MicrobiologyBytes

Assessing the quality of information on the internet is all about filtering – whether it’s a blog post or a peer-reviewed journal. I don’t want to shock you, but not everything published in peer-reviewed journals is correct, you still need to use your judgement. And some blogs provide some of the best information out there. The best example of this I’ve come across recently is How do adamantane drugs block M2? by Michael Clarkson:

Vaccination plays such an important role in our seasonal influenza strategy in part because we don’t have many medicines that can be brought to bear on the disease. The neuraminidase inhibitors (specifically Tamiflu) are widely stockpiled, and continue to work for now, but the specter of resistance is already lurking. If these drugs are too widely or too improperly used, there is a good chance that resistance mutations will eventually render these drugs ineffective. Universal drug resistance may already be the fate of the drugs amantadine and rimantadine, built on an adamantane backbone. The adamantane drugs inhibit the M2 proton channel from influenza A, a tiny tetrameric protein that equalizes pH between the virus and the endosome of the cell that has swallowed it. This process releases the virus contents so that they can do their damage to the cell, so these medicines can significantly retard the infection process. Or rather, they could, if so many influenza strains didn’t harbor the S31N mutation that almost completely nullifies their effect. If we are to develop new drugs to attack the M2 channel, it would be helpful to know how this mutation causes drug resistance. Over the past few years a great deal of structural evidence has accumulated showing how adamantane drugs work on the older, non-resistant channels. The problem is that the evidence supports two different models of M2 inhibition, and so far it has proven difficult to determine which of them is probably correct…

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Related:

• The Biology of Influenza
• Antiviral Drugs
• Viroporins

Classifying microbes has always been difficult because they are constantly evolving and changing, but nevertheless they have an accepted place on the tree of life. Although modern molecular techniques are of great help to microbial taxonomists, 16S rRNA gene sequencing has limitations when it comes to differentiating between species of bacteria. In this article in Microbiology Today (pdf) Jim Staley proposes an alternative approach – the phylogenomic species concept:

Speciation is the process whereby organisms evolve to form new strains and species. Like speciation in plants and animals, bacterial speciation is driven by ecological and geographical factors. For example, consider the bacteria that have evolved to become pathogens of specific plant and animal species. These pathogenic bacterial species are illustrative products of ecological speciation. Geographic separation in which divergence to form new species is caused by mutation, selection and genetic drift, is common in animals and plants. Evidence for the effect of geographic factors on bacterial speciation has been more difficult to establish. Recently, however, Rachel Whitaker and colleagues showed that Sulfolobus islandicus, a thermoacidophilic archaeon isolated from globally separated hot springs, forms different clades depending on the their location. Strains isolated from hot springs in Iceland differ from those from Yellowstone and Lassen National Parks of North America, and these groups differ from strains isolated from Kamchatka, Russia. This finding indicates that geography also plays a role in bacterial speciation and quite probably a major one, although more research is needed to better understand the importance and commonality of it among bacteria and archaea…

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Related:

• What is a bacterial species?

The asexual erythrocytic phase of the life cycle of Plasmodium falciparum produces the clinical symptoms, disease and pathology associated with malaria. During this phase, merozoites released from schizont-infected erythrocytes invade uninfected erythrocytes. Invasion depends on distinct molecular interactions between ligands on the merozoite, the invasive form of the parasite, and host receptors on the erythrocyte membrane. To avoid infection, humans have evolved to eliminate or modify erythrocyte surface proteins that serve as receptors for parasite invasion. Perhaps one of the best examples of this evolutionary process is the loss of the Duffy blood group in Africa. Plasmodium vivax depends on two ligands for erythrocyte invasion: the Duffy-binding protein (DBP) that binds the Duffy blood group antigen and the reticulocyte homology protein that binds to an unknown receptor on reticulocytes.

Unlike P. vivax, P. falciparum has highly redundant, alternate invasion pathways that use several different receptor families. P. vivax has only one gene, DBP, in the Duffybinding-like erythrocyte-binding protein (DBL-EBP) family, whereas P. falciparum has four DBL-EBP genes: erythrocytebinding antigen 175 (EBA-175), erythrocyte-binding antigen 140 (BAEBL/EBA-140), erythrocyte-binding antigen 181 (JESEBL/ EBA-181), and erythrocyte-binding ligand-1 (EBL-1). Consequently, no erythrocyte has been identified that is refractory to P. falciparum invasion. A recent paper provides evidence that the fourth DBL-EBP family member, EBL-1, binds to glycophorin B.

Theoretical studies indicate that a null allele of glycophorin B would need to afford only a modest level of protection against malaria in heterozygous to increase in frequency from a single mutant to an allele frequency of 0.59. Assuming a constant population of size 1,000–10,000 individuals, one need invoke a selective advantage of only 1% in homozygous-null genotypes to have a single copy of the null mutant allele increase to a frequency of 59% across an interval of 100,000 years (5,000 generations). A shorter time entails stronger selection, but even for 10,000 years (500 generations), a selective advantage of only 10% in homozygous-null genotypes is required. Both cases require partial dominance corresponding to 10–20% as much protection in heterozygous genotypes as in the homozygous-null.

