Heat Helped Hasten Life's Beginnings on Earth, Research Suggests

ScienceDaily (Dec. 5, 2010) — There has been controversy about whether life originated in a hot or cold environment, and about whether enough time has elapsed for life to have evolved to its present complexity.


Lava flow. (Credit: USGS)

But new research at the University of North Carolina at Chapel Hill investigating the effect of temperature on extremely slow chemical reactions suggests that the time required for evolution on a warm earth is shorter than critics might expect.

The findings are published in the Dec. 1, 2010, online early edition of the Proceedings of the National Academy of Sciences.

Enzymes, proteins that jump-start chemical reactions, are essential to life within cells of the human body and throughout nature. These molecules have gradually evolved to become more sophisticated and specific, said lead investigator Richard Wolfenden, PhD, Alumni Distinguished Professor of biochemistry and biophysics at the UNC School of Medicine.

To appreciate how powerful modern enzymes are, and the process of how they evolved, scientists need to know how quickly reactions occur in their absence.

Wolfenden's group measured the speed of chemical reactions, estimating that some of them take more than 2 billion years without an enzyme.

In the process of measuring slow reaction rates, "it gradually dawned on us that the slowest reactions are also the most temperature-dependent," Wolfenden said.

In general, the amount of influence temperature has on reaction speeds varies drastically, the group found. In one slow reaction, for instance, raising the temperature from 25 to 100 degrees Celsius increases the rate 10 million fold. "That is a shocker," Wolfenden said. "That's what's going to surprise people most, as it did me."

That is surprising, Wolfenden said, because a textbook rule in chemistry -- for more than a century -- has been that the influence of temperature is modest. In particular, a doubling in reaction rate occurs when the temperature rises 10 degree Celsius, according to experiments done in 1866.

High temperatures were probably a crucial influence on reaction rates when life began forming in hot springs and submarine vents, Wolfenden said. Later, the cooling of the earth provided selective pressure for primitive enzymes to evolve and become more sophisticated, the Wolfenden's group hypothesizes.

Using two different reaction catalysts -- which are not protein enzymes but that may have resembled early precursors to enzymes -- the group put the hypothesis to the test. The catalyzed reactions are indeed far less sensitive to temperature, compared with reactions that are accelerated by catalysts. The results are consistent with our hypothesis, Wolfenden said.

Wolfenden's group plans to test the hypothesis using other catalysts. In the meantime, these findings are likely to influence how scientists think of the first primitive forms of life on earth, and may affect how researchers design and enhance the power of artificial catalysts, he added.

Study co-authors from UNC are Randy Stockbridge, PhD, Charles Lewis, Jr., PhD and research specialist Yang Yuan, MS. Support for the research came from the National Institute of General Medicine, a component of the National Institutes of Health.

http://www.sciencedaily.com/releases/2010/12/101202124321.htm

Sewage Water Bacteria: 'Missing Link' in Early Evolution of Life on Earth?

ScienceDaily (Nov. 27, 2010) — A common group of bacteria found in acid bogs and sewage treatment plants has provided scientists with evidence of a 'missing link' in one of the most important steps in the evolution of life on Earth -- the emergence of cells with a nucleus containing DNA (eukaryotic cells).


New research shows that PVC (Planctomycetes, Verrucomicrobiae, Chlamydiae) bacteria -- members of which are commonly found in today's sewage treatment plants or acid bogs -- represent an intermediate type of cell structure. (Credit: iStockphoto/Viktor Balabanov).

For billions of years, bacteria (single celled organisms without a nucleus) were the only cellular life form on Earth. Then, about 1.6 to 2.1 billion years ago, eukaryotic cells emerged. These cells (with a nucleus) heralded the evolution of multi-cellular life on Earth including: plants, insects, animals and humans.

Until now scientists have been unable to identify an 'ancestral cell' linking the early prokaryotes with the later eukaryotes, so fusion theory -- where two cells merge to form a new cell -- is often put forward to explain the appearance of these new cell types.

But new findings by scientists from University College Dublin, Ireland, and the European Molecular Biology Laboratory in Heidelberg, Germany, published in Science (Nov. 26, 2010), have put paid to the fusion theory explanation, and suggest that an intermediate or 'missing link' cell did exist all those billions of years ago.

