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Evolution - Wikipedia

An example of such a speciation event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa crossbred to give the new species Arabidopsis suecica.

DNA - Wikipedia

This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases.

Gene - Wikipedia

However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer.

Last universal common ancestor - Wikipedia

The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent population of organisms from which all organisms now living on Earth have a common descent—the most recent common ancestor of all current life on Earth. A related concept is that of progenote. LUCA is not thought to be the first life on Earth, but rather the only type of organism of its time to still have living descendants.

While there is no specific fossil evidence of LUCA, it can be studied by comparing the genomes of all modern organisms, its descendants. By these means, a 2016 study identified a set of 355 genes most likely to have been present in LUCA. The genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to RNA to proteins. The study concluded that the LUCA probably lived in the high-temperature water of deep sea vents near ocean-floor magma flows.

Studies from 2000 to 2018 have suggested an increasingly ancient time for LUCA. In 2000, estimations suggested LUCA existed 3.5 to 3.8 billion years ago in the Paleoarchean era, a few hundred million years before the earliest fossil evidence of life, for which there are several candidates ranging in age from 3.48 to 4.28 billion years ago. A 2018 study from the University of Bristol, applying a molecular clock model, places the LUCA shortly after 4.5 billion years ago, within the Hadean.

Charles Darwin first proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859: "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." Later biologists have separated the problem of the origin of life from that of the LUCA.

Features

By analysis of the presumed LUCA's offspring groups, the LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. However, Carl Woese et al., who first proposed the currently-used three domain system based on an analysis of ribosomal RNA (rRNA) sequences of bacteria, archaea, and eukaryotes, stated that in its genetic machinery, the LUCA would have been a "... simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".

While the gross anatomy of LUCA can only be reconstructed with much uncertainty, its biochemical mechanisms can be described in some detail, based on the properties currently shared by all independently living organisms on Earth.

Its genetic code was likely based on DNA, so that it lived after the RNA world. If DNA was present, it was composed exclusively of the four modern-day nucleotides: deoxyadenosine, deoxycytidine, deoxythymidine, and deoxyguanosine. The DNA was kept double-stranded by a template-dependent enzyme, DNA polymerase, which was recently proposed to belong to the family D. The integrity of the DNA benefited from a group of maintenance and repair enzymes including DNA topoisomerase. If the genetic code was DNA-based, it was expressed via single-stranded RNA intermediates. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA, with the exception that the DNA nucleotide thymidine was replaced by uridine in RNA. It had multiple DNA-binding proteins, such as histone-fold proteins.

The genetic code was expressed into proteins. These were assembled from free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins. The ribosomes were composed of two subunits, a big 50S and a small 30S. Each ribosomal subunit was composed of a core of ribosomal RNA surrounded by ribosomal proteins. Both types of RNA molecules (ribosomal and transfer RNAs) played an important role in the catalytic activity of the ribosomes. Only 20 amino acids were used, only in L-isomers, to the exclusion of countless other amino acids. ATP served as an energy intermediate. Several hundred protein enzymes catalyzed chemical reactions to extract energy from fats, sugars, and amino acids, and to synthesize fats, sugars, amino acids, and nucleic acid bases through various chemical pathways.

The cell contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane. The cell tended to exclude sodium and concentrate potassium by means of specific ion transporters (or ion pumps). The cell multiplied by duplicating all its contents followed by cellular division. The cell used chemiosmosis to produce energy. It also reduced CO2 and oxidized H2 (methanogenesis or acetogenesis) via acetyl-thioesters.

The LUCA probably lived in the high-temperature conditions found in deep sea vents caused by ocean water interacting with magma beneath the ocean floor.

Hypotheses

In 1859, Charles Darwin published On the Origin of Species, in which he twice stated the hypothesis that there was only one progenitor for all life forms. In the summation he states:

"Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed."

The last sentence begins with a restatement of the hypothesis:

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one ..."

When the LUCA was hypothesized, cladograms based on genetic distance between living cells indicated that Archaea split early from the rest of living things. This was inferred from the fact that the archaeans known at that time were highly resistant to environmental extremes such as high salinity, temperature or acidity, leading some scientists to suggest that the LUCA evolved in areas like the deep ocean vents, where such extremes prevail today. Archaea, however, were later discovered in less hostile environments, and are now believed to be more closely related to the Eukaryota than to the Bacteria, although many details are still unknown.

