Posts Tagged ‘mimivirus’

Do big viruses make you really sick?

Friday, August 2nd, 2013

Mimivirus For most of my research career, I worked on viruses with small genomes, such as poliovirus and HIV. For me, the attraction of these viruses is that it is easier to understand all the interactions that go on within a small genome than with an unfeasibly large genome such as that of a cell. However, in the past few years I have become fascinated with a group of viruses that are not only considerably bigger than the little guys I worked on, but indeed the biggest of all known viruses. It has to be said that virologists are possibly not the most imaginitive people when it comes to names, so we called them all Giruses – giant viruses.

It all started in 2003 with the discovery of a new virus with a very big genome which was found hiding inside another microbe, Acanthamoeba polyphaga. This virus was so big that it had in fact first been seen ten years earlier in a Gram stain and mistakenly thought to be a small Gram-positive bacterium. Yes, these viruses are bigger than some bacteria, which finally puts paid to the persistent exam answer that size is one of the differences between bacteria and viruses. This giant virus (400 nm in diameter and with a genome of 1.18 million base pairs (bp, Mbp) of double-stranded DNA) was called Mimivirus for “mimicking microbe” – because we were dumb enough to think it was a bacterium for 10 years. (Embarrassingly, that’s not the first time this has happened. Poxviruses are just about large enough to be seen with very good light microscopes and were originally though to be bacterial spores, and in the 1903 Adelchi Negri thought that the virus factories now named after him found in rabies virus-infected cells were sub-cellular organelles.)

 

They’re getting bigger
As the years went by, the viruses got bigger. In 2010 we found Megavirus chilensis in a water sample collected in off the coast of Chile. At 500-600 nm diamater and with a genome of 1.25 Mbp, Megavirus just outpips Mimivirus. Then it started to get weird. Not only were these viruses bigger than some small bacteria such as Mycoplasma, we also found they had their own viruses. The Sputnik virophage replicates in amoeba cells that are already infected by a giant helper virus – Mamavirus.

There’s no reason to think this trend is going to stop just yet, and just this week the largest virus yet discovered has hit the press. Pandoraviruses are amoeba viruses with genomes of up to 2.5 Mbp, reaching the size of not only bacterial genomes but even some simple parasitic Eukaryotes. At 700 nm diamater and with well over 1,000 genes, the Pandoraviruses were named because they open a big box of trouble for people who still cling to the thought that you can classify organisms based on how big they are.

Do big viruses make you really sick?
Having a big genome isn’t really that important, it’s what you do with it that counts. And with viruses, a key question is – do they make you sick? The jury’s still out on that point. Although you can find antibodies against Mimivirus and some of it’s relatives in people with pneumonia, and Mimivirus has recently been isolated direct from patients with pneumonia, that is not definitive proof that the virus is causing the disease rather than simply being a passenger. The association of these viruses with amoebal hosts is particularly difficult in this respect. Until we have been properly able to satisfy Koch’s Postulates we won’t know for sure. And Robert Koch wasn’t working in the era of modern medical ethics, so those experiments are a lot harder to do now. Mamavirus and Pandovirus was pulled out of seawater so we have no idea if it has disease-causing potential, large or small.

 

So have all these giant viruses has blown my reason for liking bonsai viruses out of the water and given me virus envy? Nah, small is still beautiful in my view :-)

 

Do Mimiviruses cause pneumonia?

Monday, July 15th, 2013

Mimivirus I’m a huge fan of Mimivirus. I love it like a geneticist loves Drosophila, or a bacteriologist loves E. coli. But so what – does Mimivirus matter outside the walls of the laboratory? In this mixed up world, if you want to get any serious money to work on something, it has to make you sick, or preferably, kill you. There’s some serological evidence that you can find Mimiviruses in people with pneumonia – patients with pneumonia have higher levels of Mimivirus-specific antibodies than control groups. But this is not proof that they cause the disease rather than just going along for the ride.