"Our discovery means that the appearance of eukaryotic cells on Earth can be explained by Darwinian evolution over billions of years rather than a 'big bang' fusion theory," says cell biologist Dr Emmanuel Reynaud from University College Dublin, one of the co-authors of the scientific paper.

"Our analysis shows that PVC [Planctomycetes, Verrucomicrobiae, Chlamydiae] bacteria, members of which are commonly found in today's sewage treatment plants or acid bogs, represent an intermediate type of cell structure. They are slightly bigger than other known bacteria, and they also divide more slowly."

"The structure of PVC suggests that it is an ancestor of a 'missing link' cell which connected prokaryotic to eukaryotic cells along an evolutionary path all those billions of years ago," says Dr Damien P Devos from the European Molecular Biology Laboratory, Heidelberg, Germany, who co-authored the scientific paper.

http://www.sciencedaily.com/releases/2010/11/101126094444.htm

Age Doesn't Matter: New Genes Are as Essential as Ancient Ones

ScienceDaily (Dec. 16, 2010) — New genes that have evolved in species as little as one million years ago -- a virtual blink in evolutionary history -- can be just as essential for life as ancient genes, startling new research has discovered.


The development process for Drosophila melanogaster stopped at the pharate stage when the new gene G32376 was knocked down. This gene originated 18 million years ago. (Credit: Manyuan Long Lab/University of Chicago)

Evolutionary biologists have long proposed that the genes most important to life are ancient and conserved, handed down from species to species as the "bread and butter" of biology. New genes that arise as species split off from their ancestors were thought to serve less critical roles -- the "vinegar" that adds flavor to the core genes.

But when nearly 200 new genes in the fruit fly species Drosophila melanogaster were individually silenced in laboratory experiments at the University of Chicago, more than 30 percent of the knockdowns were found to kill the fly. The study, published December 17 in Science, suggests that new genes are equally important for the successful development and survival of an organism as older genes.

"A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."

The study used technology called RNA interference to permanently block the transcription of each targeted gene into its functional product from the beginning of a fly's life. Of the 195 young genes tested, 59 were lethal (30 percent), causing the fly to die during its development. When the same method was applied to a sample of older genes, a statistically similar figure was found: 86 of 245 genes (35 percent) were lethal when silenced.

Because the young genes tested only appeared between 1 and 35 million years ago, the data suggests that new genes with new functions can become an essential part of a species' biology much faster than previously thought. A new gene may become indispensable by forming interactions with older genes that control important functions, said Sidi Chen, University of Chicago graduate student and first author of the study.

"New genes come in and quickly interact with older genes, and if that interaction is favorable by helping the organism survive or reproduce better, it is favored by natural selection and stays in the genome," Chen said. "After a while, it becomes essential, and the organism literally cannot live without the gene any more. It's something like love: You fall in love with someone and then you cannot live without them."

The indispensable nature of new genes also questions long-held beliefs about the shared features of development across different species. In 1866, German zoologist Ernst Haeckel famously hypothesized that "ontogeny recapitulates phylogeny" after observing that the early steps of development are shared by animals as different as fly and man.

Biologists subsequently predicted and confirmed that the same ancient, essential genes would be the conductors of this early development in all species. This principle enabled the use of model organisms, including flies, mice, and rats, to be used for research on the mechanisms of human disease.

Intriguingly, in the new study, deleting many of the new genes causes flies to die during middle or late stages of development, while older genes were lethal during early development. So while ancient genes essential for the early steps of development are shared, newer genes unique to each species may take over the later developmental stages that make each species unique. For example, many new genes in the study were found to be involved with metamorphosis, the mid-life stage that drastically transforms the body plan in animals.

"This may change the way we view the developmental program," Long said. "Each species has a different species-specific developmental program shaped by natural selection, and we can no longer say that from Drosophila to humans the development of different organisms is just encoded by the same genetic program. The story is much more complicated than what we used to believe."

As such, a full understanding of biological diversity may require a new focus on genes unique to each organism.

"I think it has important implications on human health," Chen said. "Animal models have proven to be very useful and important for dissecting human disease. But if our intuition is correct, some important health information for humans will reside in the unique parts of the human genome."

