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PubMed1997

Inactivation of mdoH leads to increased expression of colanic acid capsular polysaccharide in Escherichia coli.

Capsule gene (cps) expression, which normally occurs at low levels in Escherichia coli lon+ cells, increased 38-fold in lon+ cells carrying a Tn10::delta kan insertion mapping to 24 min on the E. coli chromosome. Null mutations in rcsA, rcsB, or rcsC abolished the effect of the Tn10::delta kan insertion. Sequencing of both sides of the Tn10::delta kan insertion localized the insertion to the previously reported mdoH gene, which encodes a protein involved in biosynthesis of membrane-derived oligosaccharides (MDOs). A model suggesting that the periplasmic levels of MDOs act to signal RcsC to activate cps expression is proposed.

ATP-Dependent Proteases↗

PubMed1994

Mycobacterium smegmatis strain for detection of Mycobacterium tuberculosis by PCR used as internal control for inhibition of amplification and for quantification of bacteria.

For the detection of Mycobacterium tuberculosis by PCR, the IS6110 sequence was used. A modified target was constructed by insertion of 56 nucleotides in the IS6110 insertion element of Mycobacterium bovis BCG. This modified insertion sequence was integrated into the genome of Mycobacterium smegmatis, a mycobacterium species which does not contain the IS6110 element. When DNA from the modified M. smegmatis 1008 strain was amplified with IS6110-specific primers INS1 and INS2, a band of 301 bp was seen on agarose gel, whereas the PCR product of M. tuberculosis complex DNA was a 245-bp fragment with these primers. The addition of a small number of M. smegmatis 1008 cells to clinical samples before DNA purification enables the detection of problems which may be due to the loss of DNA in the isolation procedure or to the presence of inhibitors. The presence of inhibitors of the amplification reaction can be confirmed by the addition of M. smegmatis 1008 DNA after the DNA isolation procedure. Furthermore, competition between the different target DNAs of M. smegmatis 1008 DNA and M. tuberculosis complex DNA enables the estimation of the number of IS6110 elements in the clinical sample.

Base Sequence↗

PubMed2005

Characterization of an iodothyronine 5'-deiodinase in gilthead seabream (Sparus auratus) that is inhibited by dithiothreitol.

Iodothyronine deiodinases catalyze the conversion of the thyroid prohormone T(4) to T(3) by outer ring deiodination (ORD) of the iodothyronine molecule. The catalytic cycle of deiodinases is considered to be critically dependent on a reducing thiol cosubstrate that regenerates the selenoenzyme to its native state. The endogenous cosubstrate has still not been firmly identified; in studies in vitro the sulfhydryl reagent dithiothreitol (DTT) is commonly used to activate ORD. We now have characterized an ORD activity in the teleost gilthead seabream (Sparus auratus) that is inhibited by DTT. DTT inhibited reverse T(3) (rT(3)) ORD by 70 and 100% in kidney homogenates (IC(50) 0.4 mmol/liter) and microsomes (IC(50) 0.1 mmol/liter), respectively. The omission of DTT from the incubation medium restored renal ORD Michaelis-Menten kinetics with a Michaelis constant value of 5 mumol/liter rT(3) and unmasked the inhibition by 6-n-propyl-2-thiouracil. A putative seabream deiodinase type 1 (saD1), derived from kidney mRNA, showed high homology (> or = 41% amino acid identity) with vertebrate deiodinases type 1. Features of this putative saD1 include a selenocysteine encoded by an in-frame UGA codon, consensus sequences, and a predicted secondary structure for a selenocysteine insertion sequence and an amino acid composition of the catalytic center that is identical with reported consensus sequences for deiodinase type 1. Remarkably, three of six cysteines that are present in the deduced saD1 protein occur in the predicted amino terminal hydrophobic region. We suggest that the effects of DTT on rT(3) ORD can be explained by interactions with the cysteines unique to the putative saD1 protein.

