Viroids

Perhaps you've thought that viruses are the simplest sort of "living" thing – if a virus can even be called "alive".

Well, maybe not. Viroids are even simpler. You're on your own as to whether you want to describe them as "alive".

Viroids are not a new discovery – they've been known since 1971. Viroids are found only in plant cells and don't seem to infect animals. They can cause plant pathology, apparently enough to be a serious economic problem.

A viroid consists entirely of a circular piece of RNA, that may be only a few hundred base units long. The smallest known viroid has only 220 units. None of this RNA codes for proteins – unlike virus RNA or DNA, which codes for proteins that (among other things) encapsulate the genetic material. The RNA or DNA of a virus is much larger than the RNA of a viroid. The smallest known virus capable of causing an infection by itself is about 2000 base units.

Viruses reproduce by co-opting machinery of the host cell. The DNA of a DNA virus, for example, is typically normal double-stranded DNA. In the virus life cycle, two separate processes are required (among others). The DNA itself has to be copied with a DNA polymerase enzyme, just as is used in making DNA copies during cell division. The proteins that the virus requires for its coat are also made in the normal way – using RNA polymerase enzyme to make messenger RNA, which can then be used to make proteins in a cell's ribosomes.

RNA viruses are trickier. Sometimes they work by using an enzyme called reverse transcriptase, which makes DNA from RNA. The HIV-1 virus responsible for AIDS is an example. Other RNA viruses, such as human polio viruses, use another enzyme, RNA replicase, which makes copies of RNA directly. RNA viruses usually encode the enzymes that they need for reproduction, to ensure a sufficient quantity of the enzyme.

So how does a viroid reproduce, given that it consists of RNA, but doesn't code for any special enzymes, or any proteins at all? The process isn't well understood, as the following explains:

Viroids: Molecular Vestiges Of The RNA World (5/17/09)

As opposed to plant viruses, which encode proteins that mediate their own replication and movement, viroids depend exclusively on host factors for these purposes. Viroids replicate through an RNA-based rolling circle mechanism with three steps: i) synthesis of longer-than-unit strands catalyzed by a host nuclear or chloroplastic RNA polymerase that reiteratively transcribes the initial circular template, ii) processing to unit-length, which remarkably is mediated by hammerhead ribozymes in the family Avsunviroidae, and iii) and circularization resulting from the action of an RNA ligase or from self-ligation.

Among the many pending issues, how viroids redirect the template specificity of certain host DNA-dependent RNA polymerases to transcribe RNA, is one of the most challenging. In addition, viroids must recruit host factors for their intracelular, cell-to-cell and long-distance movement within the plant. There are also pending questions in this context, the most appealing of which is how members of the family Avsunviridae gain access into the chloroplast; because essentially no other RNA has been reported to traffic inside this organelle, the answer to this question may reveal novel transport pathways in plant cells.

In order to understand what this is saying, the first fact needed is that viroid RNA comes in the form of a circle – no loose ends. In this respect, it is somewhat like bacterial DNA, which consists partly of circular loops of double-stranded DNA, called plasmids.

The interesting part is that viroids are apparently replicated by RNA polymerase, which normally produces RNA from a DNA template, rather than an RNA template. The process is called rolling circle replication, because the enzyme may travel around the loop a number of times, since there are no clear start and stop points. Later, in a separate operation, an RNA enzyme (ribozyme) of the host, cuts the multiply copied segments of viroid RNA back into unit segments, which join at the ends to form a circle again.

What's especially interesting about viroids is that they may give some insight into mechanisms that would be important in the RNA world hypothesis. This is the idea that before proteins existed, or even DNA itself, there was RNA – see here for some recent findings about how RNA itself may have originated.

RNA is capable of carrying genetic information just as DNA does – after all, that's what happens in RNA viruses. The main problem is how it was possible for RNA to reproduce itself. Viroids hardly give us a complete answer to this problem, since proteins (such as RNA polymerase) are still required for replication. But at least, in viroids, we have an example of a replicating entity that consists entirely of genetic information, with no proteins of its own.

