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At least 217 records · Page 12Linked to original sources
PubMed1991

Cloning, sequence analysis, and expression in Escherichia coli of a gene coding for a beta-mannanase from the extremely thermophilic bacterium "Caldocellum saccharolyticum".

A lambda recombinant phage expressing beta-mannanase activity in Escherichia coli has been isolated from a genomic library of the extremely thermophilic anaerobe "Caldocellum saccharolyticum." The gene was cloned into pBR322 on a 5-kb BamHI fragment, and its location was obtained by deletion analysis. The sequence of a 2.1-kb fragment containing the mannanase gene has been determined. One open reading frame was found which could code for a protein of Mr 38,904. The mannanase gene (manA) was overexpressed in E. coli by cloning the gene downstream from the lacZ promoter of pUC18. The enzyme was most active at pH 6 and 80 degrees C and degraded locust bean gum, guar gum, Pinus radiata glucomannan, and konjak glucomannan. The noncoding region downstream from the mannanase gene showed strong homology to celB, a gene coding for a cellulase from the same organism, suggesting that the manA gene might have been inserted into its present position on the "C. saccharolyticum" genome by homologous recombination.

Amino Acid Sequence↗
PubMed2005

Comparative genomic sequence analysis coupled to chromatin immunoprecipitation: a screening procedure applied to search for regulatory elements at the RET locus.

RET gene expression is characterized by high tissue and stage specificity during the development of neural crest derivatives and in the pathogenesis of inherited cancer syndromes and Hirschsprung disease. Identifying all elements contributing to its transcriptional regulation might provide new clues to clarify both developmental and pathogenic mechanisms. We previously demonstrated that chromatin acetylation affects RET transcription; therefore, we have set up a strategy based on analysis of sequences conserved among species at the RET locus, combined with the characterization of their chromatin structure, to identify new potential regulatory elements. The histone acetylation level was evaluated by the chromatin immunoprecipitation method applied to cells displaying different degrees of endogenous RET expression. Real-time quantitative PCR of immunoprecipitated DNA-protein complexes and transfection experiments, with constructs expressing a reporter gene in which the putative regulatory regions are inserted, indicate a correlation between histone acetylation and endogenous RET expression and highlight conserved sequences with potential regulatory roles. This paper presents a reliable screening procedure to unearth elements able to affect gene regulation at the transcriptional level in a large genomic region.

Acetylation↗
PubMed1999

[Sequence analysis of the mutated AOX2 promoter region in the Pichia pastoris].

Spontaneous revertants of the AOX1-defective P. pastoris strain have been isolated, which were identified as phenotypically utilize methanol to grow as the wild type. The promoter region of the AOX2 gene from the revertant has been obtained by PCR amplification, and the DNA fragment is 1022 base pair in size. By the analysis of sequencing result and compared with the AOX2 gene sequences recorded in Gene Bank, two point mutations which at positions of -529 and -255(relative to the translation initiation codon) respectively, have been found. Since the positions are located in the AOX2 upstream repression sequences, the mutations may act interfere the repressor to combine with the functional sequences, and increase transcriptional activity. The above result implicated that the P. pastoris' ability to utilize methanol could be increased through modification the upper stream transcriptional regulation region in the AOX2 gene.

Alcohol Oxidoreductases↗
PubMed1986

Purification and partial sequence analysis of a 37-kDa protein that inhibits phospholipase A2 activity from rat peritoneal exudates.

