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PubMed1991

Primary structure of rat ribosomal protein S2. A ribosomal protein with arginine-glycine tandem repeats and RGGF motifs that are associated with nucleolar localization and binding to ribonucleic acids.

The amino acid sequence of the rat 40 S ribosomal subunit protein S2 was deduced from the sequence of nucleotides in two recombinant cDNAs and confirmed from the amino acid sequence of a cyanogen bromide peptide obtained from the protein. Ribosomal protein S2 has 293 amino acids and has a molecular weight of 31,211. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 23-28 copies of the S2 gene. The mRNA for the protein is about 1,000 nucleotides in length. The highly conserved repetitive mammalian gene family designated LLRep3, but not identified before, encodes ribosomal protein S2. Rat S2 is related to Saccharomyces cerevisiae S4, Methanococcus vannielii S5, Escherichia coli S5, and other members of the prokaryotic S5 family. S. cerevisiae S4 and E. coli S5 are involved in the binding of aminoacyl-tRNA to ribosomes and in conditioning the fidelity of translation; it is plausible to assume that rat S2 serves similar functions. The NH2-terminal region of S2 is rich in arginine-glycine repeats including eight that occur in tandem and has two consecutive copies of the motif RGGF; these sequences have been associated with nucleolar localization and binding to RNA.

Amino Acid Sequence↗
PubMed1990

Free amino acid turnover in methanogens measured by 15N NMR spectroscopy.

Turnover of the nitrogen moiety from free amino acid pools in two thermophilic methanogens, Methanobacterium thermautotrophicum delta H and Methanococcus thermolithotrophicus SN1, has been monitored with 15N NMR spectroscopy. In cells growing exponentially on 15NH4Cl, glutamate was the major soluble 15N-labeled species in both organisms. When the Mb. thermoautotrophicum cells were harvested, washed, and resuspended into medium containing 14NH4Cl, the resonance for [15N]glutamate decreased with a half-life of 0.5 h. This is considerably faster than the turnover rate for the carbon side chain of glutamate (7 h) obtained when a 13CO2 pulse followed by a 12CO2 chase was incorporated into the 15N/14N-labeling experiment. Such behavior is consistent with recycling of the glutamate carbon skeleton via alpha-ketoglutarate after transamination reactions remove the 15N for biosynthesis of other amino acids, nucleic acids, etc. When the cells were in stationary phase, 15N turnover was considerably slower indicating that transaminase activity had also decreased. Mc. thermolithotrophicus has a much more fragile cell wall and easily lyses. To avoid cell loss in the 15N/14N experiment, 15NH+4 growth followed by 14NH4+ dilution was used. In this organism the glutamate-labeled nitrogen turns over quite rapidly (t1/2 approximately 9 min), at a rate comparable to that for the carbon skeleton (t1/2 approximately 10 min). Beta-Glutamate, the second major carbon and nitrogen pool in this organism, turns over its 15N label very slowly. Therefore, this beta-amino acid does not appear to serve as a nitrogen donor in Mc. thermolithotrophicus.

Amino Acids↗
PubMed1990

Novel, acid-labile, hydroxydiether lipid cores in methanogenic bacteria.

Polar ether lipids extracted from 15 methanogenic bacteria, representative of seven genera, were screened by nuclear magnetic resonance and thin layer chromatography for the presence of hydroxyl groups on the C20-phytanyl moieties. Major amounts of hydroxydiether core lipid were confirmed for Methanosaeta concilii and discovered in two Methanosarcina species, Methanococcus voltae, and tentatively in several Methanobacterium species. Signals at 1.24 and 1.8-1.9 ppm in 1H NMR spectra are characteristic of Methanosaeta concilii lipids hydroxylated on carbon-3 (sn-3 chain). Related signals, which were shifted slightly, appeared in spectra of the polar lipids extracted from both Methanosarcina species. Following mild hydrolysis to remove the polar head groups, only two chromatographically distinct core lipids were found in significant amounts in Methanosarcina barkeri (and Methanosarcina mazei) consisting of 43% 2,3-di-O-phytanyl-sn-glycerol (C20,20-diether) and 57% C20,20-hydroxydiether. This latter core lipid differed from the hydroxydiether from M. concilii by hydroxylation, on carbon-3, of the phytanyl chain in ether linkage to the sn-2 carbon of glycerol. The structural assignment was based on identification of the novel hydroxydiether core and its methylation products by 1H NMR, 13C NMR, and mass spectroscopy. The hydroxy core lipid degraded to various products during standard methanolic HCl and sulfuric acid procedures, including a methoxy derivative (methanolic HCl) and the 3-mono-O-phytanyl-sn-glycerol.