Further reading:

Viroids and Virusoids

Proto-eukaryotes and LUCA

LUCA stands for "last universal common ancestor". It refers to the presumed common ancestor of the three presently recognized "domains" of life – Archaea, Bacteria, and Eukarya.

This common ancestor must have been very primitive, of course. One is tempted to think it might resemble modern-day religious fundamentalists, but in fact it was probably even more primitive, if you can imagine such a thing.

It's not absolutely clear there was actually one common ancestor, but that's what evidence currently indicates. But assuming there was, it's fascinating to speculate about what this ancestor was like.

Here's a very detailed blog post that discusses the issue: Ur... Again (Sort of).

It's based on an original research paper: The origins of phagocytosis and eukaryogenesis. The paper is open access and appears to be great reading, though it's conjectural and requires a little familiarity with fundamental biochemistry and cellular biology. Probably a good excuse to learn some of the details if you need to. These are topics that everybody ought to know about, even though our public educational system is way too inadequate to have done a good job of that.

Try reading at least the blog post, with a copy of Wikipedia close at hand.

RNA may form spontaneously

I'd pay attention to this one. Could be a very big story.

Chemist Shows How RNA Can Be the Starting Point for Life

An English chemist has found the hidden gateway to the RNA world, the chemical milieu from which the first forms of life are thought to have emerged on earth some 3.8 billion years ago.

He has solved a problem that for 20 years has thwarted researchers trying to understand the origin of life — how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth. The discovery, if correct, should set researchers on the right track to solving many other mysteries about the origin of life. It will also mean that for the first time a plausible explanation exists for how an information-carrying biological molecule could have emerged through natural processes from chemicals on the primitive earth.

Here are some more references:

• How RNA got started
• Life’s First Spark Re-Created in the Laboratory
• Origin of life: building an RNA world from simple chemicals
• RNA world easier to make
• Chemists see first building blocks to life on Earth
• New clue to origins of life on Earth
• Molecule of life emerges from laboratory slime

Amino acid chirality

We've discussed the mystery of amino acid chirality – the fact that all biological amino acids on Earth seem to be left-handed. Previous discussion and background are here.

In that earlier discussion we considered a hypothesis that was described last year. It is known that amino acids can be formed in interstellar space. The hypothesis suggests that the first amino acids on Earth were carried here by meteorites. Further, there was some excess of left-handed over right-handed amino acids (but not necessarily entirely the left-handed kind) that arrived this way.

The last detail is to explain how the imbalance of one handedness over the other occurred in space. That could be explained by the fact that light that is strongly polarized could selectively destroy one enantiomer (alternative chiral form of a molecule) of an amino acid. Such light is emitted by rapidly spinning neutron stars. But, as we'll see, there are other possibilities.

This hypothesis was expounded by Ronald Breslow of Colombia University. He has conducted experiments that showed a small initial imbalance could be amplified by successive evaporations of solutions containing phenylalanine, a process that could easily have occurred on Earth. [2] [3]

Although experiments were done to verify the plausibility of the various mechanisms required, there's no direct evidence that the supposed sequence of events is actually responsible for the observed chirality. However, ten years ago analyses of the Murchison meteorite by Sandra Pizzarello and John Cronin did find a preponderance of left-handed amino acids. There was a possibility that this finding could have resulted from some process occurring after the meteorite hit the ground. But last year Pizzarello and others analyzed another meteorite that fell in Antarctica and seemed especially pristine. The researchers reported that there was a similar chiral imbalance in that sample as well, and not only in amino acids but also in precursor aldehydes. [1]

Now there is still more evidence for chiral imbalances – in the Orgueil meteorite, which fell almost 150 years ago:

Clues To A Secret Of Life Found In Meteorite Dust (3/17/09)

Over the last four years, the team carefully analyzed samples of meteorites with an abundance of carbon, called carbonaceous chondrites. The researchers looked for the amino acid isovaline and discovered that three types of carbonaceous meteorites had more of the left-handed version than the right-handed variety – as much as a record 18 percent more in the often-studied Murchison meteorite. "Finding more left-handed isovaline in a variety of meteorites supports the theory that amino acids brought to the early Earth by asteroids and comets contributed to the origin of only left-handed based protein life on Earth," said [Dr. Daniel] Glavin.

