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Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level.Genes Oct 2020Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient... (Review)
Review
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
Topics: Biofilms; DNA, Bacterial; Drug Resistance, Bacterial; F Factor; Fimbriae, Bacterial; Gene Transfer, Horizontal; Gram-Negative Bacteria
PubMed: 33105635
DOI: 10.3390/genes11111239 -
International Journal of Molecular... Jul 2021Spinal muscular atrophy (SMA) is a leading genetic cause of infant death worldwide that is characterized by loss of spinal motor neurons leading to muscle weakness and... (Review)
Review
Spinal muscular atrophy (SMA) is a leading genetic cause of infant death worldwide that is characterized by loss of spinal motor neurons leading to muscle weakness and atrophy. SMA results from the loss of () gene but retention of its paralog . The copy numbers of and are variable within the human population with copy number inversely correlating with SMA severity. Current therapeutic options for SMA focus on increasing expression and alternative splicing so as to increase the amount of SMN protein. Recent work has demonstrated that not all , or genes are equivalent and there is a high degree of genomic heterogeneity with respect to the genes. Because SMA is now an actionable disease with being the primary target, it is imperative to have a comprehensive understanding of this genomic heterogeneity with respect to hybrid - genes generated by gene conversion events as well as partial deletions of the genes. This review will describe this genetic heterogeneity in SMA and its impact on disease phenotype as well as therapeutic efficacy.
Topics: Genetic Therapy; Genetic Variation; Humans; Molecular Targeted Therapy; Muscular Atrophy, Spinal; Survival of Motor Neuron 1 Protein; Survival of Motor Neuron 2 Protein
PubMed: 34360669
DOI: 10.3390/ijms22157896 -
Biomedicines Jan 2022Epidermolysis bullosa (EB) is a group of genetic blistering diseases characterized by mechanically fragile skin and mucocutaneous involvement. Historically, disease... (Review)
Review
Epidermolysis bullosa (EB) is a group of genetic blistering diseases characterized by mechanically fragile skin and mucocutaneous involvement. Historically, disease management has focused on supportive care. The development of new genetic, cellular, and recombinant protein therapies has shown promise, and this review summarizes a unique gene and cell therapy phenomenon termed revertant mosaicism (RM). RM is the spontaneous correction of a disease-causing mutation. It has been reported in most EB subtypes, some with relatively high frequency, and has been observed in both keratinocytes and fibroblasts. RM manifests as identifiable patches of unaffected, blister-resistant skin and can occur through a variety of molecular mechanisms, including true back mutation, intragenic crossover, mitotic gene conversion, and second-site mutation. RM cells represent a powerful autologous platform for therapy, and leveraging RM cells as a therapeutic substrate may avoid the inherent mutational risks of gene therapy/editing. However, further examination of the genomic integrity and long-term functionality of RM-derived cells, as well in vivo testing of systemic therapies with RM cells, is required to realize the full therapeutic promise of naturally occurring RM in EB.
PubMed: 35052793
DOI: 10.3390/biomedicines10010114 -
Frontiers in Endocrinology 2022Congenital adrenal hyperplasia (CAH) secondary to 21-hydroxylase deficiency is an autosomal recessive disorder. The 21-hydroxylase enzyme P450c21 is encoded by the gene... (Review)
Review
Congenital adrenal hyperplasia (CAH) secondary to 21-hydroxylase deficiency is an autosomal recessive disorder. The 21-hydroxylase enzyme P450c21 is encoded by the gene located on chromosome 6p21.33 within the HLA major histocompatibility complex. This locus also contains the , a non-functional pseudogene, that is highly homologous to the gene. Other duplicated genes are and , that encode two isoforms of complement factor C4, the gene that encodes a serine/threonine protein kinase, and the gene that, encodes the extracellular matrix glycoprotein tenascin-X (TNX). TNX plays a role in collagen deposition by dermal fibroblasts and is expressed in the dermis of the skin and the connective tissue of the heart and skeletal muscle. During meiosis, misalignment may occur producing large gene deletions or gene conversion events resulting in chimeric genes. Chimeric recombination may occur between and Three chimeras have been described that differ in the junction site (CH1 to CH3) and result in a contiguous and gene deletion, causing CAH-X syndrome. deficiency is associated with Ehlers Danlos syndrome (EDS). EDS comprises a clinically and genetically heterogeneous group of connective tissue disorders. As molecular analysis of the gene is challenging, the TNX-deficient type EDS is probably underdiagnosed. In this minireview, we will address the different strategies of molecular analysis of the -gene, as well as copy number variations and genetic status of in different cohorts. Furthermore, clinical features of EDS and clinical recommendations for long-term follow-up are discussed.
