Tree of life gets a total makeover (Introduction)

by David Turell @, Saturday, August 22, 2015, 21:15 (3141 days ago)

Using genetic studies, what seems related isn't and whole new classes are created:-https://www.sciencenews.org/article/tree-life-gets-makeover-"In the new vision — based on increasingly sophisticated genetic analyses — people and other animals are closer cousins to single-celled choanoflagellates than to other multi­cellular organisms. Giant kelp that grow as wavering undersea forests off the California coast are closer relatives to single­-celled plankton called diatoms than to multicelled red seaweeds or plants.-"The old tree isn't exactly wrong. The kingdoms that used to crown its top — plants, fungi and animals — still exist. But they've moved. In the new diagram, the tree's former crowning glories shrink to mere side branches, three among hundreds, crowded by the vast diversity of complex single cells.-"Biologists analyzing this treetop rarely use the word kingdom anymore. They talk of five or maybe seven bigger branches called supergroups. And the story of demoting kingdoms and introducing supergroups is far from over. A 2014 review noted five proposals for designating the most ancient stretch of supergroup branches, the bit that goes lowest on the new tree. A paper appearing in the Proceedings of the National Academy of Sciences in February described a new method for resolving this debate, and discussions continue.-***-"The new arrangement, summarized in 2012 by Sina Adl of the University of Saskatchewan and colleagues in the Journal of Eukaryotic Micro­biology, makes a fabulous mix of convergence and divergence. Animals are close relatives of fungi. Both are opisthokonts, along with some one-celled cousins. A Phytophthora potato pathogen, once famous as the “fungus” that caused famine in Ireland in the 1840s, is not a fungus at all. It belongs in the same supergroup as the giant kelp. Red and green seaweeds join plants in a distinct group called the archaeplastids."-Comment: What has resemblance on the outside may not show genetic relationships.

Tree of life gets a total makeover

by David Turell @, Saturday, August 22, 2015, 21:19 (3141 days ago) @ David Turell

It is very bushy as we have noted:-http://www.sciencedaily.com/releases/2015/08/150818153509.htm-"New species evolve whenever a lineage splits off into several. Because of this, the kinship between species is often described in terms of a 'tree of life,' where every branch constitutes a species. Now, researchers have found that evolution is more complex than this model would have it, and that the tree is actually more akin to a bush. -***-
"By using the jumping genes, or so-called retrotransposed elements, the Uppsala researchers have found that, for instance, a cuckoo can be more closely related to a hummingbird than a pigeon in a certain part of its genome, while the opposite holds true in another part. The study found numerous examples to corroborate the existence of the phenomenon.-"This is one of the first cases in evolutionary research where researchers have been able to document and quantify incomplete lineage sorting far back in time. It is likely a far more common occurrence than previously thought.-"'The more complex kinship patterns that result from this phenomenon mean that the Tree of Life should often be understood as a Bush of Life', Alexander Suh and Hans Ellegren say."

Tree of life gets a total makeover

by David Turell @, Sunday, September 20, 2015, 14:26 (3113 days ago) @ David Turell

Very bushy. A diagram:-http://www.uncommondescent.com/tree-of-life/encyclopedia-of-the-tree-of-life/

Tree of life gets a total makeover: now giant viruses

by David Turell @, Friday, May 04, 2018, 20:31 (2155 days ago) @ David Turell

New giant viruses are found to be very complex:

https://www.quantamagazine.org/new-giant-viruses-further-blur-the-definition-of-life-20...

"Several families of giant viruses are now known, and some of those giants have more than 1,000 genes; one has a whopping 2,500. (By comparison, some small viruses have only four genes.) Among those genes are ones involved in translation, the synthesis of proteins — a finding that came as a shock. “It appears that giant viruses are as complex as living organisms,” said Chantal Abergel, an evolutionary biologist at Aix-Marseille University in France.

"That conclusion was reinforced last week when scientists reported in Nature Communications that they had found two new giant amoeba-infecting viruses in Brazil, which they named tupanviruses (after Tupã, a thunder god of the regional people). Tupanviruses are striking, and not just because they possess long tails: They have the most complete set of translation-related genes seen to date, including those for all 20 of the enzymes that determine the specificity of the genetic code. The only components they are missing are full-length ribosomal genes. Whether all those elements actually function still needs to be tested.

