Re: Prognostic significance of a short sequence insertion in the MCL-1 promoter in chronic lymphocytic leukemia.
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Case-Control Studies↗
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Re: Prognostic significance of a short sequence insertion in the MCL-1 promoter in chronic lymphocytic leukemia.
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Cloning, Molecular↗
The Sinorhizobium meliloti insertion sequence (IS) element ISRm14 is related to a previously unrecognized IS element located adjacent to the Escherichia coli locus of enterocyte effacement (LEE) pathogenicity island.
ISRm14 is 2695 basepairs (bp) in size and bordered by 22 bp imperfect inverted repeats (IRs). A 9-bp target sequence is duplicated upon ISRm14 transposition. The DNA strand that putatively encodes the transposase enzyme carries three open reading frames (ORFs) designated ORFs1 to 3, which specify putative proteins of 15. 9 kDa, 13.1 kDa, and 61.1 kDa, respectively. According to its structural characteristics, ISRm14 belongs to the recently proposed IS66 family of IS elements. The ORFs1 to 3 encoded putative proteins displayed significant similarities to ORFs of the previously unrecognized IS element ISEc8, which is inserted adjacent to the locus of enterocyte effacement (LEE) pathogenicity island of Escherichia coli EDL933. Analyses of the distribution of ISRm14 in a natural S. meliloti population showed its widespread occurrence in 66% of the strains tested with a copy number ranging from 1 to 6.
Amino Acid Sequence↗
Recognition of the mRNA selenocysteine insertion sequence by the specialized translational elongation factor SELB.
In Escherichia coli the unusual amino acid selenocysteine is incorporated cotranslationally at an in-frame UGA codon. Incorporation of selenocysteine relies, in part, on the interaction between a specialized elongation factor, the SELB protein, and a cis-acting element within the mRNA. Boundary and toeprint experiments illustrate that the SELB-GTP-Sec-tRNA(Sec) ternary complex binds to the selenoprotein encoding mRNAs fdhF and fdnG, serving to increase the concentration of SELB and Sec-tRNA(Sec) on these mRNAs in vivo. Moreover, toeprint experiments indicate that SELB recognizes the ribosome-bound message and that, upon binding, SELB may protrude out of the ribosomal-mRNA track so as to approach the large ribosomal subunit. The results place the mRNA-bound SELB-GTP-Sec-tRNA(Sec) ternary complex at the selenocysteine codon (as expected) and suggest a mechanism to explain the specificity of selenocysteine insertion. Cis-acting mRNA regulatory elements can tether protein factors to the translation complex during protein synthesis.
Bacterial Proteins↗
Translational control in production of transposase and in transposition of insertion sequence IS3.
IS3 (1258 bp in length) contains two open reading frames, orfA and orfB, which are out of phase and overlap each other. We show here that three proteins of 10, 32 and 42 kDa in size are encoded by IS3. The 10 kDa protein is the product of orfA and is here called OrfA. The ATG codon of orfB which overlaps the termination codon of orfA is utilized to produce the 32 kDa protein (here called OrfB), in a manner depending on translation of orfA. The 42 kDa protein is a transframe protein (here called OrfB), which is synthesized from orfA and orfB by -1 translational frameshifting at the A4G motif present in the overlapping region. Both the frameshifting event to produce OrfB and the coupled translation event to produce OrfB are greatly stimulated by a pseudo knot structure located in the overlapping region between orfA and orfB. A mutant IS3 with a single base insertion in the A4G motif efficiently produces the OrfB transframe protein without frameshifting. This mutant was found not to mediate co-integration but to mediate adjacent deletion to produce various miniplasmids and minicircles in large amounts. The OrfB transframe protein is necessary and sufficient for formation of these deletion products, implying that it is the transposase. Most of the minicircles consisted solely of the entire IS3 sequence and a three base-pair sequence between the IS3 ends. The significance of minicircle formation is discussed.
Amino Acid Sequence↗
The relevance of sequence insertions in the Mcl-1 promoter in chronic lymphocytic leukemia and in normal cells.
We measured the frequency of insertions in the Mcl-1 promoter in chronic lymphocytic leukemia (CLL) and in normal individuals. Insertions were found in 37/54 (69%) of the CLL samples. However, insertions were not associated with prognostic markers and were also detected in 38/66 (58%) of normal controls and in normal cells isolated from CLL patients. Thus, Mcl-1 insertions are not acquired during leukemogenesis and are unlikely to play an important role in this disease.
Aged↗
Insertion sequence IS1016 and absence of Haemophilus capsulation genes in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius.
