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Licensure, Medical↗
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Identification of new candidate vaccine antigens made by Streptococcus pyogenes: purification and characterization of 16 putative extracellular lipoproteins.
Putative extracellular lipoproteins made by group A Streptococcus (GAS) are the focus of this study, which was designed to identify new candidate vaccine antigens. Bioinformatic analysis of a serotype M1 GAS strain identified 30 open-reading frames encoding putative lipoproteins. The genes encoding the mature form of 29 of these proteins were cloned, and 16 recombinant proteins were overexpressed in Escherichia coli and purified to apparent homogeneity. The genes encoding these 16 proteins were highly conserved in GAS strains for which genome sequence data are available (serotypes M1, M3, M5, M12, M18, and M28). Mice inoculated subcutaneously with GAS and humans with GAS pharyngitis and invasive infections seroconverted to most of the 16 recombinant proteins, which indicates that these lipoproteins were produced during infection. The blood of mice actively immunized with 5 of the 16 recombinant proteins had significantly (P<.05) increased growth-inhibitory activity, compared with the blood of unimmunized mice, which identified these proteins as potential new vaccine candidates.
Amino Acid Sequence↗
Chemistry in bioinformatics.
Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.
Access to Information↗
Transposition of IntAs into the conserved regions of IS3 family elements.
Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to +10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.
Amino Acid Motifs↗
Sequencing analysis of a 36.8 kb fragment of yeast chromosome XV reveals 26 open reading frames including SEC63, CDC31, SUG2, GCD1, RBL2, PNT1, PAC1 and VPH1.
The complete sequence of a 36775 bp DNA segment located on the right arm of chromosome XV of Saccharomyces cerevisiae has been determined and analysed. The sequence encodes 26 open reading frames of at least 100 amino acids. Eight of these correspond to known genes, whereas 18 correspond to new genes.
Chromosomes, Fungal↗
Nucleotide sequence relationships of double-stranded RNAs in flax rust, Melampsora lini.
Flax rust, Melampsora lini strain SP6, contains 11 double-stranded (ds) RNA molecules with a total length of about 25 kbp. The dsRNAs are inherited in three genetic units: the L unit comprising a single 5.2 kbp dsRNA and contained within a 40-nm virus-like particle, and the A and B units each consisting of five dsRNAs (A1-A5, and B1-B5) ranging in size from 1.2 to 2.7 kbp. This paper reports the isolation of a cDNA library representing 10 of the 11 dsRNAs. By nucleic-acid hybridization techniques it has been shown that all ten sequences are unique showing no detectable cross-hybridization with any other dsRNA present in the rust. A near full-length sequence of 1932 bp of the B3 dsRNA is reported and contains several open reading frames, the largest of which comprises most of the molecule.
Amino Acid Sequence↗
Cloning, restriction mapping and phylogenetic relationship of genomic components of MYMIV from Lablab purpureus.
The present work describes cloning of genomic components of whitefly transmitted geminivirus infecting Lablab purpureus syn. Dolichos lablab (commonly known as Dolichos bean or Hyacinth bean). The genome characterization using PCR with geminiviral degenerate primers and DNA sequencing were used to describe the bipartite virus associated with yellow mosaic disease of Dolichos lablab. Full-length DNA-A and DNA-B clones were obtained. The DNA-A sequence analysis showed that the isolate was similar to other Mungbean yellow mosaic India virus (MYMIV) isolates reported earlier. The nucleotide sequence analysis of the full-length DNA-A of virus isolate revealed more than 97% homology with Mungbean yellow mosaic India virus-[Cowpea] (AF481865), while the DNA-B also showed >95% homology with MYMIV-[Cp] (AF503580) and MYMIV-[Sb] (AY049771). The phylogenetic analysis of present isolate showed close relationship to legume geminiviruses. The nucleotide sequence analysis showed presence of six open reading frames (ORFs) in DNA-A, with 2 ORFs aligned in sense and 4 ORFs in antisense orientation. Similarly, DNA-B contained two open reading frames (ORFs), one in sense and another in antisense orientation.
