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Prokaryote

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Diagram of a typical prokaryotic cell

Aprokaryote(/proʊˈkærioʊt,-ət/;less commonly spelledprocaryote)[1]is asingle-cell organismwhosecelllacks anucleusand othermembrane-boundorganelles.[2]The wordprokaryotecomes from theAncient Greekπρό(pró), meaning 'before', andκάρυον(káruon), meaning 'nut' or 'kernel'.[3][4]In thetwo-empire systemarising from the work ofÉdouard Chatton,prokaryotes were classified within the empireProkaryota.[5]However in thethree-domain system,based uponmolecular analysis,prokaryotes are divided into twodomains:Bacteria(formerly Eubacteria) andArchaea(formerly Archaebacteria). Organisms with nuclei are placed in a third domain:Eukaryota.[6]

Prokaryotesevolvedbefore eukaryotes, and lack nuclei,mitochondria,and most of the other distinctorganellesthat characterize the eukaryotic cell. It was once thought that prokaryotic cellular components were unenclosed within thecytoplasmexcept for an outercell membrane,butbacterial microcompartments,which are thought to be quasi-organelles enclosed inproteinshells (such as theencapsulin protein cages), have been discovered,[7][8]along with otherprokaryotic organelles.[9]While being unicellular, some prokaryotes, such ascyanobacteria,may formcoloniesheld together bybiofilms,and large colonies can create multilayeredmicrobial mats.Others, such asmyxobacteria,have multicellular stages in theirlife cycles.[10]Prokaryotes areasexual,reproducing viabinary fissionwithout any fusion ofgametes,althoughhorizontal gene transfermay take place.

Molecular studieshave provided insight into the evolution and interrelationships of the three domains of life.[11]The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization; only eukaryotic cells have an enveloped nucleus that contains its chromosomalDNA,and other characteristic membrane-bound organelles including mitochondria. Distinctive types of prokaryotes includeextremophilesandmethanogens;these are common in some extreme environments.[2]

History

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The distinction between prokaryotes and eukaryotes was firmly established by the microbiologistsRoger StanierandC. B. van Nielin their 1962 paperThe concept of a bacterium[12](though spelled procaryote and eucaryote there). That paper citesÉdouard Chatton's 1937 bookTitres et Travaux Scientifiques[13]for using those terms and recognizing the distinction. One reason for this classification was so that what was then often calledblue-green algae(now calledcyanobacteria) would not be classified as plants but grouped with bacteria.

Structure

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

Prokaryotes have aprokaryotic cytoskeletonthat is more primitive than that of the eukaryotes. Besideshomologuesof actin and tubulin (MreBandFtsZ), the helically arranged building-block of theflagellum,flagellin,is one of the most significant cytoskeletal proteins of bacteria, as it provides structural backgrounds ofchemotaxis,the basic cell physiological response of bacteria. At least some prokaryotes also contain intracellular structures that can be seen as primitive organelles.

Membranous organelles (or intracellular membranes) are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, such asphotosynthesisorchemolithotrophy.In addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles (e.g.carboxysomesor gas vacuoles).

Most prokaryotes are between 1 μm and 10 μm, but they can vary in size from 0.2 μm (Mycoplasma genitalium) to 750 μm (Thiomargarita namibiensis).

Prokaryotic cell structure Description
Flagellum(not always present) Long, whip-like protrusion that aids cellular locomotion used by bothgram-positiveandgram-negative bacteria.
Cell membrane Surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell.
Cell wall(except generaMycoplasmaandThermoplasma) Outer covering of most cells that protects the bacterial cell and gives it shape.
Cytoplasm A gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules.
Ribosome Cell structures responsible for protein production.
Nucleoid Area of the cytoplasm that contains the prokaryote's single DNA molecule.
Glycocalyx(only in some types of prokaryotes) Aglycoprotein-polysaccharidecovering that surrounds the cell membranes.
Cytoplasmic inclusions Theinclusionssuch asribosomesand larger masses scattered in the cytoplasmic matrix.

Morphology

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Prokaryotic cells have various shapes; the four basic shapes of bacteria are:[14]

  • Cocci– A bacterium that is spherical or ovoid is called a coccus (Plural, cocci). e.g.Streptococcus, Staphylococcus.
  • Bacilli– A bacterium with cylindrical shape called rod or a bacillus (Plural, bacilli).
  • Spiral bacteria– Some rods twist into spiral shapes and are called spirilla (singular, spirillum).
  • Vibrio– comma-shaped

The archaeonHaloquadratumhas flat square-shaped cells.[15]

Reproduction

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Bacteria and archaea reproduce through asexual reproduction, usually bybinary fission.Genetic exchange and recombination still occur, but this is a form ofhorizontal gene transferand is not a replicative process, simply involving the transference of DNA between two cells, as inbacterial conjugation.

