bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.11.21.689801

Horizontal Gene Transfer of E. coli by direct DNA uptake from extracellular liquid phase

Wood, C.·Smith, Z.·Johnson, L.·Lee, J. W.
View original source ↗Export metadata ↓

Abstract

The "fate of naked DNA" or "environmental DNA (eDNA)" from genetically engineered (GE) biomasses in relation to possible horizontal gene transfer (HGT) is an emerging area of biosafety research. Using a broad-host plasmid (pAM5409) as a mimic of eDNA containing a yellow fluorescent protein gene (yfp) and conferring spectinomycin/streptomycin (Sp/Sm) resistance, we incubated each of the E. coli strains DH5, DH10B and K12 with the plasmid eDNA to evaluate HGT through direct uptake of plasmid DNA from extracellular liquid phase. According to experimental observations, the HGT can occur within 1 day of donor (eDNA) and recipient cells liquid incubation in E. coli strains DH5 and DH10B, but not in K12 which has its intact genes encoding restriction enzymes and endonucleases. HGT occurrences were observed by analyzing colony forming units (CFU) expression of yellow fluorescent protein (YFP). The HGT frequency by direct uptake of plasmid DNA from the liquid phase was determined to be 1.2 x 10-8 per cell day for both DH5 and DH10B. The frequency of HGT was slightly higher than that of spontaneous mutation for natural antibiotic resistance development that was estimated to be 4.8 x 10-9 per cell day. Extension of the liquid eDNA and recipient cells incubation time from 1 day to 3 and 5 days did not increase the HGT frequency under the current experimental conditions. Despite K12 failing to form CFUs following exposure to eDNA, this does not imply K12 did not uptake eDNA; eDNA acquired could have been fragmented by K12 restriction enzymes into non-functional oligomers incapable of HGT.

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Wood, C., Smith, Z., Johnson, L., Lee, J. W.. 2025-11-21. Horizontal Gene Transfer of E. coli by direct DNA uptake from extracellular liquid phase. https://doi.org/10.1101/2025.11.21.689801

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

How perennial, postmitotic multinucleated tissues, such as skeletal myofibers, maintain their identity and transcriptional adaptation to homeostatic perturbations through adult life is an outstanding question. To address this issue, we investigated the consequences of loss of 3D-genome architecture in skeletal muscles by generating myofiber-specific Ctcf-deficient (CtcfmKO) mice. CtcfmKO mice did not exhibit muscular phenotype at birth but spontaneously developed a severe myopathy. Integrated analysis of snRNAseq, ATACseq and promoter-capture Hi-C revealed both common and fiber-type specific patterns of dysregulated gene expression associated with alterations in chromatin accessibility and promoter-based interactions in Ctcf-deficient myonuclei at distinct stages of myopathy development. Decreased chromatin accessibility at promoters and changes in their connectivity with distal elements were observed across all myonuclei as a direct consequence of Ctcf deficiency at early stages and associated with downregulation of genes implicated in myofiber contraction and anabolism, metabolism, adhesion and neuromuscular transmission. Conversely, at later stages, upregulation of genes leading to persistent activation of ER stress/UPR and catabolism resulted from global reconfiguration of chromatin structure and connectivity, partly as indirect consequence of Ctcf deficiency. Notably, type-IIB myonuclei exhibited specific alterations in gene expression that culminated in loss of fiber-type identity and ectopic expression of inflammatory genes. These results reveal a requirement of Ctcf for maintenance of fiber-type identity and transcriptional adaptation in vivo, through multilayered control of 3D genome integrity. They also indicate an unprecedented association between Ctcf deficiency in myofibers and susceptibility to develop myopathies, whereby Ctcf dispensability for developmental myogenesis confers vulnerability to develop myopathic syndromes.

molecular biology↗
bioRxiv2026

Thiomorpholino antisense oligonucleotides inhibit telomerase and limit cancer cell proliferation

Reactivation of telomerase confers immortality to approximately 90% of human tumors by enabling continuous elongation of the DNA at chromosome ends, or telomeres. The telomerase catalytic subunit TERT adds TTAGGG repeats using a portion of the telomerase RNA component hTR as a template. Because telomerase is inactive in most normal somatic cells, it remains an attractive therapeutic target; however, no telomerase inhibitor has yet demonstrated robust clinical efficacy with acceptable safety. Here we evaluate thiomorpholino oligonucleotides (TMOs) as a new class of antisense oligonucleotides targeting the template region of hTR. TMOs incorporate morpholino rings and phosphorothioate linkages, which enhance nuclease resistance, RNA binding and nuclear uptake. Two anti-hTR TMOs inhibited telomerase activity in vitro with an IC50 below 1 nM, whereas two control TMOs were at least 100-fold less active. HeLa cells treated with anti-hTR TMOs showed progressive telomere shortening, detectable after one week of treatment. Growth inhibition was observed after substantial telomere erosion, and both telomere length and proliferation recovered upon withdrawal of TMOs. These findings establish TMOs as a promising new chemistry for telomerase-targeted therapeutics.

molecular biology↗
bioRxiv2026

Msp1-dependent extraction promotes ubiquitylation of translocation-stalled mitochondrial precursor proteins

The translocase of the outer membrane (TOM complex) imports more than 1,000 proteins into mitochondria. Clogging of the TOM pore with a precursor protein causes proteotoxic stress and eventually cell death. Two quality control pathways remove translocation-stalled precursor proteins. In the mitochondrial protein translocation-associated degradation (mitoTAD), Ubx2 recruits the cytosolic AAA-ATPase Cdc48 to clear precursor proteins from the TOM complex. In the mitochondrial compromised protein import response (mitoCPR), the stress-induced Cis1 recruits the AAA-ATPase Msp1 to Tom70. The role of Msp1 for the removal of mitochondrial precursor proteins remains unknown. Here, we demonstrate that parallel loss of Msp1 and Ubx2 strongly affects removal of precursor proteins and cell viability. Msp1 and Ubx2 bind independently of import stress and Cis1 to the TOM complex to remove a large variety of precursor proteins. Msp1-dependent extraction promotes ubiquitylation of precursor proteins, which in turn allows Ubx2-recruited Cdc48 to transfer the substrates to proteasomal degradation. We conclude that two AAA-ATPases cooperate in mitochondrial precursor quality control. Msp1-dependent extraction from the TOM complex facilitates precursor ubiquitylation and Cdc48-mediated transfer to proteasomal degradation.

molecular biology↗