Research in Microbiology 160 (2009) 437e440 www.elsevier.com/locate/resmic

From the to the latest universal common ancestor

Mario Vaneechoutte a,*, Renato Fani b

a Laboratory Bacteriology Research, Faculty Medicine & Health Sciences, University of Ghent, 3 Blok A, De Pintelaan 185, 9000 Gent, Belgium b Dept. of Evolutionary , Via Romana 17-19, University of Florence, I-50125 Florence, Italy Received 4 September 2009; accepted 7 September 2009 Available online 12 September 2009

Abstract

This special issue of Research in Microbiology is dedicated to the origin of and of microbiology. One hundred and fifty years after Darwin’s ‘Origin of the Species’, which is basically about the principles of , the origin of Life, which largely coincides with the origin of natural selection, remains the most enigmatic and fascinating problem in biology. Ó 2009 Elsevier Masson SAS. All rights reserved.

Keywords: Life; Natural selection; Darwin; Last universal common ancestor; Horizontal gene transfer

1. Introduction metabolic activity e or the potential for metabolic activity, as in seeds and spores e of unicellular and multicellular organ- This fascinating dilemma exists not only because the origin isms, which is only a transient state of being. When of Life requires the explanation of many origins, i.e. those of a prokaryote cell divides, it is no longer alive, because it is nucleotides, proteins, lipid membranes, bacterial cell walls and replaced by two other living cells. Multicellular organisms are those of and genetic coding, but especially because metabolically active with the purpose of getting their germ these and processes are so intrinsically intertwined cells into the next generation and as such are only transient, within each cell that resolving the problems related to one origin temporary constructions. E.g., when devoid of oxygen, water immediately poses new problems in understanding the origin(s) or food, a human multicellular colony ceases to be alive within of other processes and building blocks. Not one, but many resp. minutes, days or weeks. Viruses, not metabolically ‘chicken and egg’ problems are involved. active, are not alive according to this definition. Obviously, a single issue is far from sufficient to present all However, the question ‘What is Life’ requires another the available data, gathered recently by origin of Life approach. Since it is generally agreed that all extant living researchers. Therefore, we have tried to cover only those cells are the descendants of the Last Universal Common aspects of the origin of Life which we consider to be most Ancestor (LUCA), which probably originated some 3e3.5 illuminating or where refreshing insights have been proposed. billion years ago, in our opinion Life can most easily and most When trying to define Life, of which we are trying to correctly be defined as the currently existing 3.5 billion year- explain the origin(s?), we suggest making the distinction old organism, consisting of all extant trillion trillion cells on between ‘Life’ and ‘being alive’ as two very different Earth, AND their associated viruses. Life is a single organism concepts, which are usually not distinguished from each other which exists since the LUCA started duplicating for the first by most philosophers, leading to several misconceptions and time, and continued to do so with, as a result, all extant cells at irrelevant discussions [14]. ‘Being alive’ concerns the this moment of which it is composed. Because Life could be considered as a single organism, we suggest writing Life with a capital ‘L’. * Corresponding author. In appreciating the model of Life as a single organism, E-mail addresses: [email protected] (M. Vaneechoutte), [email protected]fi.it (R. Fani). derived by continued and uninterrupted duplication of the first

