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Mycoplasmas (class Mollicutes, kingdom Procaryotae) are able to induce large-scale chromosome rearrangements in the infected cells. Repeated DNA sequences including mobile elements (as IS and Tn) turn out to play a considerable part in mutation events of mycoplasmas and host cells.
Sex differentiation provides for testing evolutionary innovations in the male genome before they are transferred to the female genetic system. This is possible with dichronous (asynchronous) evolution, when evolution in males precedes that in females [3-7]. Hence, along with common autosomal genes for stable characters, exclusively male and exclusively female genes must exist. The male genes are already acquired by the male genome but are not yet transferred to the female one. The female genes are already lost by the male genome but still remain in the female genome. They constitute temporary evolutionary genotypic sexual dimorphism. Common genes cannot exhibit genotypic sexual dimorphism; they show only constant phenotypic hormonal sexual dimorphism. On the basis of the interpretation of genotypic sexual dimorphism as a consequence of sex dichronism, the evolutionary role of sex chromatins is clarified and a new concept for them is suggested. According to this concept, the Y chromosome is the "conductor" of ecological information into the genome, the "place of birth" and testing of new genes, the accelerator and regulator of genotypic sexual dimorphism. By contrast, the X chromosome of the heterogametic sex provides the transportation of new genes from the Y chromosome to autosomes. This chromosome stabilizes, relaxes, and suppresses genotypic sexual dimorphism and accumulates genes that will be eliminated. This concept sheds light on many problems: the chromosomal localization of genes and their transfer to other chromosomes, the inactivation of chromosomes, mobile genes, mutation bursts, insertional mutagenesis, the association of the Y chromosome with stress, retroviruses, etc. In particular, it explains why genes "jump," why transpositions of mobile elements depend on ecological stress, why different genes mutate simultaneously, etc.
Mobile genetic elements have been identified in several eukaryotic organisms and some classes have been found to share common structural features with the proviral forms of animal retroviruses. The representatives of this class of mobile elements in the yeast Saccharomyces cerevisiae are called Ty elements, which could be a useful model system for studying the transposition of retrovirus-like elements. Here we have attempted to answer two questions often raised in discussions of the biological importance of transposition: what is the frequency of spontaneous Ty transposition, and are there certain chromosomal regions into which Ty elements preferentially integrate? We chose the LYS2 gene to investigate these questions because it allows direct selection of both mutants and revertants. We have found that 2% of spontaneous lys2 mutants are caused by Ty transposition with a preferential integration into the transcription initiation region.
We isolated a novel halophilic archaeon, strain DSL9, representing the proposed new species Haloliberatus hailidukes gen. nov., sp. nov., from Dishui Lake, China. Unlike most obligate halophiles, DSL9 survives in low salinity, even distilled water, without lysis. Genomic analysis revealed dual salinity adaptation strategies: salt-in and compatible solutes, including a complete trehalose biosynthesis pathway. The strain harbors multiple plasmids, notably a 111,311 bp large plasmid (pHdsl9-3) encoding replication (Orc1/Cdc6, SSB), transcription (TFIIB), transmission (T4SS cluster, ArdC-like protein), and recombination (XerA) modules. pHdsl9-3 provides auxiliary functions such as defense, genome diversification, ion detoxification, and suggests active horizontal gene transfer. Similar elements are widespread in Halobacteriales, highlighting their role in haloarchaeal genetic diversity and plasticity. The encoded XerA hinted at a function beyond DNA dimer resolution, suggesting it may have been adapted by other archaeal mobile genetic elements. These findings underscore the need to investigate plasmid-driven evolution and environmental adaptation mechanisms in haloarchaea.IMPORTANCEThis study reports the isolation and characterization of DSL9, a novel halophilic archaeon from a freshwater lake. Remarkably, DSL9 defies the typical obligate halophilic lifestyle by surviving in low-salinity environments, including distilled water, without cell lysis. A key discovery is the identification of a 111,311 bp large plasmid harboring essential modules for replication, transcription, transmission, and integration. Widespread distribution of similar elements across Halobacteriales suggests their crucial role in haloarchaeal genetic diversity and plasticity, warranting further study of plasmid-mediated evolution and adaptation strategies.