In 2010, based on "the vast array of molecular sequences now available from all domains of life," a formal test of universal common ancestry was published. The formal test favored the existence of a universal common ancestor over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles make it overwhelmingly likely that all organisms do have a single common ancestor. It is extremely unlikely that organisms descended from separate incidents of cell-formation would be able to complete a horizontal gene transfer without garbling each other's genes, converting them into noncoding segments. Further, many more amino acids are chemically possible than the 22 found in protein molecules. These lines of chemical evidence, incorporated into the formal statistical test point to a single cell having been the LUCA. While the test overwhelmingly favored the existence of a single LUCA, this does not imply that the LUCA was ever alone: Instead, it was one of many early microbes but the only one whose descendants survived beyond the Paleoarchean Era.

With the later gene pool of the LUCA's descendants, with their common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have been feasible and could have been very common.

In an earlier hypothesis, Carl Woese (1988) had proposed that:

  1. no individual organism can be considered a LUCA, and
  2. the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.

While the results of Theobald (2010) and Saey (2010) demonstrated the existence of a single LUCA, Woese's argument can still be applied to Ur-organisms (initial products of abiogenesis) before the LUCA. At the beginnings of life, ancestry was not as linear as it is today because the genetic code had not evolved. Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. However, the LUCA lived after the origin of the genetic code and at least some rudimentary early form of molecular proofreading.

Location of the root

The most commonly accepted tree of life, based on several molecular studies, has its root between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota. However, a very small minority of studies place the root in the domain Bacteria, in the phylum Firmicutes, or state that the phylum Chloroflexi is basal to a clade with Archaea and Eukaryotes and the rest of Bacteria (as proposed by Thomas Cavalier-Smith).

Research by William F. Martin (2016) genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes of various phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results "depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms." The cofactors also reveal "dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." The results are "quite specific": they show that methanogenic clostridia was a basal clade in the 355 lineages[clarification needed] examined, and that the LUCA may therefore have inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H2, CO2, and iron.

These findings could mean that life on Earth originated in such hydrothermal vents, but it is also possible that life was restricted to such locations at some later time, perhaps by the Late Heavy Bombardment. The identification of these genes as being present in LUCA has also been criticized, as they may simply represent later genes which migrated via horizontal gene transfers between archaea and bacteria.

Viruses

Based on the extant distribution of viruses across the two primary domains of life, bacteria and archaea, it has been suggested that LUCA was associated with a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea and that extensive virus evolution has antedated, or preceded in time, the LUCA. This ancestral virome was likely dominated by dsDNA viruses from the realms Duplodnaviria and Varidnaviria. In addition, two groups of single-stranded DNA viruses (realm Monodnaviria), namely Microviridae and Tubulavirales, can be traced to the last bacterial common ancestor (LBCA), whereas spindle-shaped viruses most likely infected the last archaeal common ancestor (LACA). The possibility that these virus groups were present in the LUCA virome but were subsequently lost in one of the two primary domains cannot be dismissed. By contrast, RNA viruses do not appear to have been a prominent part of the LUCA virome, even though straightforward thinking might have envisaged the LUCA virome as a domain of RNA viruses descending from the primordial RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been largely supplanted by the more efficient DNA virosphere.


Questions

1) The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent ________ of organisms from which all organisms now living on Earth have a common descent - the most recent common ancestor of all current life on Earth.

2) While there is no specific fossil ________ of LUCA, it can be studied by comparing the genomes of all modern organisms, its descendants.

3) The ________ was produced by a DNA-dependent ________ polymerase using nucleotides similar to those of DNA, with the exception that the DNA nucleotide thymidine was replaced by uridine in ________ .

4) In an earlier hypothesis, Carl Woese (1988) had proposed that: no individual organism can be considered a LUCA, and the genetic heritage of all modern organisms derived through horizontal ________ transfer among an ancient community of organisms.

5) While the test overwhelmingly favored the ________ of a single LUCA, this does not imply that the LUCA was ever alone: Instead, it was one of many early microbes but the only one whose descendants survived beyond the Paleoarchean Era.

6) Research by William F. Martin (2016) genetically analyzed 6.1 million ________ -coding genes and 286,514 ________ clusters from sequenced prokaryotic genomes of various phylogenetic trees, and identified 355 ________ clusters that were probably common to the LUCA.

7) By contrast, RNA viruses do not appear to have been a prominent part of the LUCA virome, even though straightforward thinking might have envisaged the LUCA virome as a ________ of RNA viruses descending from the primordial RNA world.