We have purified from rat peritoneal exudates a 37-kDa protein that inhibits phospholipase A2 activity. It is the predominant phospholipase inhibitor protein in these preparations and also is detected in a wide variety of cell lines. Levels of expression range from 0 to 0.5% of total protein. In the peritoneal preparations, the inhibitor is partially proteolyzed into a series of lower mass forms, including species at 30, 24, and 15 kDa. These fragments all are immunoreactive with an antibody raised against the 37-kDa protein. The rat protein also is immunoreactive with an antibody developed against a 6-kDa phospholipase inhibitor protein from snake venom. The primary structure of more than half of the rat inhibitor has been deduced by protein microsequence analysis. These sequences are closely related to sequences from its human analogue, which we recently cloned and expressed (Wallner, B. P., Mattaliano, R. J., Hession, C., Cate, R. L., Tizard, R., Sinclair, L. K., Foeller, C., Chow, E. P., Browning, J. L., Ramachandran, K. L., and Pepinsky, R. B. (1986) Nature, in press), and thus we infer that the inhibitor is highly conserved evolutionarily. Properties of the molecule suggest that it is a member of a family of steroid-induced anti-inflammatory proteins collectively referred to as lipocortin.

Amino Acid Sequence↗
PubMed1998

[Hemoglobin Sydney--alpha beta 2 67 (E11) Val-Ala and hemoglobin Olomouc alpha 2 beta 2 86 (F 2) Ala-Asp in Czech families. DNA sequence analysis for a more accurate diagnosis of hemoglobinopathies].

The paper demonstrates the importance of sequence analysis of DNA for the identification of Hb-Sydney [alpha2-beta2 67 (E11) Val-Ala]. The latter was considered erroneously, based on results of biochemical analyses to be Hb-M-Milwaukee [alpha2 beta2 67 (E 11) Val-Glu]. With the unstable Hb-Sydney correspond also phenotypical manifestations of disease (haemolytic anaemia with Heinz bodies in red blood cells). Sequence analysis of DNA of patients with Hb-Olomouc [alpha 2 beta 2 (F 2) Ala-Asp] revealed that mutation of Ala-Asp in position 86 (F 2) of the beta globin chain is coded by mutation C-->A (GCC-GAC).

Czech Republic↗
PubMed1980

Genes and sites involved in replication and incompatibility of an R100 plasmid derivative based on nucleotide sequence analysis.

The nucleotide sequence of the entire region required for autonomous replication and incompatibility of an R100 plasmid derivative, pSM1, has been determined. This region includes the replication region and all plasmid encoded information required for replication. Numerous reading frames for possible proteins can be found in this region. The existence of one of these proteins called RepA1 (285 amino acids; 33,000 daltons) which is encoded within the region known by cloning analysis to be required for replication is supported by several lines of evidence. These include an examination of the characteristic sequences on the proximal and distal ends of the coding region, a comparison of the sequence of the replication regions of pSM1 and the highly related R1 plasmid derivative Rsc13 as well as other biochemical and genetic evidence. The existence of two other proteins, RepA3 (64 amino acis; 7000 daltons) and RepA2 (103 amino acids; 11,400 daltons) is also consistent with most of the criteria mentioned above. However, the region encoding RepA3, which by cloning analysis is within the region responsible for both replication and incompatibility, has never been demonstrated to produce a 7,000 dalton polypeptide. Since a large secondary structure can be constructed in this region, it is possible that the region contains structure or other information that is responsible for incompatibility. RepA2, encoded entirely within the region identified by cloning analysis to be responsible for incompatibility but not for replication can be visualized in vivo and in vitro. However, the nucleotide sequence of the region encoding RepA2 is completely different in mutually incompatible plasmid derivatives of R1 and R100. It is therefore unlikely that RepA2 plays a major role in incompatibility. Thus, we predict that RepA2 is required to initiate DNA synthesis at the replication origin and that the region proximal to RepA2 either encodes a gene product or structure information that is responsible for incompatibility.

Base Sequence↗
PubMedDate not supplied

[Reclassification of thermophylic methane-oxidizing bacteria with the use of sequence-analysis of 16S rRNA genes].

