Plant viruses with positive sense RNA genomes ( +RNA) genomes are likely to have a number of advantages over DNA or negative strand RNA viruses, which could be a reason why +RNA viruses are predominant in plants.

+RNA genomes serve as mRNAs and virus-encoded proteins are produced immediately after entry of viral RNA to cell cytoplasm. There is no need, as in the case of DNA viruses, to transport genetic material to the nucleus, where viral DNA has to be transcribed and reproduced. Therefore, using viral genomic RNAs as mRNAs make possible to reduce the number of steps from virus entry to replication, which could be targeted by host defences. All this could be more important for plant viruses because of the differences between viral spread between plant cells and between animal cells.

In the case of animal viruses, their genomes ( +RNA, -RNA, or DNA) enter cell as a part of viral particle, which may be relatively large and contain a variety of proteins facilitating transport within the cell, including nucleus (or other functions such as production of complementary RNA strands in the case of negative strand RNA viruses). Plant viruses invade cell mainly by transporting genomic RNA via plasmodesmata, cytoplasmic channels connecting cytoplasms of neighbouring cells. Although such transport require virus-encoded “movement proteins”, often no formation of virus particles is required, and viral genome entering new cells is less protected, and, in general, not all viral proteins could be easily transported through plasmodesmata.

Therefore it may be advantageous for virus to initiate production of viral proteins immediately after the entry of viral genome; - this is instantly achieved when viral genome act as mRNA. (In particular, viral proteins translated form viral genomic RNA/mRNA are known to suppress host plant defences , e.g. antiviral RNAi responses).

I think it depends on machinery in service for RNA reduplication. First object are proteins involved in the process. Unfortunately, we are limited in knowledge here.

Wish you success in the project.

Regards,

Yuri Drygin

May helicases play a role? http://jxb.oxfordjournals.org/content/54/391/2201.full; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799361/pdf/pp1520255.pdf

I don't know the right answer, but i agree it is a very interesting aspect. I can add that in general, RNA replication machinery are able to introduce mutations and they are the fuel for fitness, host adaptation, etc, evolution in general. However, it is necessary to remember that in case of ssDNA (Geminiviridae) high mutation frequency are probably to occurs.

When you have replication of the viral RNA you also have proteins synthesis. These two steps are believed to be simultaneous. So maybe, it's faster.

But also, don't forget that lots of viruses are unknown yet and maybe in several years, you see that the % will change... Work, wait & see!

Good luck!

Probably has to do with the rate of mutation of ssRNA if compared to dsDNA. ssRNA genome enables much higher rates of mutation.

There are different things to consider. When I was at school a few years ago, we were talking about 80 to 85% for RNA viruses in plants. Now it is 70% and just as Lucille said above there are lots of viruses still to be discovered. Just in the geminiviridae family (ssDNA), when we published our favorite virus back in '93, it was the 6th or 7th full genome. Right know there are hundreds in the databases and still growing strong. A few new DNA families have also emerged. On the other hand, when we say "viruses infecting plants" we are talking, in general, about crops and other associated plants. In other words, we have only noticed those viruses that are "closed" to us (humans) because they infect our crops, our gardens, etc. There are many, many plants that have not been analysed yet. Yes, there are examples of viruses infecting plants that are not "human-related" but I believe they are a minority.

In regards to biochemical pathways, they might be some advantages in being a RNA vs DNA virus in terms of efficiency. But those advantages could be also present in other systems (bacteria, fungi, animals, etc). So I am not sure what it will be the difference. Something that have not been mentioned yet is the transmission mechanisms. Is it possible that insect vectors and other transmission mechanisms "favored" in plants will be part of the equation?

Something to think about.

I agree with colleagues on more open (appropriate) form of ss RNA for selection by mutations in evolution. And I agree that future works for discovery of new viruses.

Interesting discussions.

I am not a virologist but I think ssRNA has better chance to escape the plant surveillance maschienery. Since the viral nucleic acids will end up in cytosol after infection, the chance of ssRNA being unrecognised there is much higher since it looks mostly like the host RNAs. On the other hand dsRNA and dsDNA/ssDNA are rather unusual in cytosol and targeted for rapid cleavage and degradation.

As other researchers suggested the speed of translation of the ssRNA message is faster to produce those key proteins that virus needs for protecting its nucleic acids, subverging the host defense and rapid cell to cell movement which is using hosts transport maschinery that is udapted to RNA transfer but not DNA transfer.

Plant viruses with positive sense RNA genomes ( +RNA) genomes are likely to have a number of advantages over DNA or negative strand RNA viruses, which could be a reason why +RNA viruses are predominant in plants.

+RNA genomes serve as mRNAs and virus-encoded proteins are produced immediately after entry of viral RNA to cell cytoplasm. There is no need, as in the case of DNA viruses, to transport genetic material to the nucleus, where viral DNA has to be transcribed and reproduced. Therefore, using viral genomic RNAs as mRNAs make possible to reduce the number of steps from virus entry to replication, which could be targeted by host defences. All this could be more important for plant viruses because of the differences between viral spread between plant cells and between animal cells.

