The Dictyostelium gelation factor shares a putative actin binding site with alpha-actinins and dystrophin and also has a rod domain containing six 100-residue motifs that appear to have a cross-beta conformation

The 120-kD gelation factor and alpha-actinin are among the most abundant F-actin cross-linking proteins in Dictyostelium discoideum. Both molecules are homodimers and have extended rod-like configurations that are respectively approximately 35 and 40 nm long. Here we report the complete cDNA sequence of the 120-kD gelation factor which codes for a protein of 857 amino acids. Its calculated molecular mass is 92.2 kD which is considerably smaller than suggested by its mobility in SDS-PAGE. Analysis of the sequence shows a region that is highly homologous to D. discoideum alpha-actinin, chicken fibroblast alpha-actinin, and human dystrophin. This conserved domain probably represents an actin binding site that is connected to the rod-forming part of the molecule via a highly charged stretch of amino acids. Whereas the sequence of alpha-actinin (Noegel, A., W. Witke, and M. Schleicher. 1987. FEBS [Fed. Eur. Biochem. Soc.] Lett. 221:391-396) suggests that the extended rod domain of the molecule is based on four spectrin-like repeats with high alpha-helix potential, the rod domain of the 120-kD gelation factor is constructed from six 100-residue repeats that have a high content of glycine and proline residues and which, in contrast to alpha-actinin, do not appear to have a high alpha-helical content. These repeats show a distinctive pattern of regions that have high beta-sheet potential alternating with short zones rich in residues with a high potential for turns. This observation suggests that each 100-residue motif has a cross-beta conformation with approximately nine sheets arranged perpendicular to the long axis of the molecule. In the high beta-potential zones every second residue is often hydrophobic. In a cross-beta structure, this pattern would result in one side of the domain having a surface rich in hydrophobic side chains which could account for the dimerization of the 120-kD gelation factor subunits.

Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius

The genes for the three large subunits A, B and C, of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius DSM 639, were identified and characterized. The three genes follow each other immediately in the order B-A-C, which corresponds to that found in the rpoBC operon of the Escherichia coli genome. The transcription products formed in vivo were studied by Northern analysis and the start-points were determined by S1-nuclease mapping and primer directed extension analysis. The three RNA polymerase subunit genes were co-transcribed together with an open reading frame (ORF) of 88 amino acid residues length situated immediately upstream of the B gene and two ORFs of 104 and 130 amino acid residues following the C gene (together 8500 nucleotides). The following ORF, encoding a protein of 118 amino acids homologous to the ribosomal protein S12 of E. coli, was weakly transcribed with the large co-transcript and strongly from an own promoter. The derived amino acid sequence of the B-subunit was found to be homologous to the B- (second largest) subunits of the eukaryotic nuclear polymerases I, II and III and to the eubacterial beta-subunit. The combined A + C-subunits correspond to the A- (largest) subunits of the eukaryotic RNA polymerases I, II and III and to the eubacterial beta'-subunit. The amino acid sequence similarity of the Sulfolobus subunits to the eukaryotic components is clearly higher than to the E. coli subunit.

Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome

Genes for DNA-dependent RNA polymerase components B, A, and C from the archaebacterium Sulfolobus acidocaldarius and for components B", B', A, and C from the archaebacterium Halobacterium halobium were cloned and sequenced. They are organized in gene clusters in the order above, which corresponds to the order of the homologous rpoB and rpoC genes in the corresponding operon of the Escherichia coli genome. Derived amino acid sequences of archaebacterial components A and C were aligned with each other and with the sequences of corresponding (largest) subunits from the archaebacterium Methanobacterium thermoautotrophicum, with sequences of various eukaryotic nuclear RNA polymerases I, II, and III, and with the sequence of the beta' component from E. coli polymerase. The archaebacterial genes for component A are homologous to about the first two-thirds of genes for the eukaryotic component A and the eubacterial component beta', and the archaebacterial genes for component C are homologous to the last third of the genes for the eukaryotic component A and the eubacterial component beta'. Unrooted phylogenetic dendrograms derived from both distance matrix and parsimony analyses show the archaebacteria are a coherent group closely related to the eukaryotic nuclear RNA polymerase II and/or III lineages. The eukaryotic polymerase I lineage appears to arise separately from a bifurcation with the eubacterial beta' component lineage.

