Prokaryote#DNA transfer

{{Short description|Unicellular organism lacking a membrane-bound nucleus}}

File:Prokaryote cell.svg with a flagellum ]]

A prokaryote ({{IPAc-en|p|r|oʊ|ˈ|k|ær|i|oʊ|t|,_|-|ə|t}}; less commonly spelled procaryote){{cite Merriam-Webster |procaryote |access-date=2023-12-30}} is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles.{{cite web |url=https://ncsu.edu/project/bio183de/Black/prokaryote/prokaryote1.html |title=Prokaryotes: Single-celled Organisms |publisher=North Carolina State University}} The word prokaryote comes from the Ancient Greek {{wikt-lang|grc|πρό}} ({{grc-transl|πρό}}), meaning 'before', and {{wikt-lang|grc|κάρυον}} ({{grc-transl|κάρυον}}), meaning 'nut' or 'kernel'.{{OEtymD|prokaryote}} 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. Horizontal gene transfer is common as well.

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 eukaryotes may be part of the archaean clade and have multiple homologies with other Archaea.

Prokaryotic cells are generally smaller and similar than eukaryotic cells. Prokaryotic cells do not enclose their genetic material within a nucleus.

Structure

{{See|Bacterial cell structure|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,{{cite journal |vauthors=Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO |title=Protein structures forming the shell of primitive bacterial organelles |journal=Science |volume=309 |issue=5736 |pages=936–8 |date=August 2005 |pmid=16081736 |doi=10.1126/science.1113397 |bibcode=2005Sci...309..936K |citeseerx=10.1.1.1026.896 |s2cid=24561197}}{{cite journal |vauthors=Murat D, Byrne M, Komeili A |title=Cell biology of prokaryotic organelles |journal=Cold Spring Harbor Perspectives in Biology |volume=2 |issue=10 |pages=a000422 |date=October 2010 |pmid=20739411 |pmc=2944366 |doi=10.1101/cshperspect.a000422}} while both bacteria and some archaea have gas vesicles.{{Cite journal |last1=Murat |first1=Dorothee |last2=Byrne |first2=Meghan |last3=Komeili |first3=Arash |date=2010-10-01 |title=Cell Biology of Prokaryotic Organelles |journal=Cold Spring Harbor Perspectives in Biology |volume=2 |issue=10 |pages=a000422 |doi=10.1101/cshperspect.a000422 |pmc=2944366 |pmid=20739411}}

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.{{cite journal |vauthors=Wickstead B, Gull K |title=The evolution of the cytoskeleton |journal=The Journal of Cell Biology |volume=194 |issue=4 |pages=513–25 |date=August 2011 |pmid=21859859 |pmc=3160578 |doi=10.1083/jcb.201102065 }}

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.{{cite web |title=Size scale of prokaryotic cells, from the largest to the smallest |url=https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=3&id=110077 |website=Bionumbers |access-date=20 December 2024}}{{cite journal |last1=Schulz |first1=H. N. |last2=Jorgensen |first2=B. B. |title=Big bacteria |journal=Annual Review of Microbiology |volume=55 |date=2001 |pmid=11544351 |doi=10.1146/annurev.micro.55.1.105 |pages=105–137}}

Bacterial cells have various shapes, including spherical or ovoid cocci, e.g., Streptococcus; cylindrical bacilli, e.g., Lactobacillus; spiral bacteria, e.g., Helicobacter; or comma-shaped, e.g., Vibrio.{{cite book |vauthors=Bauman RW, Tizard IR, Machunis-Masouka E |title=Microbiology |publisher=Pearson Benjamin Cummings |date=2006 |isbn=978-0-8053-7693-7 |url-access=registration |url=https://archive.org/details/microbiology00robe_yj2 }} Archaea are mainly simple ovoids, but Haloquadratum is flat and square.{{cite journal |vauthors=Stoeckenius W |title=Walsby's square bacterium: fine structure of an orthogonal procaryote |journal=Journal of Bacteriology |volume=148 |issue=1 |pages=352–60 |date=October 1981 |pmid=7287626 |pmc=216199 |doi=10.1128/JB.148.1.352-360.1981}}

class="wikitable"
+ Parts of the prokaryote cell{{cite book \|last1=Raven \|first1=Peter \|last2=Singer \|first2=Susan \|last3=Mason \|first3=Kenneth \|last4=Losos \|first4=Jonathan \|last5=Johnson \|first5=George \|title=Biology \|year=2013 \|chapter=4. Cell structure: Prokaryotic cells \|page=63 \|publisher=McGraw-Hill Education \|isbn=978-0073383071}}
style="width: 180px;" \| 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.

