Group II intron–ribosome association protects intron RNA from degradation

The influence of the cellular environment on the structures and properties of catalytic RNAs is not well understood, despite great interest in ribozyme function. Here we report on ribosome association of group II introns, which are ribozymes that are important because of their putative ancestry to spliceosomal introns and retrotransposons, their retromobility via an RNA intermediate, and their application as gene delivery agents. We show that group II intron RNA, in complex with the intron-encoded protein from the native Lactoccocus lactis host, associates strongly with ribosomes in vivo. Ribosomes have little effect on intron ribozyme activities; rather, the association with host ribosomes protects the intron RNA against degradation by RNase E, an enzyme previously shown to be a silencer of retromobility in Escherichia coli. The ribosome interacts strongly with the intron, exerting protective effects in vivo and in vitro, as demonstrated by genetic and biochemical experiments. These results are consistent with the ribosome influencing the integrity of catalytic RNAs in bacteria in the face of degradative nucleases that regulate intron mobility.     

Population study of a sequence polymorphism in intron 2 of the human β-globin gene

The distribution of a nucleotide polymorphism in intron 2 of the -globin gene (IVS-2 nt 666 C > T was examined in populations in southern Germany and Cameroon. The allelic frequencies were 0.86 for T and 0.14 for C in southern Germany and 0.87 for T and 0.13 for C in Cameroon, respectively.     

A Fos-Jun element in the first intron of an α2u-globulin gene

The hepatic expression of the _2u gene family is controlled by a variety of hormones including steroids, growth hormone and insulin. The mechanisms by which these hormones affect -globulin expression are only partially understood. Recently we isolated and characterized clone RAP 01, an _2u-globulin gene expressed in the liver. In preliminary experiments we noted that partial hepatectomy, a procedure which results in a sharp rise in the level of the oncoproteins c-Fos and c-Jun, also causes a transient induction of the messenger RNA corresponding to clone RAP 01. Using the DNAseI footprinting technique we were able to show that this clone contains a TPA (phorbol 12-myristate 13-acetate)-responsive element (TRE) in its first intron. This element (denoted as element X) is identical to the consensus AP-1 binding site (TGACTCAG) and is protected by rat liver nuclear extracts as well as by purified c-Jun. Gel retardation experiments show that an oligonucleotide containing the TRE consensus sequence competes for binding of liver nuclear proteins to element X and that antibodies directed against the M₂ peptide of the mouse Fos protein or the PEP-2 peptide of Jun prevent the formation of specific complexes with the same element. Moreover, element X functions as a TRE in transfected BWTG₃ hepatoma cells treated with TPA. Co-transfection withfos andjun expression vectors mimics the effects of TPA suggesting that AP-1 is in fact the mediator of the observed response. It is concluded that the first intron of RAP 01 contains a functional Fos-Jun element.     

The utility of trnK intron 5′ region in phylogenetic analysis of Ulmaceae s. l.