Cloning, Molecular↗
Nucleotide and predicted amino acid sequences of all genes encoded by the 3' genomic portion (9.5 kb) of respiratory bovine coronaviruses and comparisons among respiratory and enteric coronaviruses.
The 3'-ends of the genomes (9538 bp) of two wild-type respiratory bovine coronavirus (RBCV) isolates LSU and OK were obtained by cDNA sequencing. In addition, the 3'-end of the genome (9545) of the wild-type enteric bovine coronavirus (EBCV) strain LY-138 was assembled from available sequences and by cDNA sequencing of unknown genomic regions. Comparative analyses of RBCV and EBCV nucleotide and deduced amino acid sequences revealed that RBCV-specific nucleotide and amino acid differences were disproportionally concentrated within the S gene and the genomic region between the S and E genes. Comparisons among virulent and avirulent BCV strains revealed that virulence-specific nucleotide and amino acid changes were located within the S and E genes, and the 32 kDa open reading frame.
Amino Acid Sequence↗
[A structural analysis of the BRS1 repeat from the genomic DNA of barley (Hordeum vulgare L.)].
The paper presents the results of analysis of the primary sequence of repetitive barley DNA called BRS1 (index number in Genbank BRS-1 U72261). The sequence encodes the open reading frame for 337 amino acids which has homology to retrotransposon-like element of Arabidopsis. There is a block consisting of 11 direct and 7 inverted repeats outside the open reading frame, the sequence ATACTAATGGCGCACC being the base of the repeats.
Amino Acid Sequence↗
Multiple-stage mass spectrometric analysis of complex oligosaccharide antibiotics (everninomicins) in a quadrupole ion trap.
Electrospray ionization (ESI) quadrupole ion-trap tandem mass spectrometry (MS/MS) was utilized to characterize a class of complex oligosaccharide antibiotics (everninomicins) that include SCH 27899, everninomicin-D, amino everninomicin (SCH 27900), and SCH 49088 (containing a hydroxylamino-ether sugar). The addition of sodium chloride (approximately 1 microg/mL) facilitates the formation of abundant metal complex ions, and this was used because protonation does not readily occur for most of these compounds. The multiple-stage mass analysis (MS(n)) of the sodiated species provides an important series of fragment ions that are specific for sugar sequence and for some sugar-ring opening. These data suggest a general charge-remote fragmentation pattern with the sodium cation residing in a specific, central location of the sugar chain and fragmentation occurring to trim the end of the molecule. For protonated everninomicin (SCH 27900), however, the proton appears to be mobile during the collisional activation process, opening different fragmentation pathways depending on the proton location. The use of water and acetonitrile with 0.1% acetic acid as the solvent in ESI-MS promotes rapid hydrolysis of the central ortho ester, resulting in the formation of abundant sodiated products that are hydrated. These product ions of the hydrated molecules are likely formed by the same charge-remote fragmentation processes as those that occur for the unhydrolyzed precursor.
Aminoglycosides↗
Addressing environmental health concerns near Trecatti landfill site, United Kingdom.
Residents near the Trecatti landfill site located in South Wales, United Kingdom, expressed concern about odors and health effects they attributed to site emissions. The authors compared routinely collected, population-based, health data from potentially exposed electoral wards (i.e., United Kingdom electoral tracts) with data from both wards nearby, matched for socioeconomic deprivation scores, and with wards where residents were likely to attend the same hospital. Mortality rates were higher for all causes and neoplastic diseases (but not respiratory disease) in the exposed wards, but there was no change in rates after the site opened. Hospital data revealed a transient increase in admissions for asthma during the 3 yr that preceded the peak in odor complaints. The birth prevalence of congenital malformations was raised in the exposed wards, but the authors could not exclude a possible artifact resulting from differences in reporting practices between hospitals. The absence of environmental monitoring in the community during the period of public concern was a significant weakness of this study.
Abortion, Spontaneous↗
Receptor structure and function: an exploratory approach using the thyrotropin receptor as a vehicle.
