Some considerations on the universality of the DNA code Giorgio Cavallari

Abstract The DNA codon code, triplets out of four bases, is found in all living organisms, with very few exceptions. It is more than an alphabet; it is a fully developed language with grammar rules that organisms understand and conform to. This explains why viral diseases, e.g. avian flu or Lyme disease, may cross species boundaries and spread from one species to another via the bite of some insects (disease vectors). In the evolutionary theory, DNA code universality confirms the idea of a common origin of all extant organisms (Last Universal Common Ancestor). But this universality has implications that extend further than the Darwinian evolutionary theory. The Horizontal Gene Transfer (HGT) is a process by which a species acquires a stretch of DNA code from a different species and thus achieves great improvements in adaptation to environmental pressure. Symbiosis has been proposed to explain the evolution from prokaryotic to eukaryotic cell, in which two cells merge to form an altogether new cell; one cell becomes the nucleus and the other, the cytoplasm and the membrane of the new cell. The new cell thus becomes more specialized, better protected from environment and may acquire large adaptation advantages. Some hypotheses have been proposed to account for such universality, namely exterritorial origin (SETI), frozen accident, optimum code.

KEYWORDS: Genetic Code, DNA acquisition, evolution theory, origin of genetic code, Genetically Modified Organism

Introduction The genetic information of living organisms (all life forms) is stored in the DNA, a linear structure forming a double helix ladder in which each rung is one of four bases whose initials are A, C, G and T. Nature uses up to 20 amino acids to build everything needed for cellular life and there is a relationship between triplets of bases and amino acids. The genetic code maps 64 three-letter words (codon) to 20 corresponding amino acids and one stop signal; the code is thus degenerate (fig. 1).

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Codons are then grouped into genes, specific sequences that encode proteins, the large complex three-dimensional molecules that perform most of life functions.

T

C

A

G

T C TTT TCT phe TTC TCC TTA TCA leu TTG TCG CTT CCT CTC CCC leu CTA CCA CTG CCG ATT ACT ile ATC ACC ATA ile ACA ATG met ACG GTT GCT GTC GCC val GTA GCA GTG GCG

ser

pro

thr

ala

A G TAT TGT tyr TAC TGC TAA TGA stop TAG TGG CAT CGT his CAC CGC CAA CGA gln CAG CGG AAT AGT asp AAC AGC AAA AGA lys AAG AGG GAT GGT asp GAC GGC GAA GGA glu GAG GGG

cys stop try arg

ser arg

gly

T C A G T C A G T C A G T C A G

Fig. 1 – DNA genetic code - ATG = Start code Almost all life on Earth - people, birds, flowers, and bacteria - uses the same genetic code in its DNA. This code is thought to have existed since the very beginning of life on this planet about 3.7 billion years ago, perhaps in a simpler form; although it is not known how many times life started on earth. In information theory a code is just a way to carry information. One needs tools to decode a message and translate information into actions; one cannot separate a code from the associated toolkit; just as as one cannot separate the alphabet from the lexicon of a human language. Cell DNA brings a whole set of information for the cell’s life: a cell is genetically a self-sufficient organism. A number of tools are in fact present within the cell to allow reproduction (duplication) and survival, namely enzymes which copy the DNA (mitosis) and ribosomes, which assemble proteins. The point to be addressed now is what does it means a universal code and why it did not evolve within the different kingdoms or species (Doolittle 2000)? Origin of the code A number of hypotheses have been proposed about the origin of the genetic code. Panspermia, for instance, is the theory of widespread life in the universe and the arrival on our planet of cells either by accident or directed by intelligent beings (Line 2002). Life could arrive from within the solar system, namely transported on meteorites from Mars (Davies1999: 227-236); pre-biotic matter in fact has been found on the Australian meteorite. The panspermia hypothesis hinges on the prolonged survival of dormant bacterial cells; research work has focused on amber reportedly containing isolations of a range of bacteria from 25-40 million-years-old (Line 2002). F. Crick explains it as a “frozen accident”; this code just happens to be functional for life; initially, the code would have used just a few amino-acids and 2