class="wikitable"

+ Parts of the prokaryote cell{{cite book |last1=Raven |first1=Peter |last2=Singer |first2=Susan |last3=Mason |first3=Kenneth |last4=Losos |first4=Jonathan |last5=Johnson |first5=George |title=Biology |year=2013 |chapter=4. Cell structure: Prokaryotic cells |page=63 |publisher=McGraw-Hill Education |isbn=978-0073383071}}

style="width: 180px;" | 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

Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. Genetic exchange and recombination occur by horizontal gene transfer, not involving replication.{{cite book |last=Bobay |first=Louis-Marie |title=The pangenome: Diversity, dynamics and evolution of genomes |year=2020 |publisher=Springer |pages=253, 282 |url=https://library.oapen.org/bitstream/handle/20.500.12657/37707/1/2020_Book_ThePangenome.pdf#page=253 |isbn=978-3-030-38280-3}} DNA transfer between prokaryotic cells occurs in bacteria and archaea.

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

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.{{cite journal |last1=Chiang |first1=Yin Ning |last2=Penadés |first2=José R. |last3=Chen |first3=John |title=Genetic transduction by phages and chromosomal islands: The new and noncanonical |journal=PLOS Pathogens |volume=15 |issue=8 |date=2019 |pmid=31393945 |pmc=6687093 |doi=10.1371/journal.ppat.1007878 |doi-access=free |page=e1007878}}

File:Bacterial conjugation.png using F-pili to exchange DNA{{cite web |last=Patkowski |first=Jonasz |title=F-pilus, the ultimate bacterial sex machine |url=https://microbiologycommunity.nature.com/posts/f-pilus-the-ultimate-bacterial-sex-machine |website=Nature Portfolio Microbiology Community |date=21 April 2023}}|alt=Black and white image of F-pili bacteria]]

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.{{cite journal |last1=Cabezón |first1=Elena |last2=Ripoll-Rozada |first2=Jorge |last3=Peña |first3=Alejandro |last4=de la Cruz |first4=Fernando |last5=Arechaga |first5=Ignacio |title=Towards an integrated model of bacterial conjugation |journal=FEMS Microbiology Reviews |date=2014 |volume=39 |issue=1 |pages=81–95 |doi=10.1111/1574-6976.12085 |doi-access=free |pmid=25154632 |url=https://academic.oup.com/femsre/article-pdf/39/1/81/10741187/12085.pdf}}

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.{{cite journal |vauthors=Chen I, Dubnau D |title=DNA uptake during bacterial transformation |journal=Nature Reviews Microbiology |volume=2 |issue=3 |pages=241–9 |date=March 2004 |pmid=15083159 |doi=10.1038/nrmicro844 |s2cid=205499369}}

The bacterium must first enter the physiological state called competence; in Bacillus subtilis, the process involves 40 genes.{{cite journal |vauthors=Solomon JM, Grossman AD |title=Who's competent and when: regulation of natural genetic competence in bacteria |journal=Trends in Genetics |volume=12 |issue=4 |pages=150–155 |date=April 1996 |pmid=8901420 |doi=10.1016/0168-9525(96)10014-7 }} The amount of DNA transferred during transformation can be as much as a third of the whole chromosome.{{cite journal |vauthors=Akamatsu T, Taguchi H |title=Incorporation of the whole chromosomal DNA in protoplast lysates into competent cells of Bacillus subtilis |journal=Bioscience, Biotechnology, and Biochemistry |volume=65 |issue=4 |pages=823–9 |date=April 2001 |pmid=11388459 |doi=10.1271/bbb.65.823 |s2cid=30118947 |doi-access=free }}{{cite journal |vauthors=Saito Y, Taguchi H, Akamatsu T |title=Fate of transforming bacterial genome following incorporation into competent cells of Bacillus subtilis: a continuous length of incorporated DNA |journal=Journal of Bioscience and Bioengineering |volume=101 |issue=3 |pages=257–62 |date=March 2006 |pmid=16716928 |doi=10.1263/jbb.101.257}} Transformation is common, occurring in at least 67 species of bacteria.{{cite journal |vauthors=Johnsborg O, Eldholm V, Håvarstein LS |date=December 2007 |title=Natural genetic transformation: prevalence, mechanisms and function |journal=Research in Microbiology |volume=158 |issue=10 |pages=767–78 |doi=10.1016/j.resmic.2007.09.004 |pmid=17997281 |doi-access=free}}

