How The Virus Does The Trick?
How are viruses such as HIV and bird flu able to make the cells within a human body work for the purpose of the virus? Researchers at the University of Copenhagen have investigated the machinery of human producing the proteins which the virus needs in order to replicate to billions of new ones. The virus penetrates into the host cell where it liberates its RNA which is a copy of the heritage material, DNA. RNA is like a ‘cook book’ which contains the recipes of which proteins the virus needs for replication.
The cell has ribosomes, a kind of ‘molecular motors’, which move along the RNA and read the code for the proteins to be produced to fulfill the needs of the living cell. The task of the ribosomes is to read the code of the host cell, but the virus has the special trick that its RNA resembles that of the host cell, and hence, the ribosomes of the host cell will start reading the viral RNA and produce the proteins requested by the virus. The switching triggers are so called ‘pseudoknots’ in the viral RNA, a three dimensional structure. When the ribosome walking along an RNA encounters a pseudoknot it needs to unravel the pseudoknot before it can proceed.
Question is, how does it do that? Lene Oddershede at the Niels Bohr Institute, University of Copenhagen has developed optical tweezers which can investigate and manipulate molecules at the nano-meter scale. Using a tightly focussed laserbeam this instrument can grab the ends of the RNA tether and follow the process of how the pseudoknot is mechanically unfolded.
A crucial slip of the cellular motor:
In their investigations the researchers used a pseudoknot which is related to bird flu. When the ribosome encounters a pseudoknot it has to unravel the knot before the reading can proceed. During this process the ribosome sometimes slips backwards and, like the letters making up a word, it now reads a new RNA sequence and hence uses another recipe to construct the protein. The researchers have found that the stronger the pseudoknot the more often this backwards slipping happens. The different protein formed is the protein needed by the virus, with possible serious consequences for the hosting organism. This is the manner in which many viruses, e.g. HIV, trick the cell into producing something which it never would have done otherwise. Understanding the role of the pseudoknots can be an important step in developing a viral vaccine.
Proc Natl Acad Sci U S A. 2007 Mar 27; [Epub ahead of print]
Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting.Hansen TM, Reihani SN, Oddershede LB, Sorensen MA.
Department of Molecular Biology, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen N, Denmark; Niels Bohr Insitute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
Programmed ribosomal frameshifting is often used by viral pathogens including HIV. Slippery sequences present in some mRNAs cause the ribosome to shift reading frame. The resulting protein is thus encoded by one reading frame upstream from the slippery sequence and by another reading frame downstream from the slippery sequence. Although the mechanism is not well understood, frameshifting is known to be stimulated by an mRNA structure such as a pseudoknot. Here, we show that the efficiency of frameshifting relates to the mechanical strength of the pseudoknot. Two pseudoknots derived from the Infectious Bronchitis Virus were used, differing by one base pair in the first stem. In Escherichia coli, these two pseudoknots caused frameshifting frequencies that differed by a factor of two. We used optical tweezers to unfold the pseudoknots. The pseudoknot giving rise to the highest degree of frameshifting required a nearly 2-fold larger unfolding force than the other. The observed energy difference cannot be accounted for by any existing model. We propose that the degree of ribosomal frameshifting is related to the mechanical strength of RNA pseudoknots. Our observations support the “9 A model” that predicts some physical barrier is needed to force the ribosome into the -1 frame. Also, our findings support the recent observation made by cryoelectron microscopy that mechanical interaction between a ribosome and a pseudoknot causes a deformation of the A-site tRNA. The result has implications for the understanding of genetic regulation, reading frame maintenance, tRNA movement, and unwinding of mRNA secondary structures by ribosomes.
PMID: 17389398 [PubMed – as supplied by publisher]