A long-standing question is why retroviruses package 2 copies of RNA genomes when each infection event generates only 1 provirus. Recombination increases genetic diversity and generates HIV-1 variants that are resistant to antivirals or can escape immune responses. It also plays an important role in shaping the HIV epidemic as evidenced by multiple circulating recombinant forms. Although the role of recombination in generating genetic diversity has been clear, it was unknown whether this process is required for efficient HIV-1 replication. This study demonstrates that when recombination is inhibited in a part of the HIV-1 genome, viral titers decreased, and proviruses had deletions in regions where recombination was blocked. These results illustrate that recombination is a mechanism required to maintain HIV-1 genome integrity and provide insights into the benefit of packaging 2 seemingly redundant RNA genomes: it allows recombination to take place to salvage genetic information.
NAR’s Breakthrough Articles present high-impact studies answering long-standing questions in the field of nucleic acids research and/or opening up new areas and mechanistic hypotheses for investigation. These articles are chosen by the Editors on the recommendation of Editorial Board Members and Referees. Articles are accompanied by a brief synopsis explaining the findings of the paper and where they fit in the broader context of nucleic acids research. They represent the very best papers published at NAR.
This article reports important new understandings in an enzyme/process used by researchers world wide: in vitro transcription by T7 RNA polymerase. While this is the system of choice for RNA synthesis, it is well known to have limitations, a primary one being “nontemplated” 3’ extensions. This is important to the burgeoning field of RNA therapeutics, but plagues researchers throughout basic science and nanotechnology, as well. Reports over two decades have been conflicting and limited in scope. This article brings a new tool, RNA-Seq, to this problem. The RNA-Seq data drive hypotheses that are tested by more conventional tools, but they also indicate a heterogeneity in this process not previously appreciated. This work will prompt development of approaches for mitigating/eliminating this undesired process. While the practical aspects of this work will be interesting to a very wide audience, the results are also of interest to those studying mechanistic elements of transcription.
In this study, the authors have generated new genome-wide tools for functional genomics of Candida albicans. An ORFeome collection has been constructed with 5,099 sequence validated ORFs cloned into a convenient recombinational cloning vector, which represents 83% of the currently annotated coding sequences of C. albicans. This resource is supported by the CandidaOrfDB database, providing information on the individual plasmids and their sequences. The authors also provide a panel of 49 expression vectors that differ in the combination of promoter/selection marker they are carrying and give different options regarding the tagging of the cloned gene product. They demonstrate a novel high-throughput approach to investigate protein-protein interactions in C. albicans. The construction of the ORFeome constitutes a novel and important step towards a systems biology analysis of C. albicans.
