Search Results (77)

The genus Siccibacter consists primarily of environmental bacteria, with strains of Siccibacter colletis previously isolated only from plant materials and related environments. This study aims to characterize the first clinical isolate of S. colletis and explore its genomic evolution and clinical relevance. Strain S25242 was isolated from the urine of a 64-year-old male with a severe urinary tract infection. The genome of S25242 is 4.19 Mb, containing 4012 coding sequences, 73 tRNAs, 10 rRNAs, and 38 snRNAs. Phylogenetic and phylogenomic analyses indicated that strain S25242 is closely related to S. colletis type strain 1383^T. The strain shared >70% of digital DNA-DNA hybridization (dDDH) values and >96% of average nucleotide identity (ANI) values with the type strain of S. colletis 1383^T, thereby confirming its taxonomic status. The isolate was susceptible to all 11 tested antimicrobials. Comparative genomics identified 1942 S. colletis-specific genes (including multidrug efflux systems) and 13 unique genes in S25242 related to transposition and DNA integration. This study reports the first clinical isolate of S. colletis, providing evidence that genomic plasticity facilitates its transition from an environmental inhabitant to an opportunistic pathogen. The findings highlight the need for enhanced clinical surveillance of the Siccibacter genus and offer insights into its genomic evolution and clinical adaptation. Full article

I developed a mathematical method to search for DNA regions that are significantly enriched in reverse complement triplets (RCTs) and are located in sequences with strongly expressed triplet periodicity (TP). The method makes it possible to exclude the influence of TP on the number of RCTs. To search for RCTs, I used the difference between triplet frequencies and their expected number, which was determined by taking into account the TP of the analyzed region. I analyzed the genomes of 42 bacteria representing all bacterial phyla, and found that the number of DNA regions containing RCTs ranged from several hundred to several thousand per genome depending on its size. The average length of the region was about 850 DNA bases. The most common inversion symmetry (IS) pattern of the RCT-containing regions was the enrichment of the first, second, and third triplet positions with {A, G}, {A, T}, and {T, C} bases, respectively. When the sequence was rotated 180 degrees and the bases were replaced with complementary ones (IS), such enrichment of triplet positions was preserved. I suggest that the emergence of IS could be a result of evolutionary processes such as inversions, transpositions, and recombinations. Full article

DNA-protecting proteins (Dps) are crucial for safeguarding chromosomal DNA in starved cells during the stationary phase under stressful conditions. In previous research, the two Dps proteins in Deinococcus geothermalis, Dgeo_0257 (Dps3) and Dgeo_0281 (Dps1), were found to complement each other in protecting DNA from oxidative damage. This study investigates the physiological changes and transposition of insertion sequences (ISs) in a double-knockout (DK) mutant lacking both dps genes. Comparisons between the wild-type and mutant strains revealed significant phenotypic differences in viability under oxidative stress conditions induced by hydrogen peroxide and ferrous ions, particularly during the stationary phase. Notably, oxidative stress triggered the transposition of the IS families IS701 and IS5, with IS66 being transposed exclusively in the DK mutant into a gene encoding phytoene desaturase. Transcriptomic analysis using RNA-seq revealed substantial fold changes in gene expression across the genome. For example, the dgeo_1459–1460 gene cluster, which encodes a DUF421 domain-containing protein and a hypothetical protein, was highly upregulated under both oxidative and non-oxidative conditions. Interestingly, catalase, encoded by a single gene in D. geothermalis, was upregulated in the DK mutant during the stationary phase, with expression levels exceeding those observed in the single dps gene-deficient mutants. Conversely, a prominent downregulation of the Fur family regulator was detected. These findings highlight the growth phase-dependent physiological adaptation of the dps-DK mutant and reveal a novel IS transposition event of the ISBst12 group involving the IS66 family. Therefore, this study provides new observations into the influence of DNA-protective protein deficiency on oxidative stress responses and IS transposition in D. geothermalis, as well as the regulatory mechanisms of the catalase induction pathway, raising the need for further investigation into the role of OxyR. Full article

