The Beginning of Life on Earth and the Genetic Code

Sequence analysis ofgenomes ofspecies from all three domains of life showed that primarily proteins related with energy processes and protein synthesis, transcription and replication can be considered to

Corresponding Author: Knud H. Nierhaus—Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, AG Ribosomen, 14195 Berlin, Germany. Email: [email protected]

Table 2.1. Approximate molecular composition of a bacterial cell. Adapted from reference 23.

Approx. Number of Molecules Number of Different Component Percent of Total Weight Per Cell Kinds

Water 70%

Protein 15%

Nucleotides and precursors 0.4%

Amino acids and precursors 0.4%

Carbohydrates (polysaccharides and precursors) 3%

Lipids 2%

Ions 1%

Waste products and intermediates 0.2%

be generally common and conserved in the three domains, in spite of differences in detail.2

Here, the undisputed steps in the beginning of life on Earth are compiled, before a retrograde approach is presented outlining a possible minimal set of components required for protein synthesis, based on our knowledge ofthe modern translational apparatus ofthe bacterium Escherichia coli, since evidence suggests that the bacterial domain is most deeply rooted in the universal evolutionary tree (see however Section 15.2). Figure 2.3 shows a universal small subunit ribosomal RNA tree with some recently established numbers ofage, which are in overall agreement with the evidence from comparisons

4 x 1010

1

1-4

1

5 x 105

3,000

1 x 106

3,000

1.2 x 107

200

3 x 107

50

2.5 x 108

200

2.5 x 107

50

2.5 x 108

20

1.5 x 107

200

of ribosomal RNA, ribosomal proteins and membrane composition. Because protein synthesis is an energy demanding process, we further continue that consideration by addressing one of the main problems of early life, namely avoiding wasteful energy loss.

Describing the evolutionary time at which a feature of live appeared is, in many cases, more like a flower arrangement, rather than a sound determination. However, a few solid data do exist. One cornerstone for our estimate of early life is seen in the stromatolites, which represent ancient cells. The oldest "stromatolites" reported are from rocks of Isua Supracrustal Belt, Greenland, dated at 3,750 million years (Ma) ago, but they have been questioned as to whether

Figure 2.1. The relative abundance of chemical elements found in the Earth's crust (the nonliving world) compared to that of living organisms. The relative abundance is expressed as a percentage of the total number of atoms present. Adapted from reference 25.
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Figure 2.2. Comparison of (A) a prokaryotic cell and (B) a eukaryotic animal cell. For explanations see text. Adapted from reference 26.

they can really be considered as the first imprint of life. More solid data exist about formations that are 3,500 Ma old containing remnants of ancient cells: (i) One is the Pilbara region of Western Australia with an age of 3,430 Ma; a recent report supports the suggestion that these Pilbara-Craton structures might be of biotic origin.3 (ii) Another of about the same age with evidence of micro -bial biomarkers is the pillow lava from the Baberton Greenstone Belt in South Africa.4 Such ancient cells must have genes (from RNA?) and a translational apparatus, i.e., the genetic code has an age of 3.2 to 3.6 billion years. This estimate has been backed up in an elegant study ofEigen and coworkers,5 where tRNA sequences from various organisms were used to conclude that the genetic code has an age of 3,300 ± 300 Ma. It follows that chemical evolution, the development of the genetic code and the existence of the "RNA world" must be squeezed into a time span of400 to 800 Ma, corresponding to the time gap between the formation of the first rocks (4,000 Ma) and the appearance of the first cells (3,600 to 3,200 Ma).

Another important landmark is the observation, in many iron deposits around the Earth at the geological layer of about 2 billion years ago (2,000 Ma), of Fe111 (ferric state) precipitates indicating the appearance of the oxidizing power of O2, a product of photosynthesis. The earliest Fe111 deposits are found in the Hamersley iron formation in Western Australia.6 At deeper layers, Fe11 (ferrous state) deposits are usually present. It follows that cyanobacterial photosynthesis developed before 2,000 Ma. Appearance of the pollutant O2 in the atmosphere was a major threat to early life, since every cell contained and still contains a reducing milieu—a relic of the origin of life when the atmosphere was reducing. The consequence was obviously a massive extinction. Only a few cells survived due to a membrane composition that prevented the passage of oxygen into the cell. Over the longer run the cells eventually turned the appearance of atmospheric oxygen into a major advantage by inventing respiration.

Figure 2.3. Small subunit ribosomal RNA phylogenetic tree of the three living domains Bacteria, Archaea and Eukarya. The n depicting dates in years ago are according to references 6,27; see also reference 28.

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Figure 2.4. The three essential energy (ATP) production lines are shown together with their rough dates of origin in red. Cellular ATP production started with anaerobic glycolysis about 3.500 Ma years ago followed by photosynthesis and finally by respiration. The last step provided the energy required for the development of highly organized multicellular life. The inset (grey) gives some additional data.

Figure 2.4. The three essential energy (ATP) production lines are shown together with their rough dates of origin in red. Cellular ATP production started with anaerobic glycolysis about 3.500 Ma years ago followed by photosynthesis and finally by respiration. The last step provided the energy required for the development of highly organized multicellular life. The inset (grey) gives some additional data.

Eukaryotic cells developed mitochondria by engulfing respiring bacteria, specifically an a-proteobacterial ancestor,7 leading to a dramatic improvement in energy production taking the form of ATP, the energy currency of life. Respiration means an 18-fold improvement in the energy efficiency of ATP formation compared to the most ancient energy-production pathway, viz. anaerobic glycolysis. We can define three important stages of evolution relating to ATP production (Fig. 2.4): (i) Before respiration (>2,600 Ma ago), the major energy production pathway was anaerobic glycolysis, where C6 sugars (glucose, fructose) were broken down to C3 carbohydrates (pyruvate). It is thought that the sugars were taken from the environment, formed by high temperatures and electrical discharges through the ancient atmosphere according to the Stanley Miller experiments mimicking the ancient atmospheric composition and physical factors (flashes, temperature8). (ii) At 2,600-2,400 Ma ago photosynthesis was invented, abolishing the dependence of life on exogenous energy-rich compounds, such as C6 sugars. (iii) <2,000 Ma ago some of the enzymes developed for

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