Glycophorin B is the erythrocyte receptor of Plasmodium falciparum erythrocyte-binding ligand, EBL-1. PNAS USA March 11, 2009
In the war against Plasmodium, humans have evolved to eliminate or modify proteins on the erythrocyte surface that serve as receptors for parasite invasion, such as the Duffy blood group, a receptor for Plasmodium vivax, and the Gerbich-negative modification of glycophorin C for Plasmodium falciparum. In turn, the parasite counters with expansion and diversification of ligand families. The high degree of polymorphism in glycophorin B found in malaria-endemic regions suggests that it also may be a receptor for Plasmodium, but, to date, none has been identified. We provide evidence from erythrocyte-binding that glycophorin B is a receptor for the P. falciparum protein EBL-1, a member of the Duffy-binding-like erythrocyte-binding protein (DBL-EBP) receptor family. The erythrocyte-binding domain, region 2 of EBL-1, expressed on CHO-K1 cells, bound glycophorin B+ but not glycophorin B-null erythrocytes. In addition, glycophorin B+ but not glycophorin B-null erythrocytes adsorbed native EBL-1 from the P. falciparum culture supernatants. Interestingly, the Efe pygmies of the Ituri forest in the Democratic Republic of the Congo have the highest gene frequency of glycophorin B-null in the world, raising the possibility that the DBL-EBP family may have expanded in response to the high frequency of glycophorin B-null in the population.

Related:

• Malaria: now you see me, now you don’t
• New ways to beat malaria
• Researchers characterize potential protein targets for malaria vaccine

Mutual exclusion occurs when a host cell is simultaneously infected with two competing viruses, but only one virus goes on to replicate itself. This phenomenon was originally described in bacteriophages by Delbrück in 1945. Mutual exclusion implies that the virus particle which infects first alters the host cell in such a way that a second infection is unlikely. Subsequent studies found that mutual exclusion not only occurs between different viruses but also with nearly identical viruses, presumably as a way to avoid “super-infection” (Dulbecco, R. 1952 Mutual exclusion between related phages. J Bacteriol 63, 209-217). While the virus that wins the race prevents infection by additional viruses, the excluded viruses may interfere with its replication, which is referred to as a “depressor effect” (Delbrück M. 1945 Interference Between Bacterial Viruses: III. The Mutual Exclusion Effect and the Depressor Effect. J Bacteriol. 50(2): 151-170). There are different mechanisms underlying mutual exclusion and depression among bacteriophages, and still, not all of them are understood.

In some instances, exclusion causes the out-competed virus to be rapidly degraded. For example, with bacteriophage T3, degradation occurs after adsorption of the primary infecting phage but before the virus genome is expressed. There is indirect evidence with phage λ that host membrane depolarization is triggered by the successful infecting particle, which initiates exclusion.

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Mutual exclusion not only occurs among bacteriophages but also in viruses infecting certain unicellular, eukaryotic chlorella-like green algae (the chlorella viruses). Plaques arising from single cells simultaneously inoculated with two different chlorella viruses usually only contain one of the two viruses. Previously, the mechanism underlying chlorella virus mutual exclusion is unknown. Chlorella viruses often encode DNA restriction endonucleases and it was originally suggested that one function of the DNA restriction endonucleases might be to exclude infection by other viruses. A new study indicates that chlorella viruses prevent multiple infections by depolarizing the host cell membrane (Chlorella Viruses Prevent Multiple Infections by Depolarizing the Host Membrane. J Gen Virol. Apr 22 2009).

The icosahedral shaped chlorella viruses initiate infection by attaching rapidly, specifically and irreversibly to their host cell wall, probably at a unique virus vertex (corner of the icosahedron). Attachment is immediately followed by cell wall degradation at the point of contact by a virus-packaged enzyme(s). Following wall degradation, the virus internal membrane fuses with the host membrane, facilitating entry of the virus DNA and virion-associated proteins into the cell, leaving an empty virus capsid attached to the cell wall. This process initiates rapid depolarization of the host membrane, triggered by a virus encoded potassium channel located in the virus internal membrane and the rapid release of potassium from the cell. The rapid loss of potassium and associated water fluxes from the host reduce cell turgor pressure, which may help entry of virus DNA into the host.

Two different chlorella viruses were used in the study because they can be distinguished by real time PCR and they have differential sensitivity to caesium, a well known potassium channel blocker. The results showed that virus-induced membrane depolarization was at least partially responsible for the exclusion phenomenon. And that’s how this virus stays one step ahead of its “friends”.

Related:

• Dissecting the Cell Entry Pathway of Dengue Virus
• Imaging Poliovirus Entry in Live Cells
• Mimivirus and the Stargate
• Virus Entry