The N-terminal amino acid sequences of the Plasmodium falciparum (FCB1) merozoite surface antigens of 42 and 36 kilodalton, both derived from the 185-195-kilodalton precursor

The N-terminal amino acid sequences of the 42- and 36-kDa Plasmodium falciparum (strain FCB1) merozoite surface polypeptides, both processing fragments from the 185-195-kDa polymorphic glycoprotein, have been obtained. The N-terminus of the 42-kDa fragment is located in the amino acid sequence of the precursor molecule at amino acid residue 1255 (numbering according to Mackay, M., Goman, M., Bone, N., Hyde, J.E., Scaife, J., Certa, U., Stunnenberg, H. and Bujard, H. (1985) EMBO J. 4, 3823-3829). The peptide bond cleaved during processing is Glu-Ala. This fragment is derived from the C-terminal end of the precursor molecule. The N-terminus of the 36-kDa fragment is located in the precursor molecule at amino acid residue 902 (numbering as above), and the bond cleaved is Asn-Asp.

Isolation and characterization of the non-fimbrial adhesin NFA-4 from uropathogenic Escherichia coli O7:K98:H6

The non-fimbrial adhesin NFA-4 from uropathogenic Escherichia coli O7:K98:H6 mediates the agglutination of human red cells (RBC), notably of blood group MM. The adhesin can be separated from the bacteria by heat extraction and was purified to homogeneity by ammonium sulphate precipitation and anion exchange chromatography in the presence of 8 M urea. NFA-4 consists of non-covalently linked 28 kDa subunits which tend to form aggregates of an apparent molecular weight in excess of 10(6) Da. The first 23 amino-terminal amino acids were sequenced, and no homology of this region was found with that of the blood group M specific non-fimbrial adhesin of an unrelated uropathogenic E. coli. It has, however, an about 70% homology to the corresponding region of the K88 antigen from animal-pathogenic enterotoxic E. coli. Both polyclonal and monoclonal antibodies against NFA-4 were prepared. One of the monoclonal antibodies strongly inhibits the hemagglutinating activity of both whole bacteria and purified NFA-4.

cDNA and derived amino acid sequence of the hypusine containing protein from Dictyostelium discoideum

The eukaryotic translation initiation factor eIF-4D is the only protein known to contain the unusual amino acid hypusine, a posttranslationally modified lysine. For the production of monoclonal antibodies the hypusine-containing protein (HP) was isolated from Dictyostelium discoideum. Using these monoclonal antibodies, a full-length cDNA clone was isolated from a lambda gt11 library. The D. discoideum HP consists of 169 amino acids and has a molecular mass of 18.3 kDa. It is encoded by a single gene. Tryptic and cyanogen bromide peptides were prepared from the purified protein and sequenced. The hypusine residue is located at amino acid position 65 of the HP. The corresponding mRNA of approx. 0.6 kb is present throughout the life cycle of D. discoideum.

Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae

The genes for the four largest subunits, A, B', B" and C, of the DNA-dependent RNA polymerase were cloned from the extreme halophile Halobacterium halobium and sequenced and their transcription was analyzed. The downstream half of this gene cluster from another extreme halophile Halococcus morrhuae was also cloned, sequenced and its transcription products characterized. The H. halobium genes were transcribed into a common transcript from an upstream promoter in the order B", B', A and C. They are flanked by, and co-transcribed with, two smaller genes coding for 75 and 139 amino acid residues, respectively. Immediately downstream from these genes were two open reading frames that are homologous to ribosomal proteins S12 and S7 from Escherichia coli. In both extreme halophiles these genes were transcribed from their own promoter, but in Hc. morrhuae there was also considerable read-through from the RNA polymerase genes. Sequence alignment studies showed that the combined B" + B' subunits are equivalent to the B subunits of the eukaryotic polymerases I and II and to the eubacterial beta subunit, while the combined A + C subunits correspond to the A subunits of eukaryotic RNA polymerases I, II and III and to the eubacterial beta' subunit. The sequence similarity to the eukaryotic subunits was always much higher than to the eubacterial subunits. Conserved sequence regions within the individual subunits were located which are likely to constitute functionally important domains; they include sites associated with rifampicin and alpha-amanitin binding and two possible zinc binding fingers. Phylogenetic analyses based on sequence alignments confirmed that the extreme halophiles belong to the archaebacterial kingdom.

