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Prokaryote

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Diagram of a prokaryotic cell, a bacterium with a flagellum

A prokaryote (/proʊˈkærioʊt, -ət/; less commonly spelled procaryote)[1] is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles.[2] The word prokaryote comes from the Ancient Greek πρό (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'.[3] In the earlier two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. However in the three-domain system, based upon molecular phylogenetics, prokaryotes are divided into two domains: Bacteria and Archaea. A third domain, Eukaryota, consists of organisms with nuclei.

Prokaryotes evolved before eukaryotes, and lack nuclei, mitochondria, and most of the other distinct organelles that characterize the eukaryotic cell. Some unicellular prokaryotes, such as cyanobacteria, form colonies held together by biofilms, and large colonies can create multilayered microbial mats. Prokaryotes are asexual, reproducing via binary fission, although horizontal gene transfer may take place.

Molecular phylogenetics has provided insight into the evolution and interrelationships of the three domains of life. The division between prokaryotes and eukaryotes reflects two very different levels of cellular organization; only eukaryotic cells have an enclosed nucleus that contains its DNA, and other membrane-bound organelles including mitochondria. More recently, the primary division has been seen as that between Archaea and Bacteria, since the eukaryotes are part of the archaean clade and have multiple homologies with other Archaea.

Structure

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Further information: Bacterial cell structure and Archaea § Structure, composition development, and operation

The cellular components of prokaryotes are not enclosed in membranes within the cytoplasm, like eukaryotic organelles. Bacteria have microcompartments, quasi-organelles enclosed in protein shells such as encapsulin protein cages,[4][5] while both bacteria and some archaea have gas vesicles.[6]

Prokaryotes have simple cell skeletons. These are highly diverse, and contain homologues of the eukaryote proteins actin and tubulin. The cytoskeleton provides the capability for movement within the cell.[7]

Most prokaryotes are between 1 and 10 μm, but they vary in size from 0.2 μm in Thermodiscus spp. and Mycoplasma genitalium to 750 μm in Thiomargarita namibiensis.[8][9]

Bacterial cells have various shapes, including spherical or ovoid cocci, e.g. Streptococcus, Staphylococcus; cylindrical bacilli; spiral bacteria (twisted rods); and the comma-shaped vibrio.[10] Archaea are mainly simple ovoids, but Haloquadratum is flat and square.[11]

Parts of the prokaryote cell[12]
Element Description
Flagellum (not always present) Long, whip-like protrusion that moves the cell.
Cell membrane Surrounds the cell's cytoplasm, regulates flow of substances in and out.
Cell wall (except in Mollicutes, Thermoplasma) Outer covering that protects the cell and gives it shape.
Cytoplasm A watery gel that contains enzymes, salts, and organic molecules.
Ribosome Structure that produces proteins as specified by DNA.
Nucleoid Region that contains the prokaryote's single DNA molecule.
Capsule (only in some groups) Glycoprotein covering outside the cell membrane.

Reproduction and DNA transfer

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Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. Genetic exchange and recombination occur by horizontal gene transfer, not involving replication.[13] DNA transfer between prokaryotic cells occurs in bacteria[14] and archaea.[15]

Gene transfer in bacteria

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In bacteria, gene transfer occurs by three processes. These are virus-mediated transduction;[14] conjugation;[16] and natural transformation.[17]

Transduction of bacterial genes by bacteriophage viruses appears to reflect occasional errors during intracellular assembly of virus particles, rather than an adaptation of the host bacteria. There are at least three ways that it can occur, all involving the incorporation of some bacterial DNA in the virus, and from there to another bacterium.[14]

Bacterial conjugation using F-pili to exchange DNA[16]

Conjugation involves plasmids, allowing plasmid DNA to be transferred from one bacterium to another. Infrequently, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium.[18]

Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the water around them. This is a bacterial adaptation for DNA transfer, because it depends on the interaction of numerous bacterial gene products.[17] The bacterium must first enter the physiological state called competence; in Bacillus subtilis, the process involves 40 genes.[19] The amount of DNA transferred during transformation can be as much as a third of the whole chromosome.[20][21] Transformation is common, occurring in at least 67 species of bacteria.[22]

