20.10: Molecules Talk- Selecting Molecular Communication and Complexity

In our complex human society, we define communication by its specificity. Without a careful choice of words, our speech would at best, be a source of magnificent misunderstanding…, or just plain babel! What does this mean for prebiotic chemistries? In any prebiotic chemical evolution, selection would have favored the protective accumulation of longer-lived molecular aggregates. Over time, the same selective imperatives would create webs of such aggregates, increasing the range and specificity of molecular interactions in a very challenging environment. If this were to have occurred in an enclosed proto-cellular space, it would have resulted in a primitive molecular communication and the potential for a growing complexity (another property of life!). In fact, all of the properties of life must have arisen before life itself, as they accompanied the achievement of more and more complex intermolecular communication. Simply put, a prebiotic (or for that matter a cellular) genetic change that alters the rate of one catalytic reaction (if not destructive) will drive the selection of changes in components of other, interconnected metabolic chemistries. If molecular communication required the evolution of catalytic specificity, then the final elaboration of complexity and order as a property of life further requires the selection of mechanisms of regulation and coordination.

20.10.1 Intermolecular Communication: Establishment of Essential Interconnected Chemistries

Earlier, we suggested that inorganic catalyst precursors to biological enzymes could be minerals embedded in clay or other substrata, providing surfaces that would naturally aggregate organic molecules and catalyze repetitive reactions. The initial objects of prebiotic selection must have included stable monomers and polymers outside, or as seems more likely, inside proto-cells. Later, chemical selection would have favored polymers that enhanced growth and reproduction of successful aggregates. These polymers were likely those that catalyzed their own synthesis, perhaps collaborating with inorganic catalytic minerals. The result would be the elaboration of a web of interconnected chemical reactions between molecules with high affinity for each other, thereby increasing the specificity of those reactions. In the context of life origins and evolution, co-catalysis describes the activities of these interconnected metabolic reactions.

As noted, high-affinity interactions are inherently protective. During prebiotic chemical and/or metabolic evolution, protected stable molecular assemblies would be targets of selection. Continuing co-evolution of catalysts, substrates, and co-catalytic reaction sets would lead to more and more sophisticated molecular communication. Once established, efficient biochemical reaction sets would be constrained against significant evolutionary change. Any change (mutation) that threatened this efficiency would mean the end of a prebiotic chemical (or for that matter, cell) lineage! This explains why we find common pathways for energy-generation (e.g., autotrophic and fermentative), reproduction (i.e., replication), and information storage and retrieval (DNA, RNA, protein synthesis) in all of LUCA’s descendants. In other words, an organizing principle must have been selected to enable communication between molecules and their reactions. Such complex and effective communication requires coordination. In fact, effective communication is defined by coordination, the capacity to make chemical decisions. Selection of molecular aggregates that sequestered metabolic reactions behind a semipermeable membrane ensures that only certain molecules communicate with each other within a protocell (or cell). This sequestration is likely to have occurred repeatedly during chemical evolution, beginning with the synthesis of larger, polymeric molecules and possibly, an aggregation of primitive lipoidal molecules. We can think of increasingly effective catalysis in an enclosed, sheltered environment as a conversation mediated by good speakers! Thus, coordination is a property that started with prebiotic chemistry and likely co-evolved with life itself.

20.10.2 Origins of Coordination

Let’s look some possible structures churning around in the prebiotic chemistry set that might have self-assembled and sequestered compatible chemistries of life. Along with the alkaline vent biofilm compartment, proteinoid microspheres, coacervates, and liposomes have been considered as possible progenitors of biological membranes. Each can be made in the laboratory, shown to be semipermeable and in some cases can even replicate! Production of coacervates, proteinoid microspheres, and liposomes is summarized in Figure 20.14.

Figure 20.14: Proteinoid microspheres, coacervates and liposomes can all be made in a laboratory and are candidates for boundary structures that could protect early prebiotic organic molecules and reactions. See more micrographs of these synthetic compartments at Candidates for Early Compartments.

