Advances in cellular evolution

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Much of the recent advance in evolution involve the early evolution of the cell, cell structure, and aspects of abiogenesis.

Source: https://scitechdaily.com/missing-link-discovered-in-the-evolution-of-photosynthesis-and-carbon-fixation/

Missing Link Discovered in the Evolution of Photosynthesis and Carbon Fixation


Rubisco is the most abundant enzyme on the planet. Present in plants, cyanobacteria (also known as blue-green algae) and other photosynthetic organisms, it’s central to the process of carbon fixation and is one of Earth’s oldest carbon-fixing enzymes. Researchers at UC Davis and LBNL have now discovered an alternative form of rubisco in environmental samples. 3D images of the form I rubisco (left) compared to the newly discovered form I-prime (right). The discovery could help understand how the enzyme works and be used in plant breeding. Credit: D. M. Banda et al, 2020

A team led by researchers at the University of California, Davis, has discovered a missing link in the evolution of photosynthesis and carbon fixation. Dating back more than 2.4 billion years, a newly discovered form of the plant enzyme rubisco could give new insight into plant evolution and breeding.

Rubisco is the most abundant enzyme on the planet. Present in plants, cyanobacteria (also known as blue-green algae) and other photosynthetic organisms, it’s central to the process of carbon fixation and is one of Earth’s oldest carbon-fixing enzymes.

“It’s the primary driver for producing food, so it can take CO₂ from the atmosphere and fix that into sugar for plants and other photosynthetic organisms to use. It’s the primary driving enzyme for feeding carbon into life that way,” said Doug Banda, a postdoctoral scholar in the lab of Patrick Shih, assistant professor of plant biology in the UC Davis College of Biological Sciences.

Form I rubisco evolved over 2.4 billion years ago before the Great Oxygenation Event, when cyanobacteria transformed the Earth’s atmosphere by producing oxygen through photosynthesis. Rubisco’s ties to this ancient event make it important to scientists studying the evolution of life.

In a study published on August 31, 2020, in Nature Plants, Banda and researche. . .rs from UC Davis, UC Berkeley and the Lawrence Berkeley National Laboratory report the discovery of a previously unknown relative of form I rubisco, one that they suspect diverged from form I rubisco prior to the evolution of cyanobacteria.

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“The discovery of an octameric rubisco that forms without small subunits allows us to ask evolutionary questions about what life would’ve looked like without the functionality imparted by small subunits,” said Banda. “Specifically, we found that form I-prime enzymes had to evolve fortified interactions in the absence of small subunits, which enabled structural stability in a time when Earth’s atmosphere was rapidly changing.”

According to the researchers, form I-prime rubisco represents a missing link in evolutionary history. Since form I rubisco converts inorganic carbon into plant biomass, further research on its structure and functionality could lead to innovations in agriculture production.

“Although there is significant interest in engineering a ‘better’ rubisco, there has been little success over decades of research,” said Shih. “Thus, understanding how the enzyme has evolved over billions of years may provide key insight into future engineering efforts, which could ultimately improve photosynthetic productivity in crops.”

Reference: “Novel bacterial clade reveals origin of form I Rubisco” by Douglas M. Banda, Jose H. Pereira, Albert K. Liu, Douglas J. Orr, Michal Hammel, Christine He, Martin A. J. Parry, Elizabete Carmo-Silva, Paul D. Adams, Jillian F. Banfield and Patrick M. Shih, 31 August 2020, Nature Plants.
DOI: 10.1038/s41477-020-00762-4

Additional authors on the study are: Albert Liu at UC Davis and LBNL; Jose Pereira and Paul Adams, Joint BioEnergy Institute, LBNL; Christine He, UC Berkeley; Michal Hammel, LBNL; and Douglas Orr, Martin Parry and Elizabete Carmo-Silva, Lancaster University, U.K. The work was partly supported by the U.S. Department of Energy, Branco Weiss Fellowship, the Biotechnology and Biological Sciences Research Council (U.K.), NIH, the Chan Zuckerberg Biohub and Innovative Genomics Institute.

