TWiV 464: Boston baked viruses

At Tufts University Dental School in Boston, Vincent speaks with Katya Heldwein and Sean Whelan about their careers and their work on herpesvirus structure and replication of vesicular stomatitis virus.

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From cell proteins to viral capsids

Origin of virusesWe have previously discussed the idea that viruses originated from selfish genetic elements such as plasmids and transposons when these nucleic acids acquired structural proteins (see A plasmid on the road to becoming a virus). I want to explore in more detail the idea that the structural proteins of  viruses likely originated from cell proteins (link to paper).

Three ideas have emerged to explain the origin of viruses: 1. viruses evolved first on Earth, before cells, and when cells evolved, the viruses became their genetic parasites; 2. viruses are cells that lost many genes and became intracellular parasites; 3. viruses are collections of genes that escaped from cells. Missing from these hypothesis is how nucleic acids became virus particles – that is, how they acquired structural proteins. It seems likely that viral structural proteins originated from cellular genes.

An analysis of the sequence an structure of major virion proteins has identified likely ancestors in cellular proteins. Following are some examples to illustrate this conclusion.

A very common motif among viral capsid proteins is called the single jelly roll, made up of eight beta strands in two four-stranded sheets. Many cell proteins have jelly role motifs, and some form 60-subunit virus-like particles in cells. The extra sequences at the N-termini of viral jelly roll capsid proteins, involved in recognizing the viral genome, likely evolved after the capture of these proteins from cells.

The core proteins of alphaviruses (think Semliki Forest virus) has structural similarity with chymotrypsin-like serine proteases. The viral core protein retains protease activity, needed for cleavage from a protein precursor.

Retroviral structural proteins also appear to have originated from cell proteins, with clear homologies with matrix, capsid, and nucleocapsid proteins. The matrix Z proteins of arenaviruses are related to cellular RING domain proteins, and the matrix proteins of some negative strand RNA viruses are related to cellular cyclophilin. There are many more examples, providing support for the hypothesis that viruses evolved on multiple instances by recruiting different cell proteins.

Given this information on the origin of viral capsid proteins, we can modify the three hypotheses for the origin of viruses into one. Self-replicating, virus like nucleic acids emerged in the pre-cellular world and from the emerged the first cells. The replicating nucleic acids entered the cells, where they replicated and became genetic parasites. At some point these genetic elements acquired structural proteins from the cells and became bona fide virus particles. As cells evolved, new viruses emerged from them.

It is important to point out that the genes do not always flow from cells to viruses. We know that viral proteins can be returned to cells, where they serve useful functions. One example is syncytin, a retroviral protein used for the construction of the mammalian placenta.

TWiV 463: We haven’t meth but these names ring Nobel

The TWiViridae review the 2017 Nobel Prizes for cryoEM and circadian rhythms, and discuss modulation of plant virus replication by RNA methylation.

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Have a methyl with your viral RNA

N6-MethyladenosineChemical modification of RNA by the addition of methyl groups is known to alter gene expression without changing the nucleotide sequence. The addition of a methyl group to adenosine has been found to regulate gene expression of animal viruses, and most recently of plant viruses.

The illustration shows a methyl (CH3-) group added to the nitrogen  that is attached to the #6 carbon of the purine base adenine. The entire molecule, with the ribose, is called N6-methyladenosine (m6A). Methylation of adenosine is carried out by enzymes that bind the RNA in the cell cytoplasm.

The m6A modification is found in multiple RNAs of most eukaryotes. It has also been found in the genome of RNA animal viruses. The modification is added to RNAs by a multi-protein enzyme complex, and is removed by demethylases. Silencing of the methylases decreases HIV-1 replication, while depletion of demethylases has the opposite effect. The replication of other viruses, including hepatitis C virus and Zika virus, is also regulated by m6A modification, but the details differ. For example, m6A negatively affects the replication of the flaviviruses hepatitis C virus and Zika virus.