There's also evidence about how the imbalance may have occurred:

The team also found a pattern to the excess. Different types of meteorites had different amounts of water, as determined by the clays and water-bearing minerals found in the meteorites. The team discovered meteorites with more water also had greater amounts of left-handed isovaline. "This gives us a hint that the creation of extra left-handed amino acids had something to do with alteration by water," said [Dr. Jason] Dworkin.

The researchers focused on the amino acid isovaline, because it can "preserve its handedness for billions of years, and it is extremely rarely used by life, so its presence in meteorites is unlikely to be from contamination by terrestrial life."

Here's the abstract of the research paper:

Enrichment of the amino acid l-isovaline by aqueous alteration on CI and CM meteorite parent bodies

A large l-enantiomeric excess (ee) of the α-methyl amino acid isovaline was found in the CM meteorite Murchison (lee = 18.5 ± 2.6%) and the CI meteorite Orgueil (lee = 15.2 ± 4.0%). The measured value for Murchison is the largest enantiomeric excess in any meteorite reported to date, and the Orgueil measurement of an isovaline excess has not been reported previously for this or any CI meteorite. The l-isovaline enrichments in these two carbonaceous meteorites cannot be the result of interference from other C5 amino acid isomers present in the samples, analytical biases, or terrestrial amino acid contamination. We observed no l-isovaline enrichment for the most primitive unaltered Antarctic CR meteorites EET 92042 and QUE 99177. These results are inconsistent with UV circularly polarized light as the primary mechanism for l-isovaline enrichment and indicate that amplification of a small initial isovaline asymmetry in Murchison and Orgueil occurred during an extended aqueous alteration phase on the meteorite parent bodies. The large asymmetry in isovaline and other α-dialkyl amino acids found in altered CI and CM meteorites suggests that amino acids delivered by asteroids, comets, and their fragments would have biased the Earth's prebiotic organic inventory with left-handed molecules before the origin of life.

Note that evidence in the samples analyzed was not consistent with circularly polarized light as a cause of the imbalance, and a process involving water seems more likely.

Other accounts of this research: [6], [7]

There's other relatively recent research that demonstrates another way enantiomeric excesses of one form of amino acid could be produced. When inorganic materials are irradiated with high-energy photons (e. g. X-rays), they may emit electrons whose spins are polarized in a specific direction by a magnetic field. Experiments showed that this could affect the chirality of organic molecules adsorbed on the surface of a magnetic material:

Electrons put a new spin on chirality (11/5/08)

Researchers in the US have shown that the presence of spin-polarized electrons can make a chemical reaction involving “right-handed” molecules occur faster than the same reaction involving “left-handed” molecules. The discovery could help scientists understand why nature favours a certain handedness in many biological molecules.

Although the organic molecule used in this experiment was butanol (not an amino acid), the researchers plan to perform a similar experiment with the amino acid alanine. While this research doesn't show this is the mechanism actually responsible for left-handedness of amino acids found on meteorites, it's a least a possibility.

Press release on this research: [4]

Glavin, D., & Dworkin, J. (2009). Enrichment of the amino acid L-isovaline by aqueous alteration on CI and CM meteorite parent bodies Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811618106

References and further reading:

[1] Key To Life Before Its Origin On Earth May Have Been Discovered (2/28/08)

[2] Amplification of enantiomeric concentrations under credible prebiotic conditions – July 2006 research paper by Ronald Breslow and Mindy S. Levine

[3] Radiation-induced racemization and amplification of chirality: implications for comets and meteorites – February 2007 research paper

[4] Possible Mechanism For Creating 'Handedness' In Biological Molecules (12/2/08)

[5] Rock Offers Mirror-Image Clues to Life's Origins (10/5/08) – good overview article in the Washington Post

[6] Did lefty molecules seed life? (3/16/09) – The Scientist

[7] Southpaw Solar System (3/16/09) – ScienceNOW

Tags: amino acid chirality

Clues to the origins of life

The question of how life originated on Earth is one of the really big open questions for science. Right up there with questions like how the universe itself started and how the human mind works.