DNA transfer

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DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has been mainly studied in bacteria. In bacteria, gene transfer occurs by three processes. These are (1) bacterial virus (bacteriophage)-mediatedtransduction,(2)plasmid-mediatedconjugation,and (3)natural transformation.Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly ofvirusparticles, rather than anadaptationof the host bacteria. The transfer of bacterial DNA is under the control of the bacteriophage's genes rather than bacterial genes. Conjugation in the well-studiedE. colisystem is controlled by plasmid genes, and is an adaptation for distributing copies of a plasmid from one bacterial host to another. Infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA (conjugation) also appears to be an accidental process rather than a bacterial adaptation.

3D animation of a prokaryotic cell that shows all the elements that it is composed of

Natural bacterialtransformationinvolves the transfer of DNA from one bacterium to another through the intervening medium. Unlike transduction and conjugation, transformation is clearly a bacterialadaptationfor DNA transfer, because it depends on numerous bacterial gene products that specifically interact to perform this complex process.[16]For a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state calledcompetence.About 40 genes are required inBacillus subtilisfor the development of competence.[17]The length of DNA transferred duringB. subtilistransformation can be as much as a third to the whole chromosome.[18][19]Transformation is a common mode of DNA transfer, and 67 prokaryotic species are thus far known to be naturally competent for transformation.[20]

Among archaea,Halobacteriumvolcaniiforms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another.[21]Another archaeon,Sulfolobus solfataricus,transfers DNA between cells by direct contact. Frols et al. (2008) found[22]that exposure ofS. solfataricusto DNA damaging agents induces cellular aggregation, and suggested that cellular aggregation may enhance DNA transfer among cells to provide increased repair of damaged DNA via homologous recombination.

Sociality

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While prokaryotes are considered strictly unicellular, most can form stable aggregate communities.[23]When such communities are encased in a stabilizing polymer matrix ( "slime" ), they may be called "biofilms".[24]Cells in biofilms often show distinct patterns ofgene expression(phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression often appear to result fromcell-to-cell signaling,a phenomenon known asquorum sensing.

Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up ofmicrocolonies(approximately dome-shaped masses of bacteria and matrix) separated by "voids" through which the medium (e.g., water) may flow easily. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity—combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout the biofilm—has led some to speculate that this may constitute acirculatory system[25]and many researchers have started calling prokaryotic communities multicellular (for example[26]). Differential cell expression, collective behavior, signaling,programmed cell death,and (in some cases) discretebiological dispersal[27]events all seem to point in this direction. However, these colonies are seldom if ever founded by a single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations ofco-operationand theevolution of multicellularityhave focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than a similar group of selfish individuals[28](seeinclusive fitnessandHamilton's rule).

Should these instances of prokaryotic sociality prove to be the rule rather than the exception, it would have serious implications for the way we view prokaryotes in general, and the way we deal with them in medicine.[29]Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them.[30]Other aspects of bacterial cooperation—such asbacterial conjugationand quorum-sensing-mediatedpathogenicity,present additional challenges to researchers and medical professionals seeking to treat the associated diseases.

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 usingphotosynthesisororganic compoundsfor energy, as eukaryotes do, prokaryotes may obtain energy frominorganic compoundssuch ashydrogen sulfide.This enables prokaryotes to thrive in harsh environments as cold as the snow surface ofAntarctica,studied incryobiology,or as hot as underseahydrothermal ventsand land-basedhot springs.

Prokaryotes live in nearly all environments on Earth. Some archaea and bacteria areextremophiles,thriving in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles).[31]Many archaea grow asplanktonin the oceans.Symbioticprokaryotes live in or on the bodies of other organisms, including humans. Prokaryote have high populations in thesoil- including therhizosphereandrhizosheath.Soil prokaryotes are still heavily undercharacterized despite their easy proximity to humans and their tremendouseconomic importance to agriculture.[32]

Phylogenetic andsymbiogenetictree of living organisms, showing the origins ofeukaryotesand prokaryotes

Classification

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In 1977,Carl Woeseproposed dividing prokaryotes into theBacteriaandArchaea(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,andradiationbut 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.[33][34]

Phylogenetic tree

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According to the phylogenetic analysis of Hug (2016), the relationships could be the following:[35]

Phylogenetic tree showing the diversity of prokaryotes.[35]

Evolution

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Main article:Molecular evolution
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.[36]

A widespread current model of the evolution of thefirst living organismsis that these were some form of prokaryotes, which may have evolved out ofprotocells,while the eukaryotes evolved later in the history of life.[37]Some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification.[38][39][40]

Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.[41]This controversy was summarized in 2005:[42]

There is no consensus among biologists concerning the position of the eukaryotes in the overall scheme of cell evolution. Current opinions on the origin and position of eukaryotes span a broad spectrum including the views that eukaryotes arose first in evolution and that prokaryotes descend from them, that eukaryotes arose contemporaneously with eubacteria and archaebacteria and hence represent a primary line of descent of equal age and rank as the prokaryotes, that eukaryotes arose through a symbiotic event entailing an endosymbiotic origin of the nucleus, that eukaryotes arose without endosymbiosis, and that eukaryotes arose through a symbiotic event entailing a simultaneous endosymbiotic origin of the flagellum and the nucleus, in addition to many other models, which have been reviewed and summarized elsewhere.