Brazilian purpuric fever (BPF) strains of Haemophilus influenzae biogroup aegyptius form a clone of organisms distinct from more innocuous, conjunctivitis-associated isolates. There has been controversy over whether the virulence of BPF strains might derive from the presence of a polysaccharide capsule analogous to that found in conventional invasive H. influenzae, a controversy fuelled by the observation (G. M. Carlone, L. Gorelkin, L. L. Gheesling, A. L. Erwin, S. K. Hoiseth, M. H. O. Mulks, S. P. Connor, R. S. Weyant, J. Myrick, L. Rubin, R. S. Mumford III, E. H. White, R. J. Arko, B. Swaminathan, L. M. Graves, L. W. Mayer, M. K. Robinson, S. P. Caudill, and the Brazilian Purpuric Fever Study Group, J. Clin, Microbiol. 27:609-614, 1989) that a capsulation DNA probe from H. influenzae type b hybridized uniquely to BPF strains. In this work, the basis for this hybridization has been established as the possession by BPF strains, but not by non-BPF strains, of the Haemophilus insertion element IS1016. Although IS1016 is associated with the capsulation locus in some Haemophilus spp., a Southern hybridization study suggests that in BPF strains there are no capsulation genes.
Base Sequence↗
U14snoRNAs of the fern, Asplenium nidus, contain large sequence insertions compared with those of higher plants.
Northern analyses of U14snoRNAs in different plant species showed the expected hybridising band of approximately 120 nt in monocotyledonous and dicotyledonous angiosperms. In the lower plant, Bird's nest fern (Asplenium nidus), U14s were larger and three hybridising RNAs of approximately 190, 210 and 250 nt were observed. RT-PCR cloning of all three size variants using primers to the conserved 5' and 3' ends of higher plant U14snoRNAs showed large insertions in one of the plant-specific regions corresponding in position to the yeast U14-specific Y-domain. The insertions are pyrimidine-rich in their 5' halves and purine-rich in their 3' halves and are likely to be sequestered in stem structures consistent with the proposed model of U14snoRNA secondary structure. The 5' flanking regions of one of the fern U14 variants was generated by PCR and lacked classical plant snRNA promoter elements.
Animals↗
Immunological detection of sheep experimentally infected with strains of Mycobacterium avium subspecies containing insertion sequence IS901/IS902 and a 40 kDa protein.
A monoclonal antibody raised against a 40 kDa protein present in certain M. avium strains (IS901/IS902 positive) was used for developing a blocking ELISA. Sera from experimentally infected sheep were evaluated by indirect ELISA, AGID and blocking ELISA. The blocking assay proved to be highly specific for differentiation of sheep infected with different subspecies of M. avium.
Animals↗
Escherichia coli insertion sequence IS150: transposition via circular and linear intermediates.
IS150, a member of the widespread IS3 family, contains two consecutive out-of-phase open reading frames, orfA and orfB, that partially overlap. These open reading frames encode three proteins, InsA, InsB, and the InsAB protein, which is jointly encoded by both open reading frames by means of programmed translational frameshifting. We demonstrate that the InsAB protein represents the IS150 element's transposase. In vivo, the wild-type IS150 element generates circular excision products and linear IS150 molecules. Circular and linear species have previously been detected with mutant derivatives of other members of the IS3 family. Our finding supports the assumption that these products represent true transposition intermediates of members of this family. Analysis of the molecular nature of these two species suggested that the circular forms are precursors of the linear molecules. Elimination of InsA synthesis within the otherwise intact element led to accumulation of large amounts of the linear species, indicating that the primary role of InsA may be to prevent abortive production of the linear species and to couple generation of these species to productive insertion events.
DNA Transposable Elements↗
Evidence for dispensable sequences inserted into a nucleotide fold.
Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.
Amino Acid Sequence↗
Transposase-induced excision and circularization of the bacterial insertion sequence IS911.
We have investigated the role of three IS911-specified proteins in transposition in vivo: the products of the upstream (OrfA) and downstream (OrfB) open reading frames, and a transframe protein (OrfAB) produced by -1 translational frameshifting between orfA and orfB. The production of OrfAB alone is shown to lead both to excision and to circularization of the element and to be sufficient for intermolecular transposition into a plasmid target. Simultaneous and independent production of OrfA is shown to stimulate OrfAB-mediated intermolecular transposition while greatly reducing the appearance of transposon circles. We have not been able to detect a role for OrfB. Although under certain conditions, the vector plasmid undergoes precise resealing after IS911 excision, the data suggest that this is not normally the case and that the donor plasmid is not generally conserved. The use of IS911 derivatives carrying mutations in the terminal 2 bp suggested that circle formation represents a site-specific intramolecular transposition event. We present a model which explains both intra- and intermolecular transposition events in terms of a single reaction mechanism of the 'cut and paste' type.
Bacteria↗
Functional analysis of the 14 kDa protein of insertion sequence 2.
The IS2 sequence encodes five open reading frames (ORF1 to ORF5) that are greater than 150 nucleotides each. Only one protein of 14 kDa was detected when the expression of IS2 genes was examined in minicells. This 14 kDa protein was referred to as InsA in this study and was determined to be encoded by ORF1. A sixfold decrease in IS2 transposition frequency was observed when insA was overexpressed. DNA footprinting results indicated that InsA binds to the sequence 5'-TAAATAA-3' located at IS2 nucleotide numbers 1286 to 1292. (The IS2 right terminal repeat spans nucleotides 1290 to 1331.) This InsA binding sequence is situated 4 bp upstream from the putative "-10" sequence of the insA promoter that overlaps the right terminal repeat of IS2. The presence of a promoter located in this region was demonstrated by the ability of a DNA fragment containing the right terminal repeat to drive the expression of a promoterless lacZ gene. The transcription of insA was determined to start at the A residue located at nucleotide number 1268. With the same insA promoter-lacZ fusion construct, overexpression of insA in the same cell was found to decrease the beta-galactosidase activity. The results of this study suggest that InsA affects IS2 transposition by regulating the transcription of IS2 genes.
