Wasous

Our prehistoric Earth, bombarded with asteroids and lightening, rife with bubbling geothermal pools, may not seem hospitable today. But somewhere in the chemical chaos of our early planet, life did form. How? For decades, scientists have attempted to create miniature replicas of infant Earth in the lab. There, they hunt for the primordial ingredients that created the essential building blocks for life.

Somewhere in the hostile environment of early Earth, life was born [Credit: Harvard University]

It's attractive to chase our origin story. But this pursuit can bring more than just thrill. Knowledge of how Earth built its first cells could inform our search for extraterrestrial life. If we identify the ingredients and environment required to spark spontaneous life, we could search for similar conditions on planets across our universe.

Today, much of the origin-of-life research focuses on one specific building block: RNA. While some scientists believe that life formed from simpler molecules and only later evolved RNA, others look for evidence to prove (or disprove) that RNA formed first. A complex but versatile molecule, RNA stores and transmits genetic information and helps synthesize proteins, making it a capable candidate for the backbone of the first cells.

To verify this "RNA World Hypothesis," researchers face two challenges. First, they need to identify which ingredients reacted to create RNA's four nucleotides--adenine, guanine, cytosine, and uracil (A, G, C, and U). And, second, they need to determine how RNA stored and copied genetic information in order to replicate itself.

So far, scientists have made significant progress finding precursors to C and U. But A and G remain elusive. Now, in a paper published in the Proceedings of the National Academy of Sciences, Jack W. Szostak, Professor of Chemistry and Chemical Biology at Harvard University, along with first-author and graduate student Seohyun (Chris) Kim suggest that RNA could have started with a different set of nucleotide bases. In place of guanine, RNA could have relied on a surrogate--inosine.

"Our study suggests that the earliest forms of life (with A, U, C, and I) may have arisen from a different set of nucleobases than those found in modern life (A, U, C, and G)," said Kim. How did he and his team arrive at this conclusion? Lab attempts to craft A and G, purine-based nucleotides, produced too many undesired side products. Recently, however, researchers discovered a way to make versions of adenosine and inosine--8-oxo-adenosine and 8-oxo-inosine--from materials available on primeval Earth. So, Kim and his colleagues set out to investigate whether RNA constructed with these analogs could replicate efficiently.

But, the substitutes failed to perform. Like a cake baked with honey instead of sugar, the final product may look and taste similar, but it doesn't function as well. The honey-cake burns and drowns in liquid. The 8-oxo-purine RNA still performs, but it loses both the speed and accuracy needed to copy itself. If it replicates too slowly, it falls apart before completing the process. If it makes too many errors, it cannot serve as a faithful tool for propagation and evolution.

Despite their inadequate performance, the 8-oxo-purines brought an unexpected surprise. As part of the test, the team compared 8-oxo-inosine's abilities against a control, inosine. Unlike its 8-oxo counterpart, inosine enabled RNA to replicate with high speed and few errors. It "turns out to exhibit reasonable rates and fidelities in RNA copying reactions," the team concluded. "We propose that inosine could have served as a surrogate for guanosine in the early emergence of life."

Szostak and Kim's discovery could help substantiate the RNA world hypothesis. In time, their work might confirm RNA's primary role in our origin story. Or, scientists might find that early Earth offered multiple paths for life to grow. Eventually, armed with this knowledge, scientists could identify other planets that have the essential ingredients and determine whether we share this universe or are, indeed, alone.

Source: Harvard University [December 03, 2018]

University of Nebraska-Lincoln researchers have found revolutionary evidence that an evolutionary phenomenon at work in complex organisms is at play in their single-celled counterparts, too.

The Grand Prismatic Spring of Yellowstone National Park houses heat- and acid-loving archaea [Credit: Shutterstock]

Species most often evolve through DNA mutations inherited by successive generations. A few decades ago, researchers began discovering that multicellular species can also evolve through epigenetics: traits originating from the inheritance of cellular proteins that control access to an organism's DNA, rather than genetic changes.

Because those proteins can respond to shifts in an organism's environment, epigenetics resides on the ever-thin line between nature and nurture. Evidence for it had emerged only in eukaryotes, the multicellular domain of life that comprises animals, plants and several other kingdoms.

But a series of experiments from Nebraska's Sophie Payne, Paul Blum and colleagues has shown that epigenetics can pass along extreme acid resistance in a species of archaea: microscopic, single-celled organisms that share features with both eukaryotes and bacteria.

"The surprise is that it's in these relatively primitive organisms, which we know to be ancient," said Blum, Charles Bessey Professor of Biological Sciences at Nebraska. "We've been thinking about this as something (evolutionarily) new. But epigenetics is not a newcomer to the planet."

The team discovered the phenomenon in Sulfolobus solfataricus, a sulfur-eating species that thrives in the boiling, vinegar-acidic springs of Yellowstone National Park. By exposing the species to increasing levels of acidity over several years, the researchers evolved three strains that exhibited a resistance 178 times greater than that of their Yellowstone ancestors.

