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 anenclosed nucleus that contains itsDNA, and other membrane-bound organelles including mitochondria. More recently, the primary division has been seen as that between Archaea and Bacteria, since eukaryotes may be part of the archaean clade and have multiplehomologies with other Archaea.
Prokaryotic cells are generally smaller and similar than eukaryotic cells. Prokaryotic cells do not enclose their genetic material within a nucleus. Bacteria are an example of prokaryotes.
Prokaryotes have simplecell skeletons. These are highly diverse, and containhomologues of the eukaryote proteinsactin andtubulin. The cytoskeleton provides the capability for movement within the cell.[7]
Transduction of bacterial genes bybacteriophage viruses appears to reflect occasional errors during intracellular assembly ofvirus particles, rather than anadaptation 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]
Conjugation involvesplasmids, 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 calledcompetence; inBacillus 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]
Among archaea,Haloferax volcanii forms cytoplasmic bridges between cells that transfer DNA between cells,[15] whileSulfolobus solfataricus transfers DNA between cells by direct contact. Exposure ofS. solfataricus to agents that damage DNA induces cellular aggregation, perhaps enhancing homologous recombination to increasethe repair of damaged DNA.[23]
Biofilm of golden hydrophobic bacteria in a cave[24]
Prokaryotes are strictlyunicellular, but most can form stable aggregate communities inbiofilms.[25] Bacterial biofilms are formed by the secretion ofextracellular polymeric substance (EPS).[26]Myxobacteria have multicellular stages in theirlife cycles.[27] Biofilms may be structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces. Bacterial biofilms are often made up ofmicrocolonies (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 structure functions as a simplecirculatory system by moving water through the biofilm, helping to provide cells with oxygen which is often in short supply.[28] The result approaches a multicellular organisation.[29] Differential cell expression, collective behavior, signaling (quorum sensing),programmed cell death, and discretebiological 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]
Prokaryotes have diversified greatly throughout their long existence. Their metabolism is far more varied than that of eukaryotes, leading to many highly distinct types. For example, prokaryotes may obtain energy bychemosynthesis.[34] Prokaryotes live nearly everywhere on Earth, including inenvironments as cold as soils inAntarctica,[35] or as hot as underseahydrothermal vents and land-basedhot springs.[33] Some bacteria arepathogenic, causingdisease in organisms including humans.[36] Some archaea and bacteria areextremophiles, thriving in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles).[37] Somearchaeans aremethanogens, living in anoxic environments and releasingmethane.[2] Many archaea grow asplankton in the oceans.Symbiotic prokaryotes live in or on the bodies of other organisms, including humans. Prokaryotes have high populations in thesoil, in the sea, and in undersea sediments. Soil prokaryotes are still heavily undercharacterized despite their easy proximity to humans and their tremendouseconomic importance to agriculture.[38]
The oldestfossilized 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. The oldest fossil eukaryotes are about 1.7 billion years old.[41]
The distinction between prokaryotes andeukaryotes was established by the microbiologistsRoger Stanier andC. B. van Niel in their 1962 paperThe concept of a bacterium (though spelled procaryote and eucaryote there).[42] That paper citesÉdouard Chatton's 1937 bookTitres et Travaux Scientifiques[43] for using those terms and recognizing the distinction.[44] One reason for this classification was so that the group then often calledblue-green algae (nowcyanobacteria) would not be classified asplants but grouped with bacteria.[42]
In 1977,Carl Woese proposed dividing prokaryotes into theBacteria andArchaea (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 oftemperature,pH, andradiation but have since been found in all types ofhabitats. The resulting arrangement of Eukaryota (also called "Eucarya"), Bacteria, and Archaea is called thethree-domain system, replacing the traditionaltwo-empire system.[45][46]
Knowledge of prokaryote taxonomy is rapidly changing in the 21st century with thesequencing of large numbers of genomes, many of these without the isolation of cultures of the organisms involved. As of 2021, consensus had not been reached among taxonomists to rely exclusively on genomes as opposed to existing practices, describing species from cultures.[47]