"Tupanviruses are not unique: Last year, for example, researchers published an analysis of a different group of new giant viruses called klosneuviruses, which similarly turned out to encode an extensive protein-making apparatus. “It’s remarkable that viruses seem to mingle into the translational domain so extensively,” said Matthias Fischer, a virologist at the Max Planck Institute

***

"As examples of this diversity, giant viruses could help illuminate more about how viruses operate and evolve. But even their own origins and evolutionary path are unsettled. One side holds that the giant viruses evolved from smaller viruses over 2 billion years by adding genes, through processes such as horizontal gene transfer and gene duplication. The other maintains that the viruses started out large from the very beginning — and may even have been autonomous organisms — before losing genes they no longer needed and diversifying into the strains we see today.

"The reason for the split lies in the fact that some of the giant viruses’ genes are related to those found in other cellular organisms — archaea, bacteria and eukaryotes — on the tree of life, while others appear to be completely unlike anything else on record. Thirty percent of the tupanvirus genome falls into the latter category, and in other viruses that fraction is even larger.

***

'If all giant viruses turn out to share translation-related genes that are unique to their group, then it would mean they had a large common ancestor, an ancient virus that diversified over time, and it would lend support to the idea that giant viruses started out big and constitute their own domain of life.

"Abergel doesn’t believe they should be their own branch, but “I do think the viruses were already large, complex systems from the outset,” she said. In her view, the origin of life witnessed coevolving protocells that used different strategies of survival. Ultimately, the ancestors of cells were the ones that emerged dominant, equipped with fully operational translation machinery, forcing the “losers of evolution” — the ancestors of the giant viruses — to become parasitic to avoid being completely wiped out. Tupanviruses and others have so many genes involved in protein-making today because of that coevolutionary process, Abergel said.

"But rather than finding genes and proteins with the same evolutionary history, “we get a mixed picture,” Fischer said. A handful of the translation components are widespread among the giant viruses, but many are present in only a few and are closely related to sequences found in eukaryotes. That implies viruses could have started out small — likely as mobile genetic elements, as was posited in 2014 by Eugene Koonin, ...Then, over time, as they infected different hosts, the viruses would have picked up new genes and incorporated them into their translational repertoire.

***

"For now, the tupanviruses provide just one more piece in the puzzle, helping to refine the relationships among the giant viruses. For further insights into their evolution, the researchers will need to analyze the translation-related genes to determine which of them are active, what they do and which are essential for the viruses to replicate successfully.

***

"In the meantime, the classification of viruses remains unclear. Tupanviruses seem to be dependent on their hosts for very little, and other viruses, according to one preprint, even encode ribosomal proteins. “The gap between cellular organisms and viruses is starting to close,” Deeg said. “Which then brings us back to: What is a virus, and what is life?'”

Comment: A bigger tree of life. Viruses have been shown to drive evolution by entering DNA. There is a lot to be learned in this new research.

Tree of life gets a total makeover: now giant viruses

by David Turell @, Friday, June 15, 2018, 15:29 (2114 days ago) @ David Turell

Now Pandoravirus family appears to make its own new genes:

https://www.sciencedaily.com/releases/2018/06/180611133505.htm

"Three new members have been isolated and added to the Pandoravirus family by researchers at the Structural and Genomic Information Laboratory (CNRS/Aix?Marseille Université), working with partners at the Large Scale Biology Laboratory (CEA/Inserm/Université Grenoble?Alpes) and at CEA-Genoscope. This strange family of viruses, with their giant genomes and many genes with no known equivalents, surprised the scientists when they were discovered a few years ago. In the 11 June 2018 edition of Nature Communications, researchers offer an explanation: pandoviruses appear to be factories for new genes -- and therefore new functions. From freaks of nature to evolutionary innovators, giant viruses continue to shake branches on the tree of life!

"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.

***

" 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."

Comment: It has been proposed that viruses drive evolution. This study suggests that might be the case.