would, later, have included additional ones. "The new amino acid should not upset too much the proteins into which it is incorporated. This upset is least likely to happen if the new and the old amino acids are related" (Crick 1968). More recently, attempts identify some criteria for optimality: for example considering the cost of translation/copying errors (Higgs 2009): “(i) The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii) These amino acids are assigned to codons with G at first position.” Subsequent amino acids were added in such a way as to not disrupt the protein assembly. A different scheme considers the number of H-bonds of each base and sorts the codons according to the sum of H-bonds of the first two letters; six, five or four. In the latter case one needs to decode the last letter, in the first the last letter is unimportant (Wilhelm 2004). Evolution Theory The DNA code universality confirms the idea of a common origin of all extant organisms. The Neo-Darwinian theory of evolution is based upon three pillars: genetic variation, natural selection and isolation (Arber 2006). Genetic variations happen rarely, most often are fatal and get discarded by natural selection. The favorable/neutral ones are transmitted to the offspring’s that will thus have a genetic structure different from their ancestors. Natural selection is the environment, both geophysical and biological; as such, it changes with time and with the pressure for survival of other populations. Finally, isolation limits the potential habitats for an organism. If genetic variations are random, natural selection and isolation favor some variations against others according to present and time varying situations (Arber 2003). Genetic variation Bacteria are probably the oldest living organisms, have quite a simple structure and use uniparental reproduction by cell fission. Nevertheless they have DNA, genetic information organized in genes, and enzymes (catalyzers), that perform replication, do the ‘housekeeping’ and control functions. Bacteria have been largely studied because of their short genome and their fast generation cycle (about 30 min in some species). Bacteria suffer, as do all living elements, from viral infections. A virus has DNA and a body but is unable to perform reproduction; it therefore seeks a host in order to ‘pirate’ the reproduction machinery. Viral infection appears to be its way to survival; a virus strand able to infect bacteria is called bacteriophage or phage. When a phage infects a bacterial cell, the phage’s DNA is injected into the bacterium. Viral DNA forces then the cell’s ribosomes (the protein production tool of a cell) to start production of hundred copies of the phage. The bacterium eventually explodes, dies and liberates the newborn phages (lyse cycle). The process of viral infection explains why diseases endemic in some species can move to other species (e.g. avian flue, Lime disease, malaria). Nature, of course, has developed barriers against viral diseases by surface compatibility and by restriction processes, by which enzymes manage to break the invading DNA. Three strategies for DNA mutation have been identified: 3

. local substitution, insertion or deletion of one nucleotide (base) in a daughter cell during binary fission. DNA copying errors are usually taken care of by specific error correction enzymes, but nature accepts, or even favors, a low rate of errors, and natural selection acts as a filter for fitness. Most of the errors are fatal and get discarded but the few beneficial/neutral ones are kept and get transferred to a new lineage. . rearrangement, translation or transformation of stretches of DNA within the bacterial genome. Some functions may become enhanced by multiple presences of some genes or by genes being associated to other genes, as each gene expresses a given protein and control genes activate it. . acquisition of foreign DNA from other cells or species by conjugation and Horizontal Gene Transfer (HGT). In conjugation, cells exchange genes by direct contact, a sort of sexual mating, one cell transferring a stretch of DNA (transposon) to another cell by punching through the cell membrane. Horizontal Gene Transfer (HGT) Sometimes virus’ DNA gets trapped into the host’s genome, becoming part of it. It then follows the fate of the host cell; it is copied at cell fission, staying dormant during many generations. It is eventually woken up by external events (e.g. chemical agent, UV irradiation) and thus starts the reproduction in hundreds copies through the lyse cycle; it might then carry stretches/genes from the host’s DNA, which thus become part of the virus genome. During following infection the latter will then inject the acquired DNA into a new bacterial cell, eventually of a different species (virus-mediated transduction of donor DNA into a recipient cell). It is known that antibiotic resistance is a major issue in present days. Some individual bacteria are naturally antibiotic-resistant by random mutations; they are thus able to spread resistance to other bacteria by horizontal gene transfer or by conjugation. It appears that such a process is enhanced by ambient pressure. HGT plays a very special role in evolutionary theory. The traditional Darwinian evolution was based on small random errors, most often fatal and thus discarded, but sometimes profitable. With HGT we encounter a new and very powerful tool to evolution. A cell obtains in one go large useful genetic information already selected through a long series of random mutations. In fact such an advantage is so large that Syvanen (Syvanen 1985) proposes HGT as the very justification as to why the code didn’t evolve in the different kingdoms and species. Genetic isolation would in fact entail a very slow evolution rate, while HGT provides an advantage great enough to overcome the burden of viral infections. At present, one doesn’t speak any longer of tree of life (TOL), for the many bridges found between species; the evolutionary pattern looks more like a mosaic ( Mayr 2001). HGT is well documented in bacteria; it is less easily identifiable in multi-cellular organisms where sexual reproduction brings a continuous reshuffling of the genetic patrimony. Eukaryotic cells Conjugation and HGT are forms of multicellular cooperation; other forms of symbiosis must have developed within bacterial colonies bringing functional