Chromatography, Thin Layer↗
PubMed1987

Eukaryotic initiation factor 4D, the hypusine-containing protein, is conserved among eukaryotes.

When mammalian cells are grown in medium containing [3H]spermidine, a single major tritiated protein identical to eukaryotic initiation factor 4D becomes labeled. This protein contains 1 residue/molecule of tritiated hypusine (N epsilon-(4-amino-2-hydroxybutyl)lysine), a rare amino acid which has been found in no other protein. In order to investigate the conservation of this protein, we examined two nonmammalian eukaryotes, the yeast Saccharomyces cerevisiae and the insect Drosophila melanogaster, and the eubacterial prokaryote Escherichia coli for the presence of the hypusine-containing protein. When the eukaryotic cells were grown in the presence of [3H]spermidine, electrophoretic analysis revealed a single labeled protein. In each case, the apparent molecular weight was near 18,000 and the relative pI was approximately 5.2, similar to the hypusine-containing protein of mammals. Amino acid analysis confirmed the presence of tritiated hypusine in each case, and silver staining of two-dimensional polyacrylamide gels demonstrated that, in yeast and fruit flies as in mammals, the protein is relatively abundant. In the eubacterium E. coli, one tritiated protein was predominant, but its molecular weight was 24,000 and we found no evidence that it contained tritiated hypusine. We found no evidence for the existence of the hypusine-containing protein in the archaebacterium Methanococcus voltae. These data suggest that the hypusine-containing protein is conserved among eukaryotes.

Amino Acids↗
PubMedDate not supplied

[Cyst formation by methanosarcina].

The morphology of a coccoid, methane producing bacterium growing on acetate was studied. The organism is capable of forming morphologically differentiated cells, nicrocysts, whose structure resembles that of bacterial surviving cells. The organism from peculiar macrocysts in the enrichment culture. In its other characteristics, the organism is similar to Methanococcus mazei. However, it clasibied as Methanosarcina, biotype 3, due to the characteristic formation of multicellular pseudococci.

Euryarchaeota↗
PubMed1994

Organization of a Sulfolobus solfataricus gene cluster homologous to the Escherichia coli str operon.

The Sulfolobus solfataricus S12, S7 and S10 ribosomal proteins and the elongation factor 1 alpha genes are organized in a sequence analogous to that in the Escherichia coli str operon. Northern analysis showed that the S12 gene belongs to a transcript different from that corresponding to the other three genes. Compared to the Sulfolobus acidocaldarius S12 and to the Methanococcus vannielii S7 proteins, the S. solfataricus S12 and S7 proteins were 33 and 47 amino acids longer respectively. These differences were eliminated if the 5' flanking regions of the S. acidocaldarius S12 and the M. vannielii S7 genes were translated from a different start codon. Despite the structural similarities between the archaeal and the bacterial str operons the S. solfataricus ribosomal proteins S12, S7 and S10 are more similar to the eukaryotic counterparts.

Amino Acid Sequence↗
PubMed1994

Cofactor contents of methanogenic bacteria reviewed.

The content of specific methanogenic cofactors was assessed for a range of hydrogenotrophic and methylotrophic methanogenic bacteria grown on different substrates using high performance liquid chromatography. In general, all methanogens were found to contain coenzyme F420 analogues, methanopterin (MPT) analogues and 5-hydroxybenzimidazolylcobamide (vitamin B12-HBI). In hydrogenotrophic methanogens of the genera Methano-bacterium and Methanobrevibacter, as a rule, coenzymes F420-2 and F420-3 as well as MPT were present. Members of the closely related genera Methanospirillum, Methanogenium, Methanoculleus and Methanoplanus contained the same coenzyme F420 analogues but tatiopterin and/or thermopterin were present instead of MPT. In contrast, methylotrophic methanogens predominantly contained coenzymes F420-5 and F420-4, and sarcinapterin (SPT). In Methanolobus tindarius, both MPT and SPT were found, whereas no MPT analogue could be detected in Methanosphaera stadtmanae. In the hydrogenotroph Methanococcus voltae, SPT occurred as the sole MPT analogue. The levels of the various cofactors varied markedly among different methanogens and also for individual methanogens as a function of growth substrate or batch number. A correlation of cofactor levels and substrate utilized was not established. However, with methylotrophic methanogens it was noticed that the ratio of the contents of vitamin B12-HBI and SPT was independent of growth substrate.

Chromatography, High Pressure Liquid↗
PubMed1993

The primary structure of rat ribosomal protein L23a. The application of homology search to the identification of genes for mammalian and yeast ribosomal proteins and a correlation of rat and yeast ribosomal proteins.

