Hydrophobic Cluster Analysis Research Articles

Endogenous cellulases in animals: isolation of beta-1, 4-endoglucanase genes from two species of plant-parasitic cyst nematodes.

beta-1,4-Endoglucanases (EGases, EC 3.2.1.4) degrade polysaccharides possessing beta-1,4-glucan backbones such as cellulose and xyloglucan and have been found among extremely variegated taxonomic groups. Although many animal species depend on cellulose as their main energy source, most omnivores and herbivores are unable to produce EGases endogenously. So far, all previously identified EGase genes involved in the digestive system of animals originate from symbiotic microorganisms. Here we report on the synthesis of EGases in the esophageal glands of the cyst nematodes Globodera rostochiensis and Heterodera glycines. From each of the nematode species, two cDNAs were characterized and hydrophobic cluster analysis revealed that the four catalytic domains belong to family 5 of the glycosyl hydrolases (EC 3.2.1, 3.2.2, and 3.2.3). These domains show 37-44% overall amino acid identity with EGases from the bacteria Erwinia chrysanthemi, Clostridium acetobutylicum, and Bacillus subtilis. One EGase with a bacterial type of cellulose-binding domain was identified for each nematode species. The leucine-rich hydrophobic core of the signal peptide and the presence of a polyadenylated 3' end precluded the EGases from being of bacterial origin. Cyst nematodes are obligatory plant parasites and the identified EGases presumably facilitate the intracellular migration through plant roots by partial cell wall degradation.

Sequence and 3D structural relationships between mammalian Ras- and Rho-specific GTPase-activating proteins (GAPs): the cradle fold

An extensive study of both sequence and recent 3D structural data concerning GTPase interacting domains of Ras- and Rho-specific GTPase-activating proteins (GAPs) shows that these two subfamilies share a same 3D scaffold and are thus related to each other. This relationship has heretofore remained undetected although these domains of similar size are both totally α-helical and activate nearly structurally identical targets (Ras and Rho proteins). In this report, sequence similarities correlated to 3D structures of p120rasGAP and p50rhoGAP were detected using the sensitive two-dimensional method hydrophobic cluster analysis (HCA). These patterns were further extended to other members in each subfamily and the geometry orientation of crucial arginines R789 in p120 and R282 in p50 and of important stabilizing residues like p120R903 and p50N391 was confirmed. This overall structural relationship is centered on an invariant motif of three consecutive helices that we suggest to name the `cradle fold'. This observation opens new perspectives to understand how small GTPases are specifically regulated.

Cloning and expression of an iron-containing superoxide dismutase in the parasitic protist, Trichomonas vaginalis.

A superoxide dismutase (SOD) gene of the parasitic protist Trichomonas vaginalis was cloned, sequenced, expressed in Escherichia coli, and its gene product characterized. It is an iron-containing dimeric protein with a monomeric mass of 22,067 Da. Southern blots analyses suggested the presence of seven iron-containing (FeSOD) gene copies. Hydrophobic cluster analysis revealed some peculiarities in the 2D structure of the FeSOD from T. vaginalis and a strong structural conservation between prokaryotic and eukaryotic FeSODs. Phylogenetic reconstruction of the SOD sequences confirmed the dichotomy between FeSODs and manganese-containing SODs. FeSODs of protists appeared to group together with homologous proteobacterial enzymes suggesting a possible origin of eukaryotic FeSODs through an endosymbiotic event.

Cloning and expression of an iron-containing superoxide dismutase in the parasitic protist, Trichomonas vaginalis

A superoxide dismutase (SOD) gene of the parasitic protist Trichomonas vaginalis was cloned, sequenced, expressed in Escherichia coli, and its gene product characterized. It is an iron-containing dimeric protein with a monomeric mass of 22 067 Da. Southern blots analyses suggested the presence of seven iron-containing (FeSOD) gene copies. Hydrophobic cluster analysis revealed some peculiarities in the 2D structure of the FeSOD from T. vaginalis and a strong structural conservation between prokaryotic and eukaryotic FeSODs. Phylogenetic reconstruction of the SOD sequences confirmed the dichotomy between FeSODs and manganese-containing SODs. FeSODs of protists appeared to group together with homologous proteobacterial enzymes suggesting a possible origin of eukaryotic FeSODs through an endosymbiotic event.

Sequence of archaeal Methanococcus jannaschii alpha-amylase contains features of families 13 and 57 of glycosyl hydrolases: a trace of their common ancestor?

