MicrobiologyBytes

Microbiology Today: The mysteries of Chlamydia

The difficulty in growing and handling Chlamydia in the laboratory has always hampered study of this important bacterium. However, recently genomics studies have allowed re-assessment and re-interpretation of what we thought we knew.

http://www.sgm.ac.uk/en/publications/microbiology-today/current-issue.cfm

I’ve spent quite a bit of time in the last week marking exam essays about papillomaviruses, so it’s good to relax by reading a few recent journal articles about …. papillomaviruses ;-)

Animal papillomaviruses. Virology. 24 May 2013 pii: S0042-6822(13)00266-3. doi: 10.1016/j.virol.2013.05.007
We provide an overview of the host range, taxonomic classification and genomic diversity of animal papillomaviruses. The complete genomes of 112 non-human papillomavirus types, recovered from 54 different host species, are currently available in GenBank. The recent characterizations of reptilian papillomaviruses extend the host range of the Papillomaviridae to include all amniotes. Although the genetically diverse papillomaviruses have a highly conserved genomic lay-out, deviations from this prototypic genome organization are observed in several animal papillomaviruses, and only the core ORFs E1, E2, L2 and L1 are present in all characterized papillomavirus genomes. The discovery of papilloma-polyoma hybrids BPCV1 and BPCV2, containing a papillomaviral late region but an early region encoding typical polyomaviral nonstructural proteins, and the detection of recombination breakpoints between the early and late coding regions of cetacean papillomaviruses, could indicate that early and late gene cassettes of papillomaviruses are relatively independent entities that can be interchanged by recombination.

Papillomavirus E6 oncoproteins. 24 May 2013 Virology pii: S0042-6822(13)00248-1. doi: 10.1016/j.virol.2013.04.026
Papillomaviruses induce benign and malignant epithelial tumors, and the viral E6 oncoprotein is essential for full transformation. E6 contributes to transformation by associating with cellular proteins, docking on specific acidic LXXLL peptide motifs found on these proteins. This review examines insights from recent studies of human and animal E6 proteins that determine the three-dimensional structure of E6 when bound to acidic LXXLL peptides. The structure of E6 is related to recent advances in the purification and identification of E6 associated protein complexes. These E6 protein-complexes, together with other proteins that bind to E6, alter a broad array of biological outcomes including modulation of cell survival, cellular transcription, host cell differentiation, growth factor dependence, DNA damage responses, and cell cycle progression.

Over the years I’ve put a lot of my microbiology videos on YouTube. Some of them have been very popular, and overall they’ve had more than a million views! But they’ve always been mixed in with other non-microbiology content on my YouTube channel. I finally figured out how to separate the microbiology videos from the others, so now you can see just the microbiology content.

Over the next few months I hope to make quite a few more videos, based on what has been most popular in the past – but if there’s a topic that you’re particularly interested in, let me know!

Microbiology Today: Syphilis – the great scourge

The Turks called it ‘the disease of the Christians’ while the Persians called it ‘the disease of the Turks’. It has variously been attributed to the French, the British, the Polish, the Germans and the Portuguese. But what cannot be denied is that syphilis has been a scourge of mankind for over 500 years at least – and unfortunately continues to be so.

The eradication of HIV-1 from infected individuals is prevented by the persistence of the virus in a stable reservoir of latently infected CD4+ T cells. Latently infected cells can be found in all HIV-1 infected individuals at a very low frequency and allow the virus to persist despite antiretroviral therapy for the lifetime of an infected patient. Current efforts are focused on identifying small molecules or immune strategies to eliminate these latently infected cells. To assess the efficacy of these elimination strategies in HIV-1 infected patients, we must be able to measure the size of the remaining latent reservoir. While a previous assay can measure the size of this latent reservoir, it is too laborious and costly to be utilized in large-scale HIV-1 eradication trials. A new paper in PLoS Pathogens describes a rapid assay to measure the size of the HIV-1 latent reservoir more amenable to eradication trials.

Rapid Quantification of the Latent Reservoir for HIV-1 Using a Viral Outgrowth Assay. (2013) PLoS Pathog 9(5): e1003398. doi:10.1371/journal.ppat.1003398
HIV-1 persists in infected individuals in a stable pool of resting CD4+ T cells as a latent but replication-competent provirus. This latent reservoir is the major barrier to the eradication of HIV-1. Clinical trials are currently underway investigating the effects of latency-disrupting compounds on the persistence of the latent reservoir in infected individuals. To accurately assess the effects of such compounds, accurate assays to measure the frequency of latently infected cells are essential. The development of a simpler assay for the latent reservoir has been identified as a major AIDS research priority. We report here the development and validation of a rapid viral outgrowth assay that quantifies the frequency of cells that can release replication-competent virus following cellular activation. This new assay utilizes bead and column-based purification of resting CD4+ T cells from the peripheral blood of HIV-1 infected patients rather than cell sorting to obtain comparable resting CD4+ T cell purity. This new assay also utilizes the MOLT-4/CCR5 cell line for viral expansion, producing statistically comparable measurements of the frequency of latent HIV-1 infection. Finally, this new assay employs a novel quantitative RT-PCR specific for polyadenylated HIV-1 RNA for virus detection, which we demonstrate is a more sensitive and cost-effective method to detect HIV-1 replication than expensive commercial ELISA detection methods. The reductions in both labor and cost make this assay suitable for quantifying the frequency of latently infected cells in clinical trials of HIV-1 eradication strategies.

Microbiology Today: HIV and the ‘functional’ cure

http://www.sgm.ac.uk/en/publications/microbiology-today/current-issue.cfm

Last week I got involved in an interesting “discussion” with a senior professor of physics about what makes a good pathogen. I wish I’d had this at the time to show him.

Experimental Evolution of Pathogenesis: “Patient” Research. (2013) PLoS Pathog 9(5): e1003340. doi:10.1371/journal.ppat.1003340
Laboratory passage has long been recognized as an effective means to modify the host range of pathogens, with successive passage of viruses in nonhuman hosts an early strategy for generating live attenuated vaccines. The principle behind this attenuation is that confined passage in one host species can modify the host range of a pathogen such that it no longer efficiently causes disease in the original host. Armed with modern molecular and genomic tools, several groups have revisited the basic outlines of this approach to directly test how natural host diversity and host cycling influence the evolutionary trajectory of pathogens.

Advice for Job Seekers - managing your online presence

One of the great member benefits of being a member of the Society for General Microbiology is all the advice and support you can get for managing your career.

My final year students will tell you – I’m obsessed with Mimivirus. It’s true – to me these giant viruses are one of the most fascinating areas of microbiology right now, at the convergence of living cells and subcellular infectious agents.

With a particle size comparable to that of small bacteria and a 1.2 Mbp double-strand DNA genome that carries more than 1000 open reading frames, the amoeba-infecting Mimivirus, along with other recently identified members of the Mimiviridae family, are the largest and most complex viruses yet identified. The Mimivirus particle includes an internal membrane that underlies an icosahedral capsid. The assembly mechanism of internal membrane during Mimivirus infection remains unclear, as is the case for other viruses containing internal membranes. By using diverse imaging techniques, this article shows that membrane biogenesis is an elaborate process that occurs at the periphery of viral factories generated at the host cytoplasm. This multistage process, which includes the formation of open membrane sheets, enables efficient and continuous assembly of multiple Mimivirus progeny. The membrane biogenesis process suggested here provides novel insights into the assembly of internal viral membranes in general.

Membrane Assembly during the Infection Cycle of the Giant Mimivirus. (2013) PLoS Pathog 9(5): e1003367. doi:10.1371/journal.ppat.1003367
Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ~70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general.