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

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 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.

scholarly journals Pre-clinical evaluation of three non-viral gene transfer agents for cystic fibrosis after aerosol delivery to the ovine lung

Gene Therapy ◽  
2011 ◽  
Vol 18 (10) ◽  
pp. 996-1005 ◽  
Author(s):  
G McLachlan ◽  
H Davidson ◽  
E Holder ◽  
L A Davies ◽  
I A Pringle ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Gene Transfer ◽  
Clinical Evaluation ◽  
Viral Gene ◽  
Aerosol Delivery ◽  
Viral Gene Transfer ◽  
Transfer Agents

scholarly journals Evaluation of polyplexes as gene transfer agents

2001 ◽  
Vol 73 (2-3) ◽  
pp. 401-416 ◽  
Author(s):  
Catherine L. Gebhart ◽  
Alexander V. Kabanov
Keyword(s):  
Gene Transfer ◽  
Transfer Agents

Gene Transfer Agents

2019 ◽  
Author(s):  
Rosemary J. Redfield ◽  
John T. Beatty ◽  
Andrew S. Lang
Keyword(s):  
Gene Transfer ◽  
Transfer Agents
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