Questions about how life began have been asked for a long time, of course. But only within roughly the last 50 years, since DNA and related biochemistry began to be understood, has it been possible to address such questions scientifically.

DNA, and its very close relative RNA, provide the framework for one essential of life: the storage of information, which allows for "blueprints" that describe a living organism to be conveniently encoded, so that individual organisms can be duplicated and, ultimately, evolve into more complex organisms. We now understand pretty well how DNA and RNA work, so one key question now is – how did DNA and RNA, the carriers of genetic information, come about?

DNA and RNA are made up of relatively simple organic molecules – sugars and phosphate groups that can polymerize to form a backbone, and a small number of bases which encode information by the way they are ordered in their attachment to the backbone. The information encoded in DNA details how to make proteins, which are also polymeric organic molelcules, consisting of amino acids attached to each other in a sequence specified (mostly) by the DNA. It is the proteins that make up the bulk of the cellular machinery that constitutes a stand-alone single-celled organism, or by grouping together makes a multi-celled organism. So a large part of the question of life's origins comes down to that of how these various organic chemicals came to exist.

In addition to the organic chemicals that make up an organism, another necessity of life is the ability to utilize energy that is ultimately obtained from the environment. In most cases, this energy is derived from sunlight, although in a few rare cases it can come from radioactive elements. Either way, an organism needs to tap into the environmental energy in order to drive chemical reactions which power cellular mechanisms that enable reproduction, locomotion, and (in multicellular organisms) growth. (More complex organisms can also derive their energy from "food", in the form of simpler organisms that have stored up environmental energy obtained more directly.) So another key question is: when and how did these energy-management processes come about?

There have been recent research findings that are relevant to various of these questions.

Let's consider the origins of organic compounds first. One line of thinking is that organic compounds were primarily synthesized from inorganic compounds in natural processes here on Earth. The names Aleksandr Oparin and J. B. S. Haldane are associate with this idea. The classic experiment testing the idea is known as the Miller-Urey experiment, after Stanley Miller and Harold Urey, and was first conducted in 1953, the same year that the structure of DNA was identified by Francis Crick and James Watson. As yet, this is still just a conjectural possibility.

An alternative scenario for the origins of organic compounds is that some simple ones formed in space, which is known to happen, and that some of the basic building blocks of life, such as amino acids, were introduced to Earth on meteorites. This possibility has gained more plausibility from the recently announced finding of apparent "organic materials" in a meteorite that fell in 2000.

NASA Scientists Find Primordial Organic Matter In Meteorite

In a paper published in the Dec. 1 issue of the journal Science, the team, headed by NASA space scientist Keiko Nakamura-Messenger, reports that the Tagish Lake meteorite contains numerous submicrometer hollow organic globules.

Because the meteorite immediately became frozen in ice after it landed, the possibility of contamination from terrestrial material was minimized. Further, the isotopic composition of hydrogen and nitrogen in the globules is quite unlike what is normally found on Earth. It also appears that the material in the meteorite formed at least 4.5 billion years ago – before the Earth and the other planets themselves.

"The isotopic ratios in these globules show that they formed at temperatures of about -260° C, near absolute zero," said Scott Messenger, NASA space scientist and co-author of the paper. "The organic globules most likely originated in the cold molecular cloud that gave birth to our Solar System, or at the outermost reaches of the early Solar System."

Additional references:

• Ancient Meteorites from Outer Solar System May Have Provided Raw Materials for Life
  
• Carbon globules in meteorite may have seeded Earth life
  
• An Ancient Building Block of Life
  
• Organic Globules in the Tagish Lake Meteorite: Remnants of the Protosolar Disk - original research article (Science sub. rqd. for full access)
  

Just about two weeks later, results from a completely different souce appeared that also showed the existence of organic compounds in primorial solar system material. This was from the Stardust mission to retrieve grains of matter from the comet 81P/Wild-2:

Comets hold life chemistry clues

Scientists studying the tiny grains of material recovered from Comet Wild-2 by Nasa's Stardust mission have found large, complex carbon-rich molecules.

