MicrobiologyBytes

I recently wrote about the top 10 plant viruses in molecular plant pathology. Well Ed didn’t like that list, so he’s published his own:

1. Tobacco mosaic virus (TMV)
2. Tomato spotted wilt virus (TSWV)
3. Tomato yellow leaf curl virus (TYLCV)
4. Cucumber mosaic virus (CMV)
5. Potato virus Y (PVY)
6. Cauliflower mosaic virus (CaMV)
7. African cassava mosaic virus (ACMV)
8. Plum pox virus (PPV)
9. Brome mosaic virus (BMV)
10. Potato virus X (PVX)

“I see only ONE virus in the major list – African cassava mosaic begomovirus (ACMV) – that infects and causes severe losses in one of the four major food crops grown on this planet: all the rest, excepting viruses infecting the also-ran potato, are pathogens of fruits, vegetables or horticulturally-important plants. Or hardly pathogenic at all, as in the case of BMV – and before anyone argues, I probably have the best collection of African (and other) isolates of the virus in the world, and a lot of experience of it in the field.”

I have a feeling this could go on for some time :-)

Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a ‘Top 10′ based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list including, in rank order:

• Tobacco mosaic virus
• Tomato spotted wilt virus
• Tomato yellow leaf curl virus
• Cucumber mosaic virus
• Potato virus Y
• Cauliflower mosaic virus
• African cassava mosaic virus
• Plum pox virus
• Brome mosaic virus
• Potato virus X

This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.

Top 10 plant viruses in molecular plant pathology. (2011) Mol Plant Pathol. 12(9): 938-954. doi: 10.1111/j.1364-3703.2011.00752.x

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It was my privilege to work with Phil Minor during my PhD. 25 years later (gulp), Phil looks back and forward to the polio endgame.

The Polio-Eradication programme and issues of the end game. J Gen Virol. Nov 29 2011
Poliovirus causes paralytic poliomyelitis, an ancient disease of humans that became a major public health issue in the 20th century. The primary site of infection is the gut where virus replication is entirely harmless; the two very effective vaccines developed in the 1950s (Oral Polio Vaccine, or OPV and Inactivated Polio Vaccine, or IPV) induce humoral immunity which prevents viraemic spread and disease. The success of vaccination in developing countries and in middle income countries encouraged the World Health Organization to commit itself to an eradication programme which has made great advances. The features of the infection including its largely silent nature and the ability of the live vaccine (OPV) to evolve and change in vaccine recipients and their contacts make eradication particularly challenging. Understanding the pathogenesis and virology of the infections is of major significance as the programme reaches its conclusion.

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Although it has not been in the news much recently, the highly pathogenic avian influenza A virus subtype H5N1 has been endemic in some bird species since its emergence in 1996 and its ecology, genetics and antigenic properties continue to evolve. This has allowed diverse virus strains to emerge in endemic areas with altered receptor specificity, including a new H5 sublineage with enhanced binding affinity to the human-type receptor. The pandemic potential of H5N1 viruses is alarming and may be increasing. This article reviews the complex and changing nature of the H5N1 virus that may contribute to the emergence of pandemic strains – with really serious consequences.

The changing nature of avian influenza A virus (H5N1). Tresnd in Microbiology, 5 December 2011

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When HIV infects a T lymphocyte, it first inserts a copy of its genome into the cell’s DNA. This inserted virus, called a provirus, then races to make as many new viruses as possible before its host cell dies. But in a few infected cells, HIV does not immediately turn its host into a viral factory. Instead, the provirus is carried around in the DNA of the cell as a transcriptionally silent (“latent”) passenger, only to explode back into action at a later time, when its host cell attempts to participate in an immune response to infection by other pathogens. Because they target the products of HIV transcription, current antiviral therapies like HAART can’t kill latent HIV. And because a full-blown infection can be re-established from a tiny reservoir of latently infected cells, viral latency is an important contributor to our struggle against HIV (Dissecting HIV’s Latent Menace. (2011) PLoS Biol 9(11): e1001209).

The following article examines the molecular mechanism responsible for the establishment and maintenance of HIV latency and its re-activation, and uncovers the role played in this process by the SWI/SNF class of chromatin remodeling complexes, which use energy from ATP to alter the structure of chromatin. Two distinct sub-classes of SWI/SNF, BAF and PBAF, play functionally opposing roles in distinct steps of the HIV promoter (or long terminal repeat, LTR) transcription cycle. The PBAF complex augments transcription of the LTR by the viral transactivator Tat. In contrast, the distinct BAF complex generates a chromatin structure at the LTR that is energetically unfavorable with respect to the intrinsic histone-DNA sequence preferences. Specifically, BAF positions a repressive nucleosome immediately downstream of the HIV transcription start site, abrogating transcription, and in this way contributes to the establishment and maintenance of HIV latency. The data describe a novel molecular mechanism for the establishment and maintenance of HIV latency, and we identify the catalytic subunit of BAF, the enzyme BRG1, as a putative molecular target to deplete the latent reservoir in infected patients.