Tree of life gets a total makeover: now giant viruses

by dhw, Saturday, June 16, 2018, 11:31 (2113 days ago) @ David Turell

DAVID: Now Pandoravirus family appears to make its own new genes:
https://www.sciencedaily.com/releases/2018/06/180611133505.htm

QUOTE: This strange family of viruses, with their giant genomes and many genes with no known equivalents, surprised the scientists when they were discovered a few years ago. In the 11 June 2018 edition of Nature Communications, researchers offer an explanation: pandoviruses appear to be factories for new genes -- and therefore new functions. From freaks of nature to evolutionary innovators, giant viruses continue to shake branches on the tree of life!
In 2013, the discovery of two giant viruses unlike anything seen before blurred the line between the viral and cellular world.

DAVID’s comment: It has been proposed that viruses drive evolution. This study suggests that might be the case.

These blurred lines between virus and cell, and new genes that lead to evolutionary innovation, seem to me to support the view that evolution has been driven by the autonomous intelligence of microorganisms. However, the following quote came as a surprise to me:
“…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.

My proposal is that adaptations and innovations arise mainly in response to the challenges and opportunities presented by environmental conditions – both local and global. The article confirms the link with different locations, so I don’t know why the researchers say they are random. If they are unique to locations, that would suggest to me that they are intentionally produced to fit in with those locations.

Tree of life gets a total makeover: now giant viruses

by David Turell @, Saturday, June 16, 2018, 15:11 (2113 days ago) @ dhw

DAVID: Now Pandoravirus family appears to make its own new genes:
https://www.sciencedaily.com/releases/2018/06/180611133505.htm

QUOTE: This strange family of viruses, with their giant genomes and many genes with no known equivalents, surprised the scientists when they were discovered a few years ago. In the 11 June 2018 edition of Nature Communications, researchers offer an explanation: pandoviruses appear to be factories for new genes -- and therefore new functions. From freaks of nature to evolutionary innovators, giant viruses continue to shake branches on the tree of life!
In 2013, the discovery of two giant viruses unlike anything seen before blurred the line between the viral and cellular world.

DAVID’s comment: It has been proposed that viruses drive evolution. This study suggests that might be the case.

dhw: These blurred lines between virus and cell, and new genes that lead to evolutionary innovation, seem to me to support the view that evolution has been driven by the autonomous intelligence of microorganisms. However, the following quote came as a surprise to me:
“…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.

My proposal is that adaptations and innovations arise mainly in response to the challenges and opportunities presented by environmental conditions – both local and global. The article confirms the link with different locations, so I don’t know why the researchers say they are random. If they are unique to locations, that would suggest to me that they are intentionally produced to fit in with those locations.

The genes are 'random' if the new ones pop up in unrelated regions to the genome in the past. Are the genes purposefully produced as you state? By the organism or by God?

Tree of life gets total makeover:now giant viruses;addendum

by David Turell @, Saturday, June 16, 2018, 18:29 (2113 days ago) @ David Turell

DAVID: Now Pandoravirus family appears to make its own new genes:
https://www.sciencedaily.com/releases/2018/06/180611133505.htm

QUOTE: This strange family of viruses, with their giant genomes and many genes with no known equivalents, surprised the scientists when they were discovered a few years ago. In the 11 June 2018 edition of Nature Communications, researchers offer an explanation: pandoviruses appear to be factories for new genes -- and therefore new functions. From freaks of nature to evolutionary innovators, giant viruses continue to shake branches on the tree of life!
In 2013, the discovery of two giant viruses unlike anything seen before blurred the line between the viral and cellular world.

DAVID’s comment: It has been proposed that viruses drive evolution. This study suggests that might be the case.

dhw: These blurred lines between virus and cell, and new genes that lead to evolutionary innovation, seem to me to support the view that evolution has been driven by the autonomous intelligence of microorganisms. However, the following quote came as a surprise to me:
“…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.

My proposal is that adaptations and innovations arise mainly in response to the challenges and opportunities presented by environmental conditions – both local and global. The article confirms the link with different locations, so I don’t know why the researchers say they are random. If they are unique to locations, that would suggest to me that they are intentionally produced to fit in with those locations.


