly higher. Dissociation and association by high temperature and differential centrifugation allow the isolation of pure flagella. Three different protein bands, of 23,500, 26,500 and 31,500 apparent molecular weights, are seen on sodium dodecyl sulphate/polyacrylamide gels. Antibodies against halobacterial flagella were produced in chicken; these antibodies interact with the flagella even in 4 M-NaCl. Rotation of tethered cells demonstrates that Halobacteria move due to the rotation of the flagella.     

The ultrastructure of a halobacterial cell in the region of the flagellum outlet

An intracellular structure previously identified in archaeal cells (Halobacterium salinarum) was studied by electron microscopy of single and serial ultrathin sections. This structure was localized under the cytoplasmic membrane near the cellular poles on both sides of the disc-like lamellar structure (DLS), which we found earlier in the motility apparatus of Hb. salinarum. The organization of this structure differs from that of DLS. Morphological characteristics of the new structure coincide with those of bacterial “polar organelle” (PO) described previously. Similar to PO, the new structure exhibited cytochemical staining that reveals the ATPase activity. The bacterial PO is compared with the analogous structure in archaea.     

Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research

The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields.     

Purification, reconstitution and polymorphic transition of halobacterial flagella

Flagellar filaments of Halobacterium halobium have been purified by dissociation and reconstitution. Three different protein bands (23,500, 26,500 and 31,500 apparent molecular weight) are seen on sodium dodecyl sulphate/polyacrylamide gels, thus confirming that all three proteins are intrinsic to the flagellar structure. We designate them as flagellin Fla I (23,500), Fla II (26,500) and Fla III (31,500). Polymorphic transitions from normal to a curly, a ring and a straight form are induced by different pH values and heat treatments.     

Isolation of a halobacterial phage with a fully cytosine-methylated genome

Summary A new bacteriophage from Halobacterium halobium has been isolated and partially characterized. It is not homologous to the phage H (Schnabel, et al. 1982) which infects the same bacterium, though it appeared spontaneously in a culture of H adapted to H. halobium NRL/JW. The size and morphology of N are comparable to that of other known halophages. The genome of N consists of linear double-stranded DNA, 56 kb in size, whose dCMP is totally replaced by 5-methyl-dCMP. This is the second case of a fully cytosine-methylated genome, the bacteriophage XP12 from Xanthomonas oryzae, being so far the only one reported. Like H, the N, genome seems to have terminal redundancy and circular permutation. N is the first halobacterial phage which survives prolonged exposure to low ionic strength environments. After 48 h incubation in distilled water a loss in infectivity of less than 50% is observed.     

Expression of the halobacterial transducer protein HtrII from Natronomonas pharaonis in Escherichia coli

Archaeal phototaxis is mediated by sensory rhodopsins which form complexes with their cognate transducers. Whereas the receptors sensory rhodopsin I and sensory rhodopsin II (SRII) have been expressed in Escherichia coli (E. coli) only shortened fragments of HtrII from Natronomonas pharaonis (NpHtrII) are available. Here we describe the heterologous expression of full length NpHtrII which was achieved in yields of up to 0.9 mg per litre cell culture. Gel filtration analysis reveals the tendency of the transducer to form dimers and higher-order oligomers which was also observed when complexed to NpSRII. A circular dichroism (CD) spectrum of NpHtrII is comparable to those obtained for the E. coli chemoreceptors indicating a similar folding with predominantly alpha-helical structure. NpHtrII dissociates from the NpSRII/HtrII complex with an apparent K(D) of about 0.6 microM. Photocycle kinetics of the complex is comparable to that obtained for NpSRII in complex with a truncated transducer with slight differences in the M-decay. The data indicate that the heterologously expressed NpHtrII adopt a native like structure, providing the means for elucidating transmembrane signal transduction and activation of microbial signalling cascades.     

Microbial glycosaminoglycan glycosyltransferases

Glycosaminoglycans, a class of linear polysaccharides composed of repeating disaccharide units containing a hexosamine, are important carbohydrates found in many organisms. Vertebrates utilize glycosaminoglycans in structural, recognition, adhesion, and signaling roles. Certain pathogenic bacteria produce extracellular capsules composed of glycosaminoglycans or glycosaminoglycan-like polymers that enhance the microbes' ability to infect or to colonize the host. In the period from 1993 to 2001, bacterial enzymes were discovered that catalyze the polymerization of the repeating unit of hyaluronan, chondroitin, or N-acetylheparosan (unsulfated, unepimerized heparin). Depending on the specific carbohydrate and the microorganism, either a dual-action enzyme (synthase) that transfers two distinct monosaccharides or a pair of single-action transferases are utilized to synthesize the glycosaminoglycan polymer. Current views on the enzymology, structures, potential evolution, and the roles of the known glycosyltransferases from Streptococcus, Pasteurella, and Escherichia are discussed.     

