TWiV 440: I hardly noumeavirus

No problem not being nice to Dickson in this episode, because he’s absent for a discussion of a new giant virus that replicates in the cytoplasm yet transiently accesses the nucleus to bootstrap infection.

You can find TWiV #440 at microbe.tv/twiv, or listen below.

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A different kind of remote control

nucleusAmong the multitudes of eukaryotic viruses with DNA genomes, some replicate in the cell nucleus, while others avoid the nuclear bureaucracy and remain in the cytoplasm. But biology is not always so rigid: a new giant virus has been found that replicates in the cytoplasm, where it seems to recruit components of the nuclear transcription machinery (link to paper).

Noumeavirus was isolated from a pond near – where else? – Noumea airport in New Caledonia. The 200 nanometer icosahedral particles infect the amoeba Acanthamoeba castellani and have a double-stranded DNA genome of 376,207 base pairs encoding 452 proteins. Sequence comparisons revealed Noumeavirus to be a new member of the family Marseilleviridae, which  includes other previously discovered giant viruses.

Other members of the Marseilleviridae replicate in the cytoplasm of the host cell, so it was assumed that the related Noumeavirus would do the same. However an analysis of the proteins in purified virus particles revealed an absence of components of the transcriptional machinery – which is needed for ths synthesis of mRNA. RNA polymerase, for example, is readily detected in other cytoplasmic viruses such as Mimivirus and poxviruses.

If proteins involved in transcription are not present in the Noumeavirus particle, and the virus does not enter the nucleus, how are viral mRNAs produced?  It appears that early in infection, the required proteins are moved from the nucleus to sites of viral replication in the cytoplasm. When nuclear proteins were labled with green fluorescent protein, within one hour after infection they can be seen moving out of the nucleus into the cytoplasm to sites of viral replication. The nuclear integrity remains intact, as host DNA does not leave the organelle. This recruitment of nuclear proteins is transient:  after 2-4 hours proteins are no longer leaving the nucleus.

This series of events suggests that nuclear proteins needed to initiate viral mRNA synthesis are recruited from the nucleus to sites of viral replication in the cytoplasm. Once viral mRNAs are made, the viral transcriptional machinery can be assembled and the nuclear proteins are no longer needed. The authors call this ‘remote control of the host nucleus.’

Confirmation of this hypothesis will require the demonstration that nuclear proteins involved in viral mRNA synthesis are recruited to early sites of viral replication in the cytoplasm. It will also be essential to identify the mechanism by which these nuclear proteins are extracted. Perhaps one or more virion proteins, such as an abundant 150 amino acid protein of unknown function, is involved.

Other giant viruses, such as Mimivirus, package the viral transcriptional machinery in the virus particle and are independent of the cell nucleus. At the other extreme are viruses that undergo transcription and DNA synthesis entirely in the nucleus (e.g., herpesviruses). Perhaps Noumeavirus is a relic of an evolutionary transition between the two replication strategies.

Image credit

A viral nucleus

Cell typesA unique feature of eukaryotic cells, which distinguishes them from bacteria, is the presence of a membrane-bound nucleus that contains the chromosomal DNA (illustrated; image credit). Surprisingly, a nucleus-like structure that forms during viral infection of bacteria is the site of viral DNA replication (link to paper).

During infection of Pseudomonas bacteria with the phage 2O1phi2-1, a separate compartment forms in which viral DNA replication takes place. A phage protein, gp105, makes up the outer layer of this compartment, which initially forms near one end of the cell, and then migrates to the center. The migration of the compartment takes place on a spindle made up of the tubulin-like protein PhuZ.

In addition to viral DNA, certain proteins gain entry into this compartment, including viral proteins involved in DNA and mRNA synthesis, and at least one host cell protein. Other proteins, such as those involved in translation and nucleotide synthesis, are excluded. This compartmentalization very much resembles that of the nucleus of eukaryotic cells.

Packaging of the viral DNA takes place on the surface of the viral nucleus. Empty phage capsids form at the bacterial cytoplasmic membrane, then migrate to the compartment where they attach firmly to the surface. By an unknown mechanism, DNA moves from the compartment into the capsid. Then  capsids are released from the surface to further mature in the cytoplasm. The completed phages are released from the cell upon bacterial lysis.

These fascinating observations raise a number of unanswered questions. Does infection with other phages lead to assembly of a viral nucleus? How do molecules selectively move in and out of the structure?

Perhaps the most interesting question relates to the origin of viruses and cells. According to one hypothesis, self-replicating, virus-like nucleic acids might have first appeared on Earth, followed by cells without a nucleus. Was the nucleus a viral invention?