Amino Acid Sequence↗

PubMed1995

[Junctional sequences of T cell receptor V delta 2-D delta 3 or D delta 2-D delta 3 rearrangements in acute lymphoblastic leukemia].

T-cell receptor (TCR) delta chain gene rearrangements were studied by polymerase chain reaction (PCR) analysis in 46 patients with acute lymphoblastic leukemia (ALL). Sixteen patients were found to have incomplete rearrangements of the TCR delta genes. Among them, 13 patients displayed V delta 2-D delta 3 rearrangement, while 3 had both V delta 2-D delta 3 and D delta 2-D delta 3 rearrangements. To determine the junctional sequence of TCR delta gene, PCR products from the 16 patients were sequenced directly or after M13 cloning. The results showed the junctional sequences of TCR delta gene are highly specific for each allele. This sequence diversity resulted from several factors including deletion of the 3' end of V delta 2 or D delta 2 segment and 5' end of D delta 3 segment, the presence of D delta 1 or D delta 2 sequences, insertion of N nucleotides and the association of P nucleotides with intact V delta 2 and D delta 3 segments. In addition, analysis of N-nucleotide contents revealed that the amount of GC was much larger than that of AT (70%: 30%), indicating the insertion of N nucleotide was not fully random. Our sequence data confirmed that the imcomplete rearrangement of TCR delta gene is an early event in the lymphoid cell ontogenesis, and its N sequences in V-(D)-J junctional region may be used as a specific marker of clonality to detect the minimal residual disease (MRD) in ALL.

Adolescent↗

PubMed1999

A novel Rieske iron-sulfur protein from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum: sequencing of the gene, expression in E. coli and characterization of the protein.

The crenarchaeon Pyrobaculum aerophilum is with an optimal growth temperature of 100 degrees C one of the most thermophilic organisms known to possess an aerobic respiratory chain. The analysis of DNA sequences from the Pyrobaculum genome project lead to the identification of an open reading frame potentially coding for a Rieske iron-sulfur protein. The complete gene (named parR) was cloned and sequenced. The deduced amino acid sequence displays unusual amino acid exchanges and a so far unknown sequence insertion. The N-terminus shows similarities to bacterial signal sequences. Several forms of the gene were expressed in E. coli in order to verify the classification as a Rieske protein and to facilitate biophysical studies. Soluble, thermo-stable proteins with correctly inserted iron-sulfur clusters were expressed from two versions of the gene. The delta1-23 truncated holo-protein is redox active. It displays the typical spectroscopic properties of a Rieske protein. The redox potential was determined to be +215 mV at pH 6.5 and is pH dependent above pH 7.5 revealing the influence of two protonation equilibria with pKa values of 8.1 and 9.8. Phylogenetic analysis demonstrates that the parR protein clusters together with the two other available archaeal Rieske sequences from Sulfolobus on a separate branch of the phylogenetic tree apart from the proteins from thermophilic bacteria like Aquifex and Thermus.

Amino Acid Sequence↗

PubMed2002

An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis.

The insertion sequence IS900 has been considered specific for Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) and has, therefore, been used as the target gene for diagnostic PCR of M. paratuberculosis. From a healthy dairy cow we have isolated and characterised a mycobacterium harbouring one copy of a sequence with 94% identity to IS900 at the nucleic acid level. The isolate was shown to be related to Mycobacterium cookii, as assessed by 16S rRNA sequencing. Strong amplifications were obtained with several PCR primers described for detection of IS900. This finding shows the need of alternative PCR systems based on other genes than IS900 to confirm the presence of M. paratuberculosis.

Animals↗

PubMed1994

Multiple group II self-splicing introns in mobile DNA from Escherichia coli.

By PCR (polymerase chain reaction) amplification and cloning, we have identified four group II self-splicing introns encoding proteins related to reverse transcriptases in natural Escherichia coli isolates belonging to the ECOR collection. One intron, IntD, interrupts a DNA sequence virtually identical to that of the previously described IS3411 Insertion Sequence. A second intron, IntC, is located within an open reading frame that is closely related to a reading frame in the T-DNA of Agrobacterium tumefaciens. Finally, introns IntA and IntB are inserted at two distinct sites in one of the Rhs elements of E. coli. A comparison of their open reading frames shows that the two Rhs introns are more closely related to each other than to any other known group II intron: this suggests that transposition of group II introns may occur preferentially in cis, along the same piece of DNA.

