Viruses invent their own genes? Then what is left of Darwinism?

_{Denyse O'Leary

June 14, 2018

Darwinism, Evolution, Intelligent Design}

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https://www.sciencedaily.com/releases/2018/06/180611133505.htm — Pandoravirus quercus/IGS- CNRS/AMU

In 2013, the discovery of two giant viruses unlike anything seen before blurred the line between the viral and cellular world. Pandoraviruses are as big as bacteria, and contain genomes that are more complex than those found in some eukaryotic organisms (1). Their strange amphora shape and enormous, atypical genome (2) led scientists to wonder where they came from.

The same team has since isolated three new members of the family in Marseille, continental France, Nouméa, New Caledonia, and Melbourne, Australia. With another virus found in Germany, the team compared those six known cases using different approaches. Analyses showed that despite having very similar shapes and functions, these viruses only share half of their genes coding for proteins. Usually, however, members of the same family have more genes in common.

Furthermore, these new members contain a large number of orphan genes, i.e. genes which encode proteins that have no equivalent in other living organisms (this was already the case for the two previously discovered pandoraviruses). This unexplained characteristic is at the heart of many a debate over the origin of viruses. What most surprised researchers was that the orphan genes differed from one pandoravirus to another, making it less and less likely that they were inherited from a common ancestor!

Bioinformatic analysis showed that these orphan genes exhibit features very similar to those of non-coding (or intergenic) regions in the pandoravirus genome. Findings indicate the only possible explanation for the gigantic size of pandoravirus genomes, their diversity and the large proportion of orphan genes they contain: most of these viruses’ genes may originate spontaneously and randomly in intergenic regions. In this scenario, genes “appear” in different locations from one strain to another, thus explaining their unique nature.

If confirmed, this groundbreaking hypothesis would make these giant viruses craftsmen of genetic creativity — a central, but still poorly explained component of any understanding of the source of life and its evolution. Paper. (public access) – Matthieu Legendre, Elisabeth Fabre, Olivier Poirot, Sandra Jeudy, Audrey Lartigue, Jean-Marie Alempic, Laure Beucher, Nadège Philippe, Lionel Bertaux, Eugène Christo-Foroux, Karine Labadie, Yohann Couté, Chantal Abergel, Jean-Michel Claverie. Diversity and evolution of the emerging Pandoraviridae family. Nature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-04698-4 More.

No wonder that French virologist got frozen out for dissing Darwin.

See also: Why viruses are not considered to be alive

Another stab at whether viruses are alive

Phil Sci journal: Special section on understanding viruses

Should NASA look for viruses in space? Actually, it’s not clear that RNA came first. Nor is it clear that viruses precede life. A good case can doubtless be made for viruses being part of the scrap heap of existing life. But no matter. If you think you can find viruses in space, boldly go.

Why “evolution” is changing? Consider viruses

The Scientist asks, Should giant viruses be the fourth domain of life? Eukaryotes, prokaryotes, archaea… and viruses?

Viruses are alive.

and

Are viruses nature’s perfect machine? Or alive?

