Host Genome Research Articles

Structures, mechanisms, and kinetic advantages of the SgrAI filament forming mechanism.

This review documents investigations leading to the unprecedented discovery of filamentation as a mode of enzyme regulation in the type II restriction endonuclease SgrAI. Filamentation is defined here as linear or helical polymerization of a single enzyme as occurs for SgrAI, and has now been shown to occur in many other enzyme systems, including conserved metabolic enzymes. In the case of SgrAI, filamentation activates the DNA cleavage rate by up to 1000-fold and also alters the enzyme's DNA sequence specificity. The investigations began with the observation that SgrAI cleaves two types of recognition sequences, primary and secondary, but cleaves the secondary sequences only when present on the same DNA as at least one primary. DNA cleavage rate measurements showed how the primary sequence is both a substrate and an allosteric effector of SgrAI. Biophysical measurements indicated that the activated form of SgrAI, stimulated by binding to the primary sequence, consisted of varied numbers of the SgrAI bound to DNA. Structural studies revealed the activated state of SgrAI as a left-handed helical filament which stabilizes an altered enzyme conformation, which binds a second divalent cation in the active site. Efforts to determine the mechanism of DNA sequence specificity alteration are ongoing and current models are discussed. Finally, global kinetic modeling of the filament mediated DNA cleavage reaction and simulations of in vivo activity suggest that the filament mechanism evolved to rapidly cleave invading DNA while protecting the Streptomyces host genome.

Tannic acid reactivates HIV-1 latency by mediating CBX4 degradation.

HIV-1 can integrate viral DNA into host cell chromosomes and establish a long-term stable latent viral reservoir, a major obstacle in curing HIV-1 infection. The reactivation of latent proviruses with latency-reversing agents (LRAs) is a prerequisite for the eradication of viral reservoirs. Previous reports have shown that tannic acid (TA) exerts several biological functions, including antioxidant and antitumor activities. Here, we identified a novel function of TA as a reactivator of HIV-1 latency. TA showed similar features to the HIV-1 transactivator of transcription (Tat) and was able to reactivate a larger number of proviruses from various integration sites. TA also showed a strong synergistic effect with other LRAs acting on different signaling pathways. Further studies revealed that the polycomb repressive complex 1 component, chromobox protein homolog 4 (CBX4), is specifically degraded by TA through ubiquitination. CBX4 is associated with the tri-methylation at lysine 27 of histone H3 (H3K27me3) which was enriched on HIV-1 long terminal repeat regions. The TA-induced CBX4 degradation decreased the H3K27me3 enrichment and subsequently enhanced the transcriptional activity of the integrated proviruses. These results suggest that TA is an efficient LRA aiming to a new target for HIV-1 latency, which could be developed to eradicate latent proviruses.IMPORTANCEHIV-1 remains a global health challenge, with its ability to integrate into the host genome and evade the effects of drugs. To overcome this obstacle, the "shock and kill" strategy was proposed, targeting the reactivation of latent HIV-1 for subsequent eradication through antiretroviral medication and immune system reinforcement. Here, we found a new reactivator for HIV-1 latency, tannic acid (TA), which can reactivate HIV-1 latency widely and deeply. Moreover, we demonstrated that TA could promote the interaction between the polycomb repressive complex 1 component CBX4 and the E3 ubiquitin ligase cullin 4A (CUL4A), resulting in CBX4 degradation through the ubiquitin-proteasome system. These events reduce H3K27me3 enrichment in the HIV-1 long terminal repeat region, thereby promoting HIV-1 transcription and ultimately reactivating HIV-1 latent infection. Our work may facilitate the identification of new latency-reversing agents and provide more theoretical evidence for the molecular mechanism of HIV-1 latency.

Repeat competition and ecological shifts drive the evolution of the mobilome in Rhynchospora Vahl. (Cyperaceae), the holocentric beaksedges.