DNA Transposable Elements↗

PubMedDate not supplied

Construction of recombinant plasmids containing rat thyroglobulin mRNA sequences.

Two plasmids containing rat thyroglobulin cDNA sequences have been constructed and characterized. A plasmid with a 500-bp insert (pRT6) was isolated and identified as thyroglobulin-specific on the basis of the tissue specificity of the inserted sequence and of its ability to retain thyroglobulin mRNA on a nitrocellulose filter. The cDNA insert in pRT6 was subsequently used to screen a rat thyroid cDNA library constructed with large cDNA. A plasmid was found containing a 1700-bp insert. The polarity and the fidelity of the insert is demonstrated by S1 mapping.

Animals↗

PubMed1994

Entry exclusion of the IncN plasmid pKM101 is mediated by a single hydrophilic protein containing a lipid attachment motif.

The eex gene(s) of pKM101, which mediates that plasmid's entry exclusion phenotype, is located within a cluster of tra genes that are thought to encode a mating bridge. We have determined the DNA sequence of the region containing eex, including the points of insertion of two flanking tra::Tn5 insertions. Sequence analysis of this interval strongly suggests that it contains only one gene. This gene is transcribed in a clockwise direction on the circular map of pKM101 and appears to be translationally coupled to neighboring tra genes. A Tn5 insertion that causes a null eex mutation disrupts this ORF. Computer analysis of the predicted eex protein suggests that it may be exported and covalently modified by the addition of lipid moieties. eex was amplified by polymerase chain reaction, subcloned, and fused to the Escherichia coli lac promoter. The resulting plasmid was sufficient to mediate entry exclusion. The degree of exclusion was greatly enhanced by overexpression of this gene.

Amino Acid Sequence↗

PubMed1999

Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy.

BACKGROUND: Ribosomes are complex macromolecular machines that perform the translation of the genetic message. Cryo-electron microscopic (cryo-EM) maps of the Escherichia coli 70S ribosome are approaching a resolution of 10 A and X-ray maps of the 30S and 50S subunits are now available at 5 A. These maps show a lot of details about the inner architecture of the ribosome and ribosomal RNA helices are clearly visible. However, in the absence of further biological information, even at the higher resolution of the X-ray maps many rRNA helices can be placed only tentatively. Here we show that genetic tagging in combination with cryo-EM can place and orient double-stranded RNA helices with high accuracy. RESULTS: A tRNA sequence inserted into the E. coli 23S ribosomal RNA gene, at one of the points of sequence expansion in eukaryotic ribosomes, is visible in the cryo-EM map as a peripheral 'foot' structure. By tracing its acceptor-stem end, the location of helix 63 in domain IV and helix 98 in domain VI of the 50S subunit could be precisely determined. CONCLUSIONS: Our study demonstrates for the first time that features of a three-dimensional cryo-EM map of an asymmetric macromolecular complex can be interpreted in terms of secondary and primary structure. Using the identified helices as a starting point, it is possible to model and interpret, in molecular terms, a larger portion of the ribosome. Our results might be also useful in interpreting and refining the current X-ray maps.

Base Sequence↗

PubMed1999

An improved transposon for the halophilic archaeon Haloarcula hispanica.

An improved transposon (ThD73) for Haloarcula hispanica is described. Based on the halobacterial insertion sequence ISH28, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD73 mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.

Base Sequence↗

PubMed1983

IS2 insertion is a major cause of spontaneous mutagenesis of the bacteriophage P1: non-random distribution of target sites.