One of those strains evolved the resistance despite no mutations in its DNA, while the other two underwent mutations in mutually exclusive genes that do not contribute to acid resistance. And when the team disrupted the proteins thought to control the expression of resistance-relevant genes—leaving the DNA itself untouched—that resistance abruptly disappeared in subsequent generations.

Sophie Payne, doctoral student in biological sciences, has co-authored a study showing that single-celled organisms known as archaea can pass on traits even without changes in their DNA. This phenomenon, known as epigenetics, was found in a species that eats crystalline sulfur (pictured at front) [Credit: Greg Nathan/University Communication]

"We predicted that they'd be mutated, and we'd follow the mutations, and that would teach us what caused the extreme acid resistance," Blum said. "But that's not what we found."

Though epigenetics is essential to some of the most productive and destructive physiological processes in humans—the differentiation of cells into roughly 200 types, the occurrence of cancers—it remains difficult to study in eukaryotes.

The simplicity of archaea, combined with the fact that their cells resemble eukaryotes' in some important ways, should allow researchers to investigate epigenetic questions much faster and more cheaply than was possible before, Blum said.

"We don't know what flips the switch in humans that changes epigenetic traits," Blum said. "And we sure don't know how to reverse it very often. That's the first thing we'll go after: how to turn it on, how to turn it off, how to get it to switch. And that has benefits when you think about (managing) traits in us or traits in plants."

Yet the discovery also raises questions, Payne said, especially about how both eukaryotes and archaea came to adopt epigenetics as a method of inheritance.

"Maybe both of them had it because they diverged from a common ancestor that had it," said Payne, a doctoral student in biological sciences. "Or maybe it evolved twice. It's a really interesting concept from an evolutionary perspective."

Blum said the team is likewise curious about whether and how epigenetics might explain why no known archaea cause disease or wage antibiotic-armed warfare against their brethren, as bacteria do.

"There are no antibiotics going on in that world," he said. "Why is that? We're thinking (that) it's got something to do with epigenetics, and so their interactions among each other are fundamentally different than bacteria."

The research introduces an even broader question, Blum said.

"What was the benefit for them to have this? We don't know."

The team reported its findings in the journal Proceedings of the National Academy of Sciences.

Author: Scott Schrage | Source: University of Nebraska-Lincoln [December 03, 2018]

One of the most fundamental unexplained questions in modern science is how life began. Scientists generally believe that simple molecules present in early planetary environments were converted to more complex ones that could have helped jumpstart life by the input of energy from the environment.

Starting from hydrogen cyanide, the one-pot synthesis of cyanamide and precursors to simple sugars in water -- using  gamma rays in the presence of ammonium and chloride salts -- offers a way forward for engineering complex  mixtures that can evolve important, potentially prebiological compounds [Credit: Chemistry Select]

Scientists consider the early Earth was suffused with many kinds of energy, from the high temperatures produced by volcanoes to the ultraviolet radiation beamed down by the sun. One of the most classic studies of how organic compounds could have been made on the early Earth is the Miller-Urey experiment, which showed you electrical discharges simulating lightning can help make a variety of organic compounds, including amino acids, which are basic building blocks of all life.

Another important source of energy in planetary environments is high-energy radiation, which has various sources including radioactive decay of naturally occurring chemical elements such as uranium and potassium. Research led by Yi Ruiqin and Albert Fahrenbach from the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology, Japan, has recently shown that a variety of compounds useful for the synthesis of RNA, are produced when simple compound, combined with sodium chloride, are exposed to gamma rays.

This work importantly brings us one step closer to understanding how RNA, which is widely thought to be a candidate molecule for helping start life, could have arisen abiotically on early Earth. Due to its complexity, making RNA "from scratch" under primitive solar system conditions is no easy task. Biology is great at it, because it has evolved over billions of years to do the job with amazing efficiency.

Before life emerged, there would have been little in the environment that would have assisted in making RNA. These researchers found that sodium chloride - or common table salt - can assist in making the necessary building blocks for RNA. Sodium chloride is the chemical compound that makes the sea salty, thus it is highly likely this process could occur on primitive planets, including Earth.

The most challenging aspect of this work was figuring out that salt, specifically the chloride component, played a crucial role in these reactions. Typically, chemists ignore chloride in their reactions. When chemists conduct reactions in water, it is highly likely at least some chloride is in there anyway, though most of the time it just sits idly by as a "spectator." It often doesn't play a significant role in the reactions chemists are interested in, it's just part of the background a lot of the time.

These researchers found out though, that this was not the case in their experiments, and it took them some time to figure that out. What they eventually deduced was that the ionizing radiation they were using as the energy source to drive their reactions causes chloride to lose an electron and become what is known as a "radical". As the name suggests, the chloride is then no longer so mild-mannered and becomes much more chemically reactive. Once the chloride is activated by gamma radiation, it is free to help construct other high energy compounds which finally can help build up complex RNA molecules.