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Evolution on the cellular level is the present cutting edge of evolution research.

Source: https://scitechdaily.com/timeline-unveiled-for-one-of-the-most-important-and-puzzling-events-in-the-evolution-of-life/

Timeline Unveiled for One of the Most Important and Puzzling Events in the Evolution of Life

TOPICS:BiodiversityBioinformaticsEvolutionGeneticsMicrobiologyPopular
By INSTITUTE FOR RESEARCH IN BIOMEDICINE (IRB BARCELONA) NOVEMBER 4, 2020

Timeline of early eukaryotic evolution unveiled the mitochondrial acquisition occurred in a scenario of increasing complexity. Credit: Utrecht University, IRB Barcelona

• By analyzing duplicates of thousands of genes, researchers have reconstructed the evolutionary events leading to the creation of eukaryotic cells, the precursors to virtually all life you can see with the naked eye.
• The evolutionary timeline from simple bacterial cells to complex eukaryotic cells progressed differently than previously thought.
• The study, a collaboration between the Comparative Genomics lab at IRB Barcelona and the University of Utrecht, has been published in Nature Ecology & Evolution.

One of the most important and puzzling events in the evolution of life has been the origin of the first complex eukaryotic cells. Almost all lifeforms that we can perceive with the naked eye, such as algae, plants, animals, and fungi, are made up of complex cells known as ‘eukaryotes.’ A collaborative study between the groups of Toni Gabaldón, ICREA researcher at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC-CNS), and Berend Snel at the University of Utrecht, has concluded that the first cell to incorporate a mitochondrion (considered the key step to the increased complexity of eukaryotic cells) already presented eukaryote-like complexity in structure and functions. This scenario serves as a bridge between the signs of complexity observed in some archaeal genomes and the proposed role of mitochondria in triggering eukaryogenesis.

“The acquisition of mitochondria was considered either to be the crucial first step or the last step in the development of eukaryotic cell complexity,” explains Gabaldón, “our findings show that it was indeed a crucial event, but that it happened in a scenario where cell complexity had already increased.”
Complexity as a prelude to the diversity of life


For roughly the first half of the history of life on Earth, the only forms of life were the relatively simple cells of bacteria. “Eukaryotic cells are larger, contain more DNA and are made up of compartments, each with their own task,” explains first author Julian Vosseberg. “In that sense, you could compare bacterial cells with a tent, while eukaryotic cells are more like houses with several rooms.”

How and when organisms traded the tent for a house is still a mystery, as there are no intermediate forms. One important moment in evolution was the origin of mitochondria, a component of eukaryotic cells that function as their ‘power plants’. Mitochondria were once free-living bacteria, but during evolution, they were absorbed by the ancestors of today’s eukaryotic cells. As gene duplication probably drove the increase in cell complexity, the researchers attempted to reconstruct the evolutionary events based on these genetic changes.
Bioinformatics for evolutionary path reconstruction


“We can use the DNA of contemporary species to reconstruct evolutionary events. Our genes were formed over aeons of evolution. They have changed dramatically over that time, but they still hold echoes of a distant past.” Vosseberg adds, “We have a vast quantity of genetic material available, from a variety of organisms, and we can use computers to reconstruct the evolution of thousands of genes, including ancient gene duplications. These reconstructions have enabled us to uncover the timing of important intermediate steps.”

The co-corresponding author, Berend Snel, from the University of Utrecht, says, “Scientists did not have a timeline of these events. But now we’ve managed to reconstruct a rough timeline.” To achieve this, the researchers adapted an existing method developed at Gabaldon’s lab to create a new protocol, which has resulted in novel insights. These indicate that a lot of complex cellular machinery had evolved even before the symbiosis with mitochondria, including the development of transport within the cell and the cytoskeleton. “The symbiosis wasn’t an event that served as the catalyst for everything else. We observed a peak in gene duplications much earlier in time, indicating that cell complexity had already increased before that moment,” says Snel.