Sequences of halobacterial tRNAs and the paucity of U in the first position of their anticodons

The sequence of three tRNAs from Halobacterium cutirubrum have been determined. The sequences of tRNAValGAC and tRNAValCAC differ by only one nucleotide which is in the 5' terminal anticodon position. These tRNAs as well as that of tRNAAlaCGC are compared to other known halobacterial tRNAs. An observed paucity (or absence) of U in the first anticodon position is unique to archaebacterial tRNAs and may be indicative of unusual decoding properties of these organisms.     

Properties and the primary structure of a new halorhodopsin from halobacterial strain mex.

A new halorhodopsin-like pigment from the new halobacterial strain mex (Otomo, J., Tomoika, H. and Sasabe, H. (1992) J. Gen. Microbiol. 138, 1027-1037) was partially purified, and its amino acid sequence from helices A to G was determined using PCR technique. Two arginine residues in the A-B interhelix loop segment, a series of six amino acid residues (EMPAGH) in the B-C interhelix segment and most of the residues near the Schiff base of the retinal were found to be conserved in three halorhodopsins (halobium, pharaonis and mex). This result strongly suggests that these residues are essential for anion pumping function in halorhodopsin. The light-induced ion-pump measurements have shown that the selectivity of anion transport between chloride and nitrate in mex halorhodopsin is lower than that of halobium halorhodopsin, but higher than that of pharaonis halorhodopsin. The number of amino acid residues in the B-C interhelix loop segments is different in each halorhodopsin, and it correlates with their anion (chloride and nitrate) selectivity. These results suggest that the length of the B-C segment affects the selectivity of anion transport in halorhodopsin.     

Sulfotransferases in glycosaminoglycan biosynthesis

Most of the sulfotransferases participating in glycosaminoglycan biosynthesis have now been identified. Their essential role in generating binding sites for proteins interacting with glycosaminoglycans is apparent. These interactions may influence important biological processes such as growth control, signal transduction, cell adhesion and lipid metabolism. Gene targeting in mice as well as studies in Drosophila melanogaster and Caenorhabditis elegans have shown that dysfunction or lack of glycosaminoglycan sulfotransferases may result in severely disturbed embryonic development.     

Nanomechanics of opposing glycosaminoglycan macromolecules

In this study, the net intermolecular interaction force between a chondroitin sulfate glycosaminoglycan (GAG)-functionalized probe tip and an opposing GAG-functionalized planar substrate was measured as a function of probe tip-substrate separation distance in aqueous electrolyte solutions using the technique of high resolution force spectroscopy. A range of GAG grafting densities as near as possible to native cartilage was used. A long-range repulsive force between GAGs on the probe tip and substrate was observed, which increased nonlinearly with decreasing separation distance between probe tip and substrate. Data obtained in 0.1 M NaCl was well predicted by a recently developed Poisson-Boltzmann-based theoretical model that describes normal electrostatic double layer interaction forces between two opposing surfaces of end-grafted, cylindrical rods of constant volume charge density and finite length, which interdigitate upon compression. Based on these results, the nanomechanical data and interdigitated rod model were used together to estimate the electrostatic component of the equilibrium modulus of cartilage tissue, which was then compared to that of normal adult human ankle cartilage measured in uniaxial confined compression.     

Regulatory aspects of glycosaminoglycan biosynthesis

The control of glycosaminoglycan biosynthesis was investigated by studying the kinetic and regulatory properties of some enzymes involved in the formation of UDP-sugar precursors: UDP-N-acetylglucosamine 4'-epimerase, catalyzing the interconversion of hexosamine precursors and UDP-glucose dehydrogenase and UDP-glucose 4'-epimerase, utilizing UDP-glucose for the formation of uronic acid and galactose precursors. The study was carried out in tissues with different glycosaminoglycan production: bovine cornea, producing both chondroitin sulfate and keratan sulfate, and newborn-pig epiphysial-plate cartilage, producing mostly chondroitin sulfate. The biosynthesis of hexosamine precursors appeared to be regulated by the value of the NAD/NADH ratio. This control mechanism regulated also the activities of both UDP-glucose dehydrogenase and UDP-glucose 4'-epimerase and, therefore, it could correlate the biosynthesis of glycosaminoglycan precursors with the redox activity of the cell. At the level of UDP-glucose utilization two other control mechanisms were demonstrated: the different affinities of UDP-glucose dehydrogenase and UDP-glucose 4'-epimerase for UDP-glucose in tissues with different glycosaminoglycan production and the cellular concentration of UDP-xylose. This sugar-nucleotide inhibited UDP-glucose dehydrogenase, but did not affect the UDP-glucose 4'-epimerase activity; therefore, and increase of its cellular concentration may result in a decreased chondroitin sulfate synthesis and in an increased keratan sulfate formation.