The newfound importance of young genes and unique developmental programs may have a dramatic impact on the field, Long said. The discovery will also inspire new research directions examining how quickly new genes can become essential and their exact role in species-specific development.

"Biologists have long assumed, quite reasonably, that ancient genes have survived natural selection because they are essential to life and that new genes are generally less critical to an organism's development," said Irene Eckstrand, PhD, who manages Dr. Long's and other evolutionary biology grants at the National Institutes of Health. "This important study suggests that this assumption is flawed, unlocking new questions that could lead to a deeper understanding of evolutionary processes and their impact on human health."

The work was funded by grants from the National Institute of General Medical Sciences, the National Science Foundation, and the Chicago Biomedical Consortium.

http://www.sciencedaily.com/releases/2010/12/101216142523.htm

Molecular Fossil: Crystal Structure Shows How RNA, One of Biology's Oldest Catalysts, Is Made

ScienceDaily (Dec. 17, 2010) — In today's world of sophisticated organisms proteins are the stars. They are the indispensible catalytic workhorses, carrying out the processes essential to life. But long, long ago ribonucleic acid (RNA) reigned supreme.

Now Northwestern University researchers have produced an atomic picture that shows how two of these very old molecules interact with each other. It is a rare glimpse of the transition from an ancient, RNA-based world to our present, protein-catalyst dominated world.

The scientists are the first to show the atomic details of how ribonuclease P (RNase P) recognizes, binds and cleaves transfer RNA (tRNA). They used the powerful X-rays produced by the Advanced Photon Source at Argonne National Laboratory to obtain images from crystals formed by these two RNA molecules. The result is a snapshot of one of the most complex models of a catalytic RNA and its target.

Details of the structure will be published Nov. 14 by the journal Nature.

"RNA is an ancient molecule, but it is pretty sophisticated," said Alfonso Mondragón, professor of molecular biosciences in the Weinberg College of Arts and Sciences. He led the research. "Our crystal structure shows that it has many of the properties we ascribe to modern molecules. RNA is a catalyst that has much of the versatility and complexity of modern-day proteins."

For billions of years and still to this day, the function of RNase P -- found in nearly all organisms, from bacteria to humans -- has been to cleave transfer tRNA. If the tRNA is not cleaved, it is not useful to the cell.

"We knew this important chemistry happened, that RNA acts as a catalyst, but we didn't know exactly how until now," Mondragón said. "We now have a better understanding of how RNA works."

RNase P is formed by a large RNA core plus a small protein, illustrating the evolutionary shift from an RNA world toward a protein-dominated world. The protein helps recognize the tRNA, but most of the recognition occurs through RNA-RNA interactions involving shape complementarity and also base pairing.

The structure shows that once RNase P recognizes tRNA, it docks and, assisted by metal ions, cuts one chemical bond. This matures the tRNA, producing a smaller RNA molecule that now can contribute to fundamental processes in the cell. The RNA-based enzyme does this over and over, cutting each tRNA in exactly the same place every time.

"The discovery nearly 30 years ago that RNA molecules can have a catalytic function raised the idea that maybe RNA was the first molecule," Mondragón said. "Our work reinforces this notion of the existence of an RNA world when life first began."

http://www.sciencedaily.com/releases/2010/11/101114161935.htm

Rise in Oxygen Drove Evolution of Animal Life 550 Million Years Ago

ScienceDaily (Dec. 18, 2010) — Researchers funded by the Biotechnology and Biological Sciences Research Council (BBSRC) at the University of Oxford have uncovered a clue that may help to explain why the earliest evidence of complex multicellular animal life appears around 550 million years ago, when atmospheric oxygen levels on the planet rose sharply from 3% to their modern day level of 21%.


Original image of Trichoplax adhaerens. (Credit: Copyright Karolin von der Chevallerie, University of Hannover)

The team, led by Professor Chris Schofield, has found that humans share a method of sensing oxygen with the world's simplest known living animal -- Trichoplax adhaerens -- suggesting the method has been around since the first animals emerged around 550 million years ago.

This discovery, published in the January 2011 edition of EMBO Reports, throws light on how humans sense oxygen and how oxygen levels drove the very earliest stages of animal evolution.