Retrotransposons are mobile genetic elements that have invaded a wide variety of organisms. While these mobile elements share gene homologies and structural features with retroviruses, they have lost the ability to produce infectious particles. Typically these elements are 5-10 kilobases (kb) in length, are conserved in their structural organization and are present in many copies in the genomes into which they have integrated(1). Retrotransposons generally interrupt their host genome promiscuously and thus cause a variety of random effects. In general, their insertion results in mutations, inversions, deletions or rearrangements among host sequences. All of these changes are thought to add to the plasticity of the host genome and thus contribute to a faster pace of evolutionary development. However, because of the random nature of insertions, it has been difficult to attribute any one specific function to these diverse elements. Here, Serap Aksoy describes a newly recognized family of mobile elements that are different from most retrotransposons in that they have the ability to integrate into specific host sequences.
The mobile insertion element IS5 is a relatively small but genetically compact DNA sequence of 1195bp found in variable copy number in the genome of Escherichia coli strains. This study presents a detailed transcript analysis of the population of IS5 elements present in E. coli strains MC4100 and MG1655. The findings indicate that the ins5A gene comprising 978bp is transcribed from its own promoter, which is located close to the right-hand end of the element. The two divergently transcribed genes ins5C and in5B form an operon, and this transcript is fully contained within the borders of the ins5A transcript. Although transcription out of IS5 from element-internal promoters was negligible, in the case of MG1655 a major transcript was found to extend into the insertion element. This suggests that IS5-specific transcription can be influenced by the specific location of the element in the chromosome, the orientation it adopts and the gene it interrupts.
Reverse transcription intermediate forms (minus and plus strong-stop DNA) are detected in Drosophila melanogaster cultured cells for mobile dispersed genetic elements mdg1, mdg3, and mdg4 (gypsy). The mdg elements studied possess a common mechanism of reverse transcription, despite their structural differences, and the comparative analysis of intermediate forms proves that mdg elements pass the same stages of reverse transcription as retroviruses. The length of minus strong-stop DNA that locates the RNA start site coincides with the data obtained from S1 nuclease analysis of transcription initiation. S1 analysis has also revealed that mdg LTRs have a U3-R-U5 structure analogous to that of retroviral LTRs. Transcription of mdg1, mdg3, and mdg4 is initiated within or immediately after the same sequence TCAGTPy. Neither the TATA box nor the CAAT box can be found at their characteristic positions upstream of the 5' ends of mRNAs.
Integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are increasingly recognized to contribute to lateral gene flow in prokaryotes. ICEs, like most temperate bacteriophages integrate into the genome and like conjugative plasmids disseminate by conjugative transfer to new hosts. Thought of schematically, the structure of ICEs is similar to that of other types of the mobile elements; ICEs have a backbone composed of three modules ensuring maintenance, dissemination and regulation. This backbone can acquire additional functions probably through the action of insertion sequences, transposons and specific recombinases. Previously, ICEs were thought of as only vectors for transfer of antibiotic resistance genes, but it is now evident that ICEs can mediate the transfer of a very diverse set of functions. ICEs allow bacteria to rapidly adapt to new environmental conditions and to colonize new niches. Like phages and conjugative plasmids they also likely mediate the transfer of virulence determinants. ICEs shape the bacterial genome, promoting variability between strains of the same species and distributing genes between unrelated bacterial genera. Finally, we propose that by utilizing conserved integration sites, ICEs may promote the mobilization of genomic islands.
The hobo transposable element from Drosophila melanogaster was found to be capable of excision, resulting in donor sites unlike those reported for any other transposable element currently known in animals. These empty sites most closely resemble those left by the transposable elements Ac and Tam3 in Zea mays and Antirrhinum majus, respectively. Like Ac and Tam3, the hobo element was found to function in a distantly related species, in this case the housefly Musca domestica. Hobo excision in M. domestica was found not to require the expression of hobo-encoded transposase but instead appears to be driven by an endogenous hobo transposase-like activity. DNA sequences displaying high homology to the hobo transposase gene were isolated from the genome of M. domestica and appear to be part of a mobile-element system related to hobo, Ac, and Tam3.
