scholarly journals Evolution of Bacterial Gene Transfer Agents

2018 ◽  
Vol 9 ◽  
Author(s):  
Rosemary J. Redfield ◽  
Shannon M. Soucy
Keyword(s):  
Gene Transfer ◽  
Bacterial Gene ◽  
Transfer Agents

scholarly journals Evolution of Bacterial Gene Transfer Agents

2018 ◽  
Author(s):  
Rosemary J. Redfield ◽  
Shannon M. Soucy
Keyword(s):  
Gene Transfer ◽  
Gene Clusters ◽  
Bacterial Gene ◽  
Chromosomal Genes ◽  
Potential Benefits ◽  
Small Virus ◽  
Fitness Benefits ◽  
The Cost ◽  
Encoding Genes ◽  
Transfer Agents

AbstractBacterial gene transfer agents (GTAs) are small virus-like particles that package DNA fragments and inject them into cells. They are encoded by gene clusters resembling defective prophages, with genes for capsid head and tail components. These gene clusters are usually assumed to be maintained by selection for the benefits of GTA-mediated recombination, but this has never been tested. We rigorously examined the potential benefits of GTA-mediated recombination, considering separately transmission of GTA-encoding genes and recombination of all chromosomal genes. In principle GTA genes could be directly maintained if GTA particles spread them to GTA−cells often enough to compensate for the loss of GTA-producing cells. However careful bookkeeping showed that losses inevitably exceed gains for two reasons. First, cells must lyse to release particles to the environment. Second, GTA genes are not preferentially replicated before DNA is packaged. A simulation model was then used to search for conditions where recombination of chromosomal genes makes GTA+populations fitter than GTA−populations. Although the model showed that both synergistic epistasis and some modes of regulation could generate fitness benefits large enough to overcome the cost of lysis, these benefits neither allowed GTA+cells to invade GTA−populations, nor allowed GTA+populations to resist invasion by GTA−cells. Importantly, the benefits depended on highly improbable assumptions about the efficiencies of GTA production and recombination. Thus, the selective benefits that maintain GTA gene clusters over many millions of years must arise from consequences other than transfer of GTA genes or recombination of chromosomal genes.

%(G+C) Variation and Prediction by a Model of Bacterial Gene Transfer and Codon Adaptation

2002 ◽  
Vol 6 (3) ◽  
pp. 259-272 ◽  
Author(s):  
Cedric O. Buckley ◽  
Desmond Stephens ◽  
Patricia A. Herring ◽  
Julius H. Jackson
Keyword(s):  
Gene Transfer ◽  
Bacterial Gene

Polyhydroxylalkyleneamines: A class of hydrophilic cationic polymer-based gene transfer agents

2009 ◽  
Vol 137 (1) ◽  
pp. 38-45 ◽  
Author(s):  
Xiang Gao ◽  
Ramalinga Kuruba ◽  
Krishnan Damodaran ◽  
Billy W. Day ◽  
Dexi Liu ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Cationic Polymer ◽  
Transfer Agents

scholarly journals Phylogenetic evidence of headful packaging strategy in gene transfer agents

2020 ◽  
Author(s):  
Emma Esterman ◽  
Yuri I. Wolf ◽  
Roman Kogay ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Large Subunit ◽  
Dna Packaging ◽  
Host Genome ◽  
Bacterial And Archaeal Communities ◽  
History Of ◽  
Viral Dna Packaging ◽  
Packaging Strategy ◽  
Transfer Agents

AbstractGene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

scholarly journals High-efficiency gene transfer and expression in normal human hematopoietic cells with retrovirus vectors

Blood ◽  
1988 ◽  
Vol 71 (3) ◽  
pp. 811-814 ◽  
Author(s):  
P Laneuville ◽  
W Chang ◽  
S Kamel-Reid ◽  
AA Fauser ◽  
JE Dick
Keyword(s):  
Bone Marrow ◽  
Gene Transfer ◽  
Progenitor Cells ◽  
High Efficiency ◽  
Bone Marrow Cells ◽  
Fibroblast Cell ◽  
Retroviral Vectors ◽  
Semisolid Medium ◽  
Bacterial Gene

Abstract Retroviral vectors containing the selectable bacterial gene for G418 resistance (neo) were used to demonstrate gene transfer into primary human bone-marrow progenitor cells. To obtain populations of cells in which a high proportion of cells were expressing the neo gene, several important modifications were made to earlier procedures. Cells from normal donors were infected in vitro, were exposed to high concentrations of G418 for two days in liquid culture to enrich for cells expressing the neo gene, and were plated in semisolid medium. Gene transfer and expression were detected in colonies arising from progenitors of granulocyte-macrophage and erythroid lineages. Survival curves indicated that a high proportion of progenitor cells, approaching 100%, were G418 resistant. Furthermore, addition of growth factors contained in 5637-conditioned medium to the bone marrow improved the recovery of G418-resistant progenitors twofold to threefold. In addition to these biological measurements of gene expression in progenitor cells, significant levels of neo-specific RNA, similar to the levels of RNA expression in the virus-producing fibroblast cell line, were detected in the bone marrow cells after preselection. These results demonstrate that retrovirus vectors can be used successfully to transfer genes at high efficiency into progenitor cells in the human blood-forming system.

scholarly journals Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents

2019 ◽  
Vol 11 (10) ◽  
pp. 2941-2953 ◽  
Author(s):  
Roman Kogay ◽  
Taylor B Neely ◽  
Daniel P Birnbaum ◽  
Camille R Hankel ◽  
Migun Shakya ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Support Vector Machine Classifier ◽  
Rhodobacter Capsulatus ◽  
Gene Clusters ◽  
Support Vector ◽  
Structural Components ◽  
Bacterial Populations ◽  
Machine Learning Classification ◽  
Bona Fide ◽  
Transfer Agents

Abstract Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the “head–tail” gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a “support vector machine” classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like “head–tail” gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.

Gene transfer agents, bacteriophages, and bacteriocins of Rhodopseudomonas capsulata

1975 ◽  
Vol 105 (1) ◽  
pp. 217-224 ◽  
Author(s):  
Judy D. Wall ◽  
Paul F. Weaver ◽  
Howard Gest
Keyword(s):  
Gene Transfer ◽  
Rhodopseudomonas Capsulata ◽  
Transfer Agents
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