Oparin had proposed that the action of sunlight in the absence of oxygen could cause ionized, oppositely charged organic molecules (e.g., amino acids, in a primordial soup to form “colloids,” or “droplets” which were immiscible with water. These coacervates were actually produced in 1932, visualized by microscopy and shown to be a semi-permeable compartment. They even behaved as if they were able to grow and reproduce (also as Oparin originally suggested they might). Sidney Fox produced proteinoid microspheres from short peptides In the 1950s; they formed spontaneously from aqueous amino acid solutions heated to dryness, not unlike what happens in the tidal pool scenario of polymer formation from organic monomers. These can be seen by light and electron microscopy.

Liposomes are also easily made in a laboratory, but it isn’t clear that they could have formed spontaneously on a pre-biotic earth. Nevertheless, cell membranes must have had acquired their phospholipid bilayer structure by the time of LUCA since we all have them! Prior to LUCA (perhaps in or soon after formation of our progenote), chemical rearrangements must have occurred to enable incorporation of a phospholipid bilayer into whatever semipermeable boundary life started with.

We have already considered the biofilm proposed for cellular origins in an alkaline vent, and that the formation of such biofilms in alkaline vents would have separated acidic ocean protons from the interior of such protocells, creating a proton gradient. Such a gradient could have driven the early evolution of chemiososis as a means of capturing chemical energy, complete with the eventual selection of ATP synthases and the enzymes of proton transport, again because all cells descendent from LUCA posess these biochemistries.

Of course, proteinoid microspheres, coacervates, biofilm-based membranes, and liposomes are not alive, and are therefore not cells. But one or another of them must have been where the enhanced coordination of molecular communication required for life began their elaboration.

354-2 Protected Molecular Communication-Semipermeable Membranes

CHALLENGE

Briefly outline an experiment to demonstrate that proteinoid microspheres, coacervates or biofilm compartments are surrounded by a semipermeable boundary.

An important take-home message here is that whatever the original structure of the first cells was, they arose soon after the organic chemical prerequisites of life began to acquire familiar metabolic functions. We need to see chemical and structural progress to cellularity as concurrent metabolic evolutionary events. At some point, selection of sequestered biochemistries led to protocells, then to the first cell or cells, each with all the properties of life. Finally, selection of highly specific pathways of communication between cellular molecules allowed cells themselves to talk to one another, engage in group activities, and eventually join to form multicellular organisms.

Multicellularity is of course a characteristic of many if not most eukaryotes. But watch an excellent TED Talk on bacterial intercellular communication by Dr. Bonnie Bassler at Intercellular Communication in Bacteria.

20.10.3 An RNA World: Origins of Information Storage and Retrieval

Let us accept for now that molecular communication began concurrently with the packaging of interconnected co-catalytic sets into semipermeable structures. Then the most ‘fit’ of these structures were selected for their efficient coordination of meaningful, timely chemical messages. Ultimately, coordination requires information processing, storage and retrieval, something we recognize in Francis Crick’s Central Dogma of information flow from DNA to RNA to protein. Cells and organisms do coordination quite well, but what do its beginnings look like? The answer may lie in the pre-biotic RNA world. Figure 20.15 below is a statement of The Central Dogma, modified to account for the role of reverse transcription in the behavior of retroviruses and retrotransposons, both sources of lateral gene transfer (the exchange of genes between cells and organisms.

Figure 20.15: Genetic information flows from DNA to RNA to protein (the Central Dogma) but can also flow from RNA to DNA by reverse transcription.

We do not really know how cells came to rely on DNA to store, pass on and mobilize genetic information, but we have presented reasons to believe that the first replicating nucleic acid was RNA, creating an RNA world. Here is the evidence that leads us to this conclusion.

