ScienceWeek

ORIGIN OF LIFE: ON REPLICATION IN THE RNA WORLD

The following points are made by William R. Taylor (Nature 2005 434:705):

1) It is now widely believed that almost 4 billion years ago, before the first living cells, life consisted of assemblies of self-reproducing macromolecules. The molecular candidate thought to have mediated this activity has been RNA, which can combine the necessary properties of encoding information and catalyzing chemical reactions -- functions that are now fulfilled largely by DNA and proteins, respectively. From theoretical arguments, it can be expected that a system of interacting molecules will give rise to complex, and even life-like, behavior, but there is still debate about whether RNA was the first or the only macromolecule to participate in such activity, with both protein and DNA (or any combination with or without RNA) representing alternatives.

2) Circumstantial evidence for the central position of RNA in the origin of life can be found in "relic" pieces of RNA that hold a few of the most important functions in the cell. Perhaps the most convincing observation is that in the synthesis of proteins on the ribosome, the key chemical event -- peptide-bond formation --is catalyzed solely by RNA, suggesting that primacy lies with RNA rather than protein. A major impediment to full acceptance of an ancient "RNA world" is that, although it can easily be imagined that a pure RNA machine (a proto-ribosome) can make proteins, there is no equivalent RNA machine to make RNA (a ribopolymerase). All the RNA we know is made by protein, leading to perhaps the original "chicken-and-egg" problem of which came first.

3) Some mechanisms for replication in the RNA world have been put forward, and following the current systems of protein polynucleotide synthesis, all involve the creation of a complementary daughter strand using Watson-Crick base-pairing. But from a mechanistic viewpoint, such a model contains a fundamental problem: if a ribopolymerase were to make a complementary copy of itself, it would need to recopy this to obtain a new functional ribopolymerase. This implies that both the ribopolymerase sequence and its complement would have to coexist. But if these two copies came together, the result would be a double stranded Watson-Crick helix (as found in some RNA viruses) -- not a new ribopolymerase. Even if both sequences had well determined secondary structures, the perfect complementarity of the Watson-Crick pairing would act as a sink, leading to a sterile population of double-stranded molecules.

4) In a world without any other type of molecule (such as protein) to prevent these unwanted interactions, it might be concluded that a pure RNA world could not have been viable. But what if the ribopolymerase did not synthesize a complementary strand? From a chemical viewpoint, there is no reason why a polymerase must make a complementary strand that runs in the reverse direction to the template strand. In modern protein polymerases, nucleotide triphosphates are added to the 3' end of the transcript without the direct participation of the template strand. If the template strand was flipped (making a parallel complement), then all that would be lost is some capacity for the template and transcript to remain base-paired, as parallel nucleic acid strands cannot form a duplex with Watson-Crick base-pairing. In an RNA world, the loss of this interaction would be an advantage -- preventing the formation of a dead-end double helix.[1-5]

References (abridged):

1. Joyce, G. F. Nature 338, 217-224 (1989)

2. Gesteland, R. F., Cech, T. R. & Atkins, J. F. (eds) The RNA World (Cold Spring Harbor Lab. Press, 1999)

3. Maynard Smith, J. & Szathmary, E. The Major Transitions in Evolution (Oxford Univ. Press, 1995)

4. Taylor, W. R. Comp. Biol. Chem. 28, 313-319 (2004)

5. Dyson, F. Origins of Life (Cambridge Univ. Press, 1985)

Nature http://www.nature.com/nature

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ORIGIN OF LIFE: IN SEARCH OF THE SIMPLEST CELL

The following points are made by Eörs Szathmary (Nature 2005 433:469):

1) In investigating the origin of life and the simplest possible life forms, one needs to enquire about the composition and working of a minimal cell that has some form of metabolism, genetic replication from a template, and boundary (membrane) production.

2) Identifying the necessary and sufficient features of life has a long tradition in theoretical biology. But living systems are products of evolution, and an answer in very general terms, even if possible, is likely to remain purely phenomenological. Going deeper into mechanisms means having to account for the organization of various processes, and such organization has been realized in several different ways by evolution. Eukaryotic cells (such as those from which we are made) are much more complicated than prokaryotes (such as bacteria), and eukaryotes harbor organelles that were once free-living bacteria. A further complication is that multicellular organisms consist of building blocks -- cells -- that are also alive. So aiming for a general model of all kinds of living beings would be fruitless; instead, such models have to be tied to particular levels of biological organization.