Genomic changes triggered by polyploidy, chromosomal rearrangements, and/ or environmental stress are among factors that affect the activity of mobile elements, particularly Long Terminal Repeats Retrotransposons (LTR-RTs) and DNA transposons. Because these elements can proliferate and move throughout host genomes, altering the genetic, epigenetic and nucleotypic landscape, they have been recognized as a relevant evolutionary force. Beaksedges (Rhynchospora) stand out for their wide cosmopolitan distribution, high diversity (~400 spp.) and holocentric chromosomes related to high karyotypic diversity and a centromere-specific satDNA Tyba. This makes the genus an interesting model to investigate the interactions between repetitive elements, phylogenetic relationships, and ecological variables. Here, we used comparative phylogenetic methods to investigate the forces driving the evolution of the entire set of mobile elements (mobilome) in the holocentric genus Rhynchospora. We statistically tested the impact of phylogenetic relationships, abundance of holocentromeric satDNA Tyba, diversity of repeatome composition, ecological variables, and chromosome number in mobile element diversification. Tyba abundance was found to be inversely correlated with LTR-RT content. Decrease of LTR abundance and diversity was also related to increase in chromosome number (likely due to fission events), and colonization of dry environments in the northern hemisphere. In contrast, we found constant LTR insertions throughout time in species with lower chromosome numbers in rainier environments in South America. A multivariate model showed that different traits drive LTR abundance, especially repeat diversity and Tyba abundance. Other mobile elements, such as non-LTR RTs and DNA transposons had insufficient abundance to be included in our models. Our findings suggest that LTR evolution is strongly impacted by the holocentric characteristics of Rhynchospora chromosomes, correlating with species diversification and biome shifts, and supporting a holokinetic drive model of evolution and a competitive scenario with Tyba. Altogether, our results present evidence of multi-trait influence on LTR-RT dynamics and provide a broader understanding of TE evolution in a macroevolutionary context.

Genetic Variants Influence the Severity of Oral Mucositis in Pediatric Osteosarcoma Patients.

The variability in patients' risk of oral mucositis (OM) has been, in part, attributed to differences in host genomics. The aim better define the role of genomics as an OM risk by investigating the association between genetic variants and the presence and severity of OM in pediatric patients with osteosarcoma (OS) undergoing chemotherapy (CT). A longitudinal observational retrospective study was conducted. Severity of OM was assessed daily using World Health Organization (WHO) criteria. Blood samples were collected, and DNA was extracted. 54 coding regions were analyzed for 17 candidate genes using next-generation sequencing. A total of 164 CT cycles were evaluated in 14 pediatric patients being treated for OS with HDMTX (66.9%) and doxorubicin + cisplatin (34.1%). OM was diagnosed in 129 cycles (78.7%). Whereas the presence of OM was associated with ABCA3 (rs13332514) in HDMTX cycles, OM severity was associated with ABCC2 (rs2273697) in multivariate analysis. In doxorubicin + cisplatin, genetic variants of ABC family genes (ABCC2 and ABCC6) were associated with OM in multivariate analysis. Oral mucositis risk and severity in a pediatric population being treated for OS with HDMTX, doxorubicin, and cisplatin were associated with genes in the ABC family (ABCA3, ABCC2, and ABCC6 genes).

Correction to: Genetic Risk, Dysbiosis, and Treatment Stratification Using Host Genome and Gut Microbiome in Inflammatory Bowel Disease.

Correction to: Genetic Risk, Dysbiosis, and Treatment Stratification Using Host Genome and Gut Microbiome in Inflammatory Bowel Disease.

Complete genomes of common bacterial hosts of RNA bacteriophage Φ6.

Bacterial plant pathogens Pseudomonas savastanoi pv. phaseolicola, P. syringae pv. tomato, P. syringae pv. atrofaciens, and P. oleovorans East River isolate A serve as common laboratory hosts for bacteriophage Φ6, a widely used model organism for enveloped viruses. Here, we report complete genome sequences for strains of these bacterial hosts.

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.

Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.

Human immunodeficiency virus-1 induces host genomic R-loops and preferentially integrates its genome near the R-loop regions

Although HIV-1 integration sites favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites has shown that the virus can integrate into a variety of host genomic locations, including non-genic regions. The invisible infection by HIV-1 integrating into non-genic regions, challenging the traditional understanding of HIV-1 integration site selection, is more problematic because they are selected for preservation in the host genome during prolonged antiretroviral therapies. Here, we showed that HIV-1 integrates its viral genome into the vicinity of R-loops, a genomic structure composed of DNA-RNA hybrids. VSV-G-pseudotyped HIV-1 infection initiates the formation of R-loops in both genic and non-genic regions of the host genome and preferentially integrates into R-loop-rich regions. Using a HeLa cell model that can independently control transcriptional activity and R-loop formation, we demonstrated that the exogenous formation of R-loops directs HIV-1 integration-targeting sites. We also found that HIV-1 integrase proteins physically bind to the host genomic R-loops. These findings provide novel insights into the mechanisms underlying retroviral integration and the new strategies for antiretroviral therapy against HIV-1 latent infection.

Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology

BackgroundBlood cultures are essential for diagnosing bloodstream infections, but current phenotypic tests for antimicrobial resistance (AMR) provide limited information. Oxford Nanopore Technologies introduces nanopore sequencing with adaptive sampling, capable of real-time host genome depletion, yet its application directly from blood cultures remains unexplored. This study aimed to identify pathogens and predict AMR using nanopore sequencing.MethodsIn this cross-sectional genomic study, 458 positive blood cultures from bloodstream infection patients in central Taiwan were analyzed. Parallel experiments involved routine microbiologic tests and nanopore sequencing with a 15-h run. A bioinformatic pipeline was proposed to analyze the real-time sequencing reads. Subsequently, a comparative analysis was performed to evaluate the performance of species identification and AMR prediction.ResultsThe pipeline identified 76 species, with 88 Escherichia coli, 74 Klebsiella pneumoniae, 43 Staphylococcus aureus, and 9 Candida samples. Novel species were also discovered. Notably, precise species identification was achieved not only for monomicrobial infections but also for polymicrobial infections, which was detected in 23 samples and further confirmed by full-length 16S rRNA amplicon sequencing. Using a modified ResFinder database, AMR predictions showed a categorical agreement rate exceeding 90% (3799/4195) for monomicrobial infections, with minimal very major errors observed for K. pneumoniae (2/186, 1.1%) and S. aureus (1/90, 1.1%).ConclusionsNanopore sequencing with adaptive sampling can directly analyze positive blood cultures, facilitating pathogen detection, AMR prediction, and outbreak investigation. Integrating nanopore sequencing into clinical practices signifies a revolutionary advancement in managing bloodstream infections, offering an effective antimicrobial stewardship strategy, and improving patient outcomes.

Signature of viral fossils: a comparative genomics approach to understand the diversity of endogenous retroviruses in bats

Endogenous retroviruses (ERVs) are traces of past viral infections commonly found in vertebrate genomes. Many ERVs are tightly regulated by the host genomes and co-opted for various functions within the hosts. Bats are the only true volant mammals, with the smallest mammalian genomes and a high fraction of ERVs within the genomes. They are important hosts for various zoonotic viral pathogens and can effectively modulate their immune response to tolerate viral infections. Integrations of retroviruses have been implicated as one of the mechanisms by which bats have co-evolved strategies to combat viral infections. In this study, we investigated the diversity of ERVs in over 40 publicly available bat genomes to understand the distribution and the evolution of ERVs within bats. We observed all classes of ERVs within bat genomes including even the complex lenti retroviruses. Alpha and spuma retroviruses which are generally considered rare in mammals, were common within bats. We observed a positive correlation between bat genome size and length of ERV elements. Interestingly, nearly 30 % of the ERVs within bats are intact suggesting a recent origin or co-option by the host genome. Future studies focusing on comparative genomic and experimental data will be critical to understand the role of these ERVs in host genome evolution.

Unlocking the Potential of CMP Synthesis: Merging Enzyme Design, Host Genome Editing, and Fermentation Optimization Strategy

Unlocking the Potential of CMP Synthesis: Merging Enzyme Design, Host Genome Editing, and Fermentation Optimization Strategy

WITHDRAWN: Mechanism of genome editing tools and their application on genetic inheritance disorders

