A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό (pro) "before" and κάρυον (karyon) "nut or kernel". Prokaryotes are divided into two domains, Archaea and Bacteria. Species with nuclei and organelles are placed in the third domain, Eukaryota. Prokaryotes reproduce without fusion of gametes. The first living organisms are thought to have been prokaryotes.
In the prokaryotes, all the intracellular water-soluble components (proteins, DNA and metabolites) are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells. Some prokaryotes, such as cyanobacteria, may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles.
Molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species. Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus (containing chromosomal DNA) and organelles. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens; these are common in some extreme environments.
The division between prokaryotes and eukaryotes was firmly 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). That paper cites Édouard Chatton's 1937 book Titres et Travaux Scientifiques for using those terms and recognizing the distinction. One reason for this classification was so that what was then often called blue-green algae (now called cyanobacteria) would not be classified as plants but grouped with bacteria.
Prokaryotes have a prokaryotic cytoskeleton, albeit more primitive than that of the eukaryotes. Besides homologues of actin and tubulin (MreB and FtsZ), the helically arranged building-block of the flagellum, flagellin, is one of the most significant cytoskeletal proteins of bacteria, as it provides structural backgrounds of chemotaxis, 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 as photosynthesis or chemolithotrophy. In addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles (e.g. carboxysomes or gas vacuoles).
|Prokaryotic cell structure|
|Flagellum (only in some types of prokaryotes)
Long, whip-like protrusion that aids cellular locomotion used by both gram positive and gram negative organisms.
Surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell.
|Cell wall (except genera Mycoplasma and Thermoplasma)
Outer covering of most cells that protects the bacterial cell and gives it shape.
A gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules.
Cell structures responsible for protein production.
Area of the cytoplasm that contains the prokaryote's single DNA molecule.
|Glycocalyx (only in some types of prokaryotes)|
It contains the inclusion bodies like ribosomes and larger masses scattered in the cytoplasmic matrix.
Prokaryotic cells have various shapes; the four basic shapes of bacteria are:
Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. Genetic exchange and recombination still occur, but this is a form of horizontal gene transfer and is not a replicative process, simply involving the transference of DNA between two cells, as in bacterial conjugation.
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)-mediated transduction, (2) plasmid-mediated conjugation, and (3) natural transformation. Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of virus particles, rather than an adaptation of 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-studied E. coli system 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.
Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the intervening medium. Unlike transduction and conjugation, transformation is clearly a bacterial adaptation for DNA transfer, because it depends on numerous bacterial gene products that specifically interact to perform this complex process. For a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence. About 40 genes are required in Bacillus subtilis for the development of competence. The length of DNA transferred during B. subtilis transformation can be as much as a third to the whole chromosome. Transformation is a common mode of DNA transfer, and 67 prokaryotic species are thus far known to be naturally competent for transformation.
Among archaea, Halobacterium volcanii forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another. Another archaeon, Sulfolobus solfataricus, transfers DNA between cells by direct contact. Frols et al. found that exposure of S. solfataricus to 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.
While prokaryotes are considered strictly unicellular, most can form stable aggregate communities. When such communities are encased in a stabilizing polymer matrix ("slime"), they may be called "biofilms". Cells in biofilms often show distinct patterns of gene expression (phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression often appear to result from cell-to-cell signaling, a phenomenon known as quorum 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 of microcolonies (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 a circulatory system  and many researchers have started calling prokaryotic communities multicellular (for example ). Differential cell expression, collective behavior, signaling, programmed cell death, and (in some cases) discrete biological dispersal 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 of co-operation and the evolution of multicellularity have 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 (see inclusive fitness and Hamilton'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. 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. Other aspects of bacterial cooperation—such as bacterial conjugation and quorum-sensing-mediated pathogenicity, present additional challenges to researchers and medical professionals seeking to treat the associated diseases.
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). Many archaea grow as plankton in the oceans. Symbiotic prokaryotes live in or on the bodies of other organisms, including humans.
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.