The oldest knownfossilizedprokaryotes 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 fromendosymbiosisof 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.[43]

While Earth is the only place in the universe where life is known to exist, some have suggested that there isevidence on Marsof fossil or living prokaryotes.[44][45]However, this possibility remains the subject of considerable debate and skepticism.[46][47]

Relationship to eukaryotes

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Comparison of eukaryotes vs. prokaryotes

The division between prokaryotes and eukaryotes is usually considered the most important distinction or difference among organisms. The distinction is that eukaryotic cells have a "true"nucleuscontaining theirDNA,whereas prokaryotic cells do not have a nucleus.

Both eukaryotes and prokaryotes contain largeRNA/proteinstructures calledribosomes,whichproduce protein,but theribosomesof prokaryotes are smaller than those of eukaryotes.Mitochondriaandchloroplasts,two organelles found in many eukaryotic cells, contain ribosomes similar in size and makeup to those found in prokaryotes.[48]This is one of many pieces of evidence that mitochondria and chloroplasts are descended from free-living bacteria. Theendosymbiotic theoryholds that early eukaryotic cells took in primitive prokaryotic cells byphagocytosisand adapted themselves to incorporate their structures, leading to the mitochondria and chloroplasts.

Thegenomein a prokaryote is held within a DNA/protein complex in thecytosolcalled thenucleoid,which lacks anuclear envelope.[49]The complex contains a single, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organizedchromosomesfound in eukaryotic cells. In addition, many important genes of prokaryotes are stored in separate circular DNA structures calledplasmids.[3]Like Eukaryotes, prokaryotes may partially duplicate genetic material, and can have ahaploidchromosomal composition that is partially replicated, a condition known asmerodiploidy.[50]

Prokaryotes lackmitochondriaandchloroplasts.Instead, processes such asoxidative phosphorylationandphotosynthesistake place across the prokaryoticcell membrane.[51]However, prokaryotes do possess some internal structures, such asprokaryotic cytoskeletons.[52][53]It has been suggested that the bacterial phylumPlanctomycetotahas a membrane around the nucleoid and contains other membrane-bound cellular structures.[54]However, further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected.[55]

Prokaryotic cells are usually much smaller than eukaryotic cells.[3]Therefore, prokaryotes 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.[3]

Phylogenetic tree showing the diversity of prokaryotes.[56]This 2018 proposal shows eukaryotes emerging from the archaeanAsgardgroup which represents a modern version of theeocyte hypothesis.Unlike earlier assumptions, the division between bacteria and the rest is the most important difference between organisms.

There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next to) the archaeanasgardgroup, perhapsHeimdallarchaeota(an idea which is a modern version of the 1984eocyte hypothesis,eocytesbeing an old synonym forThermoproteota,ataxonto be found nearby the then-unknown Asgard group).[56]For example,histoneswhich usually package DNA in eukaryotic nuclei, have also been found in several archaean groups, giving evidence forhomology.This idea might clarify the mysterious predecessor of eukaryotic cells (eucytes) which engulfed anAlpha proteobacteriumforming the first eucyte (LECA,lasteukaryoticcommonancestor) according toendosymbiotic theory.There might have been some additional support by viruses, calledviral eukaryogenesis. The non-bacterial group comprising archaea and eukaryota was calledNeomurabyThomas Cavalier-Smithin 2002.[57] However, in acladisticview, eukaryotaarearchaea in the same sense asbirdsaredinosaursbecause they evolved from themaniraptoradinosaur group. In contrast, archaeawithouteukaryota appear to be aparaphyleticgroup, just like dinosaurs without birds.

Prokaryotes may be split into two groups

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Unlike the above assumption of a fundamental split between prokaryotes and eukaryotes, the most important difference betweenbiotamay be the division between bacteria and the rest (archaea and eukaryota).[56]For instance,DNA replicationdiffers fundamentally between bacteria and archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups.[58]Moreover,ATP synthase,though common (homologous) in all organisms, differs greatly between bacteria (including eukaryoticorganellessuch asmitochondriaandchloroplasts) and the archaea/eukaryote nucleus group. The last common antecessor of all life (calledLUCA,lastuniversalcommonancestor) 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 hypothesismight clarify this scenario, as LUCA might have been aribocyte(also called ribocell) lacking DNA, but with anRNAgenome built byribosomesasprimordial self-replicating entities.[59]APeptide-RNA world(also calledRNPworld) hypothesis has been proposed based on the idea thatoligopeptidesmay have been built together with primordial nucleic acids at the same time, which also supports the concept of aribocyteas 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 by help of some viruses (possiblyretrovirusesas they couldreverse transcribeRNA to DNA).[60]As a result, prokaryota comprising bacteria and archaea may also bepolyphyletic.

See also

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