The primary structure of the Chloroflexus aurantiacus reaction-center polypeptides

The complete nucleotide sequence of two Chloroflexus aurantiacus reaction-center genes has been obtained. The amino acid sequence deduced from the first gene showed 40% similarity to the L subunit of the Rhodobacter sphaeroides reaction center. This L subunit was 310 amino acids long and had an approximate molecular mass of 35 kDa. The second gene began 17 bases downstream from the first gene. The amino acid sequence deduced from it (307 amino acids; 34950 Da) was 42% similar to the M subunit of the Rhodobacter sphaeroides reaction center. 20% of the deduced primary structure were confirmed through automated Edman degradation of cyanogen bromide peptide fragments or N-chlorosuccinimide peptide fragments isolated from the purified reaction-center complex or from the individual subunits. The peptides were isolated by preparative gel electrophoresis combined with molecular sieve chromatography in the presence of a mixture of formic acid, acetonitrile, 2-propanol and water. This method appeared to be applicable to the isolation of other hydrophobic proteins and their peptides.

Evidence for two closely related isozymes of arylamine N-acetyltransferase in human liver

Acetyl CoA-dependent arylamine N-acetyltransferase (EC 2.3.1.5) is the target of a genetic polymorphism in the metabolism of drugs and carcinogens. N-Acetyltransferase was purified 1000-fold from cytosol of human liver and its identity was verified by amino acid sequence homology of two of its tryptic peptides with published rabbit and chicken N-acetyltransferase sequences. Enzyme activity correlated with the presence of two proteins, NAT-1 and NAT-2, with indistinguishable molecular masses (31 kDa). NAT-1 and NAT-2 could be separated by anion-exchange chromatography and were functionally distinguished by their different apparent affinities for the acceptor amine sulfamethazine (SMZ). Antibodies raised against NAT-1 were able to recognize both isozymes on Western blots.

Production, purification and characterization of hemolysins from Listeria ivanovii and Listeria monocytogenes Sv4b

In culture supernatants of both Listeria ivanovii and Listeria monocytogenes Sv4b, for the first time a hemolysin of molecular weight 58 kDa was identified, which had all the characteristics of an SH-activated cytolysin, and which was therefore identified as listeriolysin O (LLO). In the case of L. ivanovii a second major supernatant protein of molecular weight 24 kDa co-purified with LLO. However, the function of this protein has to be determined. In culture supernatants of L. ivanovii a sphingomyelinase and a lecithinase activity could be detected, both enzymatic activities together contributing to the pronounced hemolysis caused by L. ivanovii. The N-terminal amino acid sequences of LLO and the 24 kDa from L. ivanovii are shown.

The triose phosphate-3-phosphoglycerate-phosphate translocator from spinach chloroplasts: nucleotide sequence of a full-length cDNA clone and import of the in vitro synthesized precursor protein into chloroplasts

The nucleotide sequence of several cDNA clones coding for the phosphate translocator from spinach chloroplasts has been determined. The cDNA clones were selected from a lambda gt10 library prepared from poly(A)+ mRNA of spinach leaves using oligonucleotide probes modeled from amino acid sequences of tryptic peptides prepared from the isolated translocator protein. A 1439 bp insert of one of the clones codes for the entire 404 amino acid residues of the precursor protein corresponding to a mol. wt of 44,234. The full-length clone includes 21 bp at the transcribed non-coding 5' region with the ribosome initiation sequence ACAATGG, a 1212 bp coding region and 199 bp at the non-coding 3' region excluding the poly(A) tail which starts 17 bp downstream from a putative polyadenylation signal, AATAAT. According to secondary structure predictions the mature part of the chloroplast phosphate translocator exhibits high hydrophobicity and consists of at least seven membrane-spanning segments. Using plasmid-programmed wheat germ lysate the precursor protein was synthesized in vitro and could be imported into spinach chloroplasts where it is inserted into the inner envelope membrane.