Topics: Adrenal Hyperplasia, Congenital; Chimera; Collagen; DNA Copy Number Variations; Ehlers-Danlos Syndrome; Female; Humans; Male; Mutation; Steroid 21-Hydroxylase; Tenascin
PubMed: 35282436
DOI: 10.3389/fendo.2022.803226 -
Molecular Therapy : the Journal of the... Jan 2020Adult mammalian brains have largely lost neuroregeneration capability except for a few niches. Previous studies have converted glial cells into neurons, but the total...
Adult mammalian brains have largely lost neuroregeneration capability except for a few niches. Previous studies have converted glial cells into neurons, but the total number of neurons generated is limited and the therapeutic potential is unclear. Here, we demonstrate that NeuroD1-mediated in situ astrocyte-to-neuron conversion can regenerate a large number of functional new neurons after ischemic injury. Specifically, using NeuroD1 adeno-associated virus (AAV)-based gene therapy, we were able to regenerate one third of the total lost neurons caused by ischemic injury and simultaneously protect another one third of injured neurons, leading to a significant neuronal recovery. RNA sequencing and immunostaining confirmed neuronal recovery after cell conversion at both the mRNA level and protein level. Brain slice recordings found that the astrocyte-converted neurons showed robust action potentials and synaptic responses at 2 months after NeuroD1 expression. Anterograde and retrograde tracing revealed long-range axonal projections from astrocyte-converted neurons to their target regions in a time-dependent manner. Behavioral analyses showed a significant improvement of both motor and cognitive functions after cell conversion. Together, these results demonstrate that in vivo cell conversion technology through NeuroD1-based gene therapy can regenerate a large number of functional new neurons to restore lost neuronal functions after injury.
Topics: Action Potentials; Animals; Astrocytes; Basic Helix-Loop-Helix Transcription Factors; Brain Ischemia; Cellular Reprogramming; Dependovirus; Disease Models, Animal; Genetic Therapy; Male; Mice; Mice, Transgenic; Nerve Degeneration; Neuroglia; Neurons; Rats; Rats, Sprague-Dawley; Treatment Outcome
PubMed: 31551137
DOI: 10.1016/j.ymthe.2019.09.003 -
International Journal of Biological... 2023Fatty acid oxidation (FAO) is a major alternate energy metabolism pathway in tumor cells subjected to metabolic stress caused by glucose deficiency during rapid...