“Our study suggests that the ancestral host that acquired the mitochondrial endosymbiont had already developed some complexity in terms of a dynamic cytoskeleton and membrane trafficking,” says Gabaldón “this might have favored the establishment of symbiotic associations with other microorganisms, including the mitochondrial ancestor, which eventually became integrated.”

Reference: “Timing the origin of eukaryotic cellular complexity with ancient duplications” by Julian Vosseberg, Jolien J. E. van Hooff, Marina Marcet-Houben, Anne van Vlimmeren, Leny M. van Wijk, Toni Gabaldón and Berend Snel, 26 October 2020, Nature Ecology & Evolution.
DOI: 10.1038/s41559-020-01320-z

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Source: https://www.quantamagazine.org/scientists-find-vital-genes-evolving-in-genomes-junkyard-20201116/

Scientists Find Vital Genes Evolving in Genome’s Junkyard

Even genes essential for life can be caught in an evolutionary arms race that forces them to change or be replaced.

Essential genes are often thought to be frozen in evolutionary time — evolving only very slowly if at all, because changing or dying would lead to the death of the organism. Hundreds of millions of years of evolution separate insects and mammals, but experiments show that the Hox genes guiding the development of the body plans in Drosophila fruit flies and mice can be swapped without a hitch because they are so similar. This remarkable evolutionary conservation is a foundational concept in genome research.

But a new study turns this rationale for genetic conservation on its head. Researchers at the Fred Hutchinson Cancer Research Center in Seattle reported last week in eLife that a large class of genes in fruit flies are both essential for survival and evolving extremely rapidly. In fact, the scientists’ analysis suggests that the genes’ ability to keep changing is the key to their essential nature. “Not only is this questioning the dogma, it is blowing the dogma out of the water,” said Harmit Malik, a Howard Hughes Medical Institute investigator who oversaw the study.

“This work is so beautiful,” said Manyuan Long, an evolutionary geneticist at the University of Chicago. “The researchers found that rapidly changing heterochromatin drives the evolution of new essential genes. Just amazing!”
Unexpected Importance of the New

That’s why Long was so surprised in 2010, when he and his students “knocked down” 200 young, novel genes in Drosophila using a technique called RNA interference. Almost 30% of those young genes turned out to be essential; the flies died without them. Even more surprisingly, though, roughly the same percentage of old genes were essential — only about 25%-35% of them. Young genes were just as likely as old ones to encode essential functions.

“I was really shocked and very excited,” Long said. “The old ideas of the field, we felt, were not right, not correct.” Because their discovery seemed so iconoclastic, Long says he decided to gather data carefully and use new technologies like CRISPR to test it further. His team updated their 2010 study in a recent preprint, which addressed some methodological challenges from the earlier study and expanded their analysis to 702 new Drosophila genes. The new paper reached the same general conclusions but posed new questions: What exactly were these young genes doing, and how did they become so vital?
Comparing the Old and the New

To find out, Malik and his graduate student Bhavatharini Kasinathan focused on the ZAD-ZNF genes, the largest family of transcription factors in insects. Some of these had been flagged as new essential genes in Long’s earlier study, but their function was not well understood. About 70 of these ZAD-ZNF genes turned out to be present in all Drosophila species, but 20 were not: They were gained and lost several times over the 40 million year evolution of the various Drosophila species.
Not only is this questioning the dogma, it is blowing the dogma out of the water.

Harmit Malik, Fred Hutchinson Cancer Research Center

To the researchers’ surprise, the 20 genes specific to melanogaster were just as likely to encode essential functions as the 70 that had been strictly conserved over 40 million years. Those results independently confirmed Long’s observations across the entire Drosophila genome in a result Long calls “beautiful.”