The amino acid sequence of the rat 60 S ribosomal subunit protein L23a was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein L23a has 156 amino acids and a molecular weight of 17,684. Hybridization of the L23a cDNA to digests of nuclear DNA suggests that there are 18-20 copies of the L23a gene. The mRNA for the protein is about 600 nucleotides in length. Rat L23a is related to the yeast Saccharomyces cerevisiae L25, to the archaebacterial Methanococcus vannielii L23, to eubacterial Escherichia coli L23, and to other members of the L23 family of ribosomal proteins. A novel application of a routine homology search procedure was employed to identify a nucleotide sequence that could be used to design an oligodeoxynucleotide probe to screen a library for a cDNA that encodes rat L23a; this same procedure uncovered a number of previously unidentified genes for yeast ribosomal proteins in the GenBank DNA data base. In a correlation of rat and yeast ribosomal proteins 48 pairs are shown to be related.

Amino Acid Sequence↗
PubMed1997

Why a "benign" mutation kills enzyme activity. Structure-based analysis of the A176V mutant of Saccharomyces cerevisiae L-asparaginase I.

A conservative and apparently harmless A176V mutation in intracellular S. cerevisiae L-asparaginase (ScerAI) completely abolishes the enzyme activity. Sequence and structural comparisons with type II bacterial L-asparaginases show that the mutated residue is in a very conservative region and plays a vital role in the cohesion of functional tetramers of these enzymes through participation in side-chain...main-chain (Ser) Oy...O (Ala) hydrogen bonds across the tetramer interface. The fact that bacterial L-asparaginases of type I show less conservation in this region suggests that they may have different quaternary structure while adopting the subunit fold and intimate dimer architecture of type II enzymes. A comparison of all available sequences of microbial L-asparaginases confirms that separate intra- and extra-cellular enzymes evolved in prokaryotes and eukaryotes independently. However, an analysis of the available complete genome sequences reveals a surprising fact that Haemophilus influenzae possesses only a type II asparaginase while the archaebacterium Methanococcus jannaschii has a type I gene, but not a type II.

Amino Acid Sequence↗
PubMed1998

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census.

Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage-whether a given fold occurs in a particular organism. Of the approximately 340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in allhelical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture-eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a "Zipf-like" law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes.

Archaea↗
PubMed2003

Phylogenomics of type II DNA topoisomerases.

Type II DNA topoisomerases (Topo II) are essential enzymes implicated in key nuclear processes. The recent discovery of a novel kind of Topo II (DNA topoisomerase VI) in Archaea led to a division of these enzymes into two non-homologous families, (Topo IIA and Topo IIB) and to the identification of the eukaryotic protein that initiates meiotic recombination, Spo11. In the present report, we have updated the distribution of all Topo II in the three domains of life by a phylogenomic approach. Both families exhibit an atypical distribution by comparison with other informational proteins, with predominance of Topo IIA in Bacteria, Eukarya and viruses, and Topo IIB in Archaea. However, plants and some Archaea contain Topo II from both families. We confront this atypical distribution with current hypotheses on the evolution of the three domains of life and origin of DNA genomes.

Animals↗
PubMed2001

Distinctive features in the SelB family of elongation factors for selenoprotein synthesis. A glimpse of an evolutionary complexified translation apparatus.

The last ten years have seen a dramatic increase in our understanding of the molecular mechanism allowing specific incorporation of selenocysteine into selenoproteins. Whether in prokaryotes or eukaryotes, this incorporation requires several gene products, among which the specialized elongation factor SelB and the tRNA(Sec) play a pivotal role. While the molecular actors have been discovered and their role elucidated in the eubacterial machinery, recent data from our and other laboratories pointed to a higher degree of complexity in archaea and eukaryotes. These findings also revealed that more needs to be discovered in this area. This review will focus on phylogenetic aspects of the SelB proteins. In particular, we will discuss the concerted evolution that occurred within the SelB/tRNA(Sec) couples, and also the distinctive roles carried out by the SelB C-terminal domains in eubacteria on the one side, and archaea and eukaryotes, on the other.

Amino Acid Sequence↗
PubMed2001

Selenocysteine incorporation directed from the 3'UTR: characterization of eukaryotic EFsec and mechanistic implications.

The mechanism of selenocysteine incorporation in eukaryotes has been assumed for almost a decade to be inherently different from that in prokaryotes, due to differences in the architecture of selenoprotein mRNAs in the two kingdoms. After extensive efforts in a number of laboratories spanning the same time frame, some of the essential differences between these mechanisms are finally being revealed, through identification of the factors catalyzing cotranslational selenocysteine insertion in eukaryotes. A single factor in prokaryotes recognizes both the selenoprotein mRNA, via sequences in the coding region, and the unique selenocysteyl-tRNA, via both its secondary structure and amino acid. The corresponding functions in eukaryotes are conferred by two distinct but interacting factors, one recognizing the mRNA, via structures in the 3' untranslated region, and the second recognizing the tRNA. Now, with these factors in hand, crucial questions about the mechanistic details and efficiency of this intriguing process can begin to be addressed.