David: The genes are 'random' if the new ones pop up in unrelated regions to the genome in the past. Are the genes purposefully produced as you state? By the organism or by God?

Note this statement by the article:

"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."

Tree of life gets a total makeover: now giant viruses

by dhw, Sunday, June 17, 2018, 12:18 (2112 days ago) @ David Turell

dhw: These blurred lines between virus and cell, and new genes that lead to evolutionary innovation, seem to me to support the view that evolution has been driven by the autonomous intelligence of microorganisms. However, the following quote came as a surprise to me:
“…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.”

My proposal is that adaptations and innovations arise mainly in response to the challenges and opportunities presented by environmental conditions – both local and global. The article confirms the link with different locations, so I don’t know why the researchers say they are random. If they are unique to locations, that would suggest to me that they are intentionally produced to fit in with those locations.

DAVID: The genes are 'random' if the new ones pop up in unrelated regions to the genome in the past. Are the genes purposefully produced as you state? By the organism or by God?

By definition all innovation has to involve something unrelated to the past. You always emphasize your God’s purposefulness, and I too assume that any adaptation or innovation will be purposeful. For you, it is your God who purposefully preprogrammed or dabbled every innovation, lifestyle and natural wonder. I propose that the organisms use their autonomous intelligence to produce them all purposefully, but I do not know where that autonomous intelligence comes from. Your God is clearly one option.

ADDENDUM:
DAVID: Note this statement by the article:
"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."

I did indeed note it, and it is integral to my proposal that cellular intelligence (to which we must add viral intelligence) is the driving force of evolution. I agree that the source is “poorly explained”! Your God, chance, and some form of atheistic panpsychism are three of the poor explanations.

Tree of life gets a total makeover: now giant viruses

by David Turell @, Sunday, June 17, 2018, 15:03 (2112 days ago) @ dhw

dhw: These blurred lines between virus and cell, and new genes that lead to evolutionary innovation, seem to me to support the view that evolution has been driven by the autonomous intelligence of microorganisms. However, the following quote came as a surprise to me:
“…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.”

My proposal is that adaptations and innovations arise mainly in response to the challenges and opportunities presented by environmental conditions – both local and global. The article confirms the link with different locations, so I don’t know why the researchers say they are random. If they are unique to locations, that would suggest to me that they are intentionally produced to fit in with those locations.

DAVID: The genes are 'random' if the new ones pop up in unrelated regions to the genome in the past. Are the genes purposefully produced as you state? By the organism or by God?

dhw: By definition all innovation has to involve something unrelated to the past. You always emphasize your God’s purposefulness, and I too assume that any adaptation or innovation will be purposeful. For you, it is your God who purposefully preprogrammed or dabbled every innovation, lifestyle and natural wonder. I propose that the organisms use their autonomous intelligence to produce them all purposefully, but I do not know where that autonomous intelligence comes from. Your God is clearly one option.

Still on he fence


ADDENDUM:
DAVID: Note this statement by the article:
"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."

dhw: I did indeed note it, and it is integral to my proposal that cellular intelligence (to which we must add viral intelligence) is the driving force of evolution. I agree that the source is “poorly explained”! Your God, chance, and some form of atheistic panpsychism are three of the poor explanations.

One is correct

Tree of life gets a total makeover: now giant viruses

by David Turell @, Wednesday, March 27, 2019, 14:01 (1829 days ago) @ David Turell

A new very complex giant virus attacks amoebas:

https://www.sciencedaily.com/releases/2019/03/190325110300.htm

the Medusavirus, a unique giant virus that gives pause to current theory on viral evolution.

"The name Medusavirus was given for the effect this virus has on its host, Acanthamoeba castellanii. Once infected, the amoeba forms cysts, a phenomenon called encystment. This is a typical response to environments hostile to survival, and leaves the amoeba with a hard, protective covering. Perhaps it was not a coincidence then that Medusavirus was found in the hot springs in northern Japan, the first giant virus to have been isolated from a heated environment.