Isolation and characterization of the alpha-galactosyl-1,4-beta-galactosyl-specific adhesin (P adhesin) from fimbriated Escherichia coli

The alpha-galactosyl-1,4-beta-galactosyl-specific adhesin (P adhesin) was isolated from the fimbria-adhesin complex (FAC) of recombinant Escherichia coli strains expressing the F7(1), F8, or F13 fimbrial antigens. Separation into fimbriae and adhesin was achieved by heating the FAC to 80 degrees C in the presence of Zwittergent 3-16. After removal of the fimbriae by precipitation with lithium chloride, the adhesin was purified by anion-exchange fast protein liquid chromatography in the presence of 4 M urea. The purified adhesins from the three strains had pIs of 4.8 to 5.0 and molecular weights of approximately 35,000. The fimbrillins were smaller, their molecular weights being different with different F antigens. The amino-terminal amino acid sequence of the F7(1)- and F13-derived adhesins were different, that of the F13-derived adhesin being identical to that extrapolated from the DNA sequence of the papG gene (B. Lund, G. Lindberg, B.-I. Marklund, and S. Normark, Proc. Natl. Acad. Sci. USA 84:5898-5902). An antiadhesive monoclonal antibody which reacted with the three P adhesins was prepared. The FAC and the purified adhesins but not the fimbriae from which the adhesins had been removed agglutinated erythrocytes and galactose-galactose-coated latex beads. The adhesion of erythrocytes to the surface-fixed adhesins could be specifically inhibited with alpha-galactosyl-1,4-beta-galactosyl-1,4-glucosyl. The results indicate that the P adhesin(s) of uropathogenic E. coli represents a group of related proteins with conserved receptor recognition domains. The F13-derived P adhesin is the PapG protein postulated by Normark and his colleagues (Lund et al., Proc. Natl. Acad. Sci. USA 84:5898-5902; B. Lund, F. Lindberg, and S. Normark, J. Bacteriol. 170:1887-1894).

Molecular characterization of an ependymin precursor from goldfish brain

Ependymins are thought to be implicated in fundamental processes involved in plasticity of the goldfish CNS. Gas-phase sequencing of purified ependymins beta and gamma revealed that they share the same N-terminal sequence. Each sequence displays microheterogeneities at several positions. Based on the protein sequences obtained, we constructed synthetic oligonucleotides and used them as hybridization probes for screening cDNA libraries of goldfish brain. In this article we describe the full-length sequence of a mRNA encoding a precursor of ependymins. A cleavable signal sequence characteristic of secretory proteins is located at the N-terminal end, followed directly by the ependymin sequence. Also, two potential N-glycosylation sites were detected. A computer search revealed that ependymins form a novel family of unique proteins.

Purification methods for the sequence-specific DNA-binding protein nuclear factor I (NFI)--generation of protein sequence information

The paper describes a potent purification method, preparative gel retention, for the purification of sequence-specific DNA-binding proteins. This procedure exploits the sequence-specific DNA-binding affinity of such proteins for their enrichment, comparable to recognition site DNA affinity chromatography. The method was employed to obtain a pure preparation of nuclear factor I (NFI) from porcine liver from which sequences of partial peptides could be obtained. Oligonucleotide probes derived from these amino-acid sequences were used to identify genomic and cDNA clones of NFI.