In the fields of medicine and bioscience, gene editing is increasingly recognized as a promising therapeutic approach for treating pathogenic variants in humans and other living organisms. With advancements in technology and knowledge, it is now understood that most genetic defects are caused by single-base pair variants. The ability to substitute genes using genome editing tools enables scientists and doctors to cure genetic diseases and disorders. Starting with CRISPR/Cas, the technology has evolved to become more efficient and safer, leading to the development of Base and Prime Editors. Furthermore, various approaches are used to treat genetic disorders such as Hemophilia, Cystic Fibrosis, and Duchenne Muscular Dystrophy. As previously mentioned, most genetic defects leading to specific diseases are caused by single base pair variants, which can occur at many locations in corresponding gene, potentially causing the same disease. This means that, even when using the same genome editing tool, results in terms of editing efficiency or treatment effectiveness may differ. Therefore, different approaches may need to be applied to different types of diseases. Prevalently, due to the safety of AAV vectors in gene therapy, most clinical trials of gene therapy are based on AAV delivery methods. However, despite their safety and non-integration into the host genome, their limitations, such as confined capacity, dosage-dependent viral toxicity, and immunogenicity, necessitate the development of new approaches to enhance treatment effects. This review provides the structure and function of each CRISPR-based gene editing tool and focuses on introducing new approaches in gene therapy associated with improving treatment efficiency.

Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis

Infectious disease is the result of interactions between host and pathogen and can depend on genetic variations in both. We conduct a genome-to-genome study of paired human and Mycobacterium tuberculosis genomes from a cohort of 1556 tuberculosis patients in Lima, Peru. We identify an association between a human intronic variant (rs3130660, OR = 10.06, 95%CI: 4.87 − 20.77, P = 7.92 × 10−8) in the FLOT1 gene and a subclavaluee of Mtb Lineage 2. In a human macrophage infection model, we observe hosts with the rs3130660-A allele exhibited stronger interferon gene signatures. The interacting strains have altered redox states due to a thioredoxin reductase mutation. We investigate this association in a 2020 cohort of 699 patients recruited during the COVID-19 pandemic. While the prevalence of the interacting strain almost doubled between 2010 and 2020, its infection is not associated with rs3130660 in this recent cohort. These findings suggest a complex interplay among host, pathogen, and environmental factors in tuberculosis dynamics.

Conservative taxonomy and quality assessment of giant virus genomes with GVClass

Large double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant Viruses; GVs) are the largest known viruses, infecting various eukaryotic hosts, particularly protists and algae. These viruses impact biogeochemical cycles and host genome evolution but are challenging to identify and classify due to their complex genomes. We present GVClass, a tool for identifying giant viruses in sequence data, providing taxonomic assignments, and estimating genome completeness and contamination. GVClass employs optimized gene calling and a conservative approach using consensus single-protein phylogenies for robust taxonomic classification, relying on highly conserved orthologous groups. Benchmarking demonstrates over 90% accuracy at the genus-level and >99% at higher taxonomic ranks. GVClass addresses classification challenges and is available as a standalone tool and integrated into the Integrated Microbial Genomes/Virus database (IMG/VR).

Rewired chromatin structure and epigenetic gene dysregulation during HTLV-1 infection to leukemogenesis.

Human T-cell leukemia virus type 1 (HTLV-1) broadly impacts host genes, affecting the infected cell population and inducing the development of a disease with a poor prognosis, adult T-cell leukemia-lymphoma (ATL). This study aimed to provide a comprehensive epigenomic characterization of the infected cell population and evaluated the transcriptome and chromatin structures of peripheral blood cells in HTLV-1-infected individuals using RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq). The infected cells showed significant changes in gene expression patterns from the polyclonal stage and before ATL onset while demonstrating similarities to tumor-forming ATL cells. These similarities were a result of large-scale open chromatin changes, supporting the independent early formation of epigenomic aberrations as an underlying mechanism for later clonal propagation. This study also demonstrated that HTLV-1 Tax directly affects the host chromatin structure, thereby developing fundamental epigenomic characteristics. Several Tax target genes, including the RASGRP3-ERK pathway, were recognized, indicating an impact on signaling pathways. This genome-wide variability in chromatin structural property is a novel feature of HTLV-1 infection and may contribute to pathogenic mechanisms. In addition, it has crucial implications for better understanding the impact of HTLV-1 on the host genome and identifying novel therapeutic targets.