TWiV 328: Lariat tricks in 3D

On episode #328 of the science show This Week in Virology, the TWiVocateurs discuss how the RNA polymerase of enteroviruses binds a component of the splicing machinery and inhibits mRNA processing.

You can find TWiV #328 at www.microbe.tv/twiv.

TWiV 269: Herpesvirus stops a nuclear attack

On episode #269 of the science show This Week in Virology, the complete TWiV team reviews evidence for sensing of herpesviral DNA in the nucleus by the cell protein IFI16.

You can find TWiV #269 at www.microbe.tv/twiv.

Prokaryotes considered

prokaryoteAs a college biology major during the 1970s I was taught that cells in which the genetic material is separated from the cytoplasm by a nuclear membrane – such as those of animals, fungi, plants, and protists – are called eukaryotes. In contrast, the DNA of bacteria is not bounded by such a structure, and hence these microbes are called prokaryotes, a name that means ‘before the nucleus’. This concept was accepted by biologists until the late-1970s, when Carl Woese used ribosomal RNA sequences to deduce the relationships among living organisms. He found that microorganisms previously thought to be bacteria, because they have no nucleus, were no more related to bacteria than to eukaryotes. He proposed that living organisms should be classified into three lineages, now called bacteria, archaea, and eukarya. Nevertheless, the prokaryotic classification is still used by many biologists. The following letter from Elio Schaecter, sent to TWiV, explains why:

“Regarding your discussion of the term prokaryote in TWiV #93, I want to pipe in as a combatant in the “P word” wars. I am firmly in the camp of the users of the term. Although the term has carried a phylogenetic burden, meaning that it originally implied a close evolutionary relationship between the Bacteria and the Archaea, no one I know uses it in that sense now. Among biologists, the three domains model is widely accepted, in fact, not even discussed. It’s true that there are leftover people who think that the prokaryote/eukaryote divide denotes a single evolutionary cleft, but that’s simply because any concept of science takes time to filter out.

“I maintain that the term, used in a broad sense, is extraordinarily useful. In a college textbook I co-authored called “Microbe”, we used the P word some 300 times. How come? Had we not used it, we would have had to say “Bacteria and Archaea” that many times (and being parsimonious of verbiage, we eschewed that). This usage illustrates the reality that these two groups of microbes, though they likely diverged very early on in evolution, share a large number of common properties. Their sizes tend to overlap, their overall body plan is generally very similar, they often occupy the same habitats, they share many homologous genes. Presented with an EM thin section, you could not tell a typical bacterium from a typical archaeon. So, dissimilar as they may be in one sense, they are very similar in a number of important attributes. Saying “prokaryotes” is much like saying “animals” or “plants,” large groups that are extremely heterogeneous and that diverged a long time ago (although certainly not as far back as the prokaryotes and eukaryotes). I agree, there is danger in the P word being misunderstood out in the big wide world, but there is none within the family of biologists.

“Anyhow, the battle has been met and, yeah!, the victors are clearly the users of the word prokaryote. The term is found all over the place, notwithstanding the astonishing campaign waged against it. Just look at titles of recent articles in major journals.

“There is a more serious issue. Making phylogeny the overarching master of relatedness is readily justified if one thinks in these terms only. But isn’t ecology just as important to understand biological behavior and relatedness? There is a tyranny to phylogeny, which demands that you view the world of living things in terms of where they came from, not what they are doing now.”

What does this nonmenclature issue have to do with virology? According to Patrick Forterre:

The discovery of unique viruses infecting archaea also corroborates the three domains concept from the virus perspective. Indeed, most viruses infecting archaea have nothing in common with those infecting bacteria, although they are still considered as “bacteriophages” by many virologists…David Prangishvili and myself have thus suggested to classify viruses into three categories, archaeoviruses, bacterioviruses and eukaryoviruses.

Woese, C. (1977). Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms Proceedings of the National Academy of Sciences, 74 (11), 5088-5090 DOI: 10.1073/pnas.74.11.5088

Prangishvili, D., Forterre, P., & Garrett, R. (2006). Viruses of the Archaea: a unifying view Nature Reviews Microbiology, 4 (11), 837-848 DOI: 10.1038/nrmicro1527

TWiV 77: Non-nuclear proliferation

Hosts: Vincent Racaniello, Alan Dove, and Rich Condit

Vincent, Alan, and Rich revisit circovirus contamination of Rotarix, then discuss poxvirus-like replication of mimivirus in the cell cytoplasm, and whether seasonal influenza immunization increases the risk of infection with the 2009 H1N1 pandemic virus.

This episode is sponsored by Data Robotics Inc. Use the promotion code TWIVPOD to receive $50 off a Drobo or $100 off a Drobo S.

Win a free Drobo S! Contest rules here.

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