Transposable elements (TEs) are ubiquitous components of plant genomes that profoundly influence plant diversity, adaptation, and genome structure. Transposition of TEs is primarily suppressed by distinct DNA methylation systems. However, the distribution of DNA methylation at the level of individual TEs in plants remains poorly understood. Here, we address this question by generating per-base cytosine methylation maps of individual long terminal repeat retrotransposons (LTR-RTEs) for the large sunflower (Helianthus annuus L.) and the small Arabidopsis thaliana genomes. A. thaliana was selected as the model species, for which genome-wide DNA methylation profiles have been extensively characterized in prior studies. Our analysis revealed significant heterogeneity in methylation patterns both between and within individual LTR-RTE lineages. We also found that the sunflower genes harboring intact or fragmented LTR-RTE insertions exhibit altered DNA methylation and expression profiles, with intact LTR-RTE insertions enriched in stress-response and regulatory pathways. Our interspecies comparison of DNA methylation patterns indicates that methylation patterns are intrinsic features of LTR-RTE lineages, conserved across diverse plant species but influenced by factors such as insertion age, element length, and proximity to genes. Furthermore, we identified epigenetically distinct clusters of Tork and Athila sunflower elements corresponding to separate phylogenetic clades, suggesting a link between epigenetic regulation and the genetic diversity of plant LTR-RTEs. Full article

Mobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their mobilization. To address this question, we examined LTR-RTE activation in Arabidopsis thaliana, Brassica napus, and Nicotiana benthamiana following infection with the RNA viruses Tobacco rattle virus (TRV), Potato virus X (PVX), and Tobacco ringspot virus (TRSV). Nanopore cDNA sequencing revealed virus-specific transcriptional responses, with PVX uniquely triggering a strong transcriptional burst of diverse LTR-RTE families in N. benthamiana. To test the role of viral suppressors of RNA silencing (VSRs) in this process, we analyzed extrachromosomal circular DNA (eccDNA) from plants infected with TRV expressing the VSR P19. This analysis identified eccDNA derived from Ty3/Gypsy Galadriel elements, demonstrating that viral infection can promote not only retrotransposon transcription but also eccDNA production, which may indicate the ability of LTR-RTEs to transpose. These findings clearly illustrate that plant–virus interactions can induce not only changes in gene transcription, but also the activation of multiple retrotransposons, highlighting a potential evolutionary interface linking antiviral defense and transposon regulation. Full article

Background/Objectives: The PB family of “cut-and-paste” DNA transposons shows great promise as genetic manipulation tools while significantly impacting eukaryotic genome evolution. However, their evolutionary profile in beetles (Coleoptera), the most species-rich animal order, remains poorly characterized. Methods: A local tBLASTN search was conducted to mine PiggyBac (PB) transposons across 136 coleopteran insect genomes, using the DDE domain of the PB transposase as the query. Multiple sequence alignment was performed with MAFFT, and a maximum likelihood phylogenetic tree of the transposase DDE domains was constructed using IQ-TREE. Evolutionary dynamics were analyzed by means of K-divergence. Results: Our study reveals PB transposons are widely distributed, highly diverse, and remarkably active across beetles. We detected PB elements in 62 of 136 examined species (45%), classifying them into six distinct clades. A total of 62 PB-containing species harbored intact copies, with most showing recent insertions (K divergence ≈ 0), indicating ongoing transpositional activity. Notably, PB elements from Harmonia axyridis, Apoderus coryli, and Diabrotica balteata exhibit exceptional potential for genetic tool development. Structurally, intact PB elements ranged from 2074 to 3465 bp, each containing a single transposase ORF (500–725 aa). All were flanked by terminal inverted repeats and generated TTAA target site duplications. Conclusions: These findings demonstrate PB transposons have not only shaped historical beetle genome evolution but continue to drive genomic diversification, underscoring their dual significance as natural genome architects and promising biotechnological tools. Full article

Transposable elements (TEs) are major components of plant genomes and play crucial roles in adaptive genome evolution and stress tolerance. Under abiotic stress, activated TEs can generate abundant genetic variation and regulate the expression of stress-responsive genes. As a pioneer species in desert and saline–alkali environments, Tamarix chinensis L. has been little studied with respect to the abundance and evolutionary relationships of its LTR retrotransposons, particularly their activation patterns under salt and alkali stresses. This study aimed to investigate the characteristics of the reverse transcriptase (RT) domain of LTR retrotransposons in T. chinensis and to determine their patterns of activation in response to salt and alkali stresses. A total of 629 Ty1-copia and 607 Ty3-gypsy RT nucleotide sequences, which displayed high AT/GC ratios and evidence of stop codon insertions, were identified in T. chinensis by amplicon sequencing. Among these, 211 Ty1-copia and 117 Ty3-gypsy RT sequences with potential transpositional activity each contained distinct domains, suggesting a high degree of conservation. Phylogenetic analysis revealed that the RT sequences of T. chinensis are closely related to those of mangrove, wild potato, and Ipomoea, and may have undergone horizontal transfer. Expression analysis showed that 634 and 181 RT sequences were activated under salt and alkali stresses, respectively, with the majority belonging to salt-induced Ty1-copia families. Compared with the control group, under salt and alkali stresses, the cTy1-copia elements (Ty1-copia with amplificated from cDNA of T. chinensis, the same below) with dominant abundance were mainly concentrated in the Angela subfamily, while the cTy3-gypsy elements induced by alkali stress were primarily distributed in the Tekay and Reina subfamilies. Furthermore, four cTy1-copia and five cTy3-gypsy were identified as candidate key LTR retrotransposons responsive to salt and alkali stresses. Overall, this study provides new insights into the epigenetic mechanisms underlying the adaptation of T. chinensis to saline and alkali stresses and offers a theoretical basis for its potential applications in saline–alkali land reclamation. Full article

