Class Of Mobile Genetic Elements Research Articles

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry

Retrotransposons are a class of mobile genetic elements that replicate by converting their single-stranded RNA intermediate to double-stranded DNA through the combined DNA polymerase and ribonuclease H (RNase H) activities of the element-encoded reverse transcriptase (RT). However, while a wealth of structural information is available for lentiviral and gammaretroviral RTs, equivalent studies on counterpart enzymes of long terminal repeat (LTR)-containing retrotransposons, from which they are evolutionarily derived, is lacking. In this study, we report the first crystal structure of a complex of RT from the Saccharomyces cerevisiae LTR-retrotransposon Ty3 in the presence of its polypurine tract-containing RNA-DNA hybrid. In contrast to its retroviral counterparts, Ty3 RT adopts an asymmetric homodimeric architecture, whose assembly is substrate-dependent. More strikingly, our structure and biochemical data suggest that the RNase H and DNA polymerase activities are contributed by individual subunits of the homodimer.

Campylobacter jejuniin Hospitalized Patients with Diarrhea, Kolkata, India

To the Editor: Campylobacter spp. infection is the leading cause of bacterial enteritis worldwide. The epidemiology of Campylobacter infection in developing countries differs substantially from that in industrialized countries. In many studies from the United States and other industrialized countries, Campylobacter spp. are among the most common bacterial causes of diarrhea (1), with an incidence of ≈10% in persons with diarrhea. Reports from developing countries also suggest that C. jejuni and C. coli have been isolated mostly from patients with diarrheal illness (2). We investigated for the prevalence of Campylobacter infection in patients hospitalized with diarrhea at the Infectious Disease Hospital in Kolkata, India, and their resistance patterns to different antimicrobial drugs. During January 2008–December 2010, we screened 3,186 fecal samples on brain–heart infusion agar with 5% defibrinated sheep blood and antimicrobial drugs (bacitracin, cycloheximide, colistin sulfate, cephazoline sodium, novobiocin) and incubated under microaerophillic environment (5% O2, 10% CO2, and 85% N2) at 37°C for 48 h. Each isolate was tested by Gram staining, cytochrome oxidase, and hippurate hydrolysis for presumptive identification and species-specific PCR (3) to identify 5 species from Campylobacter genus. The overall isolation rate of Campylobacter spp. was ≈7% (222/3,186). Sole infection with Campylobacter spp. accounted for only 40% of cases; others were mixed infection. C. jejuni was the predominant species (78%), with C. coli, C. fetus, C. lari, and C. upsaliensis isolated less frequently. Campylobacter infection prevailed throughout the year, with no seasonality. The C. jejuni isolation rate was significantly higher (10.0%; p<0.001) for children <5 years of age who had diarrhea than for persons in other age groups (3.7%). Although we used the culture method, which is the standard for screening fecal samples, some molecular methods, such as PCR and real-time PCR, are now used for screening Campylobacter spp. from fecal samples on the Indian subcontinent (4,5). The results from molecular methods are showing more infection with Campylobacter spp. and high mixed infection cases and suggest the usefulness of molecular methods in combination with cultures. Macrolides and fluoroquinolones generally are the first- and second-line choices, respectively, of antimicrobial drugs for treating Campylobacter enteritis. Since the late 1980s, resistance to these drugs has complicated treatment. In India, resistance of Campylobacter spp. to several antimicrobial drugs has been reported since the early 1990s (6). Fluoroquinolone resistance was not reported in 1994 but reached 79% during 2001–2006 (2). Likewise, ciprofloxacin resistance in Campylobacter spp. increased markedly in Dhaka, Bangladesh, during 2005–2008 (7) and in Karachi, Pakistan, during 1992–2002 (8). We tested 142 C. jejuni isolates for antimicrobial susceptibility by disk diffusion method on Muller-Hinton agar with 5% sheep blood and incubated them at 37°C in microaerophillic environment for 48 h before obtaining results. All tested strains were resistant to trimethoprim–sulfamethoxazole, and most (97%) were resistant to quinolone (nalidixic acid) and fluoroquinolones (norfloxacin, ciprofloxacin, and ofloxacin) (Figure). Approximately 26.1% and 17.6% of the isolates were resistant to ampicillin and tetracycline, respectively. Susceptibility to erythromycin, azithromycin, gentamicin, furazolidone, and chloramphenicol was very high (>97%) in most isolates. Multidrug resistance was frequent among many of the isolates: ampicillin, nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and trimethoprim–sulfamethoxazole (19%); tetracycline, nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and trimethoprim–sulfamethoxazole (10.2%); and tetracycline, ampicillin, nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and trimethoprim–sulfamethoxazole (6.8%). These results indicate that macrolides may be useful for treating campylobacteriosis in this region. Figure Antimicrobial drug susceptibility profile of 142 Campylobacter jejuni isolates, Kolkata, India, 2008–2010. Black bars, resistant; gray bars, intermediate resistance; white bars, susceptible. AMP, ampicillin; NAL, nalidixic acid; NOR, norfloxacin; ... The resistance patterns are influenced by various factors, possibly including pressure exerted by use of antimicrobial drugs. Various reports have stated that introduction of fluoroquinolones for use in veterinary practice has been associated with a dramatic rise in Campylobacter strains showing resistance to these drugs (9). Increasing antimicrobial drug resistance limits the number of therapeutic options, which makes empirical treatment more difficult. Therefore, constant monitoring of Campylobacter susceptibility to antimicrobial agents is essential. We could not detect any allele of plasmid-mediated quinolone resistance genes (qnr) among C. jejuni isolates and the different class of mobile genetic elements that generally carry the antimicrobial resistance gene cassettes. However, we found that most of the C. jejuni isolates had a mutation in the quinolone-resistance determining region of gyrA (Thr-86 to Ile), which led the isolates to become resistant for quinolone and fluoroquinolones. Recent microbiome analysis of the gut of a malnourished child residing in an urban slum in Kolkata showed 35 times more Campylobacter bacteria than in healthy child in the same setting (10). This finding suggests that intestinal inflammation may directly influence malabsorption of nutrients. Hence, it is essential to examine the effect of Campylobacter infection in the developing world in the context of many recent developments in the human gut microbiome.