Olfactory sensitivity and locomotor activity was assayed in Drosophila melanogaster strains carrying a mutation of the flamenco gene, which controls transposition of the mobile genetic element 4 (MGE4) retrotransposon the gypsy mobile element. A change in olfactory sensitivity was detected. The reaction to the odor of acetic acid was inverted in flies of the mutator strain (MS), which carried the flam mutation and active MGE4 copies and were characterized by genetic instability. Flies of the genetically unstable strains displayed a lower locomotor activity. The behavioral changes in MS flies can be explained by the pleiotropic effect of the flam mutation or by insertion mutations which arise in behavior genes as a result of genome destabilization by MGE4.
To evaluate the prospects for transposon mutagenesis in the autogamous diploid legume Lotus japonicus, the behaviour of the maize transposable element Ac was analysed in the progeny of 38 independent transgenic plants. The conditions for monitoring donor site excision using histochemical localization of beta-glucuronidase activity or the alternative spectinomycin resistance assay were established, and used to follow Ac mobility through two generations. Somatic excision was monitored as variegated cotyledons in the T2 generation and germinal excision events were scored in segregating T3 families as complete beta-glucuronidase-mediated staining of cotyledons or as a fully green spectinomycin-resistant phenotype. Using these assays an average germinal excision frequency of 12% was estimated in the T3 offspring from variegated plants. The fidelity of the excision assays was ascertained by comparing the frequency of germinal excision to the frequency of Ac reinsertion at new positions of the genome. Transposition of Ac in 42% of the plants and detection of the characteristic Ac insertion/excision footprints suggests that insertion mutagenesis with the autonomous maize Activator element is feasible in Lotus japonicus. Parameters influencing Ac behaviour, such as dosage, position effects and modification of the element itself, were also investigated comparing homozygous and hemizygous plants from the same family and by analysing different transformants.
DNA-RNA complexes were detected in cultured Drosophila melanogaster cells. These complexes are practically perfect hybrid molecules of mobile dispersed genes DNA (mdg1 and mdg3) and suitable poly(A)+RNA. Three species of single-stranded DNA have been found in hybrid molecules: full-sized mdg DNA containing either one or two LTRs (both minus strands) and single LTR sequences (plus strand). The properties of hybrid molecules are consistent with those being expected from the model of reverse transcription pathway of transposition and amplification of mdg elements.
Mobile genetic elements have a crucial role in spreading antibiotic resistance genes among bacterial populations. Environmental and genetic factors that regulate conjugative transfer of antibiotic resistance genes in bacterial populations are largely unknown. Integrating conjugative elements (ICEs) are a diverse group of mobile elements that are transferred by means of cell-cell contact and integrate into the chromosome of the new host. SXT is a approximately 100-kilobase ICE derived from Vibrio cholerae that encodes genes that confer resistance to chloramphenicol, sulphamethoxazole, trimethoprim and streptomycin. SXT-related elements were not detected in V. cholerae before 1993 but are now present in almost all clinical V. cholerae isolates from Asia. ICEs related to SXT are also present in several other bacterial species and encode a variety of antibiotic and heavy metal resistance genes. Here we show that SetR, an SXT encoded repressor, represses the expression of activators of SXT transfer. The 'SOS response' to DNA damage alleviates this repression, increasing the expression of genes necessary for SXT transfer and hence the frequency of transfer. SOS is induced by a variety of environmental factors and antibiotics, for example ciprofloxacin, and we show that ciprofloxacin induces SXT transfer as well. Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes.
After six decades of widespread antibiotic use, bacterial pathogens of human and animal origin are becoming increasingly resistant to many antimicrobial agents. Antimicrobial resistance develops through a limited number of mechanisms: (a). permeability changes in the bacterial cell wall/membrane, which restrict antimicrobial access to target sites; (b). active efflux of the antimicrobial from the cell; (c). mutation in the target site; (d). enzymatic modification or degradation of the antimicrobial; and (e). acquisition of alternative metabolic pathways to those inhibited by the drug. Numerous bacterial antimicrobial resistance phenotypes result from the acquisition of external genes that may provide resistance to an entire class of antimicrobials. These genes are frequently associated with large transferable extrachromosomal DNA elements called plasmids, on which may be other mobile DNA elements such as transposons and integrons. An array of different resistance genes may accumulate on a single mobile element, presenting a situation in which multiple antibiotic resistance can be acquired via a single genetic event. The versatility of bacterial populations in adapting to toxic environments, along with their facility in exchanging DNA, signifies that antibiotic resistance is an inevitable biological phenomenon that will likely continue to be a chronic medical problem. Successful management of current antimicrobials, and the continued development of new ones, is vital to protecting human and animal health against bacterial pathogens.