Among archaea, Haloferax volcanii forms cytoplasmic bridges between cells that transfer DNA between cells,{{cite journal |vauthors=Rosenshine I, Tchelet R, Mevarech M |title=The mechanism of DNA transfer in the mating system of an archaebacterium |journal=Science |volume=245 |issue=4924 |pages=1387–9 |date=September 1989 |pmid=2818746 |doi=10.1126/science.2818746 |bibcode=1989Sci...245.1387R}} while Sulfolobus solfataricus transfers DNA between cells by direct contact. Exposure of S. solfataricus to agents that damage DNA induces cellular aggregation, perhaps enhancing homologous recombination to increase the repair of damaged DNA.{{cite journal |vauthors=Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV |title=UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation |journal=Molecular Microbiology |volume=70 |issue=4 |pages=938–52 |date=November 2008 |pmid=18990182 |doi=10.1111/j.1365-2958.2008.06459.x |s2cid =12797510 |url=https://www.rug.nl/research/portal/files/56956856/UV_inducible_cellular_aggregation_of_the_hyperthermophilic_archaeon_Sulfolobus_solfataricus_is_mediated_by_pili_formation.pdf |doi-access=free}}

Colonies and biofilms

File:A114, Lava Beds National Monument, California, USA, Golden Dome Lava Tube Cave, 2004.jpg

Prokaryotes are strictly unicellular, but most can form stable aggregate communities in biofilms.{{cite book |edition=13th |publisher=Benjamin Cummings |isbn=9780321649638 |vauthors=Madigan T |title=Brock biology of microorganisms |location=San Francisco |date=2012}} Bacterial biofilms are formed by the secretion of extracellular polymeric substance (EPS).{{cite book |doi=10.1007/978-3-540-68022-2_2 |chapter=Direct Observations |title=The Biofilm Primer |series=Springer Series on Biofilms |volume=1 |pages=3–4 |year=2007 |isbn=978-3-540-68021-5 |last1=Costerton |first1=J. William |publisher=Springer |location=Berlin, Heidelberg |name-list-style=vanc}} Myxobacteria have multicellular stages in their life cycles.{{cite journal |vauthors=Kaiser D |title=Coupling cell movement to multicellular development in myxobacteria |journal=Nature Reviews. Microbiology |volume=1 |issue=1 |pages=45–54 |date=October 2003 |pmid=15040179 |doi=10.1038/nrmicro733 |s2cid=9486133}} Biofilms may be 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 structure functions as a simple circulatory system by moving water through the biofilm, helping to provide cells with oxygen which is often in short supply.{{cite journal |vauthors=Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM |title=Microbial biofilms |journal=Annual Review of Microbiology |volume=49 |pages=711–745 |date=October 1995 |issue=1 |pmid=8561477 |doi=10.1146/annurev.mi.49.100195.003431}} The result approaches a multicellular organisation.{{cite journal |vauthors=Shapiro JA |title=Thinking about bacterial populations as multicellular organisms |journal=Annual Review of Microbiology |volume=52 |pages=81–104 |date=1998 |issue=1 |pmid=9891794 |doi=10.1146/annurev.micro.52.1.81 |url=http://www.sci.uidaho.edu/newton/math501/Sp05/Shapiro.pdf |author-link=James A. Shapiro |archive-url=https://web.archive.org/web/20110717183759/http://www.sci.uidaho.edu/newton/math501/Sp05/Shapiro.pdf |url-status=dead |archive-date=2011-07-17 }} Differential cell expression, collective behavior, signaling (quorum sensing), programmed cell death, and discrete biological dispersal events all seem to point in this direction.{{cite journal |vauthors=Chua SL, Liu Y, Yam JK, Chen Y, Vejborg RM, Tan BG, Kjelleberg S, Tolker-Nielsen T, Givskov M, Yang L |title=Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles |journal=Nature Communications |volume=5 |pages=4462 |date=July 2014 |issue=1 |pmid=25042103 |doi=10.1038/ncomms5462 |bibcode=2014NatCo...5.4462C |doi-access=free}}{{cite book |vauthors=Balaban N, Ren D, Givskov M, Rasmussen TB |chapter=Introduction |doi=10.1007/7142_2007_006 |title=Control of Biofilm Infections by Signal Manipulation |series=Springer Series on Biofilms |volume=2 |pages=1–11 |year=2008 |publisher=Springer |location=Berlin, Heidelberg |isbn=978-3-540-73852-7}} Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells, making them difficult to remove from surfaces they have colonized.{{cite journal |vauthors=Costerton JW, Stewart PS, Greenberg EP |title=Bacterial biofilms: a common cause of persistent infections |journal=Science |volume=284 |issue=5418 |pages=1318–22 |date=May 1999 |pmid=10334980 |doi=10.1126/science.284.5418.1318 |bibcode=1999Sci...284.1318C |s2cid=27364291 |url=https://scholarworks.montana.edu/xmlui/handle/1/14368 }}