Identification of mouse brain proteins after two-dimensional electrophoresis and electroblotting by microsequence analysis and amino acid composition analysis

Two-dimensional electrophoretic separation and immobilization of proteins onto inert membranes for subsequent amino acid sequence and amino acid composition analysis is described as a rapid procedure for the identification or characterization of proteins from complex mixtures. This method avoids the drawbacks of classical purification and isolation methods which involve time-consuming operations with low resolution and, often, insufficient yields. Excellent overall yields of minor amounts (in the low microgram range) using this method allow for sequence determination of yet inaccessible proteins. Solubilized cell proteins of mouse brain were separated by high resolution two-dimensional electrophoresis and electroblotted onto a siliconized glass fiber membrane. The immobilized proteins were stained with Coomassie Brilliant Blue R-250, and twelve proteins spots were then submitted to both Edman degradation and amino acid analysis. Proteins were identified by comparison of the experimentally determined amino acid composition with a dataset derived from the Protein Identification Resource (PIR) protein sequence database. Eight out of twelve proteins tested were identified by amino acid analysis and confirmed by N-terminal sequence determination.

Purification of yolk protein 2 of Drosophila melanogaster and identification of its site of tyrosine sulfation

We have identified the site of tyrosine sulfation in an insect secretory protein, yolk protein 2 of Drosophila melanogaster. Yolk proteins were purified from [35S]sulfate-labeled flies, and yolk protein 2 was separated from yolk protein 1 and yolk protein 3 by preparative two-dimensional polyacrylamide gel electrophoresis. After digestion of yolk protein 2 with trypsin and reversed-phase high performance liquid chromatography, the sulfate label was recovered in two distinct sulfopeptides which, however, had identical NH2-terminal sequences and contained 3 tyrosine residues each. After chymotryptic digestion of the two tryptic sulfopeptides, the sulfate label was recovered in one sulfopeptide which contained a single tyrosine residue. NH2-terminal sequencing showed that this tyrosine residue corresponded to tyrosine 172 of the yolk protein 2 precursor (Hung, M.-C., and Wensink, P. C. (1983) J. Mol. Biol. 164, 487-492) in the sequence Glu-Thr-Thr-Asp-Tyr(S)-Ser-Asn-Glu-Glu. This insect tyrosine sulfation site is very similar to the known vertebrate tyrosine sulfation sites in terms of amino acid composition and secondary structure. In the accompanying paper (Friederich, E., Baeuerle, P. A., Garoff, H., Hovemann, B., and Huttner, W. B. (1988) J. Biol. Chem. 263, 14930-14938), we report on the expression of Drosophila yolk protein 2 in mouse fibroblasts and show the in vivo sulfation of tyrosine 172 by the vertebrate tyrosylprotein sulfotransferase.

Amino-acid sequence homology of a polymorphic cellular protein from human lymphocytes and the chaperonins from Escherichia coli (groEL) and chloroplasts (Rubisco-binding protein)

The human p60 (Mr 60,000) is an abundant protein in the two-dimensional electrophoresis pattern of the cellular proteins of human mitogen-stimulated lymphocytes. The p60 shows as remarkable characteristic a genetic polymorphism with two different alleles. Electrotransfer of this protein from two-dimensional gels onto siliconized glass fiber sheets and subsequent amino-acid sequence analysis has revealed a striking homology to the known bacteria and plant chaperonins, the groEL and the Rubisco-subunit-binding protein. From this sequence homology we conclude that we have identified the human chaperonin homologue.

A new siliconized-glass fiber as support for protein-chemical analysis of electroblotted proteins

A new hydrophobic glass-fiber support is presented, which is well suited to the electrophoretic transfer of proteins from polyacrylamide gels and subsequent protein-chemical analysis. Modified glass-fiber sheets are easily prepared by chemical reaction of the surface with poly(methyl-3,3,3-trifluoropropylsiloxane) in trifluoroacetic acid. The modification is stable during electroblotting, amino acid sequence analysis and hydrolysis. The siliconized glass fiber exhibits a high protein-binding capacity, allows the application of well-established staining procedures, and does not interfere with the analytical methods of modern protein chemistry at the low picomole level. Samples separated by electrophoresis and immobilized on hydrophobic supports fail to exhibit any detectable contamination in amino acid sequence analysis hence allowing the high performance of the available protein-chemical methods to be exploited.