Two sequentially different, seemingly unrelated alpha-amylase families exist, known as family-13 and family-57 glycosyl hydrolases. Despite the common enzyme activity, it has as yet been impossible to detect any sequence similarity between the two families. The detailed analysis of the recently determined sequence of the alpha-amylase from methanogenic archaeon Methanococcus jannaschii using the sensitive Hydrophobic Cluster Analysis method revealed that this alpha-amylase contains features of both families of alpha-amylases. Thus the M. jannaschii alpha-amylase is similar to the Pyrococcus furiosus alpha-amylase from family 57 while it obviously contains most of the sequence fingerprints characteristic for alpha-amylase family 13. Importantly, a glutamic acid residue equivalent with the family-13 catalytic glutamate positioned in the beta 5-strand segment was identified in members of family 57. The results presented in this report indicate that the two families, 13 and 57, are either the products of a very distant common ancestor or have evolved from each other, although at present they can represent two different alpha-amylase families with evolved different catalytic mechanisms, catalytic machinery and folds.

Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues.

A genomic library of Pseudomonas fluorescens subsp. cellulosa DNA was screened for galactanase-positive recombinants. The nine galactanase positive phage isolated contained the same galactanase gene designated galA. The deduced primary structure of the enzyme (galactanase A; GalA) encoded by galA had a Mr of 42 130 and exhibited significant sequence identity with a galactanase from Aspergillus aculeatus, placing GalA in glycosyl hydrolase family 53. The enzyme displayed properties typical of an endo-beta1, 4-galactanase and exhibited no activity against the other plant structural polysaccharides evaluated. Analysis of the stereochemical course of 2,4-dinitrophenyl-beta-galactobioside (2,4-DNPG2) hydrolysis by GalA indicated that the galactanase catalyzes the hydrolysis of glycosidic bonds by a double displacement general acid-base mechanism. Hydrophobic cluster analysis (HCA) suggested that family 53 enzymes are related to the GH-A clan of glycosyl hydrolases, which have an (alpha/beta)8 barrel structure. HCA also predicted that E161 and E270 were the acid-base and nucleophilic residues, respectively. Mutants of GalA in which E161 and E270 had been replaced with alanine residues were essentially inactive against galactan. Against 2,4-DNPG2, E161A exhibited a much lower Km and kcat than native GalA, while E270A was inactive against the substrate. Analysis of the pre-steady-state kinetics of 2,4-DNPG2 hydrolysis by E161A showed that there was an initial rapid release of 2,4-dinitrophenol (2,4-DNP), which then decayed to a slow steady-state rate of product formation. No pre-steady-state burst of 2,4-DNP release was observed with the wild-type enzyme. These data are consistent with the HCA prediction that E161 and E270 are the acid-base and nucleophilic catalytic residues of GalA, respectively.

Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives.

Ten years after the idea of hydrophobic cluster analysis (HCA) was conceived and first published, theoretical and practical experience has shown this unconventional method of protein sequence analysis to be particularly efficient and sensitive, especially with families of sequences sharing low levels of sequence identity. This extreme sensitivity has made it possible to predict the functions of genes whose sequence similarities are hardly if at all detectable by current one-dimensional (1D) methods alone, and offers a new way to explore the enormous amount of data generated by genome sequencing. HCA also provides original tools to understand fundamental features of protein stability and folding. Since the last review of HCA published in 1990 [1], significant improvements have been made and several new facets have been addressed. Here we wish to update and summarize this information.

Domain evolution in the alpha-amylase family.

The available amino acid sequences of the alpha-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (beta/alpha)8-barrel between the strand beta3 and the helix alpha3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an alpha-helix succeeded by a three-stranded antiparallel beta-sheet. These enzymes are alpha-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few alpha-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (beta/alpha)8-barrel elements throughout the entire sequence of enzymes from the oligo-1, 6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the alpha-amylase family.

Hydrophobic Cluster Analysis Reveals a Third Chromodomain in theTetrahymenaPdd1p Protein of the Chromo Superfamily

The protein Pdd1p (for programmed DNA degradation) links heterochromatin assembly and DNA elimination inTetrahymenaand has recently been identified as a new member of the chromo superfamily that contains two chromodomains. Using the sensitive bidimensional Hydrophobic Cluster Analysis (HCA) method, we have identified a third, highly divergent chromodomain in the Pdd1p sequence. Based on similarity to chromo shadow domains that mediate protein-protein interactions, this newly identified chromodomain may direct the binding of Pdd1p to other proteins. These findings suggest that Pdd1p may be the prototypical member of a new class in the chromo superfamily as all other members contain only one or two chromodomains. The results also demonstrate the power of HCA in identifying relationships which are not detected by conventional methods of sequence analysis.