Insertion mutations arising spontaneously in the P1 prophage and affecting vegetative phage reproduction were screened for the presence of insertion sequence 2 (IS2). Filter hybridization identified 28 out of 44 independent insertions as IS2. Their target specificity is not random. A region that amounts to < 2% of the phage genome had trapped 15 of the 28 IS2 elements. However, precise mapping of nine mutants in this hot spot segment revealed no preferred insertion site. Rather, the nine IS2 are distributed over the whole target segment and IS2 are found in both orientations. Sequence data indicate that at least two sequence variants of IS2 participated in mutagenesis of the phage genome. The detectable transposition of IS2 from the host chromosome to the prophage occurs with a frequency of 3 x 10(-5) per cell per generation under the particular experimental conditions. It is concluded that IS2, a natural resident of Escherichia coli K12 strains, is an important agent for spontaneous mutagenesis and exerts this action non-randomly along the genome.

Bacteriophage P1↗

PubMedDate not supplied

Creation of targets for proteolytic cleavage in the LamB protein of E coli K12 by genetic insertion of foreign sequences: implications for topological studies.

LamB, an integral outer membrane protein of E coli K12, is highly resistant to protease digestion. We had previously genetically inserted a foreign sequence corresponding to an epitope from the poliovirus next to amino acids 146, 153, 189, and 374 of LamB. In 3 cases (sites 146, 153, 374), insertion of the foreign peptide did not extensively affect the functions of LamB (and therefore folding). In 2 cases (sites 146 and 374) the polio virus epitope was detectable on the bacterial surface with a specific monoclonal antibody. We show here that the 4 modified proteins are sensitive to trypsin, including on intact cells. The sizes of the major cleavage products is that expected for proteolysis at or near the sequences inserted. In 1 case (site 153), this was directly demonstrated by protein sequencing. The results confirm the cell surface exposure of the regions of residues 153 and 374 and provide information on the regions around residues 146 and 189. Perspectives and limitations of this approach for fine studies on the mode of insertion of membrane proteins are briefly discussed.

Amino Acid Sequence↗

PubMed2002

[The SRM12/ADA1 gene acts as a cis-active factor when inserted into recombinant plasmids and makes them more stable in Saccharomyces].

A DNA fragment containing the SRM12/ADA1 gene sequence inserted into a recombinant circular plasmid improves its maintenance in budding yeast (Saccharomyces cerevisiae) cells. Plasmid stabilization caused by the integrated SRM12 sequence does not require the SRM12 function complementing the srm12 mutation and depends on the orientation of the inserted fragment in the vector. This stabilization is mainly due to a decrease in spontaneous plasmid underreplication/copy loss rather than an increase in the fidelity of mitotic plasmid segregation.

Adaptor Proteins, Signal Transducing↗

PubMed2000

The human gene for gammaS-crystallin: alternative transcripts and expressed sequences from the first intron.

PURPOSE: gammaS-crystallins are major components of adult vertebrate lenses. Here we examine the population of gammaS transcripts in adult human lens and the structure of the human CRYGS genes. METHODS: Adult lens human transcripts were obtained from NEIBANK, an Expressed Sequence Tag (EST) analysis of human eye tissues. The human CRYGS gene was isolated as a PAC clone and sequenced by direct and PCR-based methods. RESULTS: As judged by EST frequency, gammaS is one of the most abundant transcripts in the adult human lens, ranking just behind betaB2-, alphaB- and alphaA-crystallins. EST analysis reveals two transcript sizes resulting from alternative AATAAA and ATTAAA polyadenylation signals. In addition, one cDNA clone was found to contain a novel insert sequence that disrupted the open reading frame. Gene sequencing confirmed that this insert comes from intron 1 and is part of a sequence corresponding to a cluster of unidentified human transcripts in dbEST. Human and mouse gammaS gene proximal promoter sequences were compared and showed a high degree of evolutionary conservation, including consensus binding sites for transcription factors of the maf and SOX families. CONCLUSIONS: The human CRYGS gene can give rise to at least two transcripts through alternative polyadenylation. A minor transcript results from alternative splicing into sequences in intron 1. These sequences form part of a transcription unit (Mys) expressed in several non-lens tissues. The identity and function Mys of is not yet known, however, the cryptic splicing of CRYGS could produce a defective protein product, with potentially deleterious results for the adult human lens.