Comments

Mimivirus was the first giant isolated "Virus". Of course it is no Virus, but a bacterium that acquired a virus-like coat (capsid proteins). Initial studies revealed ist characteristic virus-like icosahedral morphology, but since the newly isolated microbe also resembled a small bacterium, it was named Mimivirus (for Mi-micking mi-crobe). Mimivirus is a nucleocytoplasmic large DNA virus. This group of viruses includes four other families, of which the enveloped Poxviruses (poxviridae) that infect vertebrates and insects are the most notorious. Additional studies revealed that the genome of Mimivirus contains around 800,000 base pairs, the units that make up the DNA, and roughly eighty percent of that is coding material for proteins. A genetic and protein comparison of Mimivirus did not reveal any sign of amoebas or other contamination, showing that the sequenced genome belongs all to Mimi. Interestingly, Mimivirus lacks universal genes, such a those encoding for ribosomal RNA or proteins, as well as other ubiquitous proteins involved in protein synthesis. The major part of its genome – approximately eighty percent – consists of DNA elements that code for proteins of unknown function with no significant similarity to any other organism. Are these organisms novel life forms? No. These organism are secondary viruses, i.e. they do not mimic bacteria, they are degenerate bacteria that mimic viruses. As usual the evolutionary biologists have teh order up-side-down. Mimivirus most likely derives from a free living soil bacterium, which became parasitic, as it succeeded in entering an amoeba without being digested. In this convenient new Situation, a static environment that provides all resources for reproduction, Mimivirus lost a major part of its DNA. In particular DNA elements that are useless or not immediately required for reproduction in this new environment rapidly degenerated. The genetic studies show that Mimivirus has several genes of the DNA repair system that strongly resemble bacterial genes. The French authors who isolate these huge "viruses" make quite something out of the finding that Mimivirus is the first identified double stranded DNA virus that apparently has a system to counteract DNA damage. But, is it really so surprising? As soon as we start to realize that Mimivirus was derived from a bacterium, there is not much left to be surprised about. Mimivirus may have its origin in a resembling the Pseudomonas, Agrobacterium, or Sinorhizobium species. Only a small number of bacteria simultaneously exhibit DNA elements – genes – that code for topoisomerase type IA, IB and IIA, proteins involved in unwinding the DNA. Both Mimivirus and the above mentioned bacteria have the genes that code for these three proteins. Is this evolution? Or degeneration? Or just opportunism of a designed frontloaded biological system?Peer_{June 15, 2018
June
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Jun
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15
2018
06:40 AM
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PST}

Mimivirus was the first giant isolated "Virus". Of course it is no Virus, but a bacterium that acquired a virus-like coat (capsid proteins). Study revealed characteristic virus-like icosahedral morphology. Because the newly isolated microbe also resembled a small bacterium, it was named Mimivirus (for Mi-micking mi-crobe). Mimivirus is a nucleocytoplasmic large DNA virus. This group of viruses includes four other families, of which the enveloped Poxviruses (poxviridae) that infect vertebrates and insects are the most notorious. Additional studies revealed that the genome of Mimivirus contains around 800,000 base pairs, the units that make up the DNA, and roughly eighty percent of that is coding material for proteins. A genetic and protein comparison of Mimivirus did not reveal any sign of amoebas or other contamination, showing that the sequenced genome belongs all to Mimi. Mimivirus lacks universal genes, such a those encoding for ribosomal RNA or proteins, as well as other ubiquitous proteins involved in protein synthesis. The major part of its genome – approximately eighty percent – consists of DNA elements that code for proteins of unknown function with no significant similarity to any other organism. Are these organisms novel life forms? No. These organism are secondary viruses, or rather they do not micmic bacteria, they mimic viruses. Mimivirus most like stems from a free living bacterium, which became parasitic, as it succeeded in entering an amoeba without being digested. In this convenient new situation that is very much like a static environment that provides all resources for reproduction, Mimivirus lost a major part of its DNA. In particular DNA elements that are useless or not immediately required for reproduction in this new environment rapidly degenerate. The genetic studies show that Mimivirus has several genes of the DNA repair system that strongly resemble bacterial genes. The French authors who isolate these huge "viruses" make quite something out of the finding that Mimivirus is the first identified double stranded DNA virus that apparently has a system to counteract DNA damage. But, is it really so surprising? As soon as we start to realize that Mimivirus was derived from a bacterium there is not much left to be surprised about. Mimivirus may have its origin in a resembling the Pseudomonas, Agrobacterium, or Sinorhizobium species. Only a small number of bacteria simultaneously exhibit DNA elements – genes – that code for topoisomerase type IA, IB and IIA, proteins involved in unwinding the DNA. Both Mimivirus and the above mentioned bacteria have the genes that code for these three proteins. Is this evolution? Or degeneration? Or just opportunism of a desigden frontloaded biological system?Peer_{June 15, 2018
June
06
Jun
15
15
2018
06:34 AM
6
06
34
AM
PST}

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