Talmudic Question #6

With the buzz created by the discovery of giant viruses, e.g., Mimivirus, the distinction between viruses and cells is said to get blurred. I maintain that this is not the case because the single most important distinction is that viruses lose their corporeal integrity, cells do not. What do you think? Are you a blurrer or a non-blurrer?

An aside: Not everyone knows what a "Talmudic Question" is. Rather than telling you what I had in mind, would those who know share their definition?

Comments

[Autumn Cochrane]

I'm a non-blurrer. Just because there are some giant viruses doesn't mean that the divisions between viruses and cells are less defined when we once thought. A virus is a virus, and a cell is a cell. But, I do believe in evolution - may be the Mimivirus is in the midst of evolving into a bacterium! That's exciting!

Now, as for what a Talmudic Question is . . . I was kind of associating the quality of these questions with the Talmud, of the Jewish religion. If my understanding is correct, there is a holy text in the Jewish religion that asks philosophical questions - questions meant to make the reader think. I have a feeling that's the Talmud; but I'm not quite sure. So, yeah, that's what I think a Talmudic Question is.

[Marika Orlov]

I personally do not understand what the big buzz is all about. Even though Mimivirus contains a “big” genome for our standards, it still acts like a virus. Mimivirus must parasitize a host cell by somehow gaining entrance, losing corporeal integrity, relying on host systems for reproduction, repackaging, and exiting the host cell. The only reason that I can see for why there is currently so much debate about whether this is a virus is that we were not expecting a virus to be so large. As Claverie et al point out, we were never looking for viruses that were larger then the standard1. All of our isolation techniques and screening protocols would have been missing these giant viruses and so our entire classification system is based on what we have found, why is it such a big deal that larger viruses exist? There are so many life forms that exist on this planet and we have such a small sampling, it should come as no surprise that we are discovering new things that put our classification systems to the test. And if bacteria can exist as both intracellular parasites with a reductive genome as well as free living organisms with an expanding genome, why can’t viruses do the same? It is also interesting to think that some of the genetic information that we have been classifying as “non-culturable bacteria” could belong to the giant virus family. The argument about these viruses having larger genomes then some of the intracellular single celled organisms doesn’t really argue anything because each parasite will evolve to be the size that it needs to be in order to survive in its host. If chlamydiae can still be labeled as bacteria even though they cannot synthesize their own ATP molecules2, I don’t see why viruses cannot harbor a genome greater then a certain size before they are no longer recognized as viruses. Another reason why I don’t think the size of the virus should matter is that we have no idea what types of cells these viruses are capable of infecting. We have identified very few organisms on this planet and some may be large enough to harbor these viruses without any problems, so why should the viruses try to reduce their genome sizes if they are not experiencing selective pressure from their hosts? I also do not see the need for stringent classification systems. When organisms are evolving, they are not trying to fit into any clade or phylum, they are simply reacting to selective pressures and trying to out compete their rivals, so why do humans have such a need to classify and order everything that exists in nature, just to more easily allocate grant money? In the end, I really don’t think that size matters, it is the mechanism of reproduction that counts.

1. Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE. Mimivirus and the emerging concept of "giant" virus. Virus Res. 2006 Apr;117(1):133-44.
2. Trentmann O, Horn M, van Scheltinga AC, Neuhaus HE, Haferkamp I. Enlightening energy parasitism by analysis of an ATP/ADP transporter from chlamydiae. PLoS Biol. 2007 Sep;5(9):e231.

Marika Orlov (student, Integrative Microbiology course)

[Marcella Erb]

I am going to argue that I am a non-blurrer. The “abnormally” large size of the mimivirus alone does not give me pause – but its large genome, which encodes for 911 genes, some never seen before in viruses, like t-RNA synthatases, is intriguing. As the wikipedia article points out, 911 genes are more than some obligate parasitic bacteria and this virus has some metabolism genes that those ultra-streamlined bacteria do not.
But the mimivirus is still firmly a virus. It does experience “corporeal disintegration” upon binding to a host cell, is a capsid based life form (as opposed to a cell based one), does not grow or divide in a traditional sense, nor does it have any way of making ribosomes, so it cannot execute any independent protein synthesis. Just because we have to strip down what we consider “unique” characteristics of cellular life to just a few does not make the classification of cellular life versus virus obsolete or blur their distinction.
The mimivirus does pose interesting questions about the evolution of viruses and early cellular life. Does the mimivirus resemble more primitive viruses, one that infected early cellular life or LUCA or is it a more “advanced” virus, specialized for amoeba, and has simply picked up a lot of genes along the way? Since we know so little about the diversity of viruses, mimivirus-like viruses may be quite common or may be a gateway to just how big and complex a virus can get and yet still be a virus.