A new paper (First Isolation of Mimivirus in a Patient With Pneumonia. Clin Infect Dis. 21 June 2013) has found a new Mimivirus in a patient with pneumonia. And it’s a big one – 1.23 million base pairs of DNA – nearly as big as Megavirus (1.3 million bp) – the largest viral genome ever isolated from a human patient. Although there’s still not difinitely proof that the virus causes the disease, it’s starting to look like Mimivirus is guilty.

How to build a giant virus

Monday, June 3rd, 2013

Mimivirus My final year students will tell you – I’m obsessed with Mimivirus. It’s true – to me these giant viruses are one of the most fascinating areas of microbiology right now, at the convergence of living cells and subcellular infectious agents.

With a particle size comparable to that of small bacteria and a 1.2 Mbp double-strand DNA genome that carries more than 1000 open reading frames, the amoeba-infecting Mimivirus, along with other recently identified members of the Mimiviridae family, are the largest and most complex viruses yet identified. The Mimivirus particle includes an internal membrane that underlies an icosahedral capsid. The assembly mechanism of internal membrane during Mimivirus infection remains unclear, as is the case for other viruses containing internal membranes. By using diverse imaging techniques, this article shows that membrane biogenesis is an elaborate process that occurs at the periphery of viral factories generated at the host cytoplasm. This multistage process, which includes the formation of open membrane sheets, enables efficient and continuous assembly of multiple Mimivirus progeny. The membrane biogenesis process suggested here provides novel insights into the assembly of internal viral membranes in general.

 

Membrane Assembly during the Infection Cycle of the Giant Mimivirus. (2013) PLoS Pathog 9(5): e1003367. doi:10.1371/journal.ppat.1003367
Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ~70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general.

 

We love you Mimi 

Friday, December 14th, 2012

Giant virus blurs the boundaries between viruses and cells further:
Translation in Giant Viruses: A Unique Mixture of Bacterial and Eukaryotic Termination Schemes. (2012) PLoS Genet 8(12): e1003122 http://goo.gl/SbKrS

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Move over Mimivirus, there’s a new Megavirus in town

Thursday, October 13th, 2011

I make no secret of my admiration for Mimivirus, the largest virus known. I make quite a play of what Mimivirus tells us about the nature of viruses and virus evolution in the new edition of Principles of Molecular Virology:

Principles of Molecular Virology
Click for more information

But of course, as soon as you publish a printed textbook, it’s out of date (that’s why I write this blog). And so it proved this week when Mimivirus was knocked off it’s throne by the latest Girus to come along – the even bigger OMGItsSoHugeItBlocksOutTheSun virus. Well, actually, they called it Megavirus (but you get the general idea). With a genome of 1.26 million base pairs of DNA (megabases), this is now the largest virus known (until we discover an even bigger one).

So what do these monsters tell us about viruses? Probably quite a lot, as this excellent Wired article describes.

See:
Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. PNAS USA 10 Oct 2011. DOI: 10.1073/pnas.1110889108
Mimivirus, a DNA virus infecting acanthamoeba, was for a long time the largest known virus both in terms of particle size and gene content. Its genome encodes 979 proteins, including the first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, and TyrRS) ever found outside of cellular organisms. The discovery that Mimivirus encoded trademark cellular functions prompted a wealth of theoretical studies revisiting the concept of virus and associated large DNA viruses with the emergence of early eukaryotes. However, the evolutionary significance of these unique features remained impossible to assess in absence of a Mimivirus relative exhibiting a suitable evolutionary divergence. 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).

 

Giruses not a new domain?