Environment

File:Aerial image of Grand Prismatic Spring (view from the south).jpg, Yellowstone National Park are produced by thermophilic bacteria.]]

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 by chemosynthesis.{{cite journal |last1=Cavenaugh |first1=Colleen M. |first2=Stephen L. |last2=Gardiner |first3=Meredith L. |last3=Jones |first4=Holger W. |last4=Jannasch |first5=John B. |last5=Waterbury |title=Prokaryotic Cells in the Hydrothermal Vent Tube Worms Riftia Jones: Possible Chemoautotrophic Symbionts |journal=Science |volume=213 |issue=4505 |year=1981 |pages=340–342 |doi=10.1126/science.213.4505.340 |pmid=17819907 }}

Prokaryotes live nearly everywhere on Earth, including in environments as cold as soils in Antarctica,{{cite journal |last1=Tribelli |first1=Paula |last2=López |first2=Nancy |title=Reporting Key Features in Cold-Adapted Bacteria |journal=Life |volume=8 |issue=1 |date=2018-03-13 |pmid=29534000 |pmc=5871940 |doi=10.3390/life8010008 |doi-access=free |page=8 |bibcode=2018Life....8....8T }} or as hot as undersea hydrothermal vents and land-based hot springs.{{cite web |last=Brock |first=Thomas D. |author-link=Thomas D. Brock |title=Colorful Yellowstone |work=Life at High Temperature |url=http://www.bact.wisc.edu/bact303/b4 |archive-url=https://web.archive.org/web/20051125213458/http://www.bact.wisc.edu/bact303/b4 |archive-date=November 25, 2005 }} Some bacteria are pathogenic, causing disease in organisms including humans.{{Cite book |last=Peterson |first=Johnny W. |url=https://www.ncbi.nlm.nih.gov/books/NBK7627/ |title=Medical Microbiology – Chapter 7 Bacterial Pathogenesis |publisher=University of Texas Press |year=1996 |isbn=0963117211 |editor-last=Baron |editor-first=Samuel |edition=4th |location=Galveston, Texas}} Some archaea and bacteria are extremophiles, thriving in harsh conditions, such as high temperatures (thermophiles) or high salinity (halophiles).{{cite book |vauthors=Hogan CM |date=2010 |chapter-url=http://www.eoearth.org/article/Extremophile?topic=49540 |chapter=Extremophile |title=Encyclopedia of Earth |publisher=National Council of Science & the Environment |veditors=Monosson E, Cleveland C}} Some archaeans are methanogens, living in anoxic environments and releasing methane. 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.{{cite journal |last1=Cobián Güemes |first1=Ana Georgina |last2=Youle |first2=Merry |last3=Cantú |first3=Vito Adrian |last4=Felts |first4=Ben |last5=Nulton |first5=James |last6=Rohwer |first6=Forest |title=Viruses as Winners in the Game of Life |journal=Annual Review of Virology |publisher=Annual Reviews |volume=3 |issue=1 |date=2016-09-29 |doi=10.1146/annurev-virology-100114-054952 |pages=197–214 |pmid=27741409 |s2cid=36517589}}

The first organisms

File:Symbiogenesis 2 mergers.svg, a merger of two prokaryotes, an archaean and an aerobic bacterium, created the eukaryotes, with aerobic mitochondria; a second merger added chloroplasts from a third prokaryote, a photosynthetic cyanobacterium, creating the green plants.]]