3) Basically, there are two approaches to the "minimal cell": the top-down and the bottom-up. The top-down approach aims at simplifying existing small organisms, possibly arriving at a minimal genome. Some research to this end takes Buchnera, a symbiotic bacterium that lives inside aphids, as a rewarding example. This analysis is complemented by an investigation of the duplication and divergence of genes. Remarkably, these approaches converged on the conclusion that genes dealing with RNA biosynthesis are absolutely indispensable in this framework. This may be linked to the idea of life's origins in an "RNA world", although such an inference is far from immediate.

4) Top-down approaches seem to point to a minimum genome size of slightly more than 200 genes. Care should be taken, however, in blindly accepting such a figure. For example, although some gene set A and gene set B may not be common to all bacteria, that does not mean that (A and B) are dispensable. It may well mean that A or B is essential, because the cell has to solve a problem by using either A or B. Only experiments can have the final word on these issues.

5) A top-down approach will not take us quite to the bottom, to the minimal possible cells in chemical terms. All putative cells, however small, will have a genetic code and a means of transcribing and translating that code. Given the complexity of this system, it is difficult to believe, either logically or historically, that the simplest living chemical system could have had these components.

6) The bottom-up approach aims at constructing artificial chemical supersystems that could be considered alive. No such experimental system exists yet; at least one component is always missing. Metabolism seems to be the stepchild in the family: what most researchers in the field used to call metabolism is usually a trivial outcome of the fact that both template replication and membrane growth need some material input. This input is usually simplified to a conversion reaction from precursors to products.

Nature http://www.nature.com/nature

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ORIGIN OF LIFE: ON TRANSITIONS FROM NONLIVING TO LIVING MATTER

The following points are made by S. Rasmussen et al (Science 2004 303:963):

1) All life forms are composed of molecules that are not themselves alive. But in what ways do living and nonliving matter differ? How could a primitive life form arise from a collection of nonliving molecules? The transition from nonliving to living matter is usually raised in the context of the origin of life. But some researchers(1) have recently taken a broader view and asked how simple life forms could be synthesized in the laboratory. The resulting artificial cells (sometimes called protocells) might be quite different from any extant or extinct form of life, perhaps orders of magnitude smaller than the smallest bacterium, and their synthesis need not recapitulate life's actual origins. A number of complementary studies have been steadily progressing toward the chemical construction of artificial cells (2-5).

2) There are two approaches to synthesizing artificial cells. The top-down approach aims to create them by simplifying and genetically reprogramming existing cells with simple genomes. The more general and more challenging bottom-up approach aims to assemble artificial cells from scratch using nonliving organic and inorganic materials.

3) Although the definition of life is notoriously controversial, there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of evolving. Regeneration and replication involve transforming molecules and energy from the environment into cellular aggregations, and evolution requires heritable variation in cellular processes. The current consensus is that the simplest way to achieve these characteristics is to house informational polymers (such as DNA and RNA) and a metabolic system that chemically regulates and regenerates cellular components within a physical container (such as a lipid vesicle).

4) Two recent workshops(1) reviewed the state of the art in artificial cell research, much of which focuses on self-replicating lipid vesicles. David Deamer (Univ. of California, Santa Cruz) and Pier Luigi Luisi (ETH Zurich) each described the production of lipids using light energy, and the template-directed self-replication of RNA within a lipid vesicle. In addition, Luisi demonstrated the polymerization of amino acids into proteins on the vesicle surface, which acts as a catalyst for the polymerization process. The principal hurdle remains the synthesis of efficient RNA replicases and related enzymes entirely within an artificial cell. Martin Hanczyc (Harvard Univ.) showed how the formation of lipid vesicles can be catalyzed by encapsulated clay particles with RNA adsorbed on their surfaces. This suggests that encapsulated clay could catalyze both the formation of lipid vesicles and the polymerization of RNA.

References (abridged):

1. http://www.ees.lanl.gov/protocells

2. C. Hutchinson et al., Science 286, 2165 (1999)

3. M. Bedau et al., Artif. Life 6, 363 (2000)

4. J. Szostak et al., Nature 409, 387 (2001)

5. A. Pohorille, D. Deamer, Trends Biotechnol. 20, 123 (2002)

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