• Based on the stem-and-loop and other structures that form when RNA molecules undergo internal H-bonding, we know that RNAs can take on varied and intricate shapes.
• Diverse conformations are consistent with the evolution of specificity in the interaction of RNAs with themselves and/or with other molecules in the prebiotic environment. RNAs, either alone as autocatalysts (for example, self-splicing mRNAs) or in catalytic ribonucleoprotein complexes (e.g., ribosomes, snRNPs) that exist in cells today.
• Some of these RNAs (specifically rRNAs), have a long phylogenetic heritage, shared by cells in all three domains of life.

The propensity of single stranded RNA molecules to fold based on internal H-bonding can lead to those diverse 3D shapes (tertiary structure). These structures could have interacted with other molecules in a prebiotic environment. Because they could be replicated according to different prebiotic scenarios, the same RNAs could also pass on simple genetic information contained in their base sequences. The combination of informational and catalytic properties in a single molecule is illustrated in Figure 20.16 below.

Figure 20.16: RNA sequences contain genetic information. In retroviruses, they are molecules of inheritance. But single stranded RNAs made in cells can fold into 3-dimensions, creating specific shapes that can act as catalysts (e.g., ribozymes) combining information storage with catalytic activities.

The capacity of RNAs to be catalysts and warehouses of genetic information at the same time speaks to an efficient candidate for the first dual or multi-purpose polymer, a property that is not known and cannot be demonstrated for DNA. To read more about the proposed ‘RNA worlds’ in which life may have begun, see Cech T. R. (2012) [The RNA Worlds in Context. In Cold Spring Harbor Perspectives in Biology (Cold Spring Harbor, NY: Cold Spring Harbor press) 4(7):a006742e].

355 Self-Replication: Information, Communication & Coordination

20.10.4 From Self-Replicating RNAs to Ribozymes to Enzymes; From RNA to DNA

What might RNA catalysis beyond self-replication have looked like in simpler times? One can envision a pair of different RNA molecules, each uniquely folded, with affinities for two different aminos acids (Figure 20.17, below). After they bind to 'their' amino acids, the RNAs are attracted to each other, presumably by refolding permitting complementary H-bonding between the RNAs (not shown). The resulting ribozyme catalyzes formation of a peptide linkage between the amino acids (i.e., a dehydration synthesis). The dipeptide and the two RNAs separate.

Figure 20.17: Hypothetical origin of RNA catalysis, suggesting how some early (prebiotic) RNAs may have evolved to catalyze peptide bond formation between amino acids.

As we know, the formation of a peptide bond requires an input of free energy (recall that this one of the most energy intensive reactions in cells). For now, assume a chemical energy source and let us focus on the specificities required for RNA catalytic activity.

We know now that tRNAs are the intermediaries between nucleic acids and polypeptide synthesis. So, it’s fair to ask how the kind of activity illustrated above could have led to the tRNA-amino acid interactions we see today. There is no obvious spontaneous binding chemistry between today’s amino acids and RNAs, but there may be a less obvious legacy of the proposed bindings. This has to do with the fact that the genetic code is universal, which means that any structural relationship between RNA and amino acids must have been selected early (at the start!) of cellular life on Earth. Here is the argument.

1. The code is indeed universal (or nearly so)
2. There is a correlation between the chemical properties of amino acids and their codons, for example:

• Triplet codons for charged (polar) amino acids contain more G (guanine) bases
• Triplet codons for uncharged amino acids more often contain a middle U (uracil) than any other base.

These correlations would mean that an early binding of amino acids to specifically folded RNAs was replaced in evolution by enzyme-catalyzed covalent attachment of an amino acid to a ‘correct’ tRNA, such as we see today.

What forces might have selected separation of the combined template and informational functions from most of the catalytic activities of RNAs? Perhaps it was the selection of the greater diversity of structure (i.e., shape) that folded polypeptides can achieve, compared to folded RNAs. After all, polypeptides are strings of 20 different amino acids compared to the four bases that make up nucleic acids. This potential for molecular diversity would in turn accelerate the pace of chemical (and ultimately cellular) evolution. A scenario for the transition from earlier self-replicating RNA events to the translation of proteins from mRNAs is suggested in Figure 20.18.