Friday, July 1st, 2011

The tree Resolving the “tree of life” is among the most interesting and challenging questions in evolutionary biology. Although it is widely held that the Archaea, Bacteria and Eukarya form three distinct domains of life, two competing hypotheses place the Eukaryotes either as a sister taxon to the Archaea – the so-called 3 domains tree. The small genomes of viruses did not contain enough information to reliably position them on the tree of life. This was changed by the discovery of Mimivirus, a nucleocytoplasmic large DNA virus (NCLDV) with a genome of unprecedented size (1.2 Mb) and coding capacity (1,000 ORFs), exceeding that of many cellular organisms. In an initial phylogenetic analysis, Mimivirus emerged from the branch joining Archaea and Eukaryotes, suggesting that it might represent a distinct fourth domain of life. New analysis suggests that the informational genes of NCLDV (RNAP2, PCNA, FEN and TFIIB) have been acquired by horizontal transfer from donors within the eukaryotic domain, and suggests that invoking an ancient “4th domain” for NCLDV, or a special primordial role for NCLDV in the formation of Eukaryotes, are not needed to explain the available molecular sequence data for this group of viruses.

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses. PLoS ONE 6(6): e21080. doi:10.1371/journal.pone.0021080
Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.

Closely related to this comes the news that in the absence of competition with other microorganisms, Mimivirus, the largest known DNA virus, loses 17% of its genome. In a natural environment Mimiviruses live in a “community.” They share their amoebal hosts with other organisms such as viruses and bacteria. Constant exchanges of genes within these organisms with intra-amoebal life, not just between each other but also with their protozoan host, have allowed this evolution towards a “community” life. Researchers cultivated Mimivirus in the laboratory, alone in an amoeba without contact with other organisms. After only 150 passages, they observed a 17% reduction in the size of its genome. This genomic loss mainly occurs in the form of deletions of both ends of the genome. In the absence of other microorganisms and thus competition within the host, the Mimivirus eliminates part of its genome by deleting in particular the genes involved in the formation of the long fibers that surround its capsid, becoming “bald.” The researchers also found that this deleted form became resistant to virophages.

 

Mimivirus shows dramatic genome reduction after intraamoebal culture. (2011) PNAS USA 108(25): 10296-10301 doi: 10.1073/pnas.1101118108
Most phagocytic protist viruses have large particles and genomes as well as many laterally acquired genes that may be associated with a sympatric intracellular life (a community-associated lifestyle with viruses, bacteria, and eukaryotes) and the presence of virophages. By subculturing Mimivirus 150 times in a germ-free amoebal host, we observed the emergence of a bald form of the virus that lacked surface fibers and replicated in a morphologically different type of viral factory. When studying a 0.40-μm filtered cloned particle, we found that its genome size shifted from 1.2 (M1) to 0.993 Mb (M4), mainly due to large deletions occurring at both ends of the genome. Some of the lost genes are encoding enzymes required for posttranslational modification of the structural viral proteins, such as glycosyltransferases and ankyrin repeat proteins. Proteomic analysis allowed identification of three proteins, probably required for the assembly of virus fibers. The genes for two of these were found to be deleted from the M4 virus genome. The proteins associated with fibers are highly antigenic and can be recognized by mouse and human antimimivirus antibodies. In addition, the bald strain (M4) was not able to propagate the sputnik virophage. Overall, the Mimivirus transition from a sympatric to an allopatric lifestyle was associated with a stepwise genome reduction and the production of a predominantly bald virophage resistant strain. The new axenic ecosystem allowed the allopatric Mimivirus to lose unnecessary genes that might be involved in the control of competitors.

Breaking the 1000-gene barrier for Mimivirus

Monday, March 14th, 2011

Mimivirus Mimivirus, a nucleocytoplasmic large double stranded DNA virus infecting Acanthamoeba species, is the largest virus identified to date. Its icosahedral fibrillated capsid has a diameter of 750 nm. Besides its outstanding particle size, the genome of Mimivirus is also exceptional both in size and complexity. The initial sequencing revealed a linear genome of 1,181,404 nt (roughly the size of the spirochaete bacterium Treponema pallidum genome) harboring 911 protein coding genes and 6 tRNAs. Some of these genes were observed for the first time in a virus, the most salient being those involved in protein translation and DNA repair. These unique features reawaked conceptual discussions on the nature of viruses and the frontier between viruses and cellular organisms.