Gene transfer in archaea

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Among archaea, Haloferax volcanii forms cytoplasmic bridges between cells that transfer DNA between cells,[15] while Sulfolobus solfataricus transfers DNA between cells by direct contact. Exposure of S. solfataricus to DNA damaging agents induces cellular aggregation, perhaps enhancing homologous recombination to increase repair of damaged DNA.[23]

Colonies and biofilms

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Biofilm of golden hydrophobic bacteria in a cave[24]

Prokaryotes are strictly unicellular, but most can form stable aggregate communities in biofilms.[25] Bacterial biofilms are formed by the secretion of extracellular polymeric substance (EPS).[26] Myxobacteria have multicellular stages in their life cycles.[27] Biofilms may be heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces. Bacterial biofilms are often made up of microcolonies (dome-shaped masses of bacteria and matrix) separated by channels through which water may flow easily. Microcolonies may join together above the substratum to form a continuous layer. This structural complexity, combined with the easing of oxygen limitation by movement of medium throughout the biofilm, functions as a simple circulatory system,[28] approaching multicellular organisation.[29] Differential cell expression, collective behavior, signaling (quorum sensing), programmed cell death, and discrete biological dispersal events all seem to point in this direction.[30][31] Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells, making them difficult to remove from surfaces they have colonized.[32]

Environment

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Phylogenetic ring showing the diversity of prokaryotes, and symbiogenetic origins of eukaryotes

Prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using photosynthesis or organic compounds for energy, as eukaryotes do, prokaryotes may obtain energy from inorganic compounds such as hydrogen sulfide. This enables prokaryotes to thrive in harsh environments as cold as the snow surface of Antarctica, studied in cryobiology, or as hot as undersea hydrothermal vents and land-based hot springs.

Prokaryotes live in nearly all environments on Earth. Some archaea and bacteria are extremophiles, thriving in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles).[33] Some archaeans are methanogens, living in anoxic environments and releasing methane.[2] Many archaea grow as plankton in the oceans. Symbiotic prokaryotes live in or on the bodies of other organisms, including humans. Prokaryotes have high populations in the soil, in the sea, and in undersea sediments. Soil prokaryotes are still heavily undercharacterized despite their easy proximity to humans and their tremendous economic importance to agriculture.[34]

Evolution

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The first organisms

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Further information: Abiogenesis
Diagram of the origin of life with the Eukaryotes appearing early, not derived from prokaryotes, as proposed by Richard Egel in 2012. This view, one of many on the relative positions of prokaryotes and eukaryotes, implies that the universal common ancestor was relatively large and complex.[35]

A widespread current model of the origin of life is that the first organisms were prokaryotes. These may have evolved out of protocells, while the eukaryotes evolved later in the history of life.[36] An alternative model is that extant prokaryotes evolved from more complex eukaryotic ancestors through a process of simplification.[37][38][39]

Another view is that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.[40][41]

The oldest known fossilized prokaryotes were laid down approximately 3.5 billion years ago, only about 1 billion years after the formation of the Earth's crust. Eukaryotes only appear in the fossil record later, and may have formed from endosymbiosis of multiple prokaryote ancestors. The oldest known fossil eukaryotes are about 1.7 billion years old. However, some genetic evidence suggests eukaryotes appeared as early as 3 billion years ago.[42]

Phylogeny

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According to the 2016 phylogenetic analysis of Laura Hug and colleagues, using genomic data on over 1000 organisms, the relationships among prokaryotes are as shown in the tree diagram.[43]

Phylogenetic tree showing the diversity of prokaryotes.[43]

Classification

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Taxonomic history

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The distinction between prokaryotes and eukaryotes was established by the microbiologists Roger Stanier and C. B. van Niel in their 1962 paper The concept of a bacterium (though spelled procaryote and eucaryote there).[44] That paper cites Édouard Chatton's 1937 book Titres et Travaux Scientifiques[45] for using those terms and recognizing the distinction.[46] One reason for this classification was so that the group then often called blue-green algae (now cyanobacteria) would not be classified as plants but grouped with bacteria.[44]

In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of the major differences in the structure and genetics between the two groups of organisms. Archaea were originally thought to be extremophiles, living only in inhospitable conditions such as extremes of temperature, pH, and radiation but have since been found in all types of habitats. The resulting arrangement of Eukaryota (also called "Eucarya"), Bacteria, and Archaea is called the three-domain system, replacing the traditional two-empire system.[47][48]

As distinct from eukaryotes

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Prokaryote
Part of a eukaryotic cell, to same scale
Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, have their DNA organised in a nucleus, and contain membrane-bound organelles.