While these researchers haven't yet coaxed their reactions all the way to RNA, this work shows that there is now nothing in principle which should stop this from occurring. The question now is not so much how to make all the necessary building blocks to make RNA, but how to combine them in a "warm little pond" to make the first RNA polymers. One of the major challenges to this is understanding how other molecules, that is, other than those important for making RNA, might affect this process.

The authors think this could be pretty "messy" chemistry in the sense that a lot of other molecules, which could interfere with this process, would be made at the same time. Whether these other molecules will interfere with RNA synthesis, or even have a beneficial effect, is the future focus of these scholars' research. Understanding very complex mixtures of chemicals is not only a challenge in origins of life research, but a major challenge for organic chemistry in general.

The findings are published in Chemistry Select.

Source: Tokyo Institute of Technology [November 29, 2018]

Microbes could have performed oxygen-producing photosynthesis at least one billion years earlier in the history of the Earth than previously thought.

Cyanobacteria in a river [Credit: Goran Cakmazovic/Shutterstock]

The finding could change ideas of how and when complex life evolved on Earth, and how likely it is that it could evolve on other planets.

Oxygen in the Earth's atmosphere is necessary for complex forms of life, which use it during aerobic respiration to make energy.

The levels of oxygen dramatically rose in the atmosphere around 2.4 billion years ago, but why it happened then has been debated. Some scientists think that 2.4 billion years ago is when organisms called cyanobacteria first evolved, which could perform oxygen-producing (oxygenic) photosynthesis.

Other scientist think that cyanobacteria evolved long before 2.4 billion years ago but something prevented oxygen from accumulating in the air.

Cyanobacteria perform a relatively sophisticated form of oxygenic photosynthesis - the same type of photosynthesis that all plants do today. It has therefore been suggested that simpler forms of oxygenic photosynthesis could have existed earlier, before cyanobacteria, leading to low levels of oxygen being available to life.

Now, a research team led by Imperial College London have found that oxygenic photosynthesis arose at least one billion years before cyanobacteria evolved. Their results, published in the journal Geobiology, show that oxygenic photosynthesis could have evolved very early in Earth's 4.5-billion-year history.

Lead author Dr Tanai Cardona, from the Department of Life Sciences at Imperial, said: "We know cyanobacteria are very ancient, but we don't know exactly how ancient. If cyanobacteria are, for example, 2.5 billion years old that would mean oxygenic photosynthesis could have started as early as 3.5 billion years ago. It suggests that it might not take billions of years for a process like oxygenic photosynthesis to start after the origin of life."

If oxygenic photosynthesis evolved early, it could mean it is a relatively simple process to evolve. The probability of complex life emerging in a distant exoplanet may then be quite high.

It is difficult for scientists to figure out when the first oxygen-producers evolved using the rock record on Earth. The older the rocks, the rarer they are, and the harder it is to prove conclusively that any fossil microbes found in these ancient rocks used or produced any amount of oxygen.

Cyanobacteria up close [Credit: Dr. Norbert Lange/Shutterstock]

Instead, the team investigated the evolution of two of the main proteins involved in oxygenic photosynthesis.

In the first stage of photosynthesis, cyanobacteria use light energy to split water into protons, electrons and oxygen with the help of a protein complex called Photosystem II.

Photosystem II is made up of two proteins called D1 and D2. Originally, the two proteins were the same, but although they have very similar structures, their underlying genetic sequences are now different.

This shows that D1 and D2 have been evolving separately - in cyanobacteria and plants they only share 30 percent of their genetic sequence. Even in their original form, D1 and D2 would have been able to perform oxygenic photosynthesis, so knowing how long ago they were identical could reveal when this ability first evolved.

To find out the difference in time between D1 and D2 being 100 percent identical, and them being only 30 percent the same in cyanobacteria and plants, the team determined how fast the proteins were changing - their rate of evolution.

Using powerful statistics methods and known events in the evolution of photosynthesis, they determined that the D1 and D2 proteins in Photosystem II evolved extremely slowly - even slower than some of the oldest proteins in biology that are believed to be found in the earliest forms of life.

From this, they calculated that the time between the identical D1 and D2 proteins and the 30 percent similar versions in cyanobacteria and plants is at least a billion years, and could be more than that.

Dr Cardona said: "Usually, the appearance of oxygenic photosynthesis and cyanobacteria are considered to be the same thing. So, to find out when oxygen was being produced for the first time researchers have tried to find when cyanobacteria first evolved.

"Our study instead shows that oxygenic photosynthesis likely got started long before the most recent ancestor of cyanobacteria arose. This is in agreement with current geological data that suggests that whiffs of oxygen or localized accumulations of oxygen were possible before three billion years ago.

"Therefore, the origin of oxygenic photosynthesis and the ancestor of cyanobacteria do not represent the same thing. There could be a very large gap in time between one and the other. It is a massive change in perspective."

Now, the team are trying to recreate what the photosystem looked like before D1 and D2 evolved in the first place. Using the known variation in photosystem genetic codes across all species alive today, they are trying to piece together the ancestral photosystem genetic code.

Author: Hayley Dunning | Source: Imperial College London [November 27, 2018]