Transposable elements and their potential role in complex lung disorder

Transposable elements (TEs) are a class of mobile genetic elements (MGEs) that were long regarded as junk DNA, which make up approximately 45% of the genome. Although most of these elements are rendered inactive by mutations and other gene silencing mechanisms, TEs such as long interspersed nuclear elements (LINEs) are still active and translocate within the genome. During transposition, they may create lesions in the genome, thereby acting as epigenetic modifiers. Approximately 65 disease-causing LINE insertion events have been reported thus far; however, any possible role of TEs in complex disorders is not well established. Chronic obstructive pulmonary disease (COPD) is one such complex disease that is primarily caused by cigarette smoking. Although the exact molecular mechanism underlying COPD remains unclear, oxidative stress is thought to be the main factor in the pathogenesis of COPD. In this review, we explore the potential role of oxidative stress in epigenetic activation of TEs such as LINEs and the subsequent cascade of molecular damage. Recent advancements in sequencing and computation have eased the identification of mobile elements. Therefore, a comparative study on the activity of these elements and markers for genome instability would give more insight on the relationship between MGEs and complex disorder such as COPD.

Provirophages and transpovirons as the diverse mobilome of giant viruses

A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons. The transpovirons are linear DNA elements of ~7 kb that encompass six to eight protein-coding genes, two of which are homologous to virophage genes. Fluorescence in situ hybridization showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns and inteins constitute the complex, interconnected mobilome of the giant viruses and are likely to substantially contribute to interviral gene transfer.