Fatty acid oxidation (FAO) is a major alternate energy metabolism pathway in tumor cells subjected to metabolic stress caused by glucose deficiency during rapid progression. However, the mechanism of metabolic reprogramming between glycolysis and FAO in tumor cells is unknown. Therefore, identifying the metabolic glucolipid conversion hub in tumor cells is crucial. We used single-cell RNA sequencing (scRNA-Seq), RNA sequencing (RNA-Seq), The Cancer Genome Atlas (TCGA), and chromatin immunoprecipitation sequencing (ChIP-Seq) to predict the critical regulator and mechanism of metabolic glucolipid conversion in colorectal cancer (CRC) tumor cells. We used Seahorse metabolic analysis, immunoblotting, immunofluorescence, and immunohistochemical (IHC) technology to verify the prediction and mechanism of this regulator in cancer cell lines, a nude mouse xenograft model, and clinical CRC samples. We demonstrated that sirtuin-1 (SIRT1) was upregulated in CRC cells in response to glucose deprivation and oxidative stress. SIRT1 was also a hub of metabolic glucolipid conversion. SIRT1 upregulation deacetylated β-catenin, translocated it from the nucleus to the cytoplasm, attenuated glycolysis, and was positively correlated with fatty acid oxidation (FAO). Clinical analysis of SIRT1 expression in tumor tissues showed the SIRT1 profile was associated with poor prognosis in CRC patients. SIRT1 interference therapy significantly suppressed tumors in the mouse xenograft model. In hostile, glucose-deficient TMEs, SIRT1 is upregulated, and CRC cells transform the Warburg phenotype to FAO. SIRT1 indicates the frequency of glucolipid transformation and rapid tumor progression and is a promising therapeutic target of CRC.
Topics: Humans; Mice; Animals; Cell Line, Tumor; Colorectal Neoplasms; Sirtuin 1; Glucose; Fatty Acids; Gene Expression Regulation, Neoplastic; Cell Proliferation
PubMed: 37063423
DOI: 10.7150/ijbs.76704 -
HGG Advances Apr 2022Paralogs and pseudogenes are abundant within the human genome, and can mediate non-allelic homologous recombination (NAHR) or gene conversion events. The locus contains...
Paralogs and pseudogenes are abundant within the human genome, and can mediate non-allelic homologous recombination (NAHR) or gene conversion events. The locus contains three paralogs situated in tandem, and is therefore prone to NAHR-mediated deletions and duplications associated with severe neurological phenotypes. To study this locus further, we aimed to generate biallelic loss-of-function variants in by CRISPR/Cas9 genome editing. Unexpectedly, two of the generated clones underwent gene conversion, as evidenced by replacement of the targeted sequence of by a donor sequence from its paralog We highlight the complexity of CRISPR/Cas9 design, end-product formation, and recombination repair mechanisms for CRISPR/Cas9 delivery as a nucleic acid molecular therapy when targeting genes that have paralogs or pseudogenes, and advocate meticulous evaluation of resultant clones in model organisms. In addition, we suggest that endogenous gene conversion may be used to repair missense variants in genes with paralogs or pseudogenes.
PubMed: 35199044
DOI: 10.1016/j.xhgg.2022.100092 -
Nature May 2023Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data....
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences.
Topics: Humans; Gene Conversion; Genome, Human; Mutation; Segmental Duplications, Genomic; Polymorphism, Single Nucleotide; Haplotypes; Exons; Cytosine; Guanine; CpG Islands
PubMed: 37165237
DOI: 10.1038/s41586-023-05895-y -
Pathogens (Basel, Switzerland) Sep 2022A key factor in the successful infection of a mammalian host by parasites is their conversion from extracellular motile promastigotes into intracellular amastigotes. We... (Review)
Review
A key factor in the successful infection of a mammalian host by parasites is their conversion from extracellular motile promastigotes into intracellular amastigotes. We discuss the physical and chemical triggers that induce this conversion and the accompanying changes at the molecular level crucial for the survival of these intracellular parasites. Special emphasis is given to the reliance of these trypanosomatids on the post-transcriptional regulation of gene expression but also to the role played by protein kinases, chaperone proteins and proteolytic enzymes. Lastly, we offer a model to integrate the transduction of different stress signals for the induction of stage conversion.
PubMed: 36145483
DOI: 10.3390/pathogens11091052 -
Genes Jun 2021The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted...
The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of - gene conversion, including 64 cases for which the direction of conversion was identified (e.g., S conversion to Y). Gene conversion also does not necessarily affect the entire homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted s revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements.
Topics: Alu Elements; Animals; Evolution, Molecular; Gene Conversion; Humans; Primates
PubMed: 34208107
DOI: 10.3390/genes12060905