The authors have performed sequence-analysis of 16S rRNA genes of thermophylic methane-oxidizing bacteria UCM B-3026, UCM B-3032, UCM B-3109, UCM B-3014 which were isolated from sludge pond of different regions in Ukraine and deposited at Ukrainian Collection of Microorganisms (UCM) as Methylococcus thermophilus and "M. gracilis". A comparative analysis of 16S rRNA gene sequences of the studied bacteria with those sequences of various strains of bacteria in the GenBank databases has shown that the level of similarity of the strains UCM B-3026, UCM B-3032, UCM B-3109 with Methylocaldum szegediense was 98.0-98.7%, strain UCM B-3014 with Methylocaldum gracile--99.1%, that allows to relate them to these species. As to other species of the genus Methylocaldum, these strains had a lower level of similarity (94.8-97.2 %) and with Methylococcus thermophilus ACM 3585T (= IMV-B-3037T = UCM B-3037T)--less than 90%. Thus, the strains UCM B-3026, UCM B-3032, UCM-3109 were reclassified as Methylocaldum szegediense, strain UCM B-3014--as Methylocaldum gracile. When constructing phylogenetic tree based on the comparison of 16S rRNA genes with the use of various algorithms realized in the packages of programs Tree View (version 1.5.2) and ClastalX (version 1.81) certain clusters have formed genera Methylocaldum, Methylococcus and Methylomonas. Genera Methylobacter and Methylomicrobium have formed three clusters, one of the clusters contained two species of Methylobacter and two species of Methylomicrobium. Apparently, the taxonomy of genera Methylobacter and Methylomicrobium is to be specified.

Genes, Bacterial↗
PubMed2004

BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.

Databases, Genetic↗
PubMed1987

Sequence analysis of the matrix protein gene of human parainfluenza virus type 3: extensive sequence homology among paramyxoviruses.

The sequences of the human parainfluenza virus type 3 (PIV3) matrix (M) mRNA [1150 nucleotides exclusive of poly(A)] and predicted M protein (353 amino acids) were determined by sequence analysis of cloned cDNA and viral genomic RNA. The gene-end sequence of the M gene differed from the semi-conserved gene-end sequence of the other PIV3 genes by an apparent insertion of eight nucleotides. The PIV3 M protein shared high sequence homology with Sendai virus and moderate homology with measles virus and canine distemper virus. Statistical analysis of the available sequences showed that the M protein was the most highly conserved parainfluenza viral protein.

Amino Acid Sequence↗
PubMed2001

ANTHEPROT: an integrated protein sequence analysis software with client/server capabilities.

Programs devoted to the analysis of protein sequences exist either as stand-alone programs or as Web servers. However, stand-alone programs can hardly accommodate for the analysis that involves comparisons on databanks, which require regular updates. Moreover, Web servers cannot be as efficient as stand-alone programs when dealing with real-time graphic display. We describe here a stand-alone software program called ANTHEPROT, which is intended to perform protein sequence analysis with a high integration level and clients/server capabilities. It is an interactive program with a graphical user interface that allows handling of protein sequence and data in a very interactive and convenient manner. It provides many methods and tools, which are integrated into a graphical user interface. ANTHEPROT is available for Windows-based systems. It is able to connect to a Web server in order to perform large-scale sequence comparison on up-to-date databanks. ANTHEPROT is freely available to academic users and may be downloaded at http://pbil.ibcp.fr/ANTHEPROT.

Algorithms↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.

Amino Acid Sequence↗
PubMed1994

Sequence analysis of a 10 kb fragment of yeast chromosome XI identifies the SMY1 locus and reveals sequences related to a pre-mRNA splicing factor and vacuolar ATPase subunit C plus a number of unidentified open reading frames.

We report the DNA sequence analysis of a region on the left arm of chromosome XI of Saccharomyces cerevisiae extending over 10 kb. The region contains five open reading frames (ORFs) of greater than 100 amino acids which do not show significant overlap with other ORFs. YKL408 contains a sequence with strong similarity to the RNA helicase pre-mRNA splicing factors PRP2, PRP16 and PRP22 (Burgess et al., 1990; Company et al., 1991; Ruby et al., 1991). YKL409 corresponds to the gene SMY1, the sequence of which was previously reported by Lillie and Brown (1992). YKL410 is identical to ATPase subunit C (Beltran et al., 1992) except for an N-terminal extension. YKL406 and YKL407 show no significant identity with any sequences in the databases searched.