Marcella Erb (student, Integrative Microbiology course)

[Laurel Monticelli]

Viruses have evolved to survive in organisms from all three domains of life, but debate rages over where viruses belong in the evolutionary tree of life. Viruses are generally considered not to be alive because they lack the necessary metabolic machinery to carry out transcription, translation, and replication. Furthermore, viruses don’t “grow” like normal eukaryotic, prokaryotic, or Archaea cells, instead they are assembled from pre-formed components. Although most scientists have reached a consensus that viruses are not living organisms, the recent discovery of the giant virus Mimivirus has challenged the relationship of viruses to prokaryotes. Personally, I maintain that viruses are a distinct group separate from living organisms like bacteria.
When Mimivirus was first discovered in the amoebae Acanthamoeba polyphaga, it was actually mistaken for a Gram positive bacteria due to its large size and gram positive staining. It earned its name mi-mi because it mimicked a microbe. Mimivirus is the largest DNA virus ever identified, at 400 mm it is over twice the size of small bacteria like Mycoplasma. While many viruses have exceptionally small genomes that code for only a few proteins, Mimivirus has a 1.2mbp genome that codes for over 900 proteins! Strikingly, Mimivirus contains strand compositional asymmetry with gene transcription from an origin of replication, a trait that is commonly seen in bacteria. Furthermore, Mimivirus contains many genes involved in DNA repair, nucleotide synthesis, protein translation, and metabolic pathways that have never been identified in a virus before but are commonplace in cellular organisms. In particular, the presence of all three types of topoisomerases (important for polysaccharide biosynthesis) is a key piece of evidence that maybe not all viruses are completely dependant on their hosts for protein synthesis. So, the question remains: what distinguishes a large complex virus like Mimivirus from small bacteria?

Obligate intracellular bacteria like Chlamydiae or Rickettsiae don’t have all the genes necessary for transcription or translation and depend on the host to carry out metabolism. Despite some highly suggestive similarities between viruses and small bacteria, the key difference between viruses and bacteria is their life cycle. Mimivirus still has the characteristic viral life cycle that assembles new progeny from pre-formed subunits. The virus enters the cell, starts early gene transcription, replicates its genome, expresses its late genes, then assembles new virions and exits the cell. Mimivirus does not grow and divide like living organisms, instead it mass produces capsid proteins and progeny genomes to be packaged all at once at the end of the lifecycle. Even more important, Mimivirus lacks protein translation machinery (such as ribosomes) that is found in all bacteria. Despite the fact that Mimivirus contains some biosynthesis genes, it still ultimately relies on the host cells to produce progeny.
I highly doubt that Mimivirus is a rare case among viruses. So much of the world’s environment is yet unexplored, especially the oceans. There are likely many more viruses that challenge the distinction between virus and bacteria. Perhaps the line between viruses and bacteria will become less clear over time as new species are discovered, but the evidence today clearly defines viruses as separate organism than living bacteria. On a side note, one important consideration about the existence of large viruses is the implications for viral isolation and metagenomic sequencing. Viruses have commonly been isolated through filtration based on particle size. The filtered material is then analyzed by metagenomic sequencing to learn about the viral community. However, large viruses like Mimivirus would not be able to pass through the filter, thereby excluding such viruses from metagenomic analysis. This could be one of the reasons that more large viruses have not yet been characterized.

References:
1. Claverie, J., Ogata, H., Audic, S., Abergel, C., Suhre, K., Fournier, P. Mimivirus and the emerging concept of “giant” virus. Virus Research. 2006. 117
2. Ghedin, E., Fraser, C.M. A virus with big ambitions. Trends Microbiol. 2005. 13:2, 56-57
3. Moreira, D., Brochier-Armanet, C., Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes. BMC Evol. Biol. 2008. 8:12
4. Suzan-Monti, M., La Scola, B., Raoult, D. Genomic and evolutionary aspects of Mimivirus. Virus Research. 2006. 117, 145-155

Laurel Monticelli (Student, Integrative Microbiology course)

[Tracey McDole]

I am a non-blurrer on this one. Still, after thinking about this question, I realized the definition of a virus I previously held falls short. Having a co-dependent lifestyle with a host organism in order to replicate and persist doesn’t quite work. There are plenty of obligate intracellular bacterial parasites that can’t replicate outside of a host cell. The Mimivirus genome (1.2Mb) is similar in size to many of them, and even encodes genes for nucleotide and amino acid synthesis, which some small obligate prokaryotic parasites lack. However, what these intracellular parasitic bacteria do have that Mimivirus (and its ginormous genome) lacks is the ability to reproduce by cell division. In my opinion, a multiplication mode which entails “loss of corporeal integrity” is probably the only distinguishing characteristic of viruses (or phage). Even in a germinating bacterial endospore, integrity of a core region is maintained. Furthermore, one secret to disassembly and reassembly of corporeal integrity are capsid proteins, which are exclusive to the viral world. In fact, most double-stranded DNA viruses encode capsid proteins, and Mimivirus is no exception.