The division between prokaryotes and eukaryotes has been considered the most important distinction or difference among organisms. The distinction is that eukaryotic cells have a "true" nucleus containing their DNA, whereas prokaryotic cells do not have a nucleus.[49]

Both eukaryotes and prokaryotes contain large RNA/protein structures called ribosomes, which produce protein, but the ribosomes of prokaryotes are smaller than those of eukaryotes. Mitochondria and chloroplasts, two organelles found in many eukaryotic cells, contain ribosomes similar in size and makeup to those found in prokaryotes.[50]

The genome in a prokaryote is held within a DNA/protein complex in the cytosol called the nucleoid, which lacks a nuclear envelope. The complex contains a single circular chromosome, a cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organized chromosomes found in eukaryotic cells.[51] In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids.[52] Like eukaryotes, prokaryotes may partially duplicate genetic material, and can have a haploid chromosomal composition that is partially replicated.[53]

Prokaryotes vs Eukaryotes[49][54]
Domain Nucleus Organelles Reproduction
Prokaryotes None, DNA is free in cytoplasm Few Asexual, with horizontal gene transfer
Eukaryotes DNA in nucleus Membrane-bound organelles, inc. endoplasmic reticulum, mitochondria, chloroplasts Sexual reproduction with haploid gametes

Prokaryotes lack mitochondria and chloroplasts. Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane.[54] However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons.[55][56] It has been suggested that the bacterial phylum Planctomycetota has a membrane around the nucleoid and contains other membrane-bound cellular structures.[57] However, further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected.[58]

Prokaryotic cells are usually much smaller than eukaryotic cells. Therefore, prokaryotes have a larger surface-area-to-volume ratio, giving them a higher metabolic rate, a higher growth rate, and as a consequence, a shorter generation time than eukaryotes.[59]

Eukaryotes as Archaea

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Phylogenetic tree showing the diversity of prokaryotes.[60] This 2018 proposal shows eukaryotes within the archaean Asgard group which represents a modern version of the eocyte hypothesis. In this view, the division between bacteria and the rest is what groups organisms into the two major domains.

There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next to) the archaean Asgard group, perhaps Heimdallarchaeota (an idea which is a modern version of the 1984 eocyte hypothesis, eocytes being an old synonym for Thermoproteota, a taxon to be found nearby the then-unknown Asgard group).[60] For example, histones which usually package DNA in eukaryotic nuclei, have been found in several archaean groups, giving evidence for homology.[61] The non-bacterial group comprising archaea and eukaryota was called Neomura by Thomas Cavalier-Smith in 2002, on the view that these form a clade.[62]

Eukaryotes as Archaea[63][61][64]
Domain Histones ATP synthase DNA replication
Archaea, inc. Eukaryota Similar in these two groups, implying homology
Bacteria (missing) Present in a very different form

Unlike the above assumption of a fundamental split between prokaryotes and eukaryotes, the most important difference between biota may be the division between Bacteria and the rest (Archaea and Eukaryota).[60] DNA replication differs fundamentally between the Bacteria and Archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups.[64]

Further, ATP synthase, though homologous in all organisms, differs greatly between bacteria (including eukaryotic organelles such as mitochondria and chloroplasts) and the archaea/eukaryote nucleus group. The last common ancestor of all life (called LUCA) should have possessed an early version of this protein complex. As ATP synthase is obligate membrane bound, this supports the assumption that LUCA was a cellular organism. The RNA world hypothesis might clarify this scenario, as LUCA might have lacked DNA, but had an RNA genome built by ribosomes as suggested by Woese.[63]

A ribonucleoprotein world has been proposed based on the idea that oligopeptides may have been built together with primordial nucleic acids at the same time, which supports the concept of a ribocyte as LUCA. The feature of DNA as the material base of the genome might have then been adopted separately in bacteria and in archaea (and later eukaryote nuclei), presumably with the help of some viruses (possibly retroviruses as they could reverse transcribe RNA to DNA).[65]

See also

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