Professor Schofield said "It's absolutely necessary for any multicellular organism to have a sufficient supply of oxygen to almost every cell and so the atmospheric rise in oxygen made it possible for multicellular organisms to exist.

"But there was still a very different physiological challenge for these organisms than for the more evolutionarily ancient single-celled organisms such as bacteria. Being multicelluar means oxygen has to get to cells not on the surface of the organism. We think this is what drove the ancesters of Trichoplax adhaerens to develop a system to sense a lack of oxygen in any cell and then do something about it."

The oxygen sensing process enables animals to survive better at low oxygen levels, or 'hypoxia'. In humans this system responds to hypoxia, such as is caused by high altitudes or physical exertion, and is very important for the prevention of stroke and heart attacks as well as some types of cancer.

Trichoplax adhaerens is a tiny seawater organism that lacks any organs and has only five types of cells, giving it the appearance of an amoeba. By analysing how Trichoplax reacts to a lack of oxygen, Oxford researcher Dr Christoph Loenarz found that it uses the same mechanism as humans -- in fact, when the key enzyme from Trichoplax was put it in a human cell, it worked just as well as the human enzyme usually would.

They also looked at the genomes of several other species and found that this mechanism is present in multi-cellular animals, but not in the single-celled organisms that were the precursors of animals, suggesting that the mechanism evolved at the same time as the earliest multicellular animals

Defects in the most important human oxygen sensing enzyme can cause polycythemia -- an increase in red blood cells. This latest work could also open up new approaches to develop therapies for this disorder.

Professor Douglas Kell, Chief Executive, BBSRC said "Understanding how animals -- and ultimately humans -- evolved is essential to our ability to pick apart the workings of our cells. Knowledge of normal biological processes underpins new developments that can improve quality of life for everyone. The more skilful we become in studying the evolution of some of our most essential cell biology, the better our chances of ensuring long term health and well being to match the increase in average lifespan in the UK and beyond."

http://www.sciencedaily.com/releases/2010/12/101217145647.htm

New Fossil Site in China Shows Long Recovery of Life from the Largest Extinction in Earth's History

ScienceDaily (Dec. 22, 2010) — A major new fossil site in south-west China has filled in a sizeable gap in our understanding of how life on this planet recovered from the greatest mass extinction of all time, according to a paper co-authored by Professor Mike Benton, in the School of Earth Sciences, and published in the Proceedings of the Royal Society B. The work is led by scientists from the Chengdu Geological Center in China.



An ichthyosaur, a one-meter long fish-eating reptile -- from the new fossil site in China. (Credit: Image courtesy of University of Bristol)

Some 250 million years ago, at the end of the time known as the Permian, life was all but wiped out during a sustained period of massive volcanic eruption and devastating global warming. Only one in ten species survived, and these formed the basis for the recovery of life in the subsequent time period, called the Triassic. The new fossil site -- at Luoping in Yunnan Province -- provides a new window on that recovery, and indicates that it took about 10 million years for a fully-functioning ecosystem to develop.

"The Luoping site dates from the Middle Triassic and contains one of the most diverse marine fossil records in the world," said Professor Benton. "It has yielded 20,000 fossils of fishes, reptiles, shellfish, shrimps and other seabed creatures. We can tell that we're looking at a fully recovered ecosystem because of the diversity of predators, most notably fish and reptiles. It's a much greater diversity than what we see in the Early Triassic -- and it's close to pre-extinction levels."

Reinforcing this conclusion is the complexity of the food web, with the bottom of the food chains dominated by species typical of later Triassic marine faunas -- such as crustaceans, fishes and bivalves -- and different from preceding ones.

Just as important is the 'debut' of top predators -- such as the long-snouted bony fish Saurichthys, the ichthyosaur Mixosaurus, the sauropterygian Nothosaurus and the prolacertiform Dinocephalosaurus -- that fed on fishes and small predatory reptiles.

Professor Shixue Hu of the Chengdu Group said: "It has taken us three years to excavate the site, and we moved tonnes of rock. Now, with thousands of amazing fossils, we have plenty of work for the next ten years!"