Adenosine Triphosphatases↗
PubMed1983

Unusual domains of human alphoid satellite DNA with contiguous non-satellite sequences: sequence analysis of a junction region.

The sequence organization of cloned segments of Human DNA carrying unusual domains of alphoid satellite was studied by restriction mapping, electron microscopy and base sequence analysis. In some cases restriction mapping revealed the absence of the typical 340 bp EcoR 1 dimer, although blot hybridizations showed the extensive presence of alphoid satellite. A variant monomeric construction was demonstrated by DNA sequencing. Furthermore, inverted repeats within these domains were detected by electron microscopy. In one case these were shown to be the result of interruptions in the satellite sequence by members of a family of repetitive, conserved elements.

Base Sequence↗
PubMed1992

Automated carboxy-terminal sequence analysis of peptides.

Proteins and peptides can be sequenced from the carboxy-terminus with isothiocyanate reagents to produce amino acid thiohydantoin derivatives. Previous studies in our laboratory have focused on solution phase conditions for formation of the peptidylthiohydantoins with trimethylsilylisothiocyanate (TMS-ITC) and for hydrolysis of these peptidylthiohydantoins into an amino acid thiohydantoin derivative and a new shortened peptide capable of continued degradation (Bailey, J. M. & Shively, J. E., 1990, Biochemistry 29, 3145-3156). The current study is a continuation of this work and describes the construction of an instrument for automated C-terminal sequencing, the application of the thiocyanate chemistry to peptides covalently coupled to a novel polyethylene solid support (Shenoy, N. R., Bailey, J. M., & Shively, J. E., 1992, Protein Sci. I, 58-67), the use of sodium trimethylsilanolate as a novel reagent for the specific cleavage of the derivatized C-terminal amino acid, and the development of methodology to sequence through the difficult amino acid, aspartate. Automated programs are described for the C-terminal sequencing of peptides covalently attached to carboxylic acid-modified polyethylene. The chemistry involves activation with acetic anhydride, derivatization with TMS-ITC, and cleavage of the derivatized C-terminal amino acid with sodium trimethylsilanolate. The thiohydantoin amino acid is identified by on-line high performance liquid chromatography using a Phenomenex Ultracarb 5 ODS(30) column and a triethylamine/phosphoric acid buffer system containing pentanesulfonic acid. The generality of our automated C-terminal sequencing methodology was examined by sequencing model peptides containing all 20 of the common amino acids. All of the amino acids were found to sequence in high yield (90% or greater) except for asparagine and aspartate, which could be only partially removed, and proline, which was found not be capable of derivatization. In spite of these current limitations, the methodology should be a valuable new tool for the C-terminal sequence analysis of peptides.

Amino Acid Sequence↗
PubMed1993

Identification of the herpes simplex virus-1 protease cleavage sites by direct sequence analysis of autoproteolytic cleavage products.

Herpes simplex virus type-1 (HSV-1) encodes a protease responsible for proteolytic processing of the virus assembly protein, ICP35 (infected cell protein 35). The coding region of ICP35 is contained within the gene that encodes the protease, and ICP35 shares amino acid identity with the carboxyl-terminal 329 amino acids of the protease. The HSV-1 protease was expressed in Escherichia coli as a fusion protein containing a unique epitope and the protein A Fc binding domain at its carboxyl terminus. The fusion protease underwent autoproteolytic cleavage at two distinct sites. The size of the cleavage products containing the carboxyl-terminal epitope mapped one cleavage site near the carboxyl terminus of the protease corresponding to the proteolytic processing site of ICP35, and the second site proximal to the amino terminus consistent with previous data. The carboxyl-terminal autoproteolytic cleavage products were partially purified on an IgG affinity column by virtue of the protein A Fc binding domain and subjected to direct amino-terminal sequence analysis. Protein sequencing revealed that cleavage occurs between the Ala and Ser residues at amino acids 610/611 and 247/248 of the HSV-1 protease. The flanking sequences share homology with each other and are highly conserved in homologous proteases of other herpes viruses.