Tracey McDole (Student, Integrative Microbiology course)

[Eric Sun]

All viruses by definition lose their corporeal integrity upon host infection, and there is no restriction placed on the size (whether in physical size or size of the genome) of the virus to exclude its membership. Criteria used to define a virus and held up consistently over the decades include hijacking of host ribosomes, which all known viruses lack, for viral propagation and the inability of a virus to synthesize its own energy. In my opinion, there should be a detailed comparative genomic analysis to validate the origin of mimivirus before declaration of a fourth domain of life. However, comparative genomic analysis may still not exclude the possibility that the virus evolved from sequestering host genes. Another possibility is to try to delete some of the viral genes that have suspected metabolic activities to confirm their roles in free viruses versus those inside the host. For instance, are some of these genes critical for survival outside the host? What are their functions in a free virus? Do they perform similar roles as their cellular homologues? These questions should help establish a boundary between small obligate prokaryotic parasites and the large DNA mimivirus. Although mimivirus contain both DNA and RNA like all cellular organisms, RNA actually plays a critical part in cellular life-form other than storing genetic information. Consequently, it would be necessary to address the role of RNA in mimivirus. Although the virus could represent a missing link between cellular life and smaller viruses of modern day, I am a non-blurrer until more evidences are shown.

Eric Sun (Student, Integrative Microbiology course)

[Rachel Rettner]

Although giant viruses, such as the Mimivirus, have unique characteristics previously unseen in viruses, I do not believe that their discovery blurs the lines between viruses and cells.
The mimivirus, with its large size of about 650 nm, is about as big as some small bacteria. It also has a large genome, 1.2 Mb in size, which is actually bigger than the genome of some bacteria, such as T. whipplei, which is only 0.9 Mb. Additionally, the genome of the mimivirus contains genes that code for enzymes involved in amino acid synthesis, such as amino-acyl tRNA synthetase, and proteins involved in amino acid metabolism. While these features make the mimivirus unique, they do not allow the mimivirus and other large viruses to be classified as cells.
Perhaps most importantly, mimiviruses do not have genes that code for ribosomal proteins, so they must rely on the host cell to provide translation machinery for its viral proteins. Furthermore, the current understanding of the mimivirus’s life cycle suggests that it is a viral cycle. The mimivirus does not undergo cellular division, but instead replicates by putting together individually synthesized components. Finally, during replication mimiviruses go through an “eclipse phase” characterized by the disappearance of the virus. This implies that, like all viruses, the mimivirus goes through an uncoating process and releases its nucleic acid into the host cells. The disassembly and reassembly of viruses distinguishes them from cellular life.

Rachel Rettner (Student, Integrative Microbiology course)

[Jing Wang]

Mimivirus is a viral genus containing a single identified species named Acanthamoeba polyphaga mimivirus (APMV). In colloquial speech, APMV is more commonly referred to as just “mimivirus”. It has the largest capsid diameter of all known viruses, as well as a large and complex genome compared to other viruses. Whilst not strictly a method of classification, Mimivirus joins a group of large viruses known as nucleocytoplasmic large DNA viruses (NCLDV). They are all large viruses, which share both molecular characteristics and large genomes. The mimivirus genome also possesses 21 genes encoding homologs to proteins which are seen to be highly conserved in the majority of NCLDVs, and further work suggests that mimivirus is an early divergent of the general NCLDV group.
Mimivirus possesses many characteristics, which place it at the boundary of living and non-living. It is as large as several bacterial species, such as Rickettsia conorii and Tropheryma whipplei, possesses a genome of comparable size to several bacteria, including those above, and codes for products previously not thought to be encoded by viruses. In addition, mimivirus possesses genes coding for nucleotide and amino acid synthesis, which even some small obligate intracellular bacteria lack. This means that unlike these bacteria, mimivirus is not dependent on the host cell genome for coding the metabolic pathways for these products. They do however, lack genes for ribosomal proteins, making mimivirus dependent for protein translation and energy metabolism.
Although the size of the virus is as big as what would be classified as a living organism, they lack the essential machinery to translate RNA into proteins. It also has no energy metabolism. Viruses were categorized as non-living due to the two reasons listed above, and the increase in size doesn’t interfere with the topology. Rocks are non-living, and they could be bigger than elephant, but the gigantic size does not mean they are living matters. I would clearly put them in the non-living phylogeny.