They are of the type that could have been important precursor components of the initial reactions that gave rise to the planet's biochemistry.

Unlike the case with the Tagish Lake meteorite, it was possible to identify many of the organic compounds in the returned material:

These Wild-2 compounds lack the aromaticity, or carbon ring structures, frequently found in meteorite organics. They are very rich in oxygen and nitrogen, and they probably pre-date the existence of our Solar System.

"It's quite possible that what we're seeing is an organic population of molecules that were made when ices in the dense cloud from which our Solar System formed were irradiated by ultraviolet photons and cosmic rays," Dr Sandford explained.

"That's of interest because we know that in laboratory simulations where we irradiate ice analogues of types we know are out there, these same experiments produce a lot of organic compounds, including amino acids and a class of compounds called amphiphiles which if you put them in water will spontaneously form a membrane so that they make little cellular-like structures."

Additional information from the special Stardust issue of Science (December 15, 2006 – sub. rqd. for full access):

• Look into the Seeds of Time – introduction and summary
  
• Organics Captured from Comet 81P/Wild 2 by the Stardust Spacecraft
  

Although these results indicate that organic material formed in or before the earliest stages of the solar system might have seeded organic chemistry on Earth, there is as yet no evidence that this actually is how it happened. An even more radical possibility is that actual living carbon-based organisms that originated outside of our solar system "transplanted" life to Earth. This idea is known as panspermia, but so far, there's little or no credible evidence for it. Short of that, we know at least that the organic compounds for life either originated on Earth or arrived from outside.

So let's move on and turn to the question of how the earliest organisms managed energy supplies in order to reproduce and move. Every organism on Earth that produces energy from the chemical processing of carbohydrates, fats, and proteins uses, a complex series or reactions known as the citric acid cycle (also known as the Krebs cycle). (There are other energy-producing processes, of course, such as photosynthesis.) The question to be answered is how this complex series of reactions first arose:

New Insights Into The Origin Of Life On Earth

In an advance toward understanding the origin of life on Earth, scientists have shown that parts of the Krebs cycle can run in reverse, producing biomolecules that could jump-start life with only sunlight and a mineral present in the primordial oceans.

The Krebs cycle is a series of chemical reactions of central importance in cells -- part of a metabolic pathway that changes carbohydrates, fats and proteins into carbon dioxide and water to generate energy.

Since the cycle can run backwards, it is possible to identify an inorganic compound that may have kickstarted the process:

Nature's Jump-Starter

Reporting in next week's Journal of the American Chemical Society, researchers at Harvard University say they may have found at least one of the original players. Called sphalerite, the compound is a mix of zinc and sulfur ejected from hydrothermal vents and known to have been plentiful in Earth's early seas. Geochemist and co-author Scot Martin says the team's new lab experiments show that when immersed in sterile water and exposed to sunlight, sphalerite can create three of the five basic organic chemicals necessary to start the Krebs cycle in relatively quick fashion. Further research is needed to isolate the other compound or compounds that could have produced the remaining two Krebs ingredients, he notes. If scientists can find their sources, then they will know that the five chemical foundations of the Krebs cycle were being manufactured easily and routinely in Earth's early oceans.

In addition to relatively simple organic chemical building blocks and chemical reactions that can release energy to make an organism that is "alive", there is a third prerequisite for life: some method of storing information about an organism's composition and structure so that the organism can replicate itself, instead of simply disappearing after each generation. In other words, genetic material.

Today, that genetic material consists of DNA and RNA, which in turn are made up of a handful of bases that act as symbols encoding the genetic message and are arranged along a linear backbone of simple sugar and phosphate groups. But are these the only possible chemical entities that can perform this kind of function?