3' Untranslated Regions↗
PubMed2005

Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes.

We have performed a comparative analysis of amino acid distributions in predicted integral membrane proteins from a total of 107 genomes. A procedure for identification of membrane spanning helices was optimized on a homology-reduced data set of 170 multi-spanning membrane proteins with experimentally determined topologies. The optimized method was then used for extraction of highly reliable partial topologies from all predicted membrane proteins in each genome, and the average biases in amino acid distributions between loops on opposite sides of the membrane were calculated. The results strongly support the notion that a biased distribution of Lys and Arg residues between cytoplasmic and extra-cytoplasmic segments (the positive-inside rule) is present in most if not all organisms.

Amino Acids↗
PubMed1998

The structure of a trimeric archaeal adenylate kinase.

The adenylate kinase from the hyperthermophilic archaean species Sulfolobus acidocaldarius has been cloned, expressed in Escherichia coli, purified and crystallized. The crystal structure was elucidated by multiple isomorphous replacement and non-crystallographic density averaging. The structure was refined at 2.6 A (1 A=0.1 nm) resolution. The enzyme is trimeric, in contrast to previous solution measurements that suggested a dimeric structure, and in contrast to the vast majority of adenylate kinases, which are monomeric. In large parts of each subunit the chain fold resembles the known enzyme structure from eubacteria and eukaryotes although the sequence homology is negligible. Since the asymmetric unit contains two trimers with and without bound AMP at the AMP sites and with an ADP at one of the six ATP sites, the analysis shows the enzyme in several states. The conformational differences between these states resemble those of other adenylate kinases. Because of sequence homology, the structure presented provides a good model for the methanococcal adenylate kinases.

Adenosine Diphosphate↗
PubMed1999

Site-directed mutations within the core "alpha-crystallin" domain of the small heat-shock protein, human alphaB-crystallin, decrease molecular chaperone functions.

Site-directed mutagenesis was used to evaluate the effects on structure and function of selected substitutions within and N-terminal to the core "alpha-crystallin" domain of the small heat-shock protein (sHsp) and molecular chaperone, human alphaB-crystallin. Five alphaB-crystallin mutants containing single amino acid substitutions within the core alpha-crystallin domain displayed a modest decrease in chaperone activity in aggregation assays in vitro and in protecting cell viability of E. coli at 50 degrees C in vivo. In contrast, seven alphaB-crystallin mutants containing substitutions N-terminal to the core alpha-crystallin domain generally resembled wild-type alphaB-crystallin in chaperone activity in vitro and in vivo. Size-exclusion chromatography, ultraviolet circular dichroism spectroscopy and limited proteolysis were used to evaluate potential structural changes in the 12 alphaB-crystallin mutants. The secondary, tertiary and quaternary structures of mutants within and N-terminal to the core alpha-crystallin domain were similar to wild-type alphaB-crystallin. SDS-PAGE patterns of chymotryptic digestion were also similar in the mutant and wild-type proteins, indicating that the mutations did not introduce structural modifications that altered the exposure of proteolytic cleavage sites in alphaB-crystallin. On the basis of the similarities between the sequences of human alphaB-crystallin and the sHsp Mj HSP16.5, the only sHsp for which there exists high resolution structural information, a three-dimensional model for alphaB-crystallin was constructed. The mutations at sites within the core alpha-crystallin domain of alphaB-crystallin identify regions that may be important for the molecular chaperone functions of sHsps.

Amino Acid Sequence↗
PubMed1990

Reductive dechlorination of 1,2-dichloroethane and chloroethane by cell suspensions of methanogenic bacteria.

Concentrated cell suspensions of methanogenic bacteria reductively dechlorinated 1,2-dichloroethane via two reaction-mechanisms: a dihalo-elimination yielding ethylene and two hydrogenolysis reactions yielding chloroethane and ethane, consecutively. The transformation of chloroethane to ethane was inhibited by 1,2-dichloroethane. Stimulation of methanogenesis caused an increase in the amount of dechlorination products formed, whereas the opposite was found when methane formation was inhibited. Cells of Methanosarcina barkeri grown on H2/CO2 converted 1,2-dichloroethane and chloroethane at higher rates than acetate or methanol grown cells.

Biodegradation, Environmental↗