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency. (2011) PLoS Biol 9(11): e1001206
Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.

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It has been argued that the smaller viruses associated with giant DNA viruses are a new biological entity. However, a short article in Nature Reviews Microbiology argues that these smaller viruses should be classified with the satellite viruses (which I tend to agree with).

Virophages or satellite viruses? Nature Reviews Microbiology 9, 762-763 (November 2011) | doi:10.1038/nrmicro2676
Studies on the giant DNA viruses Acanthamoeba polyphaga mimivirus (APMV) and Cafeteria roenbergensis virus (CroV) have revealed that much smaller viruses – Sputnik and Mavirus, respectively – are associated with them. These smaller viruses depend on the giant viruses for propagation, although the giant viruses can grow without the smaller viruses. It has been argued that Sputnik represents a new, previously unknown biological entity: a ‘virophage’. This term is now used by an increasing number of researchers. However, the virophage concept and its status as a new biological entity requires objective assessment of the similarities and differences between the virophages and the ‘classical’ satellite viruses that have been described previously.

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Studies of virus particles and the steps in their life cycle have spearheaded our understanding of biological systems at the molecular level. These studies, however, relied on virus specimens isolated from nature. This dependency changed forever in 2002 when the chemical synthesis of poliovirus, in the absence of any natural template, was published. The work caused a shock wave because it led to excitement as well as revulsion, reflecting the new reality that, for better or worse, all of the more than 2,000 viruses whose genome sequences are deposited by the National Center for Biotechnology Information can be recreated in the laboratory in the absence of natural isolates. So what have we learned?

Synthetic poliovirus and other designer viruses: what have we learned from them? (2011) Annu Rev Microbiol. 65:583-609
Owing to known genome sequences, modern strategies of DNA synthesis have made it possible to recreate in principle all known viruses independent of natural templates. We describe the first synthesis of a virus (poliovirus) in 2002 that was accomplished outside living cells. We comment on the reaction of laypeople and scientists to the work, which shaped the response to de novo syntheses of other viruses. We discuss those viruses that have been synthesized since 2002, among them viruses whose precise genome sequence had to be established by painstakingly stitching together pieces of sequence information, and viruses involved in zoonosis. Synthesizing viral genomes provides a powerful tool for studying gene function and the pathogenic potential of these organisms. It also allows modification of viral genomes to an extent hitherto unthinkable. Recoding of poliovirus and influenza virus to develop new vaccine candidates and refactoring the phage T7 DNA genome are discussed as examples.

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To deliver their genomes into host cells during entry, enveloped viruses contain glycoproteins that bind to cellular receptors and cause fusion of viral and cellular membranes. The influenza virus Hemagglutinin (HA) protein is the archetypal viral fusion glycoprotein, promoting entry by undergoing irreversible structural changes that drive membrane merger. HA trimers on the surfaces of infectious influenza virions are trapped in a metastable, high-energy conformation and are triggered to refold and cause membrane fusion after the virus is internalized and exposed to low pH.

This paper provides biochemical and x-ray crystallographic evidence that naturally occurring amino-acid variations at the interface of the esterase and fusogenic domains alter HA acid stability for highly pathogenic H5N1 influenza, resulting in a shift in the threshold pH required to activate HA protein structural changes that cause membrane fusion. Furthermore, the data reveals that an increased HA activation pH correlates with increased H5N1 virulence in chickens. Overall, the acid stability of the HA protein is identified as a novel virulence factor for emerging H5N1 influenza viruses. A major implication of this work is that the fitness of enveloped viruses may be fine-tuned by mutations that alter the activation energy thresholds of their fusion glycoproteins.

Acid Stability of the Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity. (2011) PLoS Pathog 7(12): e1002398. doi:10.1371/journal.ppat.1002398
Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 Å resolution and two structures of HP HA at 2.95 and 3.10 Å resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.

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Viruses infecting higher plants are typically small RNA viruses that encode only a few genes. Although small viruses have recently been discovered that infect algae, many viruses infecting eukaryotic algae are huge dsDNA viruses with genomes ranging from 160 to 560 kb with up to 600 protein-encoding genes and are the subject of this review. These large viruses (family Phycodnaviridae), are found in aqueous environments throughout the world and play dynamic, albeit largely undocumented, roles in regulating algal communities such as the termination of massive algal blooms commonly referred to as red and brown tides.

This review focuses on one genus in the Phycodnaviridae, the chloroviruses, which are large, icosahedral, plaque-forming, dsDNA-containing viruses that replicate in certain unicellular, chlorella-like green algae. Their structure, their initial stages of infection, and many of their genes resemble bacteriophages more than viruses that infect eukaryotes – i.e. they are not your everyday plant virus.

Chloroviruses: not your everyday plant virus. Trends Plant Sci. Nov 17 2011
Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.

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