Jing Wang (Student, Integrative Microbiology course)

[Jennifer Cisson]

I do not believe that the distinction between virus and cellular life has been blurred simply because a large virus has entered the picture. Throughout evolution there is considerable evidence that size can in many cases confer a selective advantage – but of course, I realize, in microbiology such a slander must be put delicately. There is certainly evidence to the contrary of this statement, and thus I believe it acceptable to argue the point that it only makes sense that some viruses are big – such it their prerogative – while others are quite happy to remain small and thrive as such. Based on size (600nm) and genome complexity (1.4Mb) the mimivirus certainly pushes the envelope of our understanding of what constitutes a virus (Raoult et al., 2007). However, the mimivirus does not seem that fantastic an idea when we consider the constant evolution of what we know about the microbial world. The first microbiologists were limited in their understanding of the microscopic world and were restricted to classify what they saw based on size or shape, and where an isolate came from. However, with the advent of gene expression profiling and sequencing we have improved upon our ability to classify and construct phylogenetic trees. So, why can’t there be a giant virus with a large genome? The mimivirus lacks the rRNA 16S coding region – specific to cellular organisms; it has a capsid, and is an obligate intracellular parasite. These characteristics alone satisfy 3 of the 4 major requirements of a virus – the last of course, being “sub-microscopic”. I also agree with Elio that this virus loses its viral tegument but is able to reconstruct it and infect new hosts – a major feat not seen in any other dimension of life. I am also very much in agreement with Merry Youle; that the major point of difference for a virus or non virus is that no virus – as of yet – has been found that has its own translation machinery (rRNA, ribosomes etc). Therefore, the main parameters for “what makes a virus” seem to be maintained in the mimivirus – based on present data and means of discernment. In another one hundred years something new and earth shattering may again push what we “know” out to a new level or even out the proverbial window. But that is the beauty of science – the constant change and evolution of our means of study and the knowledge each new tool brings. It is not so much a “blurring” of the picture, but a high definition view of what is truly there.

Jennifer Cisson (Student, Integrative Microbiology course)

[Di Hu]

- I’m a non-blurrer, because my personal definition of a virus is an obligate parasite. For me, the most important distinction of a virus is that they are “non-living” under most definitions of “life,” as they do not self-reproduce, and do not carry out metabolic processes in the absence of host machinery. Even though mimivirus has been shown to carry transcripts of DNA polymerase and some tRNA synthetases (and genes that even some bacteria don’t have), they do not contain the genes for ribosomes and thus most likely cannot synthesize proteins, and thus cannot carry out the majority of functions that are considered integral to being “alive.” This, then, maintains the line between viruses and cells for me.

Di Hu (Student, Integrative Microbiology course)

[Anne Lamsa]

I am a non blurrer. Even if the viruses are as big as a cell, they are still fundamentally different from cells. They do not encode or have all of the machinery to replicate themselves. No viruses encode their own ribosomes, even if they do sometimes encode their own RNA polymerase. They do not have cell membranes, only protein coat, and they must uncoat and empty their contents in order to replicate. There are some obligate parasites that are bacteria, but these retain their cellular structure inside the host cell. Viruses are lacking in too many of the necessities of a cell, and thus do not come even close to blurring the line between cells and viruses, no matter the size. Something that would start to blur the line would be a virus that can be infected by another virus. I see the ability to be infected by a virus as an important characteristic of a cell.

Anne (Student, Integrative Microbiology course)

[debbie spector]

I particularly enjoyed Talmudic Question #6 regarding the giant viruses blurring the distinction between viruses and cells. Since I give many lectures in Virology and Molecular Biology, I have given this question some thought. In my opinion, the major distinction that remains between a cell and a virus is that no virus has been found that encodes ribosomal RNA and ribosomal proteins. Hence, the one host function that every virus requires is the protein translation machinery. It might be argued that the cells provide a source of energy, but I believe that this is simply a matter of encoding a few enzymes in an energy conserving or energy producing metabolic pathway; translation, however, is required to produce these enzymes. Likewise there is no a priori reason that a viral membrane could not provide an electron gradient and transport system; in the case of poxviruses, the viral membrane is formed de novo within the cytoplasm.