Characterization and genomic analysis of bacteriophage VT223 infecting Salmonella enterica subsp enterica serovar Enteritidis

Bacteriophages are increasingly considered a promising alternative to antibiotics for treating bacterial infections. For the bacteriophage VT223, which was isolated from shrimp pond wastewater, a thorough analysis of its host range, morphology, and genome sequencing was performed. Bacteriophage VT223 exhibits high specificity towards Salmonella spp. strains, highlighting its potential as a targeted therapy for Salmonella spp. infections. Electron microscopy revealed that VT223 belongs to the Caudoviricetes, Jerseyvirus, with an icosahedral head and a non-contractile tail. This phage can infect three species within the Salmonella spp., with a short latent period of 30 minutes and a burst size of 446 PFU/infected cells. Genome sequencing revealed a 43,062 bp double-stranded DNA genome with a GC content of 49.6%. Stability tests showed that VT223 is stable over various temperatures and pH levels. Biofilm formation inhibition testing revealed that phage VT223 reduced biofilm by up to 57.7% after a four-hour treatment. In vitro studies demonstrated the lytic activity of VT223 against Salmonella enterica subsp enterica serovar Enteritidis ATCC 49223. These findings provide valuable insights into the biological properties of bacteriophage VT223 and its potential use as a biocontrol agent in livestock production and aquaculture to combat bacterial growth. Published on November 15, 2024

Impact of endogenous viral elements on glioma clinical phenotypes by inducing OCT4 in the host.

Endogenous viral elements (EVEs) are viral sequences integrated within the host genome that can influence gene regulation and tumor development. While EVEs have been implicated in cancer, their role in regulating key transcription factors in glioblastoma (GBM) remains underexplored. This study investigates the relationship between EVEs and the activation of OCT4, a critical transcription factor in GBM progression. We utilized CancerHERVdb and HervD Atlas databases to identify potential interactions between EVEs and key genes involved in GBM. Data from 273 GBM patient samples in the TCGA database were analyzed to examine the correlation between OCT4 expression and mutations in glioma-related genes. Furthermore, glioblastoma stem cells (GSCs) were assessed for the expression levels of OCT4 and SOX2, and Pearson correlation analysis was performed. Our analysis revealed that OCT4 is a pivotal gene activated by EVEs in GBM. OCT4 expression was significantly correlated with mutations in key glioma-associated genes. Higher OCT4 levels were associated with poorer patient prognosis, higher tumor grades, and older age. Additionally, GSCs exhibited elevated expression of both OCT4 and SOX2, with a positive correlation observed between these two genes in GBM patients. This study highlights the potential role of EVEs in driving GBM progression through the activation of OCT4. The findings emphasize the importance of OCT4 in GBM malignancy and suggest that targeting EVE-mediated pathways may provide new therapeutic approaches for GBM treatment.

From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs.

Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE-1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause-effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non-coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non-coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.

Refining dual RNA-seq mapping: sequential and combined approaches in host-parasitic plant dynamics.

Transcriptional profiling in host plant-parasitic plant interactions is challenging due to the tight interface between host and parasitic plants and the percentage of homologous sequences shared. Dual RNA-seq offers a solution by enabling in silico separation of mixed transcripts from the interface region. However, it has to deal with issues related to multiple mapping and cross-mapping of reads in host and parasite genomes, particularly as evolutionary divergence decreases. In this paper, we evaluated the feasibility of this technique by simulating interactions between parasitic and host plants and refining the mapping process. More specifically, we merged host plant with parasitic plant transcriptomes and compared two alignment approaches: sequential mapping of reads to the two separate reference genomes and combined mapping of reads to a single concatenated genome. We considered Cuscuta campestris as parasitic plant and two host plants of interest such as Arabidopsis thaliana and Solanum lycopersicum. Both tested approaches achieved a mapping rate of ~90%, with only about 1% of cross-mapping reads. This suggests the effectiveness of the method in accurately separating mixed transcripts in silico. The combined approach proved slightly more accurate and less time consuming than the sequential approach. The evolutionary distance between parasitic and host plants did not significantly impact the accuracy of read assignment to their respective genomes since enough polymorphisms were present to ensure reliable differentiation. This study demonstrates the reliability of dual RNA-seq for studying host-parasite interactions within the same taxonomic kingdom, paving the way for further research into the key genes involved in plant parasitism.

Towards development of the 4c-based method detecting interactions of plasmid dna with host genome

Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.