According to the 2016 phylogenetic analysis of Laura Hug and colleagues, using genomic data on over 1,000 organisms, the relationships among prokaryotes are as shown in the tree diagram. Bacteria dominate the diversity of organisms, shown at left, top, and right in the diagram; the archaea are shown bottom centre, and the eukaryotes in the small green area at bottom right. As represented by red dots on the diagram, there are multiple major lineages where no representative has been isolated: such lineages are common in both bacteria (such asOmnitrophica andWirthbacteria) and archaea (such asParvarchaeota andLokiarchaeota). At the lower levels (species to class) and up to the level of phylum, the data provide strong support for the groupings, but the deepest (oldest) branches of the phylogeny are more uncertain.[48]
The large diversity of bacterial lineages shown in purple on the right of the diagram. These represent the so-called "candidate phyla radiation of bacteria", namely those with a combination of small genomes and reduced metabolic capabilities: none of them have been found to be able to carry out the whole of thecitric acid cycle by which many cellsrelease usable energy, and few can synthesiseamino acids andnucleotides, building blocks ofproteins andnucleic acids. This may represent an ancient condition, or a loss of capabilities of symbiotic organisms.[48]
Phylogenetic tree showing the diversity of prokaryotes, mainly Bacteria. The eukaryotes appear bottom right as a branch of the Archaea.[48]
Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, have their DNA organised in a nucleus, and containmembrane-bound organelles.[49]
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 theirDNA, whereas prokaryotic cells do not have a nucleus.[50] Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, and containmembrane-bound organelles.[49]
Both eukaryotes and prokaryotes containribosomes whichproduce proteins as specified by the cell's DNA. Prokaryote ribosomes are smaller than those in eukaryote cytoplasm, but similar to those insidemitochondria andchloroplasts, one of several lines of evidence that those organelles derive from bacteria incorporated bysymbiogenesis.[51][52]
Thegenome in a prokaryote is held within a DNA/protein complex in thecytosol called thenucleoid, which lacks anuclear envelope. The complex contains a singlecircular chromosome, a cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organizedchromosomes found in eukaryotic cells.[53] In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids.[54] Like eukaryotes, prokaryotes may partially duplicate genetic material, and can have ahaploid chromosomal composition that ispartially replicated.[55]
Prokaryotes lackmitochondria and chloroplasts. Instead, processes such asoxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane.[56] Prokaryotes possess some internal structures, such asprokaryotic cytoskeletons.[57][58] It was previously suggested that the bacterial phylumPlanctomycetota has a membrane around the nucleoid and contains other membrane-bound cellular structures.[59] Further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected.[60]
Prokaryotic cells are usually much smaller than eukaryotic cells. This causes prokaryotes to have a largersurface-area-to-volume ratio, giving them a highermetabolic rate, a higher growth rate, and as a consequence, a shorter generation time than eukaryotes.[61]
Phylogenetic tree showing the diversity of prokaryotes.[62] This 2018 proposal shows eukaryotes within the archaeanAsgard group which represents a modern version of theeocyte 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 the archaeanAsgard group, perhapsHeimdallarchaeota.[62] For example,histones, which usually package DNA in eukaryotic nuclei, are found in several archaean groups, giving evidence for homology.[63] A proposed non-bacterial group comprising Archaea and Eukaryota was calledNeomura byThomas Cavalier-Smith in 2002.[64]
All are similar in these two groups, implyinghomology and relatedness
Bacteria
(missing)
Present in a very different form
Another view is that the most important difference betweenbiota may be the division between Bacteria and the rest (Archaea and Eukaryota).[62]DNA replication differs fundamentally between the Bacteria and Archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups.[66]
Further,ATP synthase, though homologous in all organisms, differs greatly between bacteria (including eukaryoticorganelles such as mitochondria and chloroplasts) and the archaea/eukaryote nucleus group. The last common ancestor of all life (calledLUCA) 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. TheRNA world hypothesis might clarify this scenario, as LUCA might have lacked DNA, but had an RNA genome built by ribosomes assuggested by Woese.[65]
Aribonucleoprotein world has been proposed based on the idea thatoligopeptides may have been built together with primordial nucleic acids at the same time, which supports the concept of aribocyte 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 (possiblyretroviruses as they couldreverse transcribe RNA to DNA).[67]
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