The purpose of this chapter is not to present the final or even correct model of TSH receptor structure and function. Rather, the current speculative model presented is used to open the door to a more broad view of the receptor problem and controversy as it has evolved today. Questions of how we define a receptor are clearly very much in flux and much more difficult than initially considered when a chemical approach is taken. Numerous binding components will be described and their relevance to the physiologic state will be debated. Some will be clearly erroneous in concept--yet the very debate and data will open new ideas and approaches other than repetitive membrane binding or response measurements. The remainder of this book will explore numerous other aspects of receptor structure, regulation and function. The reader may be disturbed by the complexity and extrapolations of data and the weakness of the models. The reader should, however, remember that the receptor is the key link of the cell to its environment. The complexities of this linkage are evident in our continued concern with knowledge of the mechanisms our bodily senses utilize. The controversy that will exist is evident in the arguments we have today over the agents in our environment which affect us and the mechanisms of these effects. It is hoped that this chapter and book will provide both the desire and some reference to follow and review the data in all receptor fields as they emerge in the next several years.
Adenylyl Cyclases↗
A genetic screen to identify sequences that mediate protein oligomerization in Escherichia coli.
Many proteins assemble as oligomeric complexes and in several cases a distinct domain mediates the interaction between the subunits. The identification of new oligomerization modules is relevant to comprehend both the architecture and the evolution of protein sequences and also for protein engineering applications. Using the bacteriophage lambda repressor dimerization assay, we searched Escherichia coli genomic libraries for sequences able to mediate protein oligomerization in vivo. We identified short peptides that can substitute very effectively the dimerizing domain of the repressor. Most of these peptides belong to open reading frames that are normally not expressed in the bacterial cell.
Amino Acid Sequence↗
Relationships between transcriptional and translational control of gene expression in Saccharomyces cerevisiae: a multiple regression analysis.
Natural selection for an increased translation efficiency has been proposed as the main determinant for the bias in codon usage observed in many genes of Saccharomyces cerevisiae. Recently, the efficiency of transcription of a large number of yeast genes has been determined, based on the cellular content of the respective mRNAs: this provides an additional dimension to the study of the multisep process of gene expression. Using a representative set of yeast genes with a known level of transcription, the relationship between transcriptional and translational steps was evaluated by a multiple linear regression model. This analysis demonstrated a positive correlation between the amount of transcript, given as the number of mRNA copies per cell for each individual gene, and indices evaluating the effects of translational selection on the corresponding codon usage pattern. This finding suggests a close association of the cellular mRNA content, regulated also at the transcriptional level, to its efficiency of translation, mediated by a fine-tuning of codon usage strategy. Moreover, multiple regression analysis demonstrated that the transcription level of a gene can be approximately predicted using indices of bias deriving from its nucleotide sequence. This allowed for an extensive investigation of uncharacterized regions of the complete genome sequence of S. cerevisiae, to detect new potential short protein coding genes that were not considered by previous searching procedures. Several small open reading frames exhibiting a statistically significant coding potential were thus identified as good candidates for functional analysis.
Amino Acid Sequence↗
Inhibition of translation of transforming growth factor-beta 3 mRNA by its 5' untranslated region.
We have cloned and sequenced the 5' untranslated region of the transforming growth factor-beta 3 (TGF-beta 3) mRNA as well as the adjacent genomic sequence. S1 nuclease analysis identified a single transcription start site. We have thus determined that the 5' untranslated region is about 1.1 kb long and contains 11 open reading frames. In vitro translation of the TGF-beta 3 precursor coding sequence was markedly inhibited by the presence of the 5' untranslated region. Similarly, when the 5' untranslated region of TGF-beta 3 was introduced upstream of the coding sequence of chloramphenicol acetyltransferase, in vitro translation was inhibited. Furthermore, upon transfection into 293 cells, chloramphenicol acetyltransferase expression was inhibited by the 5' untranslated region of TGF-beta 3. The degree of translational inhibition was inversely proportional to the amount of transfected DNA. Mutation analysis implicated multiple segments of the 5' untranslated region as contributing to the inhibitory effect. Deletion of much of the 5'-most 640 nucleotides, including 8 of the 11 upstream ATGs, relieved much but not all of the inhibitory influence of the 5' untranslated region of TGF-beta 3 mRNA. The two upstream open reading frames closest to the initiator codon for the TGF-beta 3 coding sequence also decreased translational efficiency, since mutation of either ATG resulted in increased translation. Transfection results with T47-D cells, a cell line which expresses TGF-beta 3 mRNA, were similar to those obtained with the 293 cell line. Thus, TGF-beta 3 mRNA is a recent example of an expanding group of growth-related mRNAs in which the 5' untranslated region contains upstream open reading frames and other sequences which inhibit translation.