"Along with the location of its discovery, Medusavirus holds a number of distinguishing features compared with other giant viruses. Its DNA codes for all five types of histones, the key proteins that help compact DNA within the nucleus. In fact, no other known virus has all five types. Further, Medusavirus encoded neither RNA polymerase nor DNA topoimerase II, whereas all other giant viruses encode at least one.

"These features could explain why the replication of Medusavirus DNA begins and completes in the host nucleus to eventually fill the amoeba nucleus with viral DNA, which again is unlike other giant viruses.

"Moreover, the morphology of the capsid surface was unique, in that it was covered with an extraordinary number of spherical-headed spikes. In addition, the amoeba genome encoded several capsid surface proteins.

"The existence of histone genes in Medusavirus and capsid protein genes in amoeba suggest lateral gene transfer going both directions -- host-to-virus and virus-to-host.

"Overall, the findings suggest that Medusavirus offers a new model for host-virus co-evolution and that the Medusavirus is a new family of large DNA viruses."

Comment: The bush of life gets stranger and stranger. Viruses attack every level of life from bacteria (called bacteriophages) to humans. Why? They are claim ed to aid in the process of evolution. No one knows why they evolved. or how, since they are dependent on living forms to survive

Tree of life gets a total makeover: Archaea to eukaryotes?

by David Turell @, Monday, December 23, 2019, 01:31 (1558 days ago) @ David Turell

A new claim:

https://arstechnica.com/science/2019/12/the-tree-of-life-may-have-only-two-major-branch...

"...in the 1970s, archaea were discovered. These organisms are single-celled and lack nuclei, like prokaryotes, but their cell membranes and the way they make proteins from DNA are similar to eukaryotes. They are dissimilar enough to both prokaryotes and eukaryotes that they became their own third domain on the tree of life. And they became contenders for the role of eukaryotic ancestor—maybe the cell that initially swallowed a bacterium was an archaea.

"Researchers were able to home in on a likely candidate for this proto-eukaryote with the advent of metagenomics, the ability to sequence the DNA of species that cannot be grown in the lab. In 2015, they found a species of archaea that had all the requisite qualifications at a site called Loki’s Castle, a hydrothermal vent under the Arctic. Researchers duly named this organism Lokiarchaea. (Mythology thus informed not only the nomenclature of geologic features on the ocean floor, but of microbes as well.)

"The identification of Lokiarchaea led scientists to related species that they inevitably called Thor-, Odin-, and Heimdallarchaeota. The whole group is obviously known as the Asgard superphylum.

"But the three-domain tree of life taxonomy—like all other taxonomies—depends on the species used to build the tree, the genetic sequences chosen from those species, and the methods used to compare those sequences to each other. New thinking in the field is that the three domain model was made using a highly limited dataset—36 genes from 104 taxa—and is too simplistic. A two-domain model, in which eukaryotes are a branch of archaea, fits the data much better.

"The 3-D camp counters that the genetic similarities between archaea and eukaryotes, upon which much of the 2-D argument relies, are due to contamination of archaea by eukaryotes and that only fast-evolving archaea were included in the analysis, thus skewing the results.
So now a group of evolutionary biologists has undertaken a larger analysis, including over 3,000 gene families from 125 species analyzed using three different methods. Unlike the former study, this one incorporated many uncultivated microbes.

"Regardless of which genomic data is used and the method by which it’s sliced and diced, the team concluded that a two-domain tree seems to fit it better. Eukaryotes seem to have arisen from the Asgard archaea branch, which has genes that were considered uniquely eukaryotic, not because they were contaminated by eukaryotic samples, but because they are the ancestral versions of the ones eukaryotes now have."

Comment: This result makes sense. Remember life started under extreme conditions and all Archaea are found in extreme conditions. Maybe prokaryotes swallowed Archaea?

Tree of life gets a total makeover: Archaea to eukaryotes?

by David Turell @, Tuesday, December 27, 2022, 18:15 (458 days ago) @ David Turell

More on Asgards:

https://www.livescience.com/asgard-archaea-striking-new-images

" Now, for the first time, scientists have grown a large enough quantity of these microbes in the lab to study their internal structure in detail,

"Researchers grew an organism called Lokiarchaeum ossiferum, which belongs to a group of microbes known as Asgard archaea, according to a new report, published Wednesday (Dec. 21) in the journal Nature(opens in new tab). Asgard archaea are thought by some scientists to be the closest evolutionary relatives of eukaryotes, cells that package their DNA in a protective bubble called a nucleus.