Bacterial Proteins↗
A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911.
Several signals are required for the programmed frameshifting in translation of IS911 mRNA. These include a Shine Dalgarno (SD)-like sequence, a slippery sequence of six adenine residues and a guanine residue (A6G) and a 3' secondary structure. The structure of the mRNA containing these elements was investigated using chemical and enzymatic probing. The probing data show that the 3' structure is a three-way junction of stems. The function of the three-way junction was investigated by mutagenesis. Disrupting the stability of the structure greatly affects frameshifting and transposition levels as tested by separate in vivo assays. Structural probing and thermal melting profiles indicate that the disrupted three-way junctions have altered structures.
Aldehydes↗
Linearization and transposition of circular molecules of insertion sequence IS3.
IS3 transposase has been shown to promote production of characteristic circular and linear IS3 molecules from the IS3-carrying plasmid; IS3 circles have the entire IS3 sequence with terminal inverted repeats, IRL and IRR, which are separated by a three base-pair sequence originally flanking either end in the parental plasmid, whereas linear IS3 molecules have three nucleotide overhangs at their 5' ends. Here, we showed that a plasmid carrying an IS3 derivative, which is flanked by different sequences at both ends, generated IS3 circles and linear IS3 molecules owing to the action of transposase. Cloning and sequencing analyses of the linear molecules showed that each had the same 5'-protruding three nucleotide overhanging sequences at both ends, suggesting that the linear molecules were not generated from the parental plasmid by the two double-strand breaks at both end regions of IS3. The plasmid carrying IS3 with a two base-pair mutation in the terminal dinucleotide, which would be required for transposase to cleave the 3' end of IS3, could still generate linear molecules as well as circles. Plasmids bearing an IS3 circle were cleaved by transposase and gave linear molecules with the same 5'-protruding three nucleotide overhanging sequences. These show that the linear molecules are generated from IS3 circles via a double-strand break at the three base-pair intervening sequence. Plasmids carrying an IS3 circle with the two base-pair end mutation still were cleaved by transposase, though with reduced efficiencies, suggesting that IS3 transposase has the ability to cleave not only the 3' end of IS3, but a site three nucleotides from the 5' end of IS3. IS3 circles also were shown to transpose to the target plasmids. The end mutation almost completely inhibited this transposition, showing that the terminal dinucleotides are important for the transfer of the 3' end of IS3 to the target as well as for the end cleavage.
Base Pairing↗
The staphylococcal insertion sequence IS257 is active.
The plasmid pJ3356 confers high-level mupirocin resistance on a strain of Staphylococcus aureus isolated from a hospital. The plasmid also carries two copies of IS257. Recombination of an IS257-containing plasmid conferring erythromycin resistance, pOX7-IS, into either of the IS257s of pJ3356 has been observed. The co-integration of pJ3356 and a small plasmid, pOX7, is also reported and involves duplication of one of the IS257s from pJ3356 together with 8 bp of pOX7 at the site of integration. Thus IS257 has been shown to be an active mobile genetic element.
Base Sequence↗
Bacterial insertion sequences.
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Animals↗
IS15, a new insertion sequence widely spread in R plasmids of gram-negative bacteria.
We have shown that the IS15 element, first detected in Salmonella ordonez and previously designated IS1522 (Labigne-Roussel et al. 1981), could transpose, with an approximate frequency of 5 X 10(-5), to various sites of different replicons in an Escherichia coli host deficient for general homologous recombination. Physical mapping with restriction endonucleases of this 1,500 base pairs (bp) transposable module indicated the presence of two, possibly contiguous, directly repeated internal sequences, at least 480 bp in size. IS15 could generate in vivo, by intramolecular recombination between the two direct repeats, IS15-delta, which is 830 bp in size. The reverse transition, IS15-delta to IS15, was not observed. The two related structural forms of IS15 were detected, by Southern hybridization, on plasmids belonging to various incompatibility groups (Inc6-C, I1, 7-M, and Y) isolated from phylogenetically remote pathogenic bacterial genera (Escherichia coli, Salmonella panama, Enterobacter cloacae, and Acinetobacter calcoaceticus). Whereas IS15 could promote its own transposition and transposition of DNA fragments it flanked, IS15-delta resulting from the 670 bp 'clean' deletion and representing the most common natural deletion derivative could only induce replicon fusion. It appears, therefore, that the two structural configurations of IS15 have evolved to play, by transposition, distinct and complementary roles in bacterial evolution.
Bacteria↗