A widespread model of the origin of life is that the first organisms were prokaryotes. These evolved out of protocells, while the eukaryotes evolved later in the history of life,{{cite journal |vauthors=Zimmer C |title=Origins. On the origin of eukaryotes |journal=Science |volume=325 |issue=5941 |pages=666–8 |date=August 2009 |pmid=19661396 |doi=10.1126/science.325_666}} by symbiogenesis: a merger of two prokaryotes, an archaean and an aerobic bacterium, created the first eukaryote, with aerobic mitochondria. A second merger added chloroplasts, from a photosynthetic cyanobacterium, creating the green plants.{{cite book |vauthors=Latorre A, Durban A, Moya A, Pereto J |chapter-url=https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |chapter=The role of symbiosis in eukaryotic evolution |title=Origins and Evolution of Life: An astrobiological perspective |veditors=Gargaud M, López-Garcìa P, Martin H |year=2011 |location=Cambridge |publisher=Cambridge University Press |pages=326–339 |isbn=978-0-521-76131-4 |access-date=27 August 2017 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055723/https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |url-status=live }}

The oldest 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. The oldest fossil eukaryotes are about 1.7 billion years old.Carl Woese, J Peter Gogarten, "[http://www.scientificamerican.com/article/when-did-eukaryotic-cells/ When did eukaryotic cells (cells with nuclei and other internal organelles) first evolve? What do we know about how they evolved from earlier life-forms?]" Scientific American, October 21, 1999.

Evolution

= Taxonomy and phylogeny =

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).{{cite journal |vauthors=Stanier RY, Van Niel CB |title=The concept of a bacterium |journal=Archiv für Mikrobiologie |volume=42 |pages=17–35 |year=1962 |issue=1 |pmid=13916221 |doi=10.1007/BF00425185 |bibcode=1962ArMic..42...17S |s2cid=29859498 |author1-link=Roger Stanier |author2-link=C. B. van Niel}} That paper cites Édouard Chatton's 1937 book Titres et Travaux Scientifiques{{cite book |last1=Chatton |first1=Édouard |name-list-style=vanc |title=Titres Et Travaux Scientifiques (1906-1937) De Edouard Chatton |date=1937 |publisher=Impr. E. Sottano |location=Sète}} for using those terms and recognizing the distinction.{{cite journal |last=Sapp |first=Jan |author-link=Jan Sapp |title=The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology |doi=10.1128/MMBR.69.2.292-305.2005 |journal=Microbiology and Molecular Biology Reviews |volume=69 |issue=2 |pages=292–305 |year=2005 |pmid=15944457 |pmc=1197417}} 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.

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.{{cite journal |vauthors=Woese CR |title=There must be a prokaryote somewhere: microbiology's search for itself |journal=Microbiological Reviews |volume=58 |issue=1 |pages=1–9 |date=March 1994 |pmid=8177167 |pmc=372949 |doi=10.1128/MMBR.58.1.1-9.1994}}{{cite journal |vauthors=Sapp J |title=The prokaryote-eukaryote dichotomy: meanings and mythology |journal=Microbiology and Molecular Biology Reviews |volume=69 |issue=2 |pages=292–305 |date=June 2005 |pmid=15944457 |pmc=1197417 |doi=10.1128/MMBR.69.2.292-305.2005}}

Knowledge of prokaryote taxonomy is rapidly changing in the 21st century with the sequencing 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.{{cite journal |last1=Hugenholtz |first1=Philip |last2=Chuvochina |first2=Maria |last3=Oren |first3=Aharon |last4=Parks |first4=Donovan H. |last5=Soo |first5=Rochelle M. |title=Prokaryotic taxonomy and nomenclature in the age of big sequence data |journal=The ISME Journal |volume=15 |issue=7 |year=2021 |pages=1879-1892 |url=https://academic.oup.com/ismej/article-pdf/15/7/1879/55257373/41396_2021_article_941.pdf}}

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 as Omnitrophica and Wirthbacteria) and archaea (such as Parvarchaeota and Lokiarchaeota). 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.