A widespread current model of the evolution of the first living organisms is that these were some form of prokaryotes, which may have evolved out of protocells, while the eukaryotes evolved later in the history of life. 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. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool. This controversy was summarized in 2005:
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 archeabacteria 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 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.
While Earth is the only place in the universe where life is known to exist, some have suggested that there is evidence on Mars of fossil or living prokaryotes. However, this possibility remains the subject of considerable debate and skepticism.
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" nucleus containing their DNA, whereas prokaryotic cells do not have a nucleus. Both eukaryotes and prokaryotes contain large RNA/protein structures called ribosomes, which produce protein.
Another difference is that ribosomes in prokaryotes are smaller than in eukaryotes. However, two organelles found in many eukaryotic cells, mitochondria and chloroplasts, contain ribosomes similar in size and makeup to those found in prokaryotes. This is one of many pieces of evidence that mitochondria and chloroplasts are themselves descended from free-living bacteria. This theory holds that early eukaryotic cells took in primitive prokaryotic cells by phagocytosis and adapted themselves to incorporate their structures, leading to the mitochondria we see today.
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, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organized chromosomes found in eukaryotic cells. In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids. Like Eukaryotes, prokaryotes may partially duplicate genetic material, and can have a haploid chromosomal composition that is partially replicated, a condition known as merodiploidy.
Prokaryotes lack mitochondria and chloroplasts. Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane. However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons. It has been suggested that the bacterial order Planctomycetes have a membrane around their nucleoid and contain other membrane-bound cellular structures. However, further investigation revealed that Planctomycetes cells are not compartmentalized or nucleated and like the other bacterial membrane systems are all interconnected.
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.
There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next by) the archaean asgard group, perhaps Heimdallarchaeota (an idea which is a modern version of the 1984 eocyte hypothesis, eocytes being an old synonym for crenarchaeota, a taxon to be found nearby the then unknown asgard group) For example, histones usually packaging DNA in eukarotic nuclei, have also been found in several archaean groups, giving evidence for homology. This idea might clarify the mysterious predecessor of eukaryotic cells (eucytes) which engulfed an alphaproteobacterium forming the first eucyte (LECA, last eukaryotic common ancestor) according to endosymbiotic theory. There might have been some additional support by viruses, called viral eukaryogenesis. The non-bacterial group comprising archaea and eukaryota has been called Neomura by Thomas Cavalier-Smith in 2002. However, in a cladistic view eukaryota are archaea in the same sense as birds are dinosaurs because they evolved from the maniraptora dinosaur group. In contrast, archaea without eukaryota appear to be a paraphyletic group, just like dinosaurs without birds.
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). For instance, DNA replication differs fundamentally between bacteria and archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups. Moreover, ATP synthase, though common (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 antecessor of all life (called LUCA, last universal common antecessor) 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 been a ribocyte (also called ribocell) lacking DNA, but with an RNA genome built by ribosomes as primordial self-replicating entities. A Peptide-RNA world (also called RNP world) hypothesis has been proposed based on the idea that oligopeptides may have been built together with primordial nucleic acids at the same time, which also 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 by help of some viruses (possibly retroviruses as they could reverse transcribe RNA to DNA). As a result, prokaryota comprising bacteria and archaea may also be polyphyletic.
CRISPR () (clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found within the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments from viruses that have previously infected the prokaryote and are used to detect and destroy DNA from similar viruses during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes.Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms. This editing process has a wide variety of applications including basic biological research, development of biotechnology products, and treatment of diseases.
The CRISPR-Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity. RNA harboring the spacer sequence helps Cas (CRISPR-associated) proteins recognize and cut foreign pathogenic DNA. Other RNA-guided Cas proteins cut foreign RNA. CRISPR are found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.Candidatus
In prokaryote nomenclature, Candidatus (Latin for candidate of Roman office, named after the white gown worn by Roman senators) is a component of the taxonomic name for a bacterium or other prokaryote, that cannot be maintained in a microbiological culture collection. It is an interim taxonomic status for yet-to-be-cultured microorganisms. An example would be "Candidatus Phytoplasma allocasuarinae". This can be abbreviated to "Ca. Phytoplasma allocasuarinae". Candidatus status may be used when a species or genus is well characterized but yet-uncultured. With today's technology much information is obtained by 16S ribosomal RNA or even near-complete genomes with modern metagenomics techniques.Circular prokaryote chromosome
A circular prokaryote chromosome is a chromosome in bacteria and archaea, in the form of a molecule of circular DNA. Unlike the linear DNA of most eukaryotes, typical prokaryote chromosomes are circular.