In an odd twist, however, Malik and Kasinathan observed that among those 20 genes specific to D. melanogaster, the most rapidly evolving ones were much more likely to encode essential functions than the more slowly evolving ones.

At this point in their investigation, Malik said, “you really begin to question everything you think about in terms of biology, because you’re like, ‘Wait a minute. What is this?’”
Racing to Stay Relevant

To dig deeper into this puzzling result, Kasinathan looked for clues to the functions of Nicknack and Oddjob, two essential ZAD-ZNF genes that evolved quickly. When she checked where they were active inside the Drosophila cells, she encountered another surprise: These transcription factors did not localize to euchromatin, the part of the genome where most genes are located.

Instead, they localized to the heterochromatin — the regions of densely packed DNA that are mainly kept in a silent state because they contain most of the noncoding DNA and other so-called genomic junk. Heterochromatin has largely been ignored by molecular biologists, who like to focus on the gene-rich euchromatin where most of the action is. But even though heterochromatin is considered the boring junkyard of the genome, it does contain a few sequences essential for cell housekeeping, such as the centromeres, the ribosomal RNAs that assist with making proteins, and some regulatory RNAs that control gene expression throughout the genome. Because it evolves so rapidly, the heterochromatin compartments in different species all perform more or less the same essential functions, but their underlying DNA sequences are totally different.
The essential function itself may not be conserved, and that’s a heretical concept.

According to Malik, this explains why Oddjob and Nicknack evolve so rapidly: They have to adjust to the changing DNA environment of the heterochromatin to remain functional. In some ways, they are like the genes of the immune system, which change quickly to keep up with rapidly evolving pathogens in a kind of arms race. But in this case, Malik said, “It’s almost like an arms race happening in the genome, just to preserve an essential function.”

To investigate the function of these two genes further, the researchers swapped copies of Nicknack between the sister species D. melanogaster and D. simulans to see whether the two versions of the gene could functionally replace each other. Curiously, they found that the Nicknack from melanogaster could save the simulans females but not the males. That’s because the males have a huge Y chromosome full of heterochromatin, Malik explains: The Nicknack from melanogaster can restore enough function to ensure survival in simulans females, but it is overwhelmed by all the rapidly evolving heterochromatin in simulans males.

“In development, we think about genes that are really important … being super highly conserved,” Kasinathan said. “But here’s a case of a gene family that is really important for development, and you swap out even closely related transcription factors and it doesn’t work. That’s surprising and kind of cool.”

How to Be Indispensable

It’s also paradoxical: If new genes are essential, how did previous organisms live without them? Malik sees two possibilities. One is that an ancestral gene ceded its function to a new gene. The other is that the new gene performs a function that ancestral organisms didn’t need. Species today face problems that their ancestors didn’t, and those new problems require new solutions. But “what if it’s actually the evolution of these heterochromatin sequences that created the need for this essential function first?” Malik asked.

“The essential function itself may not be conserved, and that’s a heretical concept,” he continued. “We’re not just saying that the essential genes are not conserved. We are actually saying that it’s possible that the essential functions are not conserved, because it’s all context-specific.”

Kasinathan and Malik are now turning their attention to the other ZAD-ZNF transcription factors, many of which also localize to the heterochromatin. “This compartment of the genome that we basically ignored because it’s so gene-poor … is actually, at least for the ZAD-ZNFs, the answer to this paradox of young genes becoming essential,” Malik said.

This insight could prove important in identifying genes relevant to a variety of medical conditions and biological mysteries. “If you’re interested in centromere function, if you only look at the genes that are totally conserved across humans, yeast and flies, you could be missing really important genes that are potential therapeutic targets,” Malik said. “We’ve let our intuition and dogma kind of bias us to the point where we might be missing a lot of important biology.”

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[shunyadragon]

The following addresses scientific research in DNA genetics that further demonstrates the dishonest use of statistics by the phony creationist ID scientists. Cellular evolution remains the cutting edge of the science of evolution in part, because its roots go to abiogenesis. The processes of cellular evolution are no random nor by chance.