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 the citric acid cycle by which many cells release usable energy, and few can synthesise amino acids and nucleotides, building blocks of proteins and nucleic acids. This may represent an ancient condition, or a loss of capabilities of symbiotic organisms.{{Cite journal |last1=Hug |first1=Laura A. |last2=Baker |first2=Brett J. |last3=Anantharaman |first3=Karthik |last4=Brown |first4=Christopher T. |last5=Probst |first5=Alexander J. |last6=Castelle |first6=Cindy J. |last7=Butterfield |first7=Cristina N. |last8=Hernsdorf |first8=Alex W. |last9=Amano |first9=Yuki |last10=Ise |first10=Kotaro |last11=Suzuki |first11=Yohey |last12=Dudek |first12=Natasha |last13=Relman |first13=David A. |last14=Finstad |first14=Kari M. |last15=Amundson |first15=Ronald |display-authors=5 |date=2016-04-11 |title=A new view of the tree of life |journal=Nature Microbiology |volume=1 |issue=5 |page=16048 |doi=10.1038/nmicrobiol.2016.48 |doi-access=free |pmid=27572647 }}

File:A Novel Representation Of The Tree Of Life.png

= As distinct from eukaryotes =

{{multiple image

|align =right

|image1 =Prokaryote cell.svg

|width1 =55

|caption1 =Prokaryote, to same scale

|image2 =Endomembrane system diagram en (edit).svg

|width2 =330

|caption2 =Part of a eukaryotic cell

|footer =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.{{cite journal |last1=Coté |first1=Gary |last2=De Tullio |first2=Mario |name-list-style=vanc |date=2010 |title=Beyond Prokaryotes and Eukaryotes: Planctomycetes and Cell Organization |url=https://nature.com/scitable/topicpage/beyond-prokaryotes-and-eukaryotes-planctomycetes-and-cell-14158971 |journal=Nature}} Eukaryotic cells are some 10,000 times larger than prokaryotic cells by volume, and contain membrane-bound organelles.{{cite book |last=DeRennaux |first=B. |name-list-style=vanc |title=Encyclopedia of Biodiversity |chapter=Eukaryotes, Origin of |publisher=Elsevier |year=2001 |volume=2 |doi=10.1016/b978-0-12-384719-5.00174-x |pages=329–332|isbn=9780123847201 }}

Both eukaryotes and prokaryotes contain ribosomes which produce proteins as specified by the cell's DNA. Prokaryote ribosomes are smaller than those in eukaryote cytoplasm, but similar to those inside mitochondria and chloroplasts, one of several lines of evidence that those organelles derive from bacteria incorporated by symbiogenesis.{{cite book |title=The Molecular Biology of the Cell |url=https://archive.org/details/molecularbiolog000wils |url-access=registration |edition=fourth |author=Bruce Alberts |display-authors=etal |publisher=Garland Science |date=2002 |pages=808 |isbn=0-8153-3218-1 }}{{cite book |last1=Latorre |first1=A. |last2=Durban |first2=A. |last3=Moya |first3=A. |last4=Pereto |first4=J. |chapter-url=https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |chapter=The role of symbiosis in eukaryotic evolution |title=Origins and Evolution of Life: An astrobiological perspective |editor1=Gargaud, M. |editor2=López-Garcìa, P. |editor3=Martin, H. |year=2011 |location=Cambridge |publisher=Cambridge University Press |pages=326–339 |isbn=978-0-521-76131-4 |access-date=27 August 2017 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055723/https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |url-status=live }}