Domain-specific Interactions of Human HP1-type Chromodomain Proteins and Inner Nuclear Membrane Protein LBR

HP1-type chromodomain proteins self-associate as well as interact with the inner nuclear membrane protein LBR (lamin B receptor) and transcriptional coactivators TIF1alpha and TIF1beta. The domains of these proteins that mediate their various interactions have not been entirely defined. HP1-type proteins are predicted by hydrophobic cluster analysis to consist of two homologous but distinct globular domains, corresponding to the chromodomain and chromo shadow domain, separated by a hinge region. We show here that the chromo shadow domain mediates the self-associations of HP1-type proteins and is also necessary for binding to LBR both in vitro and in the yeast two-hybrid assay. Hydrophobic cluster analysis also predicts that the nucleoplasmic amino-terminal portion of LBR contains two globular domains separated by a hinge region. The interactions of the LBR domains with an HP1-type protein were also analyzed by the yeast two-hybrid and in vitro binding assays, which showed that a portion of the second globular domain is necessary for binding. The modular domain organization of HP1-type proteins and LBR can explain some of the diverse protein-protein interactions at the chromatin-lamina-membrane interface of the nuclear envelope.

Polysaccharide hydrolase folds diversity of structure and convergence of function

Polysaccharide glycosyl hydrolases are a group of enzymes that hydrolyze the glycosidic bond between carbohydrates or between a carbohydrate and a noncarbohydrate moiety. Here we illustrate that traditional schemes for grouping enzymes, such as by substrate specificity or by organism of origin, are not appropriate when thinking of structure-function relationships and protein engineering. Instead, sequence comparisons and structural studies reveal that enzymes with diverse specificities and from diverse organisms can be placed into groups among which mechanisms are largely conserved and insights are likely to be transferrable. In particular, we illustrate how enzymes have been grouped using protein sequence alignment algorithms and hydrophobic cluster analysis. Unfortunately for those who seek to improve cellulase function by design, cellulases are distributed throughout glycosyl hydrolase Families 1,5,6,7,9, and 45. These cellulase families include members from widely different fold types, i.e., the TIM-barrel, betaalphabeta-barrel variant (a TIM-barrel-like structure that is imperfectly superimposable on the TIM-barrel template), beta-sandwich, and alpha-helix circular array. This diversity in cellulase fold structure must be taken into account when considering the transfer and application of design strategies between various cellulases.

From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair

Inherited mutations in BRCA1 predispose to breast and ovarian cancer, but the biological function of the BRCA1 protein has remained largely elusive. The recent correspondence of Koonin et al. [Koonin, E.V., Altschul, S.F. and Bork, P. (1996) Nature Genet. 13, 266–267] has emphasized the potential importance of the BRCA1 C-terminal region for BRCA1-mediated breast cancer suppression, as this domain shows similarities with the C-terminal regions of a p53-binding protein (53BP1), the yeast RAD9 protein involved in DNA repair, and two uncharacterized, hypothetical proteins (KIAA0170 and SPAC19G10.7). The highlighted domain has been suggested to be the result of an internal duplication, each of the tandem domains being designated as a `BRCT domain' (for BRCA1 C-terminus). Sequence analysis using hydrophobic cluster analysis reveals here the presence of 50 copies of the BRCT domain in 23 different proteins, including, in addition to BRCA1, 53BP1 and RAD9, XRCC1, RAD4, Ect2, REV1, Crb2, RAP1, terminal deoxynucleotidyltransferases (TdT) and three eukaryotic DNA ligases. Most of these proteins are known to be involved in DNA repair. The BRCT domain is not limited to the C-termini of protein sequences and can be found in multiple copies or in a single copy as in RAP1 and TdT, suggesting that it could well constitute an autonomous folding unit of approx. 90–100 amino acids.

Herpesvirus of turkeys homologue of HSV VP16 is structurally related to varicella zoster virus trans-inducing protein encoded by ORF 10.