How mobile genetic elements molded eukaryotic genomes is a key evolutionary question that gained wider popularity when mobile DNA sequences were shown to comprise about half of the human genome. Although Saccharomyces cerevisiae does not suffer such "genome obesity", five families of LTR-retrotransposons, Ty1, Ty2, Ty3, Ty4, and Ty5 elements, comprise about 3% of its genome. The availability of complete genome sequences from several Saccharomyces species, including members of the closely related sensu stricto group, present new opportunities for analyzing molecular mechanisms for chromosome evolution, speciation, and reproductive isolation. In this review I present key experiments from both the pre- and current genomic sequencing eras suggesting how Ty elements mediate genome evolution.
IS1999 and a point mutant derivative, IS1999.2, have been described inserted upstream of emerging antibiotic resistance genes bla(VEB-1) and bla(OXA-48). 5' Rapid amplification of cDNA ends experiments revealed that expression of these beta-lactamase genes was driven by the outward-directed promoter, P(out), located in the IS1999 elements. These findings led us to study IS1999-mediated gene mobilization. Thus, the transposition properties of IS1999 and of IS1999-based composite transposons, made of two copies of IS1999 in different orientations, were investigated. IS1999 or IS1999-based composite transposons were capable of transposing onto the conjugative plasmid pOX38-Gen. Sequence analysis of the insertion sites revealed that IS1999 inserted preferentially into DNA targets containing the consensus sequence NGCNNNGCN. Transposition was more efficient when at least one left inverted repeat end was located at an outside end of the transposon. The transposition frequency of IS1999.2 was 10-fold lower than that of IS1999, and transposition frequencies of the putative natural transposon, Tn1999, were below detection limits of our transposition assay. This reduced transposition frequency of IS1999.2-based elements may result from a lower transcription of the transposase gene, as revealed by reverse transcription-PCR analyses.
We describe here two new transposable elements, CemaT4 and CemaT5, that were identified within the sequenced genome of Caenorhabditis elegans using homology based searches. Five variants of CemaT4 were found, all non-autonomous and sharing 26 bp inverted terminal repeats (ITRs) and segments (152-367 bp) of sequence with similarity to the CemaT1 transposon of C. elegans. Sixteen copies of a short, 30 bp repetitive sequence, comprised entirely of an inverted repeat of the first 15 bp of CemaT4's ITR, were also found, each flanked by TA dinucleotide duplications, which are hallmarks of target site duplications of mariner-Tc transposon transpositions. The CemaT5 transposable element had no similarity to maT elements, except for sharing identical ITR sequences with CemaT3. We provide evidence that CemaT5 and CemaT3 are capable of excising from the C. elegans genome, despite neither transposon being capable of encoding a functional transposase enzyme. Presumably, these two transposons are cross-mobilised by an autonomous transposon that recognises their shared ITRs. The excisions of these and other non-autonomous elements may provide opportunities for abortive gap repair to create internal deletions and/or insert novel sequence within these transposons. The influence of non-autonomous element mobility and structural diversity on genome variation is discussed.
Maize Suppressor-mutator (Spm) transposable elements have been introduced into tobacco cells and a visual assay for Spm activity has been developed using a bacterial beta-glucuronidase gene. The Spm element is mobile in tobacco and can trans-activate excision of a transposition-defective Spm (dSpm) element either from a different site on the same transforming Ti plasmid or from a second plasmid. An Spm element expressed from the stronger cauliflower mosaic virus 35S promoter trans-activates transposition of a dSpm element earlier after its introduction into tobacco cells than an element expressed from its own promoter.