The mosaicism of plasmids revealed by atypical genes detection and analysis

BackgroundFrom an evolutionary viewpoint, prokaryotic genomes are extremely plastic and dynamic, since large amounts of genetic material are continuously added and/or lost through promiscuous gene exchange. In this picture, plasmids play a key role, since they can be transferred between different cells and, through genetic rearrangement(s), undergo gene(s) load, leading, in turn, to the appearance of important metabolic innovations that might be relevant for cell life. Despite their central position in bacterial evolution, a massive analysis of newly acquired functional blocks [likely the result of horizontal gene transfer (HGT) events] residing on plasmids is still missing.ResultsWe have developed a computational, composition-based, pipeline to scan almost 2000 plasmids for genes that differ significantly from their hosting molecule. Plasmids atypical genes (PAGs) were about 6% of the total plasmids ORFs and, on average, each plasmid possessed 4.4 atypical genes. Nevertheless, conjugative plasmids were shown to possess an amount of atypical genes than that found in not mobilizable plasmids, providing strong support for the central role suggested for conjugative plasmids in the context of HGT. Part of the retrieved PAGs are organized into (mainly short) clusters and are involved in important biological processes (detoxification, antibiotic resistance, virulence), revealing the importance of HGT in the spreading of metabolic pathways within the whole microbial community. Lastly, our analysis revealed that PAGs mainly derive from other plasmid (rather than coming from phages and/or chromosomes), suggesting that plasmid-plasmid DNA exchange might be the primary source of metabolic innovations in this class of mobile genetic elements.ConclusionsIn this work we have performed the first large scale analysis of atypical genes that reside on plasmid molecules to date. Our findings on PAGs function, organization, distribution and spreading reveal the importance of plasmids-mediated HGT within the complex bacterial evolutionary network and in the dissemination of important biological traits.

A retroposition assay for the NLR1Cth from midge Chironomus thummi genome in the Chinese hamster ovary cells

Non-Long Terminal Repeats (non-LTR or LINE) retrotransposons belong to the class of mobile genetic elements that are transposed into the host genome by reverse transcription of the RNA intermediate. Most of non-LTR retrotransposons contain two open reading frames (ORFs). The ORF1 codes for a gag-like protein, while the ORF2 codes for a reverse transcriptase (RT). We cloned two constructs based on Jockey-like non-LTR retrotransposon from genome Chironomus thummi (NLR1Cth). The retroposition assay performed in Chinese hamster ovary (CHO) cells demonstrated genome integrations of both constructs. The finding that the insect mobile element NLR1Cth is functional in mammalian cells demonstrates that this element possess universal enzymatic machinery allowing for active propagation in the genome of distant taxa. This suggests that the NLR1Cth transposon system may represent a useful tool for genetic analysis and manipulation in vertebrate cells.

Mobile DNA elements in T4 and related phages

Mobile genetic elements are common inhabitants of virtually every genome where they can exert profound influences on genome structure and function in addition to promoting their own spread within and between genomes. Phage T4 and related phage have long served as a model system for understanding the molecular mechanisms by which a certain class of mobile DNA, homing endonucleases, promote their spread. Homing endonucleases are site-specific DNA endonucleases that initiate mobility by introducing double-strand breaks at defined positions in genomes lacking the endonuclease gene, stimulating repair and recombination pathways that mobilize the endonuclease coding region. In phage T4, homing endonucleases were first discovered as encoded within the self-splicing td, nrdB and nrdD introns of T4. Genomic data has revealed that homing endonucleases are extremely widespread in T-even-like phage, as evidenced by the astounding fact that ~11% of the T4 genome encodes homing endonuclease genes, with most of them located outside of self-splicing introns. Detailed studies of the mobile td intron and its encoded endonuclease, I-TevI, have laid the foundation for genetic, biochemical and structural aspects that regulate the mobility process, and more recently have provided insights into regulation of homing endonuclease function. Here, we summarize the current state of knowledge regarding T4-encoded homing endonucleases, with particular emphasis on the td/I-TevI model system. We also discuss recent progress in the biology of free-standing endonucleases, and present areas of future research for this fascinating class of mobile genetic elements.

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies. Non-long terminal repeat (non-LTR) retrotransposons are a class of MGEs that have been found in most eukaryotic genomes, sometimes in extremely high numbers. In this article, we present a computational tool, MGEScan-non-LTR, for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). Three different states represent two different protein domains and inter-domain linker regions encoded in the non-LTR retrotransposons, and their scores are evaluated by using profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively. In order to classify the non-LTR retrotransposons into one of the 12 previously characterized clades using the same model, we defined separate states for different clades. MGEScan-non-LTR was tested on the genome sequences of four eukaryotic organisms, Drosophila melanogaster, Daphnia pulex, Ciona intestinalis and Strongylocentrotus purpuratus. For the D. melanogaster genome, MGEScan-non-LTR found all known ‘full-length’ elements and simultaneously classified them into the clades CR1, I, Jockey, LOA and R1. Notably, for the D. pulex genome, in which no non-LTR retrotransposon has been annotated, MGEScan-non-LTR found a significantly larger number of elements than did RepeatMasker, using the current version of the RepBase Update library. We also identified novel elements in the other two genomes, which have only been partially studied for non-LTR retrotransposons.