Expression of the immediate-early genes of alpha-herpesviruses is stimulated by a family of trans-inducing factors represented by VP16 of HSV-1 and ORF10 gene product of VZV. We have identified and determined the nucleotide sequence of the UL48 gene encoding the herpesvirus of turkeys (HVT) homologue of HSV VP16. The gene maps to the BamHI-J fragment and appears to be expressed in a form of bicistronic transcript together with UL49. The deduced amino acid sequence of the protein encoded by HVT UL48 gene shows 55% identity with MDV UL48 gene product. Like the majority of related proteins in other alpha-herpesviruses, the protein encoded by HVT UL48 gene lacks the acidic C-terminal tail, known to possess the transactivation capacity of HSV VP16. Hydrophobic cluster analysis has revealed that its predicted domain composition is closely related to the transactivator protein encoded by ORF10 of VZV. However, the putative amino-terminal activation domain of the HVT homologue of HSV VP16 does not contain a typical horseshoe-like hydrophobic cluster found in other alpha-herpesvirus homologues, suggesting either that it acts as a transactivator via a different activation domain or that its transactivation potential is diminished.

Identification of Candidate Active Site Residues in Lysosomal β-Hexosaminidase A

The beta-hexosaminidases (Hex) catalyze the cleavage of terminal amino sugars on a broad spectrum of glycoconjugates. The major Hex isozymes in humans, Hex A, a heterodimer of alpha and beta subunits (alphabeta), and Hex B, a homodimer of beta subunits (betabeta), have different substrate specificities. The beta subunit (HEXB gene product), hydrolyzes neutral substrates. The alpha subunit (HEXA gene product), hydrolyzes both neutral and charged substrates. Only Hex A is able to hydrolyze the most important natural substrate, the acidic glycolipid GM2 ganglioside. Mutations in the HEXA gene cause Tay-Sachs disease (TSD), a GM2 ganglioside storage disorder. We investigated the role of putative active site residues Asp-alpha258, Glu-alpha307, Glu-alpha323, and Glu-alpha462 in the alpha subunit of Hex A. A mutation at codon 258 which we described was associated with the TSD B1 phenotype, characterized by the presence of normal amounts of mature but catalytically inactive enzyme. TSD-B1 mutations are believed to involve substitutions of residues at the enzyme active site. Glu-alpha307, Glu-alpha323, and Glu-alpha462 were predicted to be active site residues by homology studies and hydrophobic cluster analysis. We used site-directed mutagenesis and expression in a novel transformed human fetal TSD neuroglial (TSD-NG) cell line (with very low levels of endogenous Hex A activity), to study the effects of mutation at candidate active site residues. Mutant HEXA cDNAs carrying conservative or isofunctional substitutions at these positions were expressed in TSD-NG cells. alphaE323D, alphaE462D, and alphaD258N cDNAs produced normally processed peptide chains with drastically reduced activity toward the alpha subunit-specific substrate 4MUGS. The alphaE307D cDNA produced a precursor peptide with significant catalytic activity. Kinetic analysis of enzymes carrying mutations at Glu-alpha323 and Asp-alpha258 (reported earlier by Bayleran, J., Hechtman, P., Kolodny, E., and Kaback, M. (1987) Am. J. Hum. Genet. 41,532-548) indicated no significant change in substrate binding properties. Our data, viewed in the context of homology studies and modeling, and studies with suicide substrates, suggest that Glu-alpha323 and Asp-alpha258 are active site residues and that Glu-alpha323 is involved in catalysis.

Identification of cellulose synthase(s) in higher plants: sequence analysis of processive β-glycosyltransferases with the common motif ’D, D, D35Q(R,Q)XRW‘

More than ten β-glycosyltransferases are now recognized that have limited similarity to the amino acid sequence of cellulose synthase from Acetobacter xylinum. Using hydrophobic cluster analysis (HCA), we recently identified two domains and putative catalytic residues in the processive β-glycosyltransferases. In this study, we have found expressed sequence tags (ESTs) from higher plants (Arabidopsis thaliana, Brassica campestris, and Oryza sativa) that exhibit a limited sequence similarity to the A. xylinum cellulose synthase. These ESTs contain some of the conserved residues identified in the processive β-glycosyltransferases. Complete sequencing of an EST clone (T88271) from A. thaliana led to the identification of all the conserved residues in the derived truncated polypeptide which appears to be part of a putative cellulose synthase. Sequence comparison of proteins with known function and several unidentified proteins have the ‘D, D, D35Q(R,Q)XRW’ motif which is considered a strong predictor for β-glycosyltransferasesthat includes, among other proteins, cellulose and chitin synthases. The first two conserved aspartic acid residues in this motif were analysed by site-directed mutagenesis, and their replacement by another amino acid led to a loss of cellulose synthase activity in A. xylinum, suggesting that they are essential for enzyme activity. A correlation between the second residue (R or Q) in the Q(R,Q)XRW sequence and the synthesis of along glucan chain (polysaccharide) or a short glucan chain(oligosaccharide) suggests that this residue may be involved in the degree of processivity

Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT.

