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Algorithms in Bioinformatics. Paul A. Gagniuc

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Название Algorithms in Bioinformatics

Год выпуска 0

isbn 9781119697992

Автор произведения Paul A. Gagniuc

Жанр Математика

Серия

Издательство John Wiley & Sons Limited

Algorithms in Bioinformatics - Paul A. Gagniuc

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the fossil record with the rise of bilaterians (bilateral symmetry in organisms) over 550–600 million years ago [15]. Nevertheless, even in the case of these fossils, some uncertainty overshadows interpretation. The macroscopic dimensions and the observed bilateral symmetry still cannot indicate with certainty the multicellular nature of these extinct organisms. Again, many of these fossils can be interpreted as multicellular organisms or as unicellular organisms (e.g. giant protists) [16]. More clear evidence suggests that multicellular organisms may have been present around 635 million years ago [17]. Recent molecular clock analyses estimate that animals started to evolve ∼650 million years ago [18]. Bilaterian metazoans (animals with bilateral symmetry) first appeared around 600 million years [12]. Moreover, the evolutionary origins of the blood vascular system date around the same period [19]. Later, bilaterians split into the protostomes and deuterostomes [12]. Protostomes give rise to bring about all the arthropods (e.g. insects, spiders, crabs, shrimp, and so on). Deuterostomes eventually give rise to all vertebrates [12]. Perhaps the most important leap made in the evolution of life was the appearance of motility in multicellular organisms. Fossilized trails of bilaterian animals suggest that eukaryotic multicellular organisms have acquired motility around 551–539 million years ago [20]. A “few” million years later, the first true vertebrate with a backbone appears in the fossil record (545–490 million years ago) [21]. Moreover, fossil evidence shows that animals were exploring the land for the first time around 500 million years ago (544–457) [22]. Plants begin colonizing the land around the same time (470 million years ago) [22]. The first four-legged animals (tetrapods) explored the land 385–359 million years ago and gave rise to all amphibians, reptiles, birds, and mammals [22, 23]. The oldest fossilized tree also dates from this period [22]. Important diversifications in eukaryotic species appear after this period, both on land and in water. The first mammal-like forms appear in the fossil record around 225 million years ago [24]. Much closer periods bring many wonders. For instance, the largest eukaryotes in Earth's history have been observed around 100 million years ago, namely the cretaceous dinosaurs (e.g. Argentinosaurus; length: 22–35 m; estimated mass: 50 000–100 000 kg) [25]. The last extinction event (Cretaceous–Tertiary extinction), which occurred over 66–65 million years ago, allowed for a relaxed evolution of mammals [26]. Our own story begins of course at the origin, of life. However, more distinguished developments start with the origins of the first primates around 55 million years ago [27]. Note that the timeline of past events is detailed in the literature and here only some general points were reached.

1.2.1 Timeline Disagreements

Microfossils (the imprint left by an organism in stone), stromatolites (layered rocks derived from photosynthetic cyanobacteria remains sedimented over time), sedimentary carbon isotope ratios or molecular fossils derived from cellular and membrane lipids (“biomarkers”), are used for estimations of the origin and diversification of life in the distant past [28]. Data expressed in billions and hundreds of millions of years are particularly subjective and can lead to variations in the literature up to plus or minus half a billion years. These issues are known and must be taken at face value. While timeline estimates may vary, the order of events is particularly objective. Note that timeline disagreements in the paleontology literature rather indicate that evolution has no milestones but trial periods that overlap; some trials more successful and others that we will probably never know about. Nevertheless, the closer the events get to the present, the more reliable the numbers become. Although relative, timeline estimations in paleontology represent a reliable reference system for important past events on our planet.

1.3 Classifications and Mechanisms

Life on Earth was classified by us into three major domains, namely Bacteria, Archaea, and Eukarya (Figure 1.1) [29]. Bacteria (Greek – bakterion, “small stick”) and Archaea (Greek – Arkhē, “origin”) are prokaryotes (Greek – pro, “before”; karyon, “kernel” or “core”). Prokaryotes are single-cell organisms (unicellular) without a “core,” namely without a nucleus, and are considered similar or close in sophistication to the first living organisms on Earth. Eukarya (Greek – eu, “well” or “true”) includes all unicellular and multicellular organisms with cells that contain nuclei, and it refers to animals (including us), plants, fungi, and single-celled protists.

Schematic illustration of the tree of life – basic diagram. The prebiotic period shown on the bottom-left represents the formation of primordial chemical molecules necessary for the ignition of life.

Figure 1.1 The tree of life – basic diagram. The prebiotic period shown on the bottom-left represents the formation of primordial chemical molecules necessary for the ignition of life. Next, the diagram indicates the appearance of LUCA (last universal common ancestor), the first “rudimentary” form of life. The first prokaryotes appear later based on the evolution of LUCA, namely bacteria and archaea. Eukaryotes appear next in the evolutionary chain. Eukaryotes divide the tree of life into four other main subdivisions (eukaryotic kingdoms), namely: protists, fungi, animals, and plants. Note that the approximate number of known species is presented for each subdivision.

Source: Refs. [29, 74, 252, 253].

All contemporary forms of life store information in DNA molecules. DNA molecules are polymers consisting of four types of organic molecules linked together by phosphate groups, namely: adenine (A), thymine (T), cytosine (C), and guanine (G). Indirectly, all cellular processes are orchestrated by the information contained in the DNA molecule. Cellular processes store and use energy in the form of discrete packets (adenosine triphosphate molecules or ATP). In prokaryotes, DNA shows a double-stranded circular (usually) form and it is located in the internal environment of the cell (cytoplasm). Cells of eukaryotic organisms contain a double-stranded linear (usually) DNA folded inside a membrane-bound organelle, named the nucleus (from Latin – nucleus, “kernel” or “seed”; pl. nuclei). The nuclear membrane is a controlled barrier that separates the DNA molecules from the cytoplasm (Figure 1.2). Naturally, images based on electron microscopy can best show the classic structure and the inner “frozen” dynamics of eukaryotic cells (Figure 1.2). In double-stranded DNA, a cytosine molecule from one strand and a guanine molecule from the other strand, form three hydrogen bonds while adenine and thymine form two hydrogen bonds. The successive alternation of these simple hydrogen bonds along the double-stranded DNA molecule dictates the energy required to separate the two strands and establishes the local stability of the duplex. In both eukaryotes and prokaryotes, the order of the four types of nucleotides defines the information structure throughout a DNA molecule. These structures include the well-known “genes” (Greek – geneá, “generation”). Genes are regions of different lengths, found along the DNA molecule. Broadly, gene regions are in turn accompanied by regulatory structures, such as gene promoters and enhancers. Genes are involved in transcription, namely in the synthesis of RNA transcripts. Note that RNA molecules are also polymers consisting of four types of organic molecules, namely: adenine (A), uracil (U), cytosine (C), guanine (G). The RNA transcript is a single-stranded nucleotide sequence that is complementary to the DNA strand harboring the gene. In turn, the information on the RNA transcript dictates whether the transcript becomes a functional molecule within the cell or whether it becomes a template for protein synthesis.

1.4 Chromatin Structure

In multicellular organisms, every cell type usually contains the same DNA information; however, it exhibits a different phenotype. What determines this behavior ? Double-stranded DNA molecules of eukaryotic organisms are folded and distributed into chromosomes, which take the form of chromatin (DNA, histone proteins, and non-histone proteins). The basic organization of chromatin consists of filaments made of repetitive units called nucleosomes.

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