Most prokaryote chromosomes contain a circular DNA molecule – there are no free ends to the DNA. Free ends would otherwise create significant challenges to cells with respect to DNA replication and stability. Cells that do contain chromosomes with DNA ends, or telomeres (most eukaryotes), have acquired elaborate mechanisms to overcome these challenges. However, a circular chromosome can provide other challenges for cells. After replication, the two progeny circular chromosomes can sometimes remain interlinked or tangled, and they must be resolved so that each cell inherits one complete copy of the chromosome during cell division.Hydrogen hypothesis
The hydrogen hypothesis is a model proposed by William F. Martin and Miklós Müller in 1998 that describes a possible way in which the mitochondrion arose as an endosymbiont within an archaeon (without doubts classified as prokaryote at then times), giving rise to a symbiotic association of two cells from which the first eukaryotic cell could have arisen (symbiogenesis).
According to the hydrogen hypothesis:
The host that acquired the mitochondrion was a hydrogen-dependent archaeon, possibly similar in physiology to a modern methanogenic archaea, which use hydrogen and carbon dioxide to produce methane;
The future mitochondrion was a facultatively anaerobic eubacterium which produced hydrogen and carbon dioxide as byproducts of anaerobic respiration;
A symbiotic relationship between the two started, based on the host's hydrogen dependence (anaerobic syntrophy).LtrA
LtrA is an open reading frame found in the Lactococcus lactis group II introns LtrB. It is an intron-encoded protein, which consists of three subdomains: a reverse-transcriptase/maturase, DNA endonuclease, and DNA/RNA binding domain. LtrA helps to capture and stabilize the catalytically active conformation of the LtrB group II intron RNA. It also functions in group II intron retrohoming.Monera
Monera () (Greek - μονήρης (monḗrēs), "single", "solitary") is a kingdom that contains unicellular organisms with a prokaryotic cell organization (having no nuclear membrane), such as bacteria. They are single-celled organisms with no true nuclear membrane (prokaryotic organisms).
The taxon Monera was first proposed as a phylum by Ernst Haeckel in 1866. Subsequently, the phylum was elevated to the rank of kingdom in 1925 by Édouard Chatton. The last commonly accepted mega-classification with the taxon Monera was the five-kingdom classification system established by Robert Whittaker in 1969.
Under the three-domain system of taxonomy, introduced by Carl Woese in 1977, which reflects the evolutionary history of life, the organisms found in kingdom Monera have been divided into two domains, Archaea and Bacteria (with Eukarya as the third domain). Furthermore, the taxon Monera is paraphyletic (does not include all descendants of their most-recent common ancestor), as Archaea and Eukarya are currently believed to be more closely related than either is to Bacteria. The term "moneran" is the informal name of members of this group and is still sometimes used (as is the term "prokaryote") to denote a member of either domain.Most bacteria were classified under Monera; however, Cyanobacteria (often called the blue-green algae) were initially classified under Plantae due to their ability to photosynthesize.Nif gene
The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. The primary enzyme encoded by the nif genes is the nitrogenase complex which is in charge of converting atmospheric nitrogen (N2) to other nitrogen forms such as ammonia which the organism can use for various purposes. Besides the nitrogenase enzyme, the nif genes also encode a number of regulatory proteins involved in nitrogen fixation. The nif genes are found in both free-living nitrogen-fixing bacteria and in symbiotic bacteria associated with various plants. The expression of the nif genes is induced as a response to low concentrations of fixed nitrogen and oxygen concentrations (the low oxygen concentrations are actively maintained in the root environment of host plants). The first Rhizobium genes for nitrogen fixation (nif) and for nodulation (nod) were cloned in the early 1980s by Gary Ruvkun and Sharon R. Long in Frederick M. Ausubel's laboratory.Nucleoid