"On the evolutionary tree of life, Asgards often appear as a "sister" of eukaryotes or as their direct ancestor, Jan Löwe, leader of the Bacterial Cytoskeleton and other Molecular Machines research group at the Medical Research Council, wrote in a commentary about the new study. Asgards don't carry nuclei themselves, but they do contain a suite of genes and proteins that were once thought to be unique to eukaryotes. Researchers have a variety of theories as to how Asgards may have gained primitive nuclei and thus birthed the first complex cells, which later gave rise to plants, animals and humans.

***

"Compared with other Asgards, L. ossiferum grows relatively fast, doubling its number of cells in seven to 14 days, Löwe noted. In comparison, P. syntrophicum replicates every 14 to 25 days. Note that the familiar bacterium Escherichia coli replicates every 20 minutes or so. (The slow growth of these archaea is one factor that makes them incredibly difficult to culture.)

"Gathered from mud in a canal on the coast of Piran, Slovenia, the L. ossiferum specimens have funky tentacles that extend from the body of each cell; odd bumps and bulges appear along the length of each appendage. These "surface protrusions" may support the idea that, at some point in evolutionary history, an Asgard grabbed a passing bacterium using similar extensions of its membrane and sucked the bacterium into its cell body, and this led to the development of the nucleus, Löwe wrote. The protrusions support the idea that such an interaction could have occurred, he explained.

"L. ossiferum also carries tiny, lollipop-like structures on its surface, which "look like they come from another planet," Thijs Ettema(opens in new tab), an environmental microbiologist at Wageningen University in the Netherlands who wasn't involved in the work, told Science. The microbe also contains structural filaments that closely resemble those seen in the cytoskeleton, or supporting scaffold, of eukaryotic cells, Löwe wrote.

More evidence:

https://www.science.org/content/article/strange-tentacled-microbe-may-resemble-ancestor...

"Additional evidence came earlier this year when Victoria Orphan, a geobiologist at the California Institute of Technology and her colleagues isolated enough of two other Asgard species—from rock collected from a hydrothermal vent in the Gulf of California—to sequence their complete genomes. The genes in those genomes bolstered the case that these genes really did arise in archaea. Moreover, the genomes harbored mobile pieces of DNA that contained bacterial genes involved in metabolism, suggesting these elements played a role in transferring genes among life’s major branches, Orphan and her colleagues reported on 13 January in Nature Microbiology.

"By comparing the proteins encoded by Asgard archaea and eukaryotes, researchers including Ettema, Baum, and Mohan Balasubramanian, a cellular microbiologist at the University of Warwick, recently connected the two domains in another way. They focused on the interacting protein complexes eukaryotic cells use to bend, cut up, and stitch together their membranes to link internal compartments. To that point, only two of those protein complexes had been found in archaea. But Asgard genomes contain instructions for making four of them, the team reported on 13 June in Nature Communications.

"After predicting the proteins’ structures, the group synthesized some of the molecules in the lab and showed they work similarly to the eukaryotic versions. To the scientists, that suggests this membrane-manipulating machinery predates the evolution of eukaryotes.

***

"Its genome is larger and has more eukaryotic genes than the other cultured Asgard, and its DNA includes four genes for the protein actin, a key component of a eukaryotic cell’s internal skeleton, Schleper’s team reports. That skeleton extends throughout the cell and into the tentacles, and it varies from cell to cell, suggesting it’s capable of being rearranged. “We show that the ‘eukaryotic’ cytoskeleton—which is crucial for eukaryotes—was an invention within archaea, meaning it evolved before the emergence of the first eukaryotic cells,” Schleper explains.

“'This study further strengthens that our ancestor is archaea,” agrees Nobu’s collaborator, Hiroyuki Imachi, a microbiologist at the Japan Agency for Marine-Earth Science and Technology.