Source: https://phys.org/news/2020-11-genetic-code-evolution-darwin-theory.html

Genetic code evolution and Darwin's evolution theory should consider DNA an 'energy code'


by Todd Bates, Rutgers University

Darwin's theory of evolution should be expanded to include consideration of a DNA stability "energy code"—so-called "molecular Darwinism"—to further account for the long-term survival of species' characteristics on Earth, according to Rutgers scientists.

The iconic genetic code can be viewed as an "energy code" that evolved by following the laws of thermodynamics (flow of energy), causing its evolution to culminate in a nearly singular code for all living species, according to the Rutgers co-authored study in the journal Quarterly Reviews of Biophysics.

"These revelations matter because they provide entirely new ways of analyzing the human genome and the genome of any living species, the blueprints of life," said senior author Kenneth J. Breslauer, Linus C. Pauling Distinguished University Professor in the Department of Chemistry and Chemical Biology in the School of Arts and Sciences at Rutgers University-New Brunswick. He is also affiliated with the Rutgers Cancer Institute of New Jersey. "The origins of the evolution of the DNA genetic code and the evolution of all living species are embedded in the different energy profiles of their molecular DNA blueprints. Under the influence of the laws of thermodynamics, this energy code evolved, out of an astronomical number of alternative possibilities, into a nearly singular code across all living species."

Scientists investigated this so-called "universal enigma," probing the origins of the astounding observation that the genetic code evolved into a nearly uniform blueprint that arose from trillions of possibilities.

The scientists expanded the underpinnings of the landmark "survival of the fittest" Darwinian evolutionary theory to include "molecular Darwinism." Darwin's revolutionary theory is based on the generational persistence of a species' physical features that allow it to survive in a given environment through "natural selection." Molecular Darwinism refers to physical characteristics that persist through generations because the regions of the molecular DNA that code for those traits are unusually stable.

Different DNA regions can exhibit differential energy signatures that may favor physical structures in organisms that enable specific biological functions, Breslauer said.

Next steps include recasting and mapping the human genome chemical sequence into an "energy genome," so DNA regions with different energy stabilities can be correlated with physical structures and biological functions. That would enable better selection of DNA targets for molecular-based therapeutics.

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Source: https://scitechdaily.com/lurking-in-genomic-shadows-how-giant-viruses-fuel-the-genetic-evolution-of-organisms/

Lurking in Genomic Shadows: How Giant Viruses Fuel the Genetic Evolution of Organisms

Viruses are tiny invaders that cause a wide range of diseases, from rabies to tomato spotted wilt virus and, most recently, COVID-19 in humans. But viruses can do more than elicit sickness — and not all viruses are tiny.

Large viruses, especially those in the nucleo-cytoplasmic large DNA virus family, can integrate their genome into that of their host — dramatically changing the genetic makeup of that organism. This family of DNA viruses, otherwise known as “giant” viruses, has been known within scientific circles for quite some time, but the extent to which they affect eukaryotic organisms has been shrouded in mystery — until now.

“Viruses play a central role in the evolution of life on Earth. One way that they shape the evolution of cellular life is through a process called endogenization, where they introduce new genomic material into their hosts. When a giant virus endogenizes into the genome of a host algae, it creates an enormous amount of raw material for evolution to work with,” said Frank Aylward, an assistant professor in the Department of Biological Sciences in the Virginia Tech College of Science and an affiliate of the Global Change Center housed in the Fralin Life Sciences Institute.

Mohammad ‘Monir’ Moniruzzaman, a postdoctoral researcher in Aylward’s lab, studies endogenous viral elements, which are fragments or whole sequences of raw viral DNA that have been inserted into the infected host’s genome.

Together, Aylward and Moniruzzaman have recently discovered that endogenous viral elements that originate from giant viruses are much more common in chlorophyte green algae than previously thought.

Their findings will be published today (November 18, 2020) in Nature.

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