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.{{cite journal |vauthors=Thanbichler M, Wang SC, Shapiro L |title=The bacterial nucleoid: a highly organized and dynamic structure |journal=Journal of Cellular Biochemistry |volume=96 |issue=3 |pages=506–21 |date=October 2005 |pmid=15988757 |doi=10.1002/jcb.20519 |s2cid=25355087 |doi-access=free}} In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids.{{cite journal |vauthors=Helinski DR |title=A Brief History of Plasmids |journal=EcoSal Plus |volume=10 |issue=1 |pages=eESP00282021 |date=December 2022 |pmid=35373578 |pmc=10729939 |doi=10.1128/ecosalplus.ESP-0028-2021 |veditors=Kaper JB }} Like eukaryotes, prokaryotes may partially duplicate genetic material, and can have a haploid chromosomal composition that is partially replicated.{{cite journal |vauthors=Johnston C, Caymaris S, Zomer A, Bootsma HJ, Prudhomme M, Granadel C, Hermans PW, Polard P, Martin B, Claverys JP |title=Natural genetic transformation generates a population of merodiploids in Streptococcus pneumoniae |journal=PLOS Genetics |volume=9 |issue=9 |pages=e1003819 |date=2013 |pmid=24086154 |pmc=3784515 |doi=10.1371/journal.pgen.1003819 |doi-access=free }}

class="wikitable" \|+ Prokaryotes vs Eukaryotes
Domain ! style="width: 120px;" \| Nucleus ! style="width: 180px;" \| Organelles ! style="width: 180px;" \| 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

class="wikitable"

|+ Prokaryotes vs Eukaryotes

Domain

! style="width: 120px;" | Nucleus

! style="width: 180px;" | Organelles

! style="width: 180px;" | 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.{{cite journal |vauthors=Harold FM |title=Conservation and transformation of energy by bacterial membranes |journal=Bacteriological Reviews |volume=36 |issue=2 |pages=172–230 |date=June 1972 |pmid=4261111 |pmc=408323 |doi=10.1128/MMBR.36.2.172-230.1972 }} Prokaryotes possess some internal structures, such as prokaryotic cytoskeletons.{{cite journal |vauthors=Shih YL, Rothfield L |title=The bacterial cytoskeleton |journal=Microbiology and Molecular Biology Reviews |volume=70 |issue=3 |pages=729–754 |date=September 2006 |pmid=16959967 |pmc=1594594 |doi=10.1128/MMBR.00017-06}}{{cite journal |vauthors=Michie KA, Löwe J |title=Dynamic filaments of the bacterial cytoskeleton |journal=Annual Review of Biochemistry |volume=75 |pages=467–92 |date=2006 |issue=1 |pmid=16756499 |doi=10.1146/annurev.biochem.75.103004.142452 |url=http://www2.mrc-lmb.cam.ac.uk/SS/Lowe_J/group/PDF/annrev2006.pdf |archive-url=https://web.archive.org/web/20061117183040/http://www2.mrc-lmb.cam.ac.uk/SS/Lowe_J/group/PDF/annrev2006.pdf |url-status=dead |archive-date=November 17, 2006}} It was previously suggested that the bacterial phylum Planctomycetota has a membrane around the nucleoid and contains other membrane-bound cellular structures.{{cite journal |vauthors=Fuerst JA |title=Intracellular compartmentation in planctomycetes |journal=Annual Review of Microbiology |volume=59 |pages=299–328 |date=2005 |issue=1 |pmid=15910279 |doi=10.1146/annurev.micro.59.030804.121258 }} Further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected.{{cite journal |vauthors=Santarella-Mellwig R, Pruggnaller S, Roos N, Mattaj IW, Devos DP |title=Three-dimensional reconstruction of bacteria with a complex endomembrane system |journal=PLOS Biology |volume=11 |issue=5 |pages=e1001565 |date=2013 |pmid=23700385 |pmc=3660258 |doi=10.1371/journal.pbio.1001565 |doi-access=free }}

Prokaryotic cells are usually much smaller than eukaryotic cells. This causes prokaryotes to 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.{{cite journal |last1=Kempes |first1=Christopher P. |last2=Dutkiewicz |first2=Stephanie |last3=Follows |first3=Michael J. |title=Growth, metabolic partitioning, and the size of microorganisms |journal=Proceedings of the National Academy of Sciences |volume=109 |issue=2 |date=10 January 2012 |pmid=22203990 |pmc=3258615 |doi=10.1073/pnas.1115585109 |doi-access=free |pages=495–500 |bibcode=2012PNAS..109..495K |url=https://www.pnas.org/content/pnas/109/2/495.full.pdf}}