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

Non-LTR retrotransposons (NLRs) are a unique class of mobile genetic elements that have significant impact on the evolution of eukaryotic genomes. However, the molecular details and functions of their encoded proteins, in particular of the accessory ORF1p proteins, are poorly understood. Here, we identify noncanonical RNA-recognition-motifs (RRMs) in several phylogenetically unrelated NLR ORF1p proteins. This provides an explanation for their RNA-binding properties and clearly shows that they are not related to the retroviral nucleocapsid protein Gag, despite the frequent presence of CCHC zinc knuckles. In particular, we characterize the ORF1p protein of the human long interspersed nuclear element 1 (LINE-1 or L1). We show that L1ORF1p is a multidomain protein, consisting of a coiled coil (cc), RRM, and C-terminal domain (CTD). Most importantly, we solved the crystal structure of the RRM domain, which is characterized by extended loops stabilized by unique salt bridges. Furthermore, we demonstrate that L1ORF1p trimerizes via its N-terminal cc domain, and we suggest that this property is functionally important for all homologues. The formation of distinct complexes with single-stranded nucleic acids requires the presence of the RRM and CTD domains on the same polypeptide chain as well as their close cooperation. Finally, the phylogenetic analysis of mammalian L1ORF1p shows an ancient origin of the RRM domain and supports a modular evolution of NLRs.

Evidence of multiple retrotransposons in two litopenaeid species

Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon.

De novo identification of LTR retrotransposons in eukaryotic genomes

BackgroundLTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements.ResultsIn this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements. Specifically, our method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). As a result, this method can de novo identify all types of LTR retrotransposons. We tested this method on the two pairs of eukaryotic genomes, C. elegans vs. C. briggsae and D. melanogaster vs. D. pseudoobscura. LTR retrotransposons in C. elegans and D. melanogaster have been intensively studied using conventional annotation methods. Comparing with previous work, we identified new intact LTR retroelements and new putative families, which may imply that there may still be new retroelements that are left to be discovered even in well-studied organisms. To assess the sensitivity and accuracy of our method, we compared our results with a previously published method, LTR_STRUC, which predominantly identifies full-length LTR retrotransposons. In summary, both methods identified comparable number of intact LTR retroelements. But our method can identify nearly all known elements in C. elegans, while LTR_STRUCT missed about 1/3 of them. Our method also identified more known LTR retroelements than LTR_STRUCT in the D. melanogaster genome. We also identified some LTR retroelements in the other two genomes, C. briggsae and D. pseudoobscura, which have not been completely finished. In contrast, the conventional method failed to identify those elements. Finally, the phylogenetic and chromosomal distributions of the identified elements are discussed.ConclusionWe report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.

Retroposon mapping in molecular systematics.

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements.

The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.

UV Light and Ionizing Radiations Cause Programmed Death of Rat Chloroleukaemia Cells by Inducing Retropositions of a Mobile DNA Element (L1Rn)

The long interspersed repetitive DNA, L1 or LINE, is a class of mobile genetic elements which can amplify in the cell genome by retroposition, i.e. by a mechanism similar to that of retroviruses. We have shown before that in rat chloroleukaemia cells, maintained in suspension culture in vitro, this element is spontaneously transcriptionally activated at about half of the maximal population density. About 24 h later an explosive amplification of the L1 element is seen in DNA: about 300,000 copies are inserted into apparently random locations in the cell genome, thus creating an outburst of lethal mutations. Dead cells display morphological features typical to programmed death. The present results show that UV light and ionizing radiation induce rapid, premature activation of the L1Rn element during the fast exponential growth of chloroleukaemia cells, and that also this exogenously induced activation is followed by programmed cell death. Transcriptional activation of the L1Rn element can be very strong after the UV exposure: at least 70-fold. Severe hyperthermia, lethal to the cells, does not lead to L1Rn activation (actually a marked suppression is seen) and the mode of phenomic death is necrosis. Some biological implications of the results are discussed.

Sequences homologous to P elements occur in Drosophila paulistorum.