"The fossils at Luoping have told us a lot about the recovery and development of marine ecosystems after the end-Permian mass extinction," said Professor Benton. "There's still more to be discovered there, and we hope to get an even better picture of how life reasserted itself after the most catastrophic global event in the history of our planet."

http://www.sciencedaily.com/releases/2010/12/101222093204.htm

Africa Has Two Elephant Species, Genetic Analysis Confirms

ScienceDaily (Dec. 22, 2010) — Contrary to the belief of many scientists (as well as many members of the public), new research confirms that Africa has two -- not one -- species of elephant. Scientists from Harvard Medical School, the University of Illinois, and the University of York in the United Kingdom used genetic analysis to prove that the African savanna elephant and the smaller African forest elephant have been largely separated for several million years.



Top: Forest elephants (shown) in Africa have now been confirmed as a new species of elephant and have been distinguished from the larger savanna elephant in Africa. Bottom: Africa's savanna elephant (shown) is as different from Africa's forest elephant as Asian elephants are to mammoths, says a new study in PLoS Biology. (Credit: Forest elephant photo by Nicholas Georgiadis; Savanna elephant photo by A. Schaefer)

The researchers, whose findings appear online in PLoS Biology, compared the DNA of modern elephants from Africa and Asia to DNA that they extracted from two extinct species: the woolly mammoth and the mastodon. Not only is this the first time that anyone has generated sequences for the mastodon nuclear genome, but it is also the first time that the Asian elephant, African forest elephant, African savanna elephant, the extinct woolly mammoth, and the extinct American mastodon have been looked at together.

"Experimentally, we had a major challenge to extract DNA sequences from two fossils -- mammoths and mastodons -- and line them up with DNA from modern elephants over hundreds of sections of the genome," says research scientist Nadin Rohland of the Department of Genetics at Harvard Medical School.

According to David Reich, associate professor in the same department, "The surprising finding is that forest and savanna elephants from Africa -- which some have argued are the same species -- are as distinct from each other as Asian elephants and mammoths."

Researchers only had DNA from a single elephant in each species, but had collected enough data from each genome to traverse millions of years of evolution to the time when elephants first diverged from each other.

"The divergence of the two species took place around the time of the divergence of the Asian elephant and woolly mammoths," says Professor Michi Hofreiter, who specializes in the study of ancient DNA in the Department of Biology at York. "The split between African savanna and forest elephants is almost as old as the split between humans and chimpanzees. This result amazed us all."

The possibility that the two might be separate species was first raised in 2001, but this is the most compelling scientific evidence so far that they are indeed distinct.

Previously, many naturalists believed that African savanna elephants and African forest elephants were two populations of the same species, despite the significant size differences. The savanna elephant has an average shoulder height of 3.5 meters whereas the forest elephant has an average shoulder height of 2.5 meters. The savanna elephant weighs between six and seven tons, roughly double the weight of the forest elephant.

DNA analysis revealed a wide range of genetic diversity within each species. The savanna elephant and woolly mammoth have very low genetic diversity, Asian elephants have medium diversity, and forest elephants have very high diversity. Researchers believe that this is due to varying levels of reproductive competition among males.

"We now have to treat the forest and savanna elephants as two different units for conservation purposes," says Alfred Roca, assistant professor in the Department of Animal Sciences at the University of Illinois. "Since 1950, all African elephants have been conserved as one species. Now that we know the forest and savanna elephants are two very distinctive animals, the forest elephant should become a bigger priority for conservation purposes."

This research was funded by the Max Planck Society and by a Burroughs Wellcome Career Development Award in Biomedical Science.

http://www.sciencedaily.com/releases/2010/12/101221172244.htm

Fossil Finger Bone Yields Genome of a Previously Unknown Human Relative

ScienceDaily (Dec. 22, 2010) — A 30,000-year-old finger bone found in a cave in southern Siberia came from a young girl who was neither an early modern human nor a Neanderthal, but belonged to a previously unknown group of human relatives who may have lived throughout much of Asia during the late Pleistocene epoch. Although the fossil evidence consists of just a bone fragment and one tooth, DNA extracted from the bone has yielded a draft genome sequence, enabling scientists to reach some startling conclusions about this extinct branch of the human family tree, called "Denisovans" after the cave where the fossils were found.