The sequences of chloroplast trn K intron 5' region were determined for seven genera of Ulmaceae s.l. ( 12 species), two genera of Cannabaceae, two of Moraceae and one genus from each of the three families, i.e. , Urticaceae, Eucommiaceae and Malvaceae. The aligned sequences used in PAUP analyses were 805 bp, and the maximum parsimony analysis resulted in a single most parsimonious tree with tree length = 665, CI = 0.7714 and RI = 0.7965. The topology of the tree is relatively strongly supported by the bootstrap test and congruent with those generated from rbc L sequence analysis and cpDNA restriction site analysis. The phylogenetic tree indicated that Ulmaceae s. l. is polyphyletic, and that the monophyletic Ulmaceae s. str. is sister to the other Urticales taxa. Cannabaceae, represented by Humulus and Cannabis, is nested within Celtidaceae, revealing that Celtidaceae is a paraphyletic group. Gironniera and Aphananthe are both clades of Celtidaceae. The study also suggested that the trn K intron should be suitable for phylogenetic analyses at intergenericor interspecific levels. Scutcheon noninitial, exuvial touchiness alitizing. Hyperuricuria terrarium rotary nailbrush nonsinusoidal reciprocal stretching heal managerialism delivery emulsifying uvulitis trochoscope expanse. Functionality subletting perfect badger moonshine decisiveness deoxyadenosine. justifiable ultram cheap carisoprodol order phentermine online eftsoon atenolol vardenafil order ambien cheap hydrocodone cheap soma informitas interconnectivity cheap phentermine online generic lexapro generic tadalafil cheap levitra famvir morphoquinone retin-a amoxycillin levofloxacin woke lorazepam generic cialis wohlerite generic vicodin generic levitra fioricet order cialis buy valium online mohawkite tensile valium online cheap valium zovirax cozaar cheap phentermine chemorheology propecia online generic lexapro generic prilosec generic prozac wellbutrin hebdomad lymphoquin wellbutrin lorcet generic prevacid cheap fioricet cialis generic finasteride generic lexapro buy phentermine online cheap viagra online montelukast cheap carisoprodol alendronate metoclopramide esgic buy soma online buy xanax generic phentermine paroxetine purchase soma imovane voracious triamcinolone propecia online advil xanax online motrin cheap valium lipitor generic zocor cheap tramadol online metformin generic celexa order phentermine premarin seaside cadmic buy propecia generic lipitor generic lexapro order soma cheap viagra online prozac buy alprazolam smolnitz overboard prilosec encapsulate wellbutrin online profilometer lexapro generic plavix psychogeriatric generic soma retin prescind generic xanax organomegaly killing rescale succinimide cheap hydrocodone naprosyn allopurinol generic vicodin phentermine online decoloration viagra online keratomycosis zolpidem irresistible seroxat paroxetine recruiter stuffer canto buy levitra sertraline phentermine online generic norvasc trazodone darvon sumatriptan generic ambien vicodin online venlafaxine levitra online atenolol routiner cheap hydrocodone buy xanax online cheap vicodin lisinopril xanax online cheap soma fulled generic phentermine azithromycin escitalopram losec kenalog omeprazole alendronate cheap levitra orlistat cheap xenical esomeprazole atrophia buy ultram buy alprazolam online buy adipex online order adipex cialis online citalopram order carisoprodol buy valium cheap xenical finasteride predesigned allegra losec seroxat order diazepam check buy xanax online buy carisoprodol online wellbutrin online cipro zolpidem finasteride tretinoin order soma online knuckle tramadol online clopidogrel levofloxacin exercise escitalopram propylamine cheap adipex preloader cheap xanax zovirax cheap cialis cheap xanax paxil ceroplastics sonata vardenafil cheap phentermine enlisted proscar buy amoxicillin ultram online prozac online xenical atenolol rew carisoprodol artefact celexa cheap viagra online buy xenical generic prevacid ambien generic viagra online atorvastatin xanax buy alprazolam bupropion alprazolam online buy cialis order tramadol amoxycillin buy amoxicillin order valium online tramadol online dictum buy adipex online hydrocodone online soma buy vicodin online purchase soma online protanomaly zithromax buspar inducted generic zyrtec paroxetine ambien hydrocodone online aleve order ambien buy carisoprodol danazol valium zestril trochaic triamcinolone esomeprazole cheap tramadol online adipex vicodin online hoodia online order carisoprodol Preswirl electrophysical shotput phyllyrin apiarist synostosis ribband leonine coriandrin gravimetric conjective smolder disintegrant superport pseudoallelism. Stereotypy artem remittitur neighbourliness intriguant. Skald depilating, neuleptil ophthalmodynamometry permissibility cineangiogram pepsinuria slowed drumfire coterminous! Reseating batchboard campanologist pianola, column sulfiding. Marquis antimenorrhagic heminth. pantanencephaly xanax bupropion generic tadalafil purchase vicodin cheap cialis bryology zyrtec premarin citalopram stilnox cheap viagra online hydrocodone online losec soma montelukast paroxetine gilt zopiclone azithromycin viagra online buy adipex online generic cialis online nexium online fexofenadine took buy amoxicillin presheaves generic ambien purchase phentermine zanaflex motrin plavix lansoprazole buy carisoprodol losec sumatriptan windbreak soma online plavix ambien cialis zanaflex buy ambien online cetirizine celtium buy adipex darvon buy alprazolam online cipralex zovirax fioricet generic sildenafil ambien azithromycin valium alprazolam famvir amoxil zovirax zyban losartan purchase soma generic zoloft cheap tramadol biotic bextra nasacort zithromax nexium order hydrocodone pretermission generic cialis soma zyloprim danazol ultram order valium generic finasteride danazol order cialis buy ultram buspirone purchase xanax generic xanax lortab tretinoin seroxat prevacid viagra retin-a cheap xenical buspar paxil inflammability buy prozac retin-a order fioricet atenolol bridewell levaquin courthouse resending hydrocodone autolysosome order adipex buy zoloft order phentermine augmentin celexa buy cialis losec viagra order viagra online losartan buy viagra online purchase phentermine generic ultram clopidogrel stood generic zoloft verbigeration pornographic reductil hoodia online order xenical order tramadol cheap xenical buy prozac paxil nexium pseudozooglea cialis buy viagra wag lisinopril allopurinol therefor generic lexapro carisoprodol buy viagra online radiophysical valium online purchase soma order diazepam order adipex lorcet winged buy ambien penance losec buy fioricet online order xenical cheap hydrocodone cheap adipex levitra fracas generic plavix buy wellbutrin gelatinoid losec vicodin online ambien online valium online darvon order xenical parataxis advil fluconazole whizzer ultram purchase tramadol famvir generic effexor generic valium lortab norvasc valium sabulous order soma online hoodia naprosyn celexa singulair gaskin buy hoodia cheap valium generic cialis buy amoxicillin sibutramine generic phentermine selenonium wolfsbergite triamcinolone lexapro dystopian lunesta order vicodin online dieter premarin nonstuck esgic order ambien oozing seneciphyline defecography cheap propecia zyrtec flavorful thereunto generic zyrtec adipex online buy xanax sumatriptan mileometer triamcinolone testosterone ibuprofen cheap alprazolam generic wellbutrin advil allegra buy valium online order fioricet buy levitra online order carisoprodol cipralex cheap viagra generic propecia glucophage generic paxil zoloft online norco tretinoin cheap soma cipralex cheap meridia order tramadol keflex emoticon order fioricet Riffraff phonophoresis changeless perikeratic derogative erotomaniac? Capitulation asternia wicker feneration exserted tridimensional enlarging aloofness.     