In the past, other possibilities have been suggested, such as peptide nucleic acids (PNAs). A PNA has a backbone formed of simple molecules consisting of carbon, nitrogen, hydrogen, and oxygen. These are liked together by peptide bonds, which form when H- and OH- units from two molecules combine to form H₂O, leaving the original molecules joined to each other. Such peptide bonds also form the backbone of proteins. But unlike proteins, PNAs have DNA-like bases attached to the backbone instead of amino acids. However, PNAs do not occur naturally, so they do not seem to have played a role in life on Earth.

If there are other ways of structuring a backbone, perhaps comparing them to what is actually used in RNA (the sugar known as ribose) and DNA (the sugar deoxyribose) would suggest why the latter proved to win out. That was the idea behind this research:

Uncovering DNA's 'Sweet' Secret

“These molecules are the result of evolution,” said Egli, professor of Biochemistry. “Somehow they have been shaped and optimized for a particular purpose.”

“For a chemist, it makes sense to analyze the origin of these molecules.”

One particular curiosity: how did DNA and RNA come to incorporate five-carbon sugars into their “backbone” when six-carbon sugars, like glucose, may have been more common? Egli has been searching for the answer to that question for the past 13 years.

Recently, Egli and colleagues solved a structure that divulges DNA's “sweet” secret. In a recent issue of the Journal of the American Chemical Society, Egli and colleagues report the X-ray crystal structure of homo-DNA, an artificial analog of DNA in which the usual five-carbon sugar has been replaced with a six-carbon sugar.

It was found that homo-DNA is more stable that DNA/RNA and it allows a wider variety of bases to be attached. So why didn't it prevail?

[D]espite homo-DNA's apparent versatility in base pairing and its thermodynamic stability, other features of the molecule's architecture probably preclude it from being a viable genetic system

For example, it cannot pair with other nucleic acids — unlike DNA and RNA which can and must pair with each other. Also the steep angle, or inclination, between the sugar backbone and the bases of homo-DNA requires that the pairing strands align strictly in an antiparallel fashion — unlike DNA which can adopt a parallel orientation. Finally, the irregular spaces between the “rungs” prevent homo-DNA from taking on the uniform structure DNA uses to store genetic information.

The findings suggest that fully hydroxylated six-carbon sugars probably would not have produced a stable base-pairing system capable of carrying genetic information as efficiently as DNA.

So that variation didn't work out. But what about the possibility of using a different set of bases than the purines and pyrimidines which actually occur? That was investigated in this study:

Origin Of Life: The Search For The First Genetic Material

To find the right track in searching for the origins of life, the team is trying to put together groups of potential building blocks from which primitive molecular information transmitters could have been made. The researchers have taken a pragmatic approach to their experiments. Compounds that they test do not need to fulfill specific chemical criteria; instead, they must pass their “genetic information” on to subsequent generations just as simply as the genetic molecules we know today—and their formation must have been possible under prebiotic conditions. Experiments with molecules related to the usual pyrimidine bases (pyrimidine is a six-membered aromatic ring containing four carbon and two nitrogen atoms), among others, seemed a good place to start. The team thus tried compounds with a triazine core (a six-membered aromatic ring made of three carbon and three nitrogen atoms) or aminopyridine core (which has an additional nitrogen- and hydrogen-containing side group). Imitating the structures of the normal bases, the researchers equipped these with different arrangements of nitrogen- and hydrogen- and/or oxygen-containing side groups.

Unlike the usual bases, these components can easily be attached to many different types of backbone, for example, a backbone made of dipeptides or other peptide-like molecules. In this way, the researchers did indeed obtain molecules that could form specific base pairs not only with each other, but also with complementary RNA and DNA strands. Interestingly, only one sufficiently strong pair was formed within both the triazine and aminopyridine families; however, for a four-letter system analogous to the ACGT code, two such strongly binding pairs are necessary.

The conclusion was that the critical factor affecting the composition of modern genetic material was the structure of the bases rather than the structure of the backbone. It was necessary to have only certain bases which are capable of pairing up in specific ways, as occurs in double-stranded DNA and DNA-RNA combinations.

Tags: origins of life, biology, biochemistry, Krebs cycle, citric acid cycle, Tagish Lake meteorite