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specialization. Endosymbiosis (Margulis 2009) is a form of permanent cohabitation, in which two cells fuse into a single cell. Eukaryotes are much larger than prokaryotes, and their nucleus, containing the genome, is surrounded by a membrane. Outside the membrane is the cytoplasm with all the cellular toolkit, namely ribosomes and mitochondria, all enclosed by the cell wall. Eukaryotes are ubiquitous and form all multicellular organisms. Genetically Modified Organism (GMO) Selected genes can be artificially transferred from one species to another: a specific DNA sequence or gene will code the same protein in all the organisms, as the DNA code is the same. One may regard Genetic Engineering as accelerated evolution, but as such it requires a lot of enforced control from the civil society. Applications in agriculture span from herbicide resistance (e.g. soybean) to resistance to pests (e.g. Bt corn), to production of beta-carotene in rice. Other possible applications are the production of drugs by plants (e.g. insulin). Most often, GMOs are patented. The surface cultivated with GMOs is larger than 1 million km2. Despite some obvious advantages, a lot of concern has been raised, some countries limiting or forbidding production or usage of GM crops. Main concerns include the risk of allergies and the risk of impairing biodiversity by spreading genes into the wild, to list just a few. Conclusion The quasi universality of the DNA code has opened the road to some strategies of foreign DNA acquisition by cells, either naturally, via conjugation and horizontal gene transfer, or artificially, via genetic engineering. The exchange of genes makes it impossible to reconstruct a tree of life (TOL) of living organisms, but it explains the formation of eukaryotic cells as well as antibiotic resistance in bacteria. Genetically modified organisms appear to be a kind of accelerated evolution with artificial fitness selection; they allow production of crops with novel properties but raise questions about the preservation of biodiversity. References Arber, W. 2003 “Elements for a theory of molecular evolution”, Gene 317, 3-11 Arber, W. 2007 “Evolutionary Strategy of DNA Acquisition as Possible Reason for Universal Genetic Code”, Hist. Phil. Life Sci. 28, 525-532 Arber, W. 2011” Private communication” Crick, F.H.C. 1968 “The origin of the genetic code”, J. Mol. Biol. 38,367–379. Davies, P. 1999 The fifth miracle, New York, Touchstone Book, Doolittle, W.F. 2000 “Uprooting the Tree of Life” Sci. Am. Feb 2000, 90-94 Higgs P. 2009, Biology Direct, 4:16 Line, M.A. 2002 “The Enigma of the Origin of Life and its Timing” Microbiology 148,21-27 Margoulis, L. 2009 “Origin of Evolutionary Novelty by Symbiogenesis” in G.Auletta, M.Leclerc, R.A. Martinez (eds), Biological Evolution: facts and Theories, Gregorian 5

and Biblical Press - Roma Mayr, E. 2001 What Evolution is, New York, Basic Books Meldolesi, A. 2001 Organismi Geneticamente Modificati, Torino, Grandi Tascabili Einaudi Praveenya P., et al. 2012 “Antibiotic resistance creating a new epoch” J. Bacteriol. Parasitol. 3:1 Syvanen, M. 1985 “Cross-species gene transfer; Implications for a new theory of Evolution” J. Theor. Biol. 112,333-343 Wilhelm, T. et al. 2004 “A New Classification Scheme of the Genetic Code” J.Mol. Biol., 59: 598–605

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Biography Retired physicist from the CERN- European Organization for Nuclear Research. The main field of activity have been neutrino beams, DC and RF superconducting components for accelerators, Gravitational Wave Experiment and interaction of ionizing particles with superconducting materials.

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