0923-2508/$ - see front matter Ó 2009 Elsevier Masson SAS. All rights reserved. doi:10.1016/j.resmic.2009.09.002 438 M. Vaneechoutte, R. Fani / Research in Microbiology 160 (2009) 437e440 cell, one should realize that all cells of the organism Life not all three domains of Life and ii) by acting as an important only share a common past but also are strongly interconnected, selective force, strongly influencing population dynamics being interdependent on each others’ metabolism. Prokaryote through infection, e.g. think of phage-driven bacterial pop- and eukaryote cells influence each others’ activity, whereby ulation dynamics [3] and of viral pandemics like the current the waste products of the metabolism of one cell provide the one caused by HIV. Viruses both made immune defense energy and building blocks for another cell, and these cells and possible (as important agents of HGT) and necessary (as their intrinsically associated viruses helped shape each others’ infectious agents). Viruses were probably around before the evolution through genetic exchange. Commensal, symbiotic, LUCA [8,12] and also played an important role in the origin of parasitic and pathogenic organisms and parasitic viruses, the first cell, i.e. the origin of Life. living on and within other organisms continuously influence In summary, Life includes the interactions among the the activity of the cells of their hosts and are mutually influ- metabolically active cells, which are all descendants of enced by them. Think of the continuous interaction between a common ancestral cell, with the biosphere as a whole, which our estimated log13 cells and the estimated log14 bacterial is a product of Life’s activity, and with the associated viruses. cells in our bodies, e.g. the way our native and adaptive The ‘being alive’ of individual living cells, whether existing as immune system is influenced by and influences bacterial separate entities or joined into clonal temporary colonies, can metabolism. Cells within each multicellular colony, as well, only be understood by considering the many interactions with interact continuously with each other by collaboration and other cells, viruses and the biosphere at present AND in the competition, e.g. the induction of apoptosis in other cells past. during embryology. And of course, multicellular colonies The success of research aiming at unravelling the origin of interact with each other and with their (multicellular) para- Life has increased exponentially due to the availability of sites. Even within most eukaryotic cells, we find remnants of completely sequenced genomes belonging to organisms of the ancient cooperations which have crystallized into irreversible three cell domains of Life, i.e. Bacteria, Archaea and Eukarya. endosymbioses, e.g. mitochondria and chloroplasts. For This sequence information made possible comparative anal- instance, at first sight, photosynthesizing plants might be ysis of genes and genomes, which has led to spectacular considered as autonomous, as long as there is sunlight and developments in the understanding of the molecular basis of fertile soil, but their ability to photosynthesize relies on the many biological phenomena, which, in turn, enabled shedding ancient acquisitions of photosynthetic cyanobacteria (or of light on the molecular mechanisms and forces driving the other eukaryotic photosynthesizing cells, already containing evolution of (micro)organisms. cyanobacterial descendants) by the first plant ancestor line- ages. And the fertile soil on which most plants depend was 2. Prebiotic chemistry itself created by and depends largely on the activity of bacteria and fungi and maybe also on complex microbial communities The first strong impulse for the study of the origin of Life inhabiting the phloem and xylem of the plants. was the MillereUrey experiment in 1953 [13], which repre- In brief, all present cells of the organism Life form one sents the starting point of prebiotic chemistry, a discipline giant network of multiple and very different interactions, which during the following years led to the demonstration that which can only be understood by considering the ‘evolu- the building blocks of cells can be easily synthesized under tionary history’, or in this context the ‘past lifetime’ of the putative primitive conditions, supporting Alexander Oparin’s organism Life. To quote Theodosius Dobzhansky [6]:‘Nothing ‘‘primordial soup’’ idea on the origin of Life on Earth [15]. in biology makes sense except in the light of evolution’. This special issue starts with a prebiotic chemistry paper. Another example of the importance of understanding the Saladino et al. [19] propose that formamide and water may biogeological record as determined by the activity of Life is have played a central role in the evolution of the first nucle- that Life itself has reshaped its own environment, including the otides, and propose plausible mechanisms whereby nucleo- atmosphere, the oceans and the soil, partially by ‘polluting’ it, sides, nucleotides and nucleotide oligomerization may have e.g. with oxygen, a pollution which turned out to enable the occurred in an environment of formamide, and later water. development of multicellular organisms. So Life includes the Their proposal is a very elegant one, e.g. because this oligo- interactions among the metabolically active cells, but also with merization does not require templates, catalysts or dry- the biosphere as a whole, largely a product of Life’s activity. chemistry conditions. Moreover, the proposed cyclic Our proposal to clearly distinguish ‘Life’ as an organism synthesis/degradation process for nucleic acid bases in form- from the ‘being alive’ of its constituent cells may help to amide reduces the relevance of their stability for molecular answer the longstanding debate about whether viruses are part evolution, since degraded products can be easily resynthesized of Life. Viruses, although not alive, because not metabolically under the same experimental conditions. Not addressed in this active, clearly are part of the organism Life, playing an issue, but worth mentioning because usually overlooked, is increasingly recognized pivotal role in evolution and in some that nucleotides not only are important as building blocks of major evolutionary transitions [8], e.g. in the origin of the RNA and DNA, but also play a central role in extant metab- innate immune system in vertebrates and the origin of pla- olism, e.g. as energy storage devices (ATP, GTP), as universal centalism in mammals. Viruses influence evolution i) through energy transporters with well-delineated roles (e.g. NADH, the possibilities of horizontal gene transfer (HGT) they offer to FADH, NADPH), or in guiding the polymerization of M. Vaneechoutte, R. Fani / Research in Microbiology 160 (2009) 437e440 439 