Archive for October, 2011

Silence(d) is Golden (mosaic)…

12 October, 2011

Geminivirus particle: characteristic doubled icosahedron containing a single ssDNA (courtesy Russell Kightley)

About that title…I read in my Nature News on the iPad about the use of siRNA in transgenic beans to silence expression of the Bean golden mosaic begomovirus, and I irresistibly thought of this…B-)

To serious matters – said article reported the following:

“Brazilian scientists roll out a transgenic pinto bean (Phaseolus vulgaris) engineered to fend off one of the crop’s most devastating enemies: the golden mosaic virus. Approved on 15 September by the Brazilian National Technical Commission on Biosafety (CTNBio), the transgenic bean uses RNA interference to shut down replication of the virus [reported originally in Mol Plant Microbe Interac in 2007].”

This paper reported the following:

“…we explored the concept of using an RNA interference construct to silence the sequence region of the AC1 viral gene and generate highly resistant transgenic common bean plants. Eighteen transgenic common bean lines were obtained with an intron-hairpin construction to induce post-transcriptional gene silencing against the AC1 gene. One line (named 5.1) presented high resistance (approximately 93% of the plants were free of symptoms) upon inoculation at high pressure (more than 300 viruliferous whiteflies per plant during the whole plant life cycle) and at a very early stage of plant development. “

OK, some background: Bean golden mosaic virus (BGMV) is a begomovirus, a representative of the largest genus of the Geminiviridae, and one of the more devastating viral plant pathogens on the planet.  It is a single-stranded circular DNA virus with a very distinct particle morphology, which replicates its genome by a rolling circle mechanism shared by all geminiviruses, nanoviruses, circoviruses, microviruses and pretty much any other ssDNA virus, as well as some plasmids.

RNA silencing – once known as post-transcriptional gene silencing, before the field was usurped by non-plant virologists – is a natural mechanism used by plants in particular as an adaptive immune response to plant viruses, as well as to control gene expression.  It is a complicated process, involving the formation of double-stranded RNAs from complementary sequences, transcribed from DNA or RNA genomes, which are then chopped up into shorter 21-25 base-length sequences.  These small interfering (si) RNAs are dissociated, and are free to bind to complementary sequences in the plant cell cytoplasm – and target them for degradation by a particular set of enzymes.  This happens frequently in transgenic plants, where the desired over-expression of a particular gene may be frustrated by the plant promptly silencing it.  It is also part of an arms race between plant viruses and plants, with nearly all plant viruses demonstrating some ability to interfere with siRNA silencing.

Geminiviruses are no exception: a number of papers have explored silencing suppression by geminiviruses, with a review by Dave Bisaro prominent among them.  Who is also famous for singing “Born to be Wild” in a Spanish karaoke bar in 1994 with a number of other geminivirologists, who called themselves “Subgroup IV” – but I digress.

It is interesting, then, that one can make transgenic plants expressing siRNA specific for a geminivirus gene – and get silencing of viral expression, and effective immunity to the virus: this would seem to have potential for a deathmatch, with the plant trying to silence virus-coded RNA, while the virus tries to suppress RNA silencing by the plant…as well as the fact that it is a DNA virus, and silencing is mediated at the level of cytoplasmic RNA.

But it obviously works – and probably because the siRNA is being expressed constitutively, meaning the virus infecting the first cell(s) gets shut down before it has a chance to get expression going.  The choice of gene – the “AC1” or Rep – is also important, as expression of mRNA from this is at a very low level, and it is crucial for virus genome replication.  This means that shutting it down stops any DNA replication from occurring.

So Viva! Brasil, Viva! as we South African are fond of saying.  Southern hemisphere rules geminivirus resistance, OK…because we have more than a passing interest in the same phenomenon…B-)

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Goodbye, Mimi – we got Mega!

11 October, 2011

Through the unlikely medium of a local online version of a local daily paper, comes the following:

“A virus found in the sea off Chile is the biggest in the world, harbouring more than 1,000 genes, surprised scientists reported on Monday. The genome of Megavirus chilensis is 6.5 percent bigger than the DNA code of the previous virus record-holder, Mimivirus, isolated in 2003. “

The relevant article is from the group led by Jean-Michel Claverie, of the Institut de Microbiologie de la Méditerranée, in Marseilles, and appears in the October 10th online issue of PNAS.

From the abstract:

An electron micrograph of Megavirus: thanks to Jean-Michel Claverie

Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the

genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).

I could argue with the choice of name as it does not conform to ICTV rules, as far as I can see – but then, neither did Mimivirus.  The important fact about the discovery – apart from the fact that it is a discovery, and therefore not amenable to hypothesising, which I rather like – is that it shows how very diverse these viruses are, and how long they must have been evolving.  For example, despite their morphological similarity, Mimi- and Megavirus genomes do not share nearly 25% of their ORFs – and sequence identities of  predicted homologous proteins are as low as 50%.

I have blogged earlier on Mimivirus structure and evolution – see “Mimivirus unveiled” – and it is nice to see that an important speculation from those earlier papers appears to be borne out here.  Namely, and quite important when considering both viral and cellular origins, is further evidence that very large viral genomes do not seem to have evolved by extensive horizontal gene transfer from cells, and in fact, the reverse may be true.  The authors state in their conclusion, in discussion of opposing views of the origin of these viruses:

“The potential origin of giant mimivirus-like genomes has been hotly debated, basically opposing two views. One is depicting Mimivirus as an extremely efficient gene “pickpocket,” explain- ing its large genome as the result of considerable HGTs from its host, bacteria, or other viruses. This scenario has been criticized in detail elsewhere [see paper for refs]. The opposite view claims that the level of HGT remained marginal (10%) and that most of the Mimivirus genes originated from an even more complex viral ancestor, itself eventually derived from an ancestral cellular genome.”

I have fond memories of an essay I won a school prize with, in about 1970, entitled “The Sea, and All that Therein Is”.  I should update it to “The Sea, and All the Viruses that Therein Are”…B-)

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Posted in Evolution, General, Viruses | 1 Comment »