[Merry Youle]

Allan asks if the quotation is Talmudic. Could be. I've encountered it in various contexts, as in...

"All instruction is but a finger pointing to the moon; and those whose gaze is fixed upon the pointer will never see beyond."

and...

"All talk, as the Chinese masters of old say, is at best a finger pointing to the moon. The finger is not the moon and cannot pull the moon down."

[allan campbell]

I won't get into the semantics, but a Talmudic question deserves a Talmudic answer. In "Viruses take center stage in cellular evolution" (Genome Biol. 7:110, 2006), Claverie supplies a quotation (he doesn't say from where)< "When the finger points to the stars, the fool looks at the finger," which seems apt. Is it Talmudic?

[Merry Youle]

I imagine a Talmudic question would be akin to these lines from the Tao de Ching:
"Work with joy without caring for the achievement. Travel with joy without focusing on the destination." In other words, the value of the question lies in the process of questioning, in the discovery and the going deeper and the unexpected insights. Such questions need not be answered today, but are to be carried with you on the way.

As to the distinction between viruses and cells--- I would argue for both viewpoints. On the one hand, I see "life" as a creative continuum where every possible strategy that we can imagine has been explored, as well as many that have taken us by surprise. When I was in high school, many decades ago, the question posed was "Is a virus alive?" ---a question which I now see as meaningless. We tend to define "life" in a very anthropocentric manner, wanting clear distinctions and neat categories. I see no sharp line between life and non-life, but rather a continuum extending from ISs and viroids through plasmids and viruses (in their incredible diversity) to obligate endobacteria to organelles to eukaryotic cells to multicellular symbionts to colonies of social insects to immense fungal mats to...

On the other hand, I see a sharp distinction between cells and viruses (and other non-cellular entities). I assumed "loss of corporeal integrity" referred to the primary difference in the modes of reproduction employed by viruses and by cells. Specifically, upon entry into a cell, a virus is "unpackaged," a process which separates its nucleic acid(s) from the proteins (and sometimes other molecules) present in the mature virus particle. Some viruses can self-assemble infectious particles in vitro from their nucleic acid and one or a few different kinds of protein. A pre-existing intact virus is not required. All the information that is needed to construct the new virus WITHIN A CELLULAR ENVIRONMENT is contained in the base sequence of its nucleic acid.

With cells, a huge amount of information is required in addition to the (over-emphasized) base sequence of the genome. New cells come from division of an existing cell, and thus inherit all the information embodied in the existing cellular organization and structure. So even though recent discoveries have found that some large viruses have genes for metabolic functions which we previously thought were the sole domain of cells, I think a significant distinction between virus and cell remains.

This must make me a fence sitter.

[Robert Murray]

Life is a game of consequences. Living cells may, given suitable environment, show their life by growing and dividing to form two or more cells. The odd one is unable to cope and dies. A virus requires living cells and some of the systems therein because on entry into the cell it releases nucleic acid instructions for its reformation in quantity. If a particle deemed a possible virus entered a cell to grow and divide retaining integrity it would not be a true virus. The complex viruses just make the task a bit more complex for the host cell.

[Stanley Maloy]

************************

I know what you mean by "lose their corporeal integrity" but I am not convinced that this concept is self-explanatory. Although I agree that this is THE defining characteristic of viruses, it is not an integral part of the definition of viruses commonly used in microbiology classes (for example, simply read the Wikopedia definition of virus).

[stan zahler]

With my mentor, Jim Moulder, I published my Ph.D. thesis on feline pneumonitis virus in 1953. It showed that FPV contained both DNA and RNA. Six or eight years later, Jim had collected enough data to conclude that FPV wsa really a bacterium: genus Chlamydia, as it happens. Having both kinds of nucleic acids is a pretty good sign of non-virus status -- except that some DNA viruses have a little teensy bit of RNA.

[Andrew]

I didn't read the piece on "Mimivirus" yet, so I probably am disqualified from this answer.

But since this is something I was hoping you'd speak to, I will put my depreciated 2 cents into the game.

Human cells pick up all sorts of dirty things. I guess most of the time they wash them clean by breaking the dirty things down into small pieces and recycle them as best they can.

Some bits and pieces are resolved to remain bits and pieces. They do not break down so easily. DNA is my choice of example.

Whatever the operation of method, some foreign DNA incorporates within genomes.

Could these DNA bits be used advantageously for the cell, or is this just another "trick" ascribed to viruses?

I am a blurrer, as I think the "trick" idea can only go so far (one way).

I am willing to blur classic understanding in order to imagine why a cell would prosper from incorporating bits here and there. DNA, membranes, what else?