Figure 20.18: Suggested steps in evolution from an RNA world to our DNA world. The first of the steps would be to divorce the self-replication activity of RNAs from their information storage function, as illustrated here.

Adaptor RNAs in the illustration will become tRNAs. The novel, relatively unfolded RNA is a presumptive mRNA (even though mRNAs can sometimes engage in intrastrand H-bonding). Thus, even before the intrusion of DNA into our RNA world, we can imagine selection of the defining features of the genetic code and mechanism of translation (protein synthesis) that characterizes all life on Earth. Next, we’ll consider “best-speculations” for how RNA-based information storage and catalytic chemistries might have made the evolutionary transition to DNA-based information storage and largely protein-based enzyme catalysis.

CHALLENGE

An early association of specific amino acids with folded RNAs, along with correlations between bases in codons and specific amino acids suggests how the present-day tRNA/amino acid relationships may have evolved. Does this argument mitigate for or against the origins of multiple “first cells” on earth?

20.10.4.a Ribozymes Branch Out: Replication, Transcription and Translation

The term co-catalysis describes biochemical reactions in which a catalyst accelerates a chemical reaction whose product feeds back in some way on its own synthesis. We saw this in action when we discussed allosteric enzyme regulation and the control of biochemical pathways. Catalytic feedback loops must have been significant events in the evolution of the intermolecular communication and the metabolic coordination required for life. Here we look at some scenarios for the transition from an RNA world to something more recognizable as today’s nucleic acid information storage and protein-based catalytic metabolism.

If early RNAs catalyzed their own replication, they were functioning as primitive ribozymes. If some of these ribozymes bound and polymerized amino acids, they may have catalyzed the synthesis of short peptides. What if some of the polypeptides occasionally bound to their shapely catalytic RNAs and enhanced the catalytic properties of the aggregate? What if one of these aggregates enhanced the rate of synthesis of its own RNA, or evolved to catalyze other reactions useful to life? Such a structure might presage the ribosome, which is a ribonucleoprotein with catalytic properties. If later in evolution, a peptide changed just enough to accomplish the catalysis on its own, it might dissociate from its RNA, flying solo as a protein enzyme catalyst, as suggested in Figure 20.19.

Figure 20.19: If RNAs could bind peptides whose synthesis they catalyze, evolution could have selected ribozymes from some RNA-peptide complexes that did not separate. Later, the peptides themselves could have evolved to take over catalytic functions from ribozymes.

Selection favoring the synthesis of short oligopeptides and polypeptides is consistent with a catalytic diversification that led to the dominance of protein catalysts, i.e., enzymes. The primitive enzyme shown here must have been selected because at first, it assisted the autocatalytic replication of the RNA itself! Over time, the enzyme would evolve along with the RNA. This co-evolution then eventually replaced autocatalytic RNA replication with the enzyme-catalyzed RNA synthesis we recognize as transcription today. In this scenario, self-splicing pre-mRNAs and ribozymes are surviving remnants of an RNA world!

356 Information Storage and Retrieval in an RNA World

Let’s turn now to some speculations about how an RNA world could make the transition to the DNA-RNA-protein world we have today.

20.10.4.b Transfer of Information Storage from RNA to DNA

The transfer of function from RNA to DNA is by no means a settled issue among students of life origins and early evolution. A best guess is that the elaboration of protein enzymes begun in the RNA world would lead to reverse transcriptase-like enzymes that copied RNA information into DNA molecules. The basic transfer scenario is illustrated below in Fig 20.20.

Figure 20.20: A final evolutionary scenario gets us from the RNA world to a DNA world that governs most life on earth today.

DNA information may have been selected because DNA is chemically more stable than RNA. All cells alive today store information in DNA (only some viruses have an RNA genome).

Therefore, transition to the use of DNA as an information molecule would have preceded the origin of life. At least, it must have occurred in the cells from which the LUCA arose. Details of this key change involve evolutionary steps yet to be worked out to everyone’s satisfaction!

357 The Transition from an RNA World to a DNA World