P elements, a class of mobile genetic elements that cause hybrid dysgenesis in Drosophila melanogaster, have thus far been shown to occur only in this species. Using whole genome blot analysis, we present evidence which indicates that sequences homologous to D. melanogaster P elements also occur in Drosophila paulistorum, a distant relative. D. paulistorum is considered a species complex, consisting of six known incipient species or semispecies. All six semispecies possess P element homologous sequences. We further show that there is conservation of restriction enzyme recognition sites between the D. melanogaster and D. paulistorum P element sequences. The presence of P elements in these two species may clarify the roles of recent invasion and rapid loss in the temporal distribution of P elements in Drosophila.

Role of reverse transcription in the generation of extrachromosomal copia mobile genetic elements.

The Drosophila genetic element copia is one of the best studied eukaryotic transposable sequences. Copia shares structural features with a wide variety of mobile elements in Drosophila, Lepidoptera, yeast and vertebrates, the last class being the retrovirus proviruses. Furthermore, retrovirus-like particles containing copia RNA have been isolated from Drosophila cells and extrachromosomal circular copias with structures closely resembling circular retrovirus proviruses have been isolated and cloned. Therefore, copia-like elements and retroviruses may be members of a class of mobile genetic elements existing throughout the eukaryotic kingdom. Consequently, there has been speculation that retroviruses evolved from transposable elements and, conversely, that copia-like elements transpose as retroviruses or retrovirus-like particles. To date, however, there has been no demonstration that copia RNA is reverse transcribed into copia DNA. The present report describes the isolation of linear extrachromosomal copias whose structure closely resembles the analogous retrovirus provirus linears and whose synthesis is unaffected by inhibitors of the cellular DNA polymerase responsible for chromosomal DNA replication.

Structure and expression of mouse VL30 genes.

DNA sequencing and blot hybridization analyses have been used to study the structure of a mouse VL30 gene and the molecular nature of VL30-related RNA which is induced upon the stimulation of cultured AKR mouse embryo cells with defined peptide growth factors. An integrated mouse VL30 gene was found to contain identical 601-base-pair long terminal repeats (LTRs) which were themselves terminated in short inverted repeats. The entire VL30 gene was flanked by a 4-base-pair direct repeat of cellular DNA. Thus, VL30 genes are structurally analogous to integrated forms of retrovirus proviruses and certain other classes of mobile genetic elements. The LTR sequence was found to contain putative promoter and polyadenylation signals and generally exhibited little sequence homology to murine leukemia virus proviral LTRs. Certain short regions of sequence conservation, however, were evident, including the inverted terminal repeat, LTR-adjacent regions corresponding to origins of murine leukemia virus proviral DNA synthesis, and a 36-base-pair direct repeat bearing homology to the 72-base-pair direct repeat (enhancer sequence) of the murine leukemia virus-related Moloney sarcoma virus. Upon mitogenic stimulation of quiescent cells with epidermal growth factor and insulin, a major 5.5-kilobase VL30-specific RNA complementary to both LTR and non-LTR sequences was rapidly induced. We conclude that a complete VL30 gene(s) is highly regulated by peptide growth factor binding to specific membrane receptors in these cells.

Structure and expression of mouse VL30 genes.

DNA sequencing and blot hybridization analyses have been used to study the structure of a mouse VL30 gene and the molecular nature of VL30-related RNA which is induced upon the stimulation of cultured AKR mouse embryo cells with defined peptide growth factors. An integrated mouse VL30 gene was found to contain identical 601-base-pair long terminal repeats (LTRs) which were themselves terminated in short inverted repeats. The entire VL30 gene was flanked by a 4-base-pair direct repeat of cellular DNA. Thus, VL30 genes are structurally analogous to integrated forms of retrovirus proviruses and certain other classes of mobile genetic elements. The LTR sequence was found to contain putative promoter and polyadenylation signals and generally exhibited little sequence homology to murine leukemia virus proviral LTRs. Certain short regions of sequence conservation, however, were evident, including the inverted terminal repeat, LTR-adjacent regions corresponding to origins of murine leukemia virus proviral DNA synthesis, and a 36-base-pair direct repeat bearing homology to the 72-base-pair direct repeat (enhancer sequence) of the murine leukemia virus-related Moloney sarcoma virus. Upon mitogenic stimulation of quiescent cells with epidermal growth factor and insulin, a major 5.5-kilobase VL30-specific RNA complementary to both LTR and non-LTR sequences was rapidly induced. We conclude that a complete VL30 gene(s) is highly regulated by peptide growth factor binding to specific membrane receptors in these cells.