= Eukaryotes as Archaea =

File:Phylogenetic Tree of Prokaryota.png |volume=172 |issue=6 |pages=1181–1197 |date=March 2018 |pmid=29522741 |doi=10.1016/j.cell.2018.02.016 |url=http://www.escholarship.org/uc/item/0299z0z4 |doi-access=free}} 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 the archaean Asgard group, perhaps Heimdallarchaeota. For example, histones, which usually package DNA in eukaryotic nuclei, are found in several archaean groups, giving evidence for homology.{{cite journal |vauthors=Mattiroli F, Bhattacharyya S, Dyer PN, White AE, Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG, Santangelo TJ, Reeve JN, Luger K |title=Structure of histone-based chromatin in Archaea |journal=Science |volume=357 |issue=6351 |pages=609–612 |date=August 2017 |pmid=28798133 |pmc=5747315 |doi=10.1126/science.aaj1849 |bibcode=2017Sci...357..609M }} A proposed non-bacterial group comprising Archaea and Eukaryota was called Neomura by Thomas Cavalier-Smith in 2002.{{cite journal |author=Cavalier-Smith T |author-link=Tom Cavalier-Smith |title=The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa |journal=International Journal of Systematic and Evolutionary Microbiology |volume=52 |issue=Pt 2 |pages=297–354 |date=March 2002 |pmid=11931142 |doi=10.1099/00207713-52-2-297 |url=http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=11931142 |archive-date=2017-07-29 |access-date=2019-03-21 |archive-url=https://web.archive.org/web/20170729113756/http://ijs.microbiologyresearch.org/content/journal/ijsem |url-status=dead }}

class="wikitable" \|+ Eukaryotes as Archaea
Domain	Histone proteins	ATP synthase	DNA replication
Archaea, inc. Eukaryota \|colspan=3 \|All are similar in these two groups, implying homology and relatedness
Bacteria \|(missing) \|colspan=2 \|Present in a very different form

class="wikitable"

|+ Eukaryotes as Archaea

Domain

Histone proteins

ATP synthase

DNA replication

Archaea, inc. Eukaryota

|colspan=3 |All are similar in these two groups, implying homology and relatedness

Bacteria

|(missing)

|colspan=2 |Present in a very different form

Another view is that the most important difference between biota may be the division between Bacteria and the rest (Archaea and Eukaryota). DNA replication differs fundamentally between the Bacteria and Archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups.{{cite journal |vauthors=Barry ER, Bell SD |title=DNA replication in the archaea |journal=Microbiology and Molecular Biology Reviews |volume=70 |issue=4 |pages=876–887 |date=December 2006 |pmid=17158702 |pmc=1698513 |doi=10.1128/MMBR.00029-06}}

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.{{cite book |vauthors=Lane N |author-link1=Nick Lane |chapter=Energy, Evolution, and the Origins of Complex Life |url=https://archive.org/details/vitalquestionene0000lane |url-access=registration |page=[https://archive.org/details/vitalquestionene0000lane/page/77 77] |title=The Vital Question |publisher=W. W. Norton |date=2015 |isbn=978-0-393-08881-6}}

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).{{cite journal |doi=10.1073/pnas.0510333103 |last1=Forterre |first1=Patrick |name-list-style=vanc |year=2006 |title=Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain |journal=PNAS |volume=103 |issue=10 |pages=3669–3674 |pmid=16505372 |pmc=1450140 |bibcode=2006PNAS..103.3669F |doi-access=free}}

References

External links

[http://wiki.biomine.skelleftea.se/wiki/index.php/Prokaryote_versus_eukaryote Prokaryote versus eukaryote, BioMineWiki] {{Webarchive|url=https://web.archive.org/web/20121025065711/http://wiki.biomine.skelleftea.se/wiki/index.php/Prokaryote_versus_eukaryote |date=2012-10-25 }}
[https://web.archive.org/web/20130502073028/http://www.taxonomicoutline.org/ The Taxonomic Outline of Bacteria and Archaea]
[http://mmbr.asm.org/content/69/2/292.full The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology]
[http://www.thatquiz.org/tq/practice.html?cells_imgmap Quiz on prokaryote anatomy]
[http://tolweb.org/Life_on_Earth/1 TOLWEB page on Eukaryote-Prokaryote phylogeny]