Cloning and sequencing of a Clostridium perfringens sialidase gene

Escherichia coli was transformed with pUC vectors containing Sau3A restriction fragments (RF) of Clostridium perfringens DNA. Two clones expressed sialidase activity when assayed with the fluorogenic substrate 4-methylumbelliferyl-alpha-D-N-acetylneuraminic acid. A synthetic oligonucleotide representing the N-terminus of the expressed enzyme hybridized with the clostridial insert and with a corresponding 2.1 kb Sau3A RF of the C. perfringens genome. The insert reduced to 1.4 kb, which still encoded active sialidase, has been sequenced. The structural gene encodes 382 amino acids representing an Mr of 42770. A hydrophobic leader sequence is absent. Upstream from the initiation codon ATG, a GA-rich region is found and considered as the Shine-Dalgarno sequence. Homology with the N-terminus of the Vibrio cholerae sialidase gene and with viral sialidase sequences was not found.

Human T cell specific proteinase (HuTSP) is encoded by the T cell and natural killer cell specific human Hanukah factor (HuHF) gene

HuTSP, a serine proteinase which is specifically associated with activated t lymphocytes, was purified to homogeneity and characterized. N-terminal amino acid sequencing revealed identity with a sequence predicted from the human Hanukah factor (HF) gene, which was isolated from a human T cell cDNA library. The dimeric structure of HuTSP, together with its extensive sequence homologies with the murine T cell specific proteinase, MTSP-1, suggests phylogenetic conservation of this serine proteinase family.

The cDNA clone for strictosidine synthase from Rauvolfia serpentina. DNA sequence determination and expression in Escherichia coli

The cDNA clone for strictosidine synthase, the enzyme which catalyzes the stereospecific condensation of tryptamine with secologanin to form the key intermediate in indole alkaloid biosynthesis, strictosidine, has been identified with a synthetic oligodeoxynucleotide hybridization probe in a lambda gt11 cDNA library of cultured cells of Rauvolfia serpentina. The DNA has been sequenced, revealing an open reading frame of 1032 base pairs encoding 344 amino acids. The sequence of 60 nucleotides in the 5'-flanking region has been determined by primer extension analysis. The encoded protein has been expressed in E. coli DH5 as detected by immunoblotting of protein extracts with antibodies raised against the native enzyme.

Nucleotide sequence of cDNA clones encoding the entire precursor polypeptides for subunits IV and V of the photosystem I reaction center from spinach

Using lambda gt11 expression cloning and immunoscreening, cDNA-containing recombinant phages for subunits IV and V of the photosystem I reaction center were isolated, sequenced and used to probe Northern blots of polyadenylated RNA prepared from spinach seedlings. The mRNA sizes for both components are approximately 1000 and 850 nucleotides, respectively. The 968 nucleotide cDNA sequence and derived amino acid sequence for subunit IV predict a single open reading frame of 231 amino acid residues (25.4 kDa). Comparison with a 13-residue N-terminal amino acid sequence determined for subunit IV suggests a mature protein of 17.3 kDa (154 residues) and a transit sequence of 77 amino acids (8.1 kDa). The corresponding data for subunit V are 677 bp (cDNA), 167 residues for the precursor protein (18.2 kDa), 98 residues for the mature polypeptide (10.8 kDa) and 69 residues for the transit peptide (7.4 kDa). Secondary structure predictions indicate that both proteins possess greatly different transit sequences and that none is membrane-spanning.

Isolation and characterization of the porcine nuclear factor I (NFI) gene

This study describes the isolation of a major portion of the gene for nuclear factor I (NFI) including its 5'-flanking region with transcriptional start sites. We screened a porcine liver, genomic DNA library in phage EMBL3A with synthetic oligonucleotides derived from tryptic and cyanogen-bromide peptide sequences obtained from purified NFI protein. The NFI gene is present as a single copy in porcine DNA.