Methylation of adenosine has been recently shown to modulate the replication of plant viruses. The RNA genomes of alfalfa mosaic virus (AMV) and cucumber mosaic virus (CMV) were found to contain m6A. An m6A demethylase was identified in Arabidopsis thaliana, a small flowering plant commonly used in research. This demethylase protein bound the capsid protein of AMV but not of CMV. Elimination of the demethylase from Arabidopsis reduced the replication of AMV but not CMV. These results show that m6A methylation negatively regulates the replication of AMV. Binding of the AMV capsid protein to the m6A demethylase might be a mechanism for ensuring that the enzyme demethylates viral RNA, allowing for efficient viral replication.

While it is clear that m6A regulates the replication of RNA viruses, the mechanisms involved are not well understood. Methylation of adenosine is likely to affect multiple functions, including the structure, celllular localization, splicing, stability, and translation of viral RNA (link to review). As m6A is also found in cellular RNAs, studies of its effect on viral processes is likely to provide insight into its role in cellular biology.

TWiV 462: Splicing RNA with Phillip A. Sharp

Vincent speaks with 1993 Nobel Laureate Phillip A. Sharp about his career and his seminal discovery of RNA splicing in mammalian cells, which changed our understanding of gene structure.

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TWiV 461: Gotta trace them all!

The TWiVers discuss the declining readability of scientific texts, and review the use of self-inactivating rabies virus for tracing neural circuits.

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TWiV 460: Penn, a great sandbox for science

Vincent travels to the University of Pennsylvania and speaks with virologists Gary Cohen, Scott Hensley, Carolina Lopez, and Susan Weiss about their careers and their research.

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TWiV 459: Polio turns over a new leaf

The TWiV team reviews the first FDA approved gene therapy, accidental exposure to poliovirus type 2 in a manufacturing plant, and production of a candidate poliovirus vaccine in plants.

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The $475,000 drug

KymriahThe US Food and Drug Administration recently approved the first gene therapy, Kymriah, to treat B-cell acute lymphoblastic leukemia. It uses a lentivirus to modify the patient’s T cells to kill tumor cells.

Acute lymphoblastic leukemia, or ALL, is caused by uncontrolled growth of B cells, which normally produce antibodies to fight off infections. It is the most common cancer in children. The uncontrolled production of these cells by the bone marrow causes a shortage of blood cell production, leading to fever, increased risk of infection, and anemia. These B cells have on their surfaces a protein called B19 – which is the key to understanding how Kymriah works.

The therapy begins with drawing blood from the patient, from which T cells are purified. These T cells are then infected with a lentivirus vector that encodes the gene for a chimeric antigen receptor (CAR) that recognizes the B19 protein. The CAR protein is synthetic – it doesn’t exist in any cell. The extracellular domain consists of a single-chain antibody directed against the B19 protein (pictured). The cytoplasmic domain of the protein contains sequences that stimulate the T cells to proliferate.

After the T cells are infected with the CAR-encoding lentivirus, they are infused back into the patient. Upon encountering a B cell producing B19, the T cells bind to the protein and kill the cells, thus eliminating the cancer.

Kymriah was licensed by the FDA after testing showed it was effective, leading to remission of cancers in the majority of children treated. But the price tag is steep – $475,000 for a treatment, and other similar drugs in the pipeline could be even more expensive. The drug makers justify the high price by arguing that it reflects the value to the patient – it saves their lives.

But vaccines also save lives, and they cost much less than Kymriah. The difference, of course, is that vaccines are given to millions of people. Kymriah, in contrast, would be given to thousands in the US.

In other words, the high cost of Kymriah reflects the need of drug companies to recoup their high investment in developing and testing the drug – not the value to the patient.  Rather than spinning a false story about the value of a drug to a patient, the drug companies should be honest about the pricing of their products. No wonder the public has a negative image of the industry.

TWiV 458: Saliva of the fittest

The TWiVians present an imported case of yellow fever in New York City, and explain how a dengue virus subgenomic RNA disrupts immunity in mosquito salivary glands to increase virus replication.

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