Our understanding of the molecular mechanisms by which DNA meiotic recombination occurs has significantly increased in the past decades. A more representative molecular model has also undergone repeated revisions and upgrades with the continuous expansion of experimental data. Considering several apparent issues in the field, we intend to make necessary upgrades to previous models and reanalyze those data, exploring structural details and molecular mechanisms of DNA meiotic recombination. Eligible studies were identified from PubMed/Medline (up to June 2024). Key related publications and experimental data were retrieved from eligible studies, displaying five major issues. Meanwhile, the biophysical modeling method was used to establish an enlacement model. Then, the model was used to wholly reanalyze the collected data. An updated molecular model was supplemented. In the current model, a copy choice mechanism can initiate DNA meiotic recombination. The copy choice is based on a branched structure of DNA, which results from relative motion between homologous single strands. The reanalysis of previous experimental data based on this model can lead to new interpretations that can better address the discrepancies between previous experimental observations and theoretical models, including (1) the intertwinement model having embodied the particular characteristics of the SDSA model; (2) hDNA arising from JM resolution rather than being followed by a JM; (3) strand specificity of hDNA mismatch repair seeming to be an illusion and copy choice more likely to be the actual state; (4) parity in resolution patterns of a dHJ leading to parity of gene conversion; (5) the cooperation of multiple HJs readily generating a high correlation between gene conversion and crossover; and (6) transpositional recombination and site-specific recombination seeming to have a common pathway to meiotic recombination. The results indicate that both revisions and reanalysis are necessary. The novel interpretations would be critical to the understanding of the mechanisms of DNA recombination as well as its role in DNA repair. Additionally, the work could have implications for how the field views the importance of factors such as Spo11 or the mechanisms that drive meiotic pairing. Full article

Insertion sequence (IS) elements are key drivers of bacterial genome plasticity, yet the overall regulation of their transposition remains poorly understood. This is especially true for the multiple-layer regulation at the donor site, which has been largely overlooked. Using multiple mutation assays, genetic manipulations and reporter genes, this study focuses on characterizing how endogenous DNA sequences, transcriptional and translational factors, and genomic context regulate IS1 transposition from its donor site. Out of six elements within the chromosome of E. coli strain BW25113, IS1A and IS1E (both with the consensus sequence) contribute to over 99.9% of the overall IS1 transposition within the genome while the other four elements without the non-consensus sequence are essentially incapable of transposing. Inducing a ribosomal -1 frameshift at the A₆C motif increases transposition over 1000-fold, but this enhancement is largely reversed by restoring InsA-mediated transcriptional regulation. Strikingly, genomic sequences flanking IS1 elements appreciably modulate transposition by promoting transcription or facilitating formation of transpososomes, a phenomenon that remains under-studied. Finally, IS1 was confirmed to undergo replicative transposition intramolecularly, a mechanism shown here to be independent of transposase levels in the cell. These findings contribute to our understanding of mobile genetic element regulation and potentially offer strategies for mitigating their potentially harmful effects. Full article

R2 retrotransposons reside exclusively within the 28S regions of 10–20% of all rDNA genes comprising the nucleolar organizer loci on the X and Y chromosomes of Drosophila melanogaster. These R2-inserted genes are normally silent and heterochromatic. When expressed, however, the R2 transcript is co-transcribed with the 28S rRNA. Self-cleavage releases a 3.6 kb mature R2 transcript that encodes a single protein with endonuclease and reverse transcriptase activities that facilitate R2 element transposition by target-primed reverse transcription. While we know the molecular details of R2 transposition, we know little about the genetic mechanisms that initiate R2 transcription. Here, we examine R2 expression in wild type versus mutant backgrounds. R2 expression in stage 1–4 wild type egg chambers was variable depending on the stock. R2 expression was silent in wild type stages 5–10 but was consistently active during nurse cell nuclear breakdown in stages 12–13 regardless of the genetic background. Massive R2 expression occurred in stages 5–10 upon loss of Udd, an RNA Pol I transcription factor. Similarly, loss of Nopp140, an early ribosome assembly factor, induced R2 expression more so in somatic tissues. Interestingly, over-expression of the Nopp140-RGG isoform but not the Nopp140-True isoform induced R2 expression in larval somatic tissues, suggesting Nopp140-RGG could potentially affect rDNA chromatin structure. Conversely, Minute mutations in genes encoding ribosomal proteins had minor positive effects on R2 expression. We conclude that R2 expression is largely controlled by factors regulating RNA Pol I transcription and early ribosome assembly. Full article