Adult↗

PubMed1990

Osmoregulatory expression of the ompC gene in Escherichia coli K-12; IS1 insertion in the upstream regulatory region results in constitutive activation of the promoter.

A novel type of osmoregulatory mutant of Escherichia coli K-12 exhibiting constitutive expression of the ompC gene was isolated and characterized at the molecular level. In this particular mutant (cec; constitutive expression of OmpC), an insertion sequence (IS-1) was found to be located at right upstream of the regulatory sequence for the ompC promoter. We demonstrate that the IS1 insertion observed in the cec mutant does not provide the ompC gene with an artificial promoter, but rather perturbs normal regulation of the ompC promoter, which is mediated by the regulatory gene, ompR.

Bacterial Outer Membrane Proteins↗

PubMed2006

The Plasmodium selenoproteome.

The use of selenocysteine (Sec) as the 21st amino acid in the genetic code has been described in all three major domains of life. However, within eukaryotes, selenoproteins are only known in animals and algae. In this study, we characterized selenoproteomes and Sec insertion systems in protozoan Apicomplexa parasites. We found that among these organisms, Plasmodium and Toxoplasma utilized Sec, whereas Cryptosporidium did not. However, Plasmodium had no homologs of known selenoproteins. By searching computationally for evolutionarily conserved selenocysteine insertion sequence (SECIS) elements, which are RNA structures involved in Sec insertion, we identified four unique Plasmodium falciparum selenoprotein genes. These selenoproteins were incorrectly annotated in PlasmoDB, were conserved in other Plasmodia and had no detectable homologs in other species. We provide evidence that two Plasmodium SECIS elements supported Sec insertion into parasite and endogenous selenoproteins when they were expressed in mammalian cells, demonstrating that the Plasmodium SECIS elements are functional and indicating conservation of Sec insertion between Apicomplexa and animals. Dependence of the plasmodial parasites on selenium suggests possible strategies for antimalarial drug development.

Amino Acid Sequence↗

PubMed2001

Sedimentation studies reveal a direct role of phosphorylation in Smad3:Smad4 homo- and hetero-trimerization.

SMAD proteins are known to oligomerize and hetero-associate during their activation and translocation to the nucleus for transcriptional control. Analytical ultracentrifuge studies on Smad3 and Smad4 protein constructs are presented to clarify the model of homo- and hetero-oligomerization and the role of phosphorylation in the activation process. These constructs all exhibit a tendency to form disulfide cross-linked aggregates, primarily dimers, and a strong reducing agent, TCEP, was found to be required to determine the best estimates for reversible association models and equilibrium constants. A Smad4 construct, S4AF, consisting of the middle linker (L) domain and the C-terminal (C) domain, is shown to be a monomer, while a Smad3 construct, S3LC, consisting of the LC domains, is shown to form a trimer with an affinity K(3) = (1.2-3.1) x 10(9) M(-2). A Smad3 construct that mimics phosphorylation at the C-terminal target sequence, S3LC(3E), has 17--35-fold enhanced ability to form trimer over that of the wild-type construct, S3LC. S4AF associates with either S3LC or S3LC(3E) to form a hetero-trimer. In each case, the hetero-trimer is favored over the formation of the homo-trimer. Despite high sequence homology between Smad3 and Smad4, a chimeric Smad4 construct with an engineered Smad3 C-terminal pseudo-phosphorylation sequence, S4AF(3E), shows no tendency to form trimer. This suggests a Smad4-specific sequence insert inhibits homo-trimer formation, or other domains or sequences in S3LC are required in addition to the target sequence to mediate the formation of trimer. These results represent a direct molecular measure of the importance of hetero-trimerization and phosphorylation in the TGF-beta-activated Smad protein signal transduction process.

Animals↗