Amino Acid Sequence↗
PubMed1992

Biochemical characterization of crystallins from pigeon lenses: structural and sequence analysis of pigeon delta-crystallin.

Crystallins from pigeon eye lenses were isolated and purified by gel-permeation chromatography and characterized by gel electrophoresis, amino-acid composition and sequence analysis. Alpha- and beta-crystallins could be obtained in relatively pure forms by single-step size-exclusion chromatography whereas an extra step of ion-exchange chromatography was needed for the separation of delta-crystallin from the beta-crystallin fraction. In contrast to most characterized vertebrate species, a large amount of glycogen is eluted as a high molecular form in the first peak of the gel filtration column. Pigeon delta-crystallin, similar to duck and reptilian delta-crystallins, exists as a tetrameric structure of about 200 kDa in the native form and is composed of one major subunit of 50 kDa with heterogeneous isoelectric points spreading in a range of 4.7 to 6.8. In contrast to those obtained from duck, goose and caiman, delta-crystallin isolated from the pigeon lens possessed very little argininosuccinate lyase activity. However, pigeon delta-crystallin can still cross-react with the antibody against enzymically active duck delta-crystallin as revealed by the sensitive immunoblotting technique. It was also shown that the delta-crystallin content of the total pigeon soluble proteins decreased with the age of the animal. Structural analysis of purified delta-crystallin fraction was made with respect to its amino-acid composition and protein primary sequence. N-terminal sequence analysis indicated the presence of blocked amino-termini in all crystallin fractions of pigeon lenses. Therefore, a sequence analysis of PCR (polymerase chain reaction) amplified delta-crystallin cDNA was employed to deduce the protein sequence of this crystallin. Structural comparison of delta-crystallin sequences from pigeon, chicken and duck lenses casts some doubts on the recent claim that His-89-->Gln mutation in the chicken delta-crystallin may account for the loss of argininosuccinate lyase activity in this avian species, as compared to high enzymic activity in the duck crystallin (Barbosa et al. (1991) J. Biol. Chem. 266, 5286-5290).

Amino Acid Sequence↗
PubMed2000

Comparative sequence analysis of the MECP2-locus in human and mouse reveals new transcribed regions.

Comparative sequence analysis facilitates the identification of evolutionarily conserved regions, that is, gene-regulatory elements, which can not be detected by analyzing one species only. Sequencing of a 152-kb region on human Chromosome (Chr) Xq28 and of the synthenic 123 kb on mouse Chr XC identified the MECP2/Mecp2 locus, which is flanked by the gene coding for Interleukin-1 receptor associated kinase (IRAK/Il1rak) and the red opsin gene (RCP/Rsvp). By comparative sequence analysis, we identified a previously unknown, non-coding 5' exon embedded in a CpG island associated with MECP2/Mecp2. Thus, the MECP2/Mecp2 gene is comprised of four exons instead of three. Furthermore, sequence comparison 3' to the previously reported polyadenylation signal revealed a highly conserved region of 8.5 kb terminating in an alternative polyadenylation signal. Northern blot analysis verified the existence of two main transcripts of 1.9 kb and approximately 10 kb, respectively. Both transcripts exhibit tissue-specific expression patterns and have almost identical short half-lifes. The approximately 10-kb transcript corresponds to a giant 3' UTR contained in the fourth exon of MECP2. The long 3' UTR and the newly identified first intron of MECP2/Mecp2 are highly conserved in human and mouse. Furthermore, the human MECP2 locus is heterogeneous with respect to its DNA composition. We postulate that it represents a boundary between two H3 isochores that has not been observed previously.

3' Untranslated Regions↗