The nucleoid (meaning nucleus-like) is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material, called genophore. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. The genome of prokaryotic organisms generally is a circular double-stranded piece of DNA, of which multiple copies may exist at any time. The length of a genome widely varies, but generally is at least a few million base pairs. As in all cellular organisms, the length of the DNA molecules of bacterial and archaeal chromosomes is very large compared to the dimensions of the cell, and the genomic DNA molecules must be compacted to fit.Nucleomorph
Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that were engulfed by a larger eukaryote. Because the nucleomorph lies between two sets of membranes, nucleomorphs support the endosymbiotic theory and are evidence that the plastids containing them are complex plastids. Having two sets of membranes indicate that the plastid, a prokaryote, was engulfed by a eukaryote, an alga, which was then engulfed by another eukaryote, the host cell, making the plastid an example of secondary endosymbiosis.Parakaryon myojinensis
Parakaryon myojinensis is a single-celled organism known from a single specimen, described in 2012. It has features of both prokaryotes and eukaryotes but is apparently distinct from either group, making it unique among organisms so far discovered.PncA
PncA is a gene encoding pyrazinamidase in Mycobacterium species. Pyrazinamidase converts the drug pyrazinamide to the active form pyrazinoic acid. There is a strong correlation between mutations in pncA and resistance of M. tuberculosis to pyrazinamide.Poribacteria
Poribacteria are a candidate phylum of bacteria originally identified in the microbiome of sea sponges (Porifera). Poribacteria were distinguished from other microorganisms associated with sea sponges by their distinctive morphology featuring a large membrane-bound cellular compartment that frequently contains DNA, a highly unusual feature for a prokaryote. Poribacteria are Gram-negative mixotrophs.Prochloron
Prochloron (from the Greek pro (before) and the Greek chloros (green) ) is a unicellular oxygenic photosynthetic prokaryote commonly found as an extracellular symbiont on coral reefs, particularly in didemnid ascidians (sea squirts). Part of the phylum cyanobacteria, it was theorized (endosymbiotic theory) that Prochloron is a predecessor of the photosynthetic components, chloroplasts, found in photosynthetic eukaryotic cells. However this theory is largely refuted by phylogenetic studies which indicate Prochloron is not on the same line of descent that lead to chloroplast-containing algae and land plants.Prochloron was discovered in 1975 by Ralph A. Lewin of the Scripps Institution of Oceanography. Prochloron is one of three known prochlorophytes, cyanobacteria that contain both chlorophyll a and b bound to a special light-harvesting protein.Prokaryotic cytoskeleton
The prokaryotic cytoskeleton is the collective name for all structural filaments in prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but advances in visualization technology and structure determination led to the discovery of filaments in these cells in the early 1990s. Not only have analogues for all major cytoskeletal proteins in eukaryotes been found in prokaryotes, cytoskeletal proteins with no known eukaryotic homologues have also been discovered. Cytoskeletal elements play essential roles in cell division, protection, shape determination, and polarity determination in various prokaryotes.Quinella (bacterium)
Quinella is a genus of bacteria in the Veillonellaceae family. Its only species, Quinella ovalis, is an extremely large motile rumen anaerobic prokaryote previously known as "Quin's Oval".In the illustrated atlas of sheep rumen organisms of Moir and Masson, their organism no. 3 represents Quinella ovalis.Zinc uptake regulator
The zinc uptake regulator (Zur) gene is a bacterial gene that codes for a transcription factor protein involved in zinc homeostasis. The protein is a member of the ferric uptake regulator family and binds zinc with high affinity. It typically functions as a repressor of zinc uptake proteins via binding to characteristic promoter DNA sequences in a dimer-of-dimers arrangement that creates strong cooperativity. Under conditions of zinc deficiency, the protein undergoes a conformational change that prevents DNA binding, thereby lifting the repression and causing zinc uptake genes such as ZinT and the ZnuABC zinc transporter to be expressed.
Prokaryotes: Archaea classification