Retroviruses insert DNA copies of themselves into the chromosomes of their hosts forming proviruses that can synthesize new transmissible viruses. Exogenous retroviruses (XRVs) insert into the DNA of somatic cells and are transmitted infectiously. Endogenous retroviruses (ERVs) become inserted in the DNA of germline cells and are transmitted genetically. ERVs can spread through the genome by transposition. ERVs originate from an initial copy of an XRV inserted into the genome of an organism infected by the XRV. Many XRVs are transmitted maternally as well as horizontally; therefore, we consider the effect of maternal transmission on the evolution of virulence of an XRV. Our model shows that the XRV either evolves high virulence with low maternal transmission, or vice versa. We then consider the spread of ERV genes in conjunction with the infectious spread of an XRV. Beginning from a single copy of an ERV, we calculate the probability that it spreads to fixation (i.e., the state where all individuals contain ERV genes). This depends on its virulence and transposition rate. If the XRV is present, the fixation probability also depends on the virulence of the XRV and whether the ERV provides resistance to the XRV. An ERV with only a small deleterious effect on host fitness has a high fixation probability, particularly if it provides resistance to the XRV. We also show that, if an ERV does not spread to fixation, it can still cause elimination of the XRV, with the end result that the population is cleared of both XRV and ERV. Full article

Long interspersed element-1 (LINE-1) is the only active autonomous transposon comprising about 17% of human genomes. LINE-1 transposition can cause the mutation and rearrangement of the host’s genomic DNA. The host has, therefore, developed multiple mechanisms to restrict LINE-1 mobility. Here, we report that SLFN11, a member of the Schlafen family, can restrict LINE-1 retrotransposition, and the inhibitory activity requires its helicase domain. Mechanistically, SLFN11 specifically binds to the LINE-1 5′ untranslated region (5′UTR) and blocks RNA polymerase II recruitment, thereby suppressing its transcription. Furthermore, SLFN11 promotes heterochromatinization, suggesting an epigenetic inhibition pathway. Full article

We investigated overlapping dispersed repeats (DRs) on the plus and minus DNA strands in 12 bacterial genomes. The use of the iterative procedure method (IP method) without taking into account insertions or deletions of nucleotides allowed speeding up the calculations by several times and increased the number of the identified DRs by 10–20%. Most of the DRs were found in the known bacterial genes. The intersection regions of the bacterial DRs contained reverse complement codons. Calculation of triplet periodicity matrices mt(i,j) (i is the position in the codon and j is the nucleotide) was performed for the intersection regions. Two classes of matrices in which the number of nucleotides was significantly greater than in random sequences were revealed: the first contained mt(1,G), mt(2,A), mt(2,T), and mt(3,C) cells and the second mt(1,G), mt(2,C), mt(3,A), and mt(3,T) cells. These classes included 10 and 2 bacterial genomes, respectively. The reverse complement transformation of the DR intersection regions preserved the cells in both classes, although cyclic matrix shifting to the right by one base was observed in the second class. The reverse complement codons in the DR intersection regions on the plus and minus DNA strands could represent sites of more frequent inversions/transpositions or participate in the formation of secondary/tertiary mRNA structures. Full article

DNA metabolism consists of crucial processes occurring in all living cells. These processes include various transactions, such as DNA replication, genetic recombination, transposition, mutagenesis, and DNA repair. While it was initially assumed that these processes might occur in the cytoplasm of prokaryotic cells, subsequent reports indicated the importance of the cell membrane in various DNA transactions. Furthermore, newly identified factors play significant roles in regulating DNA-related cellular processes. One such factor is the Hfq protein, originally discovered as an RNA chaperone but later shown to be involved in several molecular mechanisms. These include DNA transactions and interaction with the cell membrane. Recent studies have suggested that Hfq plays a role in the regulation of DNA replication, mutagenesis, and recombination. In this narrative review, we will focus on the importance of membranes in DNA transactions and discuss the potential role of Hfq-mediated regulation of these processes in Escherichia coli, where the protein is the best characterized. Special attention is given to the affinity of this small protein for both DNA and membranes, which might help explain some of the findings from recent experiments. Full article