When routinely analysing protein sequences, detailed analysis of database search results made with BLAST and FASTA becomes exceedingly time consuming and tedious work, as the resultant file may contain a list of hundreds of potential homologies. The interpretation of these results is usually carried out with a text editor which is not a convenient tool for this analysis. In addition, the format of data within BLAST and FASTA output files makes them difficult to read. To facilitate and accelerate this analysis, we present for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition. Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.

The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development.

The human p100 protein was recently identified as a coactivator of the Epstein-Barr virus nuclear antigen 2. On the basis of sequence analysis with the hydrophobic cluster analysis method, we predict that this protein consists of a repeat of four similar domains. Their fold can be related to the staphylococcal nuclease structure whose first subdomain belongs to the large oligonucleotide/oligosaccharide-binding (OB)-fold superfamily. The catalytic amino acids present in nucleases are missing, however, suggesting that these repeated motifs could only serve to bind DNA without catalytic activity, as in many other OB-folds. A highly modified fifth domain follows the four nuclease-like domains, conserving the second subdomain of the nuclease structure but not the first one (the OB-fold), which is replaced by an original domain found in multiple copies in the tudor protein, a Drosophila melanogaster protein required during oogenesis for establishment of a functional posterior organizing centre. We named this heretofore undescribed domain the 'tudor domain' and highlight within it five invariant residues which could be involved in one of the essential roles played by these proteins.

A Novel Pathway for O-Polysaccharide Biosynthesis in Salmonella enterica Serovar Borreze

The plasmid-encoded gene cluster for O:54 O-polysaccharide synthesis in Salmonella enterica serovar Borreze (rfbO:54) contains three genes that direct synthesis of a ManNAc homopolymer with alternating beta1,3 and beta1,4 linkages. In Escherichia coli K-12, RfbAO:54 adds the first ManNAc residue to the Rfe (UDP-GlcpNAc::undecaprenylphosphate GlcpNAc-1-phosphate transferase)- modified lipopolysaccharide core. Hydrophobic cluster analysis of RfbAO:54 indicates this protein belongs to the ExoU family of nonprocessive beta-glycosyltransferases. Two putative catalytic residues and a potential substrate-binding motif were identified in RfbAO:54. Topological analysis of RfbBO:54 predicts four transmembrane domains and a large central cytoplasmic domain. The latter shares homology with a similar domain in the processive beta-glycosyltransferases Cps3S of Streptococcus pneumoniae and HasA of Streptococcus pyogenes. Hydrophobic cluster analysis of RfbBO:54 and Cps3S indicates both possess the structural features characteristic of the HasA family of processive beta-glycosyltransferases. Four potential catalytic residues and a putative substrate-binding motif were identified in RfbBO:54. In Deltarfb E. coli K-12, RfbAO:54 and RfbBO:54 direct synthesis of smooth O:54 lipopolysaccharide, indicating that this O-polysaccharide involves a novel pathway for O-antigen transport. Based on sequence and structural conservation, 15 new ExoU-related and 17 new HasA-related transferases were identified.

The Biosynthesis of Cellulose

Abstract Cellulose is one of the major commercial products of Sweden and constitutes the most abundant of the natural polymer systems. Thus, it is of interest to review the molecular design and architecture of cellulose with particular reference to the controls of its biosynthesis. The bioassembly process is highly ordered and structured, reflecting the intricate series of events which must occur to generate a thermodynamically metastable crystalline submicroscopic, ribbonlike structure. The plant cell wall is an extremely complex composite of many different polymers. Cellulose is the “reinforcing rod” component of the wall. True architectural design demands a polymer which can withstand great flexing and torsional strain. Using comparative Hydrophobic Cluster Analysis of a bacterial cellulose synthase and other glycosyl transferases, the multidomain architecture of glycosyl transferases has been analyzed. All polymerization reactions which are processive require at least three catalytic sites located on ...

Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic alpha-mannosyltransferases.

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial alpha-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309-316].