Amino Acid Sequence↗
Tn5044, a novel Tn3 family transposon coding for temperature-sensitive mercury resistance.
We report the discovery and characterization of the mercury resistance transposon, Tn5044, from a Xanthomonas strain from the Kamchatka peninsula. In addition to the standard set of merRTPCAD genes, the mer operon of Tn5044 contains a gene named sigY that encodes the RNA polymerase sigma factor-like protein. Mercury resistance determined by Tn5044 is expressed at low (30 degrees C) but not at elevated temperatures (37 degrees C). None of the mer operon genes downstream of merA is responsible for the temperature-sensitive mercury resistance. The transposition module of Tn5044 is closely related to those of Tn1412 isolated from medical sources and to Tn5563 and ISXc5 from environmental sources. However, Tn5044 differs from these transposons in that it has unusually long terminal inverted repeats. Sequence analysis of the transposase (tnpA) genes places Tn5044 and its close relatives into the Tn3 subgroup of the Tn3 family. However, the orientation of their resolvase and transposase genes is unusual for the Tn3 family: tnpR is proximal to the end of the transposon, while divergently transcribed tnpA is oriented inwardly. The region between tnpA and tnpR genes is unusually large and contains two short conserved open reading frames. In addition to the complete set of sequence motifs common to true resolvases, the resolvase of Tn5044 and its close relatives possesses a C-terminal extension showing no homology to known proteins. Despite this peculiarity, Tn5044 resolvase can resolve cointegrates formed during Tn5044 transposition controlled by tnpA. Genetic data suggest that the extension is essential for TnpR functioning.
Amino Acid Sequence↗
Nucleotide sequence of the 7 K gene of Helenium virus S.
The sequence of 380 nucleotides upstream of the start codon of the open reading frame (ORF) of the coat protein of the carlavirus Helenium virus (HelVS) was determined from cloned cDNA. This portion of the viral RNA contained one complete ORF encoding a protein of 7 K which had homology with similar sized proteins from other members of the carla- and potexvirus groups. Sequence data was also obtained beyond the start codon of the 7 K ORF into what was presumed to be the 12 K protein gene of the previously identified triple gene block of carla- and potexviruses. Significant sequence similarity of 46.3% and 41.6% was evident at the amino acid level with the equivalent regions of the 12 K proteins of potato virus S, Andean strain (PVSA) and potato virus M (PVM), respectively, with 25.4% similarity detected with the equivalent region of potato virus X (PVX).
Amino Acid Sequence↗
Characterization of a gene encoding a Pichia pastoris protein disulfide isomerase.
Protein disulphide isomerases belong to the thioredoxin superfamily of protein-thiol oxidoreductases that have two double-cysteine redox-active sites and take part in protein folding in the endoplasmic reticulum (ER). We report here the cloning of a Pichia pastoris genomic DNA fragment (2919 bp) that encodes the full length of a protein disulphide isomerase (PpPDI). The deduced amino acid sequence of PDI consists of 517 residues and carries the two characteristic PDI-type redox-active domains -CGHC-, separated by 338 residues, and two potential N-glycosylation sites. The N-terminal end forms a putative signal sequence, and an acidic C-terminal region represents a possible calcium-binding domain. Together with the -HDEL ER retrieval sequence at the C-terminus, these features indicate that the gene encodes a redox-active ER-resident protein disulphide isomerase. The nucleotide sequence, which also contains two other open reading frames, has been submitted to the EMBL Nucleotide Sequence Database, Accession No. AJ302014.
Amino Acid Sequence↗