monosaccharides, whereby monosaccharide activation by UTP a complex process requiring factors some of which are shared guides polymerization into polysaccharides with a structural by Bacteria and Archaea, whereas others are specific to each function (e.g. peptidoglycane and cellulose), whereas ATP domain. The discovery of leaderless mRNA, that is mRNA leads to polysaccharides for energy storage (e.g. starch and molecules transcribed from genes lacking a Shine and Dal- glycogen). garno sequence, led to the suggestion that in the primordial gene, the transcription startpoint was coincidental with the first 3. The ‘‘RNA world’’ codon. This issue is reviewed by Benelli and Londei [1], where they also suggest that the machinery of translational More than 40 years ago Woese [23], Crick [4] and Orgel initiation in the LUCA consisted of at least two factors and [16] proposed the existence of a hypothetical stage, the ‘‘RNA operated in leaderless mRNA. world’’ predating the appearance of proteins and DNA-based molecules during which the first cells were based on ribo- 5. Metabolic pathways zymes [11]. An insight into the RNA world and in the func- tion(s) that might have been performed by ancient RNA The origin of the genetic code, the appearance of trans- molecules is provided by the contribution of Talini et al. [20]. lation and its refinement were very likely concomitant with the One of the key steps in the appearance of the first cells should assembly of most of the metabolic pathways and the increase have been the possibility of confining the ancestral spontane- in metabolism and genome complexity. This represented ously formed catalytic molecules capable of growth and another milestone in the evolution of living beings because the replication (RNA or pre-RNA molecules) within membranous possibility of autonomously synthesizing those abiotically boundaries. In the last few years, considerable progress has produced substances whose concentration was (rapidly) been made in understanding the self-assembly and function of decreasing in the primitive Earth rendered the first microbial primitive cell membranes as permeability barriers. This issue communities less dependent on the external supply of nutri- as well as the emergence of protein-mediated ion transport ents. Fondi et al. [7] describe the molecular mechanisms and across membranes is reviewed in the contribution by Pohorille forces that are thought to have driven the origin and evolution and Deamer [17]. of metabolic routes and the expansion of genomes. This issue is considered in conjunction with the organization of the 4. Origin of the genetic code and ribosomes primordial genes, by discussing the origin and evolution of operons. The appearance of proteins and DNA genomes required complex and still unclear steps which include the origin of the 6. HGT and evolution genetic code and of ribosomes and how ancestral ribosomes recognized and translated primordial RNA messenger mole- Once assembled, the first metabolic abilities, i.e. entire cules. According to the ingenious analysis of protein and gene metabolic routes possibly encoded by operonically organized sequences by Trifonov [21], the very first genes were genes, rapidly spread in the ancestral microbial communities complementary to each other, consisting of GGC and GCC by HGT mechanisms, which very likely also included cell triplets, encoding respectively ala and gly, which e not fusion in addition to virus-mediated gene transfer (trans- coincidentally, we may assume e also happen to be the most duction), plasmid-mediated transfer (transconjugation) and ancient and stable amino acids. Moreover, the two earliest uptake of naked DNA (transformation). complementary genes code for ATP/GTP binding and ATPase HGT has been recognized as one of the major forces activity, which might throw light on the intriguing question on driving the evolution of genomes. It was particularly important how e nucleotide-centered e metabolism (see above for the during the early stages of molecular and cellular evolution role of nucleotides in extant metabolism) and early encoding when, according to Woese [24], the primordial DNA mole- can be brought together. cules might easily have flowed between cells. In this way, the The paper by Davidovich et al. [5] provides biochemical progenote community could exchange its new metabolic evidence to support the existence of an ancestral proto-ribo- tricks. This issue has been reviewed by Poole [18], who some, consisting of two identical subunits, i.e. two self-folding addresses the difficult problem of how strong HGT and natural RNA chains that spontaneously assembled to give a pocket selection might be reconciled. A related problem has been favoring the positioning of substrates involved in peptide bond dubbed the COSMIC-LOPER problem: the capability of formation and elongation. According to these authors, the searching mutation space independently of concern over loss relics of this ancestral pocket are still embedded in the core of of properties essential to replication [2]. Indeed, the RNA the modern ribosome. At the start of the ‘translational world’, world hypothesis relies on natural selection between self- protein synthesis was most probably inaccurate and many replicating nucleotides to explain prebiotic evolution, but errors occurred during translation, leading to inefficient natural selection too early confronts us with a limitation of the protein molecules. Thus, the refinement of this process should possibilities for variation that can be explored [22]. have been of great importance for the further evolution of As addressed above, viruses play a central role in HGT, but primitive cells. In this context, one of the most important steps their origin and evolution is still heavily debated. Forterre and in gene expression is represented by translational initiation, Prangishvili [8] shed some light on possible virus origins and 440 M. Vaneechoutte, R. Fani / Research in Microbiology 160 (2009) 437e440 report that at least two types of virions originated indepen- of this multi-dimensional puzzle finally all fall into place. dently before the appearance of the LUCA. Maybe, for that to happen, we need another Darwin. The last two papers in this special issue deal with later stages of cellular evolution. The first one, by the late Glans- dorff (please see the obituary in his honor, in this issue) et al. References [9], addresses several basic questions regarding the nature of the LUCA. Their argumentation requesting us to not neglect [1] Benelli, D., Londei, P. (2009) Begin at the beginning: evolution of translational initiation. Res. Microbiol. 160, 493e501. alternatives to ‘assertions that originally had the status of [2] Benner, S. (1999) Old views of ancient events. 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