In the case of animal viruses, their genomes ( +RNA, -RNA, or DNA) enter cell as a part of viral particle, which may be relatively large and contain a variety of proteins facilitating transport within the cell, including nucleus (or other functions such as production of complementary RNA strands in the case of negative strand RNA viruses). Plant viruses invade cell mainly by transporting genomic RNA via plasmodesmata, cytoplasmic channels connecting cytoplasms of neighbouring cells. Although such transport require virus-encoded “movement proteins”, often no formation of virus particles is required, and viral genome entering new cells is less protected, and, in general, not all viral proteins could be easily transported through plasmodesmata.

Therefore it may be advantageous for virus to initiate production of viral proteins immediately after the entry of viral genome; - this is instantly achieved when viral genome act as mRNA. (In particular, viral proteins translated form viral genomic RNA/mRNA are known to suppress host plant defences , e.g. antiviral RNAi responses).

Interesting point ( see Andrey's comment), should consider differences between dsDNA and ssRNA vrisess in the opposite process, - "virion" disassembly, which have to take place in initiate infection in a newly infected cell. Moreover, in the case of some plant virus, for example Tobacco mosaic virus, plasmodesmal movement does not require capsid protein and vision formation, - transport form of virus in plasmodesmal translocation is a likely to be complex of genomic +RNA and virus-encoded RNA binding protein, so-called "movement protein". Those structures are less "rigid" than capsids, basically there is much less protein in these structures than in the case of rod-shaped particles. Which, possibly, makes RNA more accessibly to translation machinery once the complex enters new cell through plasmodesmata.

As to viral molecular "motors", ssRNA viruses encode RNA helicases (which have NTPAse activity), these proteins are required for replication of RNA genomes. Interestingly, for some plant RNA viruses are known to replicate in vicinity of plasmodesmata (e.g. Potato virus X), which suggest connection between RNA movement through plasmodesmata and viral replication.

ssDNA viruses can also move without CP. At least some geminiviruses have been reported that in some hosts no CP is needed.

A question that remains is: Is there something characteristic in plant cells that favored RNA viruses? What happens in other systems (animal, bacteria, fungi)? If there is an inherent advantage of RNA viruses over DNA viruses why we do not see the same ratio on those other systems? Any ideas?

It is an excellent question, and one which I have wondered about since I was first introduced as a summer student to the world of plant viruses.

Respondents to this question have pointed to the functional advantages in replication, evasion of defence mechanisms and spread within the host that accrue to plant viruses as a consequence of being small, positive-sense, ssRNA-containing obligate parasites. I will suggest here an additional perspective that entails a 'big-picture' view from a Darwinian perspective that looks at flows of biological information.

In the broadest sense, (biological) viruses (and their attendant replication mechanisms) can be seen as arising from the escape of certain necessary biological information flows that "have gone 'rogue' and 'taken on a life of their own' ". The parallel with "computer viruses" is more than just a linguistic convenience. In both kinds of viruses, the replication and processing of information has escaped or subverted host control mechanisms and, entirely dependent on host machinery, has 'hijacked' that machinery to make copies of itself and spread.

The frequency and preponderance of a certain basic design of information parasite (whether 'computer virus' or 'biological virus') in a certain class of host may tell us something about how important or central the specific type of information flow (out of which the virus originally evolved and 'went rogue') is to that class of host. If viruses containing small, positive-sense ssRNA are a much larger proportion of the universe of plant viruses than they are of their counterparts infecting (say) vertebrates or bacteria, then perhaps it is because in the evolution of the class of complex, coordinated information flows that became modern higher plants, certain kinds of RNA processing steps were that much more integral or characteristic.

What, if any, consequences might follow from such speculation? When their existence is known (even if incompletely understood), 'rogue elements' (as I have characterized viruses as hijackers of flows of certain specific streams of biological information) can be made to serve a useful purpose as 'criminal informants'. We (Dallas Seifers, KSU and I) hypothesized that the response of a plant host to a virus infection and its 'knock-on' effects on the host's (and its descendants') information flows might reveal something about the evolutionary trajectory of higher plants that distinguished them from other classes of hosts. In very simple terms, we observed that in generations of wheat plants directly descended from progenitors that had responded to inoculation with Wheat Streak Mosaic Virus (WSMV; small, positive-sense ssRNA; replicates in cytoplasm), there was an easily detectable proportion of individuals with altered gene expression, i.e. epigenetic effects. With a small number of additional generations of selection, a subset of the thus evolved sublines came to express the altered traits (such as de novo disease resistances, altered morphology, and in some cases, de novo disease susceptibility) in a uniform fashion and serve as 'quasi-conventional' Mendelian gene donors in crossing experiments. Examples of such phenomena are described in several publications available from this site (one of these is attached right here to this answer).

The evolutionary path that led to the modern higher plants took certain critical turns that distinguished it from the counterpart paths leading to the other modern kingdoms. We think these distinctions may be reflected in the composition of the universes of viruses that hijack their information flows, and that we might be able to exploit some of these aspects to 'guide' certain aspects of plants' evolution for our own purposes.

This is necessarily a brief and very simplified exposition, but I hope it will be provocative. I look forward to the responses of ResearchGate members.