***

"Some scientists now believe the most likely scenario for the emergence of eukaryotes, some 2 billion years after bacteria and archaea arose, is that an Asgard-like microbe enveloped an oxygen-using bacterium, turning it into an extra energy producer for its host. The archaea may have also acquired other bacteria to make the combined cell that comprise eukaryotes."


Comment: More evidence our ancestors are Archaea.

Bush of life: role of giant viruses in food web

by David Turell @, Friday, April 17, 2020, 15:30 (1442 days ago) @ David Turell

They live on ocean forms at the bottom of the web:

https://www.sciencemag.org/news/2020/04/giant-viruses-aren-t-alive-so-why-have-they-sto...

Viruses might not be alive, but they may be altering life on a global scale. Researchers have found that a bizarre group of microbes known as “giant viruses” contain genes associated with metabolism, which they likely use to convert their zombified hosts into supercharged energy factories. Because many of their victims are important players in dampening climate change and in controlling ocean ecosystems, the megaviruses may be exerting an unexpected power over life on Earth.

There are more than 200,000 kinds of viruses in the world’s oceans. Some are giant viruses, so named because they tend to be about 10 times bigger than the average virus. They’re still tiny—the largest is only one-fifth the size of a red blood cell—which may explain why they went undiscovered until 2003. Since then, researchers have learned some basic facts—the viruses mostly infect amoebas and phytoplankton, for example—but scientists are still trying to figure out what makes them tick.

***

Their results, published this month in Nature Communications, show that giant viruses are extremely diverse, splitting into 54 distinct groups. Several genomes were new to science and likely represent new species.

In addition to the usual genes that allow a virus to infect its host and multiply, many also contained genes for metabolism, the process that converts food into energy in all living cells. This was a surprise because viruses don’t eat. And strangely, these genes weren’t a recent addition, says first author Mohammad “Monir” Moniruzzaman: Many had been evolving in the viruses for millions of years. “If your goal is simply to find a new host and multiply,” he asks, why do you need these genes?

All of this could have a dramatic impact on sea life. Phytoplankton suck the greenhouse gas carbon dioxide from the atmosphere as they photosynthesize. They also form the base of the entire food web, the interconnected “who-eats-whom” relationships between predator and prey. Still, researchers are just beginning to study what the larger impacts could be. (my bold)

Frederik Schulz, a microbiologist at the Joint Genome Institute, says the new work comes to “similar conclusions” as those found by his own team. But he cautions against speculating too broadly. Just because a gene helps living organisms metabolize, doesn’t mean it does the same thing for viruses.

Comment: Since these viruses are part of the lowest sections of the sea food web, and affect phytoplankton photosynthesis, using CO2 and producing free O2., it can be proposed they are a significant part of God's design plan.

Bush of life: how giant viruses attack

by David Turell @, Tuesday, May 26, 2020, 23:33 (1402 days ago) @ David Turell

More research on how they release their DNA. Like all viruses they lack RNA and cannot replicate without it:

https://www.livescience.com/triggers-for-giant-virus-infection.html?utm_source=Selligen...

"Viruses, giant or otherwise, lack the machinery required to make copies of their DNA; the microbes are essentially just a coil of genetic material tucked inside an envelope, called a capsid. In order to survive, viruses must sneak inside a host cell, hijack the machinery within and set up a so-called viral factory to produce new viruses. Giant viruses have a special portal for this job: the stargate.

***

"Since their initial discovery, giant viruses have been recovered from melting permafrost in Siberia, the depths of the Antarctic ocean and highly alkaline soda lakes, as well as less exotic environments, said Chantal Abergel, research director of the Structural and Genomic Information laboratory at the French National Centre for Scientific Research, who was not involved in the study. The viruses have mostly been found to infect amoebas and phytoplankton, but laboratory studies suggest that they can also infect animal cells, including rodent and human cells. However, "no direct link between GVs and human disease has yet been established," the authors noted.

***

"For example, Parent and her coauthors studied several giant viruses that look like 20-sided dice, including the mimivirus, Antarctica virus, Samba virus and Tupanvirus. The structure and outer shells of these viruses "are very complex, as never seen before in the virosphere," Jônatas Abrahão, an associate professor of virology at the Universidade Federal de Minas Gerais in Brazil, told Live Science in an email. The stargate found on the surfaces of these viruses particularly fascinates scientists "due its beauty and symmetry," and the fact that no smaller viruses contain such a structure, said Abrahão, who was not involved in the study.