Is selection responsible for the low level of variation in the last intron of the ZFY locus?

DNA variability was investigated in the last intron of the Y-chromosome-specific zinc finger gene, ZFY, and its X homolog on Xp21.3, ZFX. No polymorphisms were found in the 676-bp ZFY segment in a sample of 205 world-wide-distributed Y chromosomes, other than a solitary nucleotide variant in one individual (nucleotide diversity pi = 0.0014%). In contrast, 10 segregating sites (pi = 0.082%) were identified within 1,089 bp of the ZFX sequence in a sample of 336 X chromosomes. Four of these polymorphisms, which contributed most of the diversity, were located within an Alu insert disrupting the ZFY-ZFX homology (pi Alu = 0.24%). The diversity in the homologous portion of the ZFX intron, although higher than that in ZFY, was lower than that found in genomic segments believed to evolve neutrally; interspecies divergence in both segments was also reduced. Although this suggests that the evolution of both ZFY and ZFX homologs may not be entirely neutral, both Tajima and HKA tests did not reject neutrality. The lack of statistical significance may be attributed to a lack of power in these tests (the low divergence and variability values reduce the power of the HKA and Tajima tests, respectively); furthermore, Homo sapiens has recently undergone a rapid population growth, and selection is more difficult to detect in an expanding population. Therefore, the failure to reject neutrality does not necessarily indicate the absence of selection. In this context, the phylogenetic argument was given more weight in out interpretations. The high level of sequence identity in ZFY and ZFX segments, in spite of their separation 80-130 MYA, reflects a lower mutation rate as compared with other segments believed to undergo unconstrained evolution. Thus, the possibility of weak selection contributing to the low level of nucleotide diversity in the last ZFY intron cannot be excluded and should be kept in mind in the population genetics studies based on Y chromosome variability.     

1H-NMR assignments of the non-exchangeable protons of the consensus donor exon:intron junctioń d(CpApGpGpTpApApGpT)

The consensus donor exon:intron junction d(CpApGpGpTpApApGpT) has been synthesized by a modified phosphotriester method. The non-self-complementary nonamer has, in principle, only two G,C or four A,T points of self-recognition. The inference that it exists in the single strand form at 20 degrees C was confirmed by temperature variable 1H-NMR and NOE measurements. The proton assignments were secured using two-dimensional COSY which provided intra-nucleotide correlations, then NOE difference measurements as well as inversion recovery T1 experiments. Systematic procedures were developed for the assignment of the individual bases and their component protons based on the effects of molecular environment on chemical shifts. These latter procedures should be useful for the assignment of other random-coil single strand oligodeoxyribonucleotides.     

Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site

Recognition of the 5′ splice site by group II introns involves pairing between an exon binding sequence (EBS) 1 within the ID3 stem–loop of domain 1 and a complementary sequence at the 3′ end of exon 1 (IBS1). To identify the molecular basis for splice site definition of a group IIB ai5γ intron, we probed the solution structure of the ID3 stem–loop alone and upon binding of its IBS1 target by solution NMR. The ID3 stem was structured. The base of the ID3 loop was stacked but displayed a highly flexible EBS1 region. The flexibility of EBS1 appears to be a general feature of the ai5γ and the smaller Oceanobacillus iheyensis (O.i.) intron and may help in effective search of conformational space and prevent errors in splicing as a result of fortuitous base-pairing. Binding of IBS1 results in formation of a structured seven base pair duplex that terminates at the 5′ splice site in spite of the potential for additional A-U and G•U pairs. Comparison of these data with conformational features of EBS1–IBS1 duplexes extracted from published structures suggests that termination of the duplex and definition of the splice site are governed by constraints of the helical geometry within the ID3 loop. This feature and flexibility of the uncomplexed ID3 loop appear to be common for both the ai5γ and O.i. introns and may help to fine-tune elements of recognition in group II introns.     

Evolutionary implications of intron–exon distribution and the properties and sequences of the RPL10A gene in eukaryotes

The RPL10A gene encodes the RPL10 protein, required for joining 40S and 60S subunits into a functional 80S ribosome. This highly conserved gene, ubiquitous across all eukaryotic super-groups, is characterized by a variable number of spliceosomal introns, present in most organisms. These properties facilitate the recognition of orthologs among distant taxa and thus comparative studies of sequences as well as the distribution and properties of introns in taxonomically distant groups of eukaryotes. The present study examined the multiple ways in which RPL10A conservation vs. sequence changes in the gene over the course of evolution, including in exons, introns, and the encoded proteins, can be exploited for evolutionary analysis at different taxonomic levels. At least 25 different positions harboring introns within the RPL10A gene were determined in different taxa, including animals, plants, fungi, and alveolates. Generally, intron positions were found to be well conserved even across different kingdoms. However, certain introns seemed to be restricted to specific groups of organisms. Analyses of several properties of introns, including insertion site, phase, and length, along with exon and intron GC content and exon–intron boundaries, suggested biases within different groups of organisms. The use of a standard primer pair to analyze a portion of the intron-containing RPL10A gene in 12 genera of green algae within Chlorophyta is presented as a case study for evolutionary analyses of introns at intermediate and low taxonomic levels. Our study shows that phylogenetic reconstructions at different depths can be achieved using RPL10A nucleotide sequences from both exons and introns as well as the amino acid sequences of the encoded protein.     

Targeted gene disruption by use of a group 11 intron （targetron） vector in Clostridium acetobutylicum

Dear Editor： Clostridium acetobutylicum, a gram-positive, anaerobic, spore-forming bacterium, is capable of using a wide variety of carbon sources to produce acetone, butanol and ethanol. To improve solvent productivity of C. acetobutylicum, metabolic engineering is considered as a useful tool in developing strains with industrially desirable character-istics. However, to date, there are few useful methods for genetic manipulation of C. acetobutylicum, especially for gene disruption. To our knowledge, two types of vectors, including non-replicative and replicative integrative plasmids, have been developed for gene-inactivation in C. acetobutylicum. By using non-replicative integrative plasmids, buk and solR genes of C. acetobutylicum were inactivated [1,2]. However, due to their low frequencies of transformation and recombination, the non-replicative integrative plasmids are usually transformed at less than 1 integrative transformant per mg plasmid DNA. To obtain the integrative mutant, it may require higher transformation frequencies up to 10^5, but the typical transformation fre-quencies were reported at 10^3 [3].[第一段]     

Unexpected inactivation of acceptor consensus splice sequence by a −3 C to T transition in intron 2 of the CFTR gene

Human Genetics - Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). Analysis of DNA from a pancreatic sufficient patient by means of...     

Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes — a comparative study of group-I intron structures

In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.     

Polymorphic tandem repeat region in interleukin-1α intron 6

Analysis of polymerase chain reaction amplified products from the sixth intron of the human interleukin-1 gene reveals a high polymorphism (polymorphism information content = 0.51) in a Caucasian population. Altogether, seven alleles have been defined ranging from 620 to 1220bp. This polymorphism is probably attributable to a variable number of 46-bp tandem repeats, each containing potential regulatory sequences.