The findings are reported in the Dec. 23 issue of Nature by an international team of scientists, including many of the same researchers who earlier this year published the Neanderthal genome. Coauthor Richard Green of the University of California, Santa Cruz, played a lead role in the analysis of the genome sequence data, for which a special portal was designed on the UCSC Genome Browser. The team was led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

By comparing the Denisovan genome sequence with the genomes of Neanderthals and modern humans, the researchers determined that the Denisovans were a sister group to the Neanderthals, descended from the same ancestral population that had separated earlier from the ancestors of present-day humans. The study also found surprising evidence of Denisovan gene sequences in modern-day Melanesians, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians, just as Neanderthals appear to have interbred with the ancestors of all modern-day non-Africans.

"The story now gets a bit more complicated," said Green, an assistant professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neanderthals, we now see these very intertwined story lines with more players and more interactions than we knew of before."

The Denisovans appear to have been quite different both genetically and morphologically from Neanderthals and modern humans. The tooth found in the same cave as the finger bone shows a morphology that is distinct from Neanderthals and modern humans and resembles much older human ancestors, such as Homo habilis and Homo erectus. DNA analysis showed that the tooth and the finger bone came from different individuals in the same population.

The finger bone was found in 2008 by Russian scientists in Denisova Cave, an archaeological site in southern Siberia. Pääbo, who had worked with the Russian scientists before, obtained the bone for his research on ancient DNA. In Leipzig, researchers extracted DNA from the bone and sequenced the mitochondrial genome, a smaller DNA sequence separate from the chromosomal DNA and easier to obtain from ancient samples. The results, published earlier this year, showed a surprising divergence from the mitochondrial genomes of Neanderthals and modern humans, and the team quickly began working to sequence the nuclear genome.

"It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome, because we already had the team assembled and ready to do another similar analysis," Green said. "This is an incredibly well-preserved sample, so it was a joy to work with data this nice. We don't know all the reasons why, but it is almost miraculous how well-preserved the DNA is."

The relationship between Denisovans and present-day Melanesians was a completely unexpected finding, he said. The comparative analysis, which included genome sequences of individuals from New Guinea and Bougainville Island, indicates that genetic material derived from Denisovans makes up about 4 to 6 percent of the genomes of at least some Melanesian populations. The fact that Denisovans were discovered in southern Siberia but contributed genetic material to modern human populations in Southeast Asia suggests that their population may have been widespread in Asia during the late Pleistocene, said David Reich of Harvard Medical School, who led the population genetic analysis.

It is not clear why fossil evidence had not already revealed the existence of this group of ancient human relatives. But Green noted that the finger bone was originally thought to be from an early modern human, and the tooth resembles those of other ancient human ancestors. "It could be that other samples are misclassified," he said. "But now, by analyzing DNA, we can say more definitively what they are. It's getting easier technically to do this, and it's a great new way to extract information from fossil remains."

In the light of the Neanderthal and Denisovan genomes, a new, more complex picture is emerging of the evolutionary history of modern humans and our extinct relatives. According to Green, there was probably an ancestral group that left Africa between 300,000 and 400,000 years ago and quickly diverged, with one branch becoming the Neanderthals who spread into Europe and the other branch moving east and becoming Denisovans. When modern humans left Africa about 70,000 to 80,000 years ago, they first encountered the Neanderthals, an interaction that left traces of Neanderthal DNA scattered through the genomes of all non-Africans. One group of humans later came in contact with Denisovans, leaving traces of Denisovan DNA in the genomes of humans who settled in Melanesia.

"This study fills in some of the details, but we would like to know much more about the Denisovans and their interactions with human populations," Green said. "And you have to wonder if there were other populations that remain to be discovered. Is there a fourth player in this story?"

The paper's 28 coauthors include scientists from Germany, Spain, China, Russia, Canada, and the United States. Reich and Green are among seven coauthors credited with contributing equally to this work. This research was supported by the Max Planck Society, the Krekeler Foundation, the U.S. National Institutes of Health, and the U.S. National Science Foundation.

http://www.sciencedaily.com/releases/2010/12/101222131119.htm