***

"Before the stargate opens, giant viruses get "gobbled up by cells" in a process called phagocytosis, Parent said. While small viruses like influenza fuse their fatty membrane with that of the cell they're infecting, giant viruses enter cells by being swallowed whole, hard outer shell and all.

"Once inside, the giant viruses open their stargates and release their infectious "seed," Abergel said. "This is an entire structure that is downloaded from the plasmid," or circular ring of viral DNA, into the cytoplasm, or the water solution of proteins and salts that surrounds the organelles in eukaryotic cells. This process jumpstarts infection, she said."

Comment: The complex parts of the giant virus suggest it is a more evolved form of virus.

Bush of life: giant viruses can create energy

by David Turell @, Monday, November 02, 2020, 14:19 (1243 days ago) @ David Turell

Do they have a metabolism?:

https://www.newscientist.com/article/2258107-viruses-have-been-shown-to-produce-their-o...

"A few giant viruses appear to generate their own energy, which viruses are not supposed to be able to do. Viruses usually consist of RNA or DNA wrapped in a protein coat or membrane, and rely on host cells to copy themselves. Giant viruses, first discovered in 2003, can be larger than bacterial cells and some have their own machinery for processes like copying DNA into RNA. Now researchers have found that some giant viruses known as pandoraviruses somehow generate an electrical voltage across their outer membrane. It takes energy to do this, which means these giant viruses must have a metabolism, but why they do so is still unclear. The finding will fuel an already fierce debate about whether giant viruses really are viruses, and if they are alive or not."

Comment: No real answers as yet

Bush of life: giant virus DNA hiding in Algae

by David Turell @, Thursday, November 19, 2020, 14:49 (1226 days ago) @ David Turell

What is it doing there?:

https://www.sciencemag.org/news/2020/11/giant-virus-genomes-discovered-lurking-dna-comm...

"In 2003, scientists discovered something huge, literally, in the virus world: viruses so big they could be seen with a standard microscope. These massive parasites were considered rare at the time, but they’ve since proved more common than anyone expected. Now, researchers have found entire giant virus genomes embedded in the genomes of several common algae. The find suggests this strange viral group is even more prolific—and potentially influential—than scientists thought.

***

"Viral matches “kept popping up in algal genomes,” Aylward recalls. So the duo and their colleagues systematically looked through genomes representing all of the sequenced DNA from the group of algae called Chlorophytes. An entire giant virus was genetically present in the DNA of a dozen of these species, the team reports today in Nature.

"In all, the viruses added between 78 and 1782 genes to the algae. Two algae even had the whole genomes of two giant viruses in their DNA, in one case making up 10% of the algae’s total gene count.

"It’s not clear why these viruses sneak their DNA into their host’s genome, instead of just replicating inside the cell. It may be a way for the virus to ensure that its genetic material will be passed down from generation to generation. HIV and other viruses also integrate their genes into human DNA—one reason they are difficult to eliminate by the immune system or drugs.

"Some of these giant viruses have likely been part of the algae for a long time, the researchers found, perhaps millions of years. Indeed, some viral DNA has acquired noncoding DNA called introns within their genes. And some of their genes are now duplicated or missing, changes that are unlikely to occur in viruses simply floating around inside algal cells.

“'They make a solid case that the viral sequences they identified are, in all likelihood, part of their host genomes,” says Matthias Fischer, an environmental virologist at the Max Planck Institute for Medical Research.

***

"The viral DNA present in algae can even include genes hijacked from other algae. The giant viruses may therefore be a way to transfer genes among species, says Andrew Roger, an evolutionary biologist at Dalhousie University. All of this new DNA can enable the host genome to take on new functions that improve the alga’s ability to survive and may have shaped the group’s diversity and distribution, he says.

“'These interactions have been going on since the origins of life,” Fischer adds. “And they continue to play a big role in cellular evolution.'”

Comment: Note the bold. This is a mystery, but perhaps the key is the role in evolution.

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