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. (2011) Virology Journal 2011, 8:99 doi:10.1186/1743-422X-8-99
Background: Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes.FindingsWe now report a much deeper analysis using the SOLiD technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation. Conclusions: This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.

Related:

Another Really, Really Big Virus

Tuesday, January 25th, 2011

Mimivirus Typically, viruses are considered to be small particles that easily pass through 0.2 µm filters and have small genomes containing a few protein-encoding genes. However, large viruses with huge dsDNA genomes that encode hundreds of proteins are being discovered with increasing frequency. These large viruses have also been referred to as giruses in order to emphasize their unique properties. Examples of giruses include:

  1. Mimivirus and its close relative Mamavirus, which infect amoebae and have the largest genomes (~1.2 Mb). Mimivirus has 979 protein-encoding sequences (CDSs), six tRNA genes and 33 non-coding RNA genes.
  2. Viruses that infect algae (phycodnaviruses) and have genomes up to ~560 kb.
  3. Viruses, such as bacterophage G, that infect bacteria and have genomes up to ~670 kb (~498 kb is unique sequence).

A recent report describes the newest girus, a lytic virus (named CroV) that infects the marine microzooplankton Cafeteria roenbergensis. CroV has a ~730 kb genome and contains 544 CDSs and 22 tRNAs encoding genes in the 618 kb central region of its genome. Viruses with genomes ranging from 100 to 280 kb, such as herpesviruses and baculoviruses, are not discussed in this commentary, and poxviruses, asfarviruses, iridoviruses, and ascoviruses are only briefly mentioned because of their evolutionary connection to some giruses. Another group of viruses with dsDNA genomes >500 kb are the polydnaviruses.

To place the size of these large viruses into perspective, the smallest free-living bacterium, Mycoplasma genitalium, encodes ~470 CDSs. Although estimates of the minimum genome size required to support life are ~250 CDSs, some symbiotic bacteria such as Carsonella ruddii and Hodgkinia cicadicola have genomes of 160 kb and 144 kb, respectively. Thus, many large viruses have more CDSs than some single-celled organisms.

Another Really, Really Big Virus. (2011) Viruses 3(1): 32-46; doi:10.3390/v3010032
Viruses with genomes larger than 300 kb and up to 1.2 Mb, which encode hundreds of proteins, are being discovered and characterized with increasing frequency. Most, but not all, of these large viruses (often referred to as giruses) infect protists that live in aqueous environments. Bioinformatic analyses of metagenomes of aqueous samples indicate that large DNA viruses are quite common in nature and await discovery. One issue that is perhaps not appreciated by the virology community is that large viruses, even those classified in the same family, can differ significantly in morphology, lifestyle, and gene complement. This brief commentary, which will mention some of these unique properties, was stimulated by the characterization of the newest member of this club, virus CroV (Fischer, M.G.; Allen, M.J.; Wilson, W.H.; Suttle, C.A. Giant virus with a remarkable complement of genes infects marine zooplankton. PNAS USA 2010, 107, 19508-19513). CroV has a 730 kb genome (with ~544 protein-encoding genes) and infects the marine microzooplankton Cafeteria roenbergensis producing a lytic infection.

Related:

DNA Viruses – Really Big Ones

Friday, August 13th, 2010

Mimivirus Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade. To date, most of the giruses are associated with aqueous environments. Many of these large viruses (phycodnaviruses and Mimiviruses) probably have a common evolutionary ancestor with the poxviruses, iridoviruses, asfarviruses, ascoviruses, and a recently discovered Marseillevirus. One issue that is perhaps not appreciated by the microbiology community is that large viruses, even ones classified in the same family, can differ significantly in morphology, lifestyle, and genome structure. This review focuses on some of these differences rather than provides extensive details about individual viruses.

DNA Viruses: The Really Big Ones (Giruses). Annu Rev Microbiol. May 12 2010 | PDF

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