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61-527: Nanoarchaeota (Greek, "dwarf or tiny ancient one") is a proposed phylum ( Candidatus Nanoarchaeota) in the domain Archaea that currently has only one representative, Nanoarchaeum equitans , which was discovered in a submarine hydrothermal vent and first described in 2002. Members of the Nanoarchaeota are associated with different host organisms and environmental conditions. Despite small size,

122-447: A nucleotide , such as the electron carriers NAD and FAD , and coenzyme A , which carries acyl groups. Most of these cofactors are found in a huge variety of species, and some are universal to all forms of life. An exception to this wide distribution is a group of unique cofactors that evolved in methanogens , which are restricted to this group of archaea . Metabolism involves a vast array of chemical reactions, but most fall under

183-447: A century earlier). The definition was posited because extinct organisms are hardest to classify: they can be offshoots that diverged from a phylum's line before the characters that define the modern phylum were all acquired. By Budd and Jensen's definition, a phylum is defined by a set of characters shared by all its living representatives. This approach brings some small problems—for instance, ancestral characters common to most members of

244-513: A cofactor has been identified. Iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor. Calcium is another special case, in that it is required as a component of the human diet, and it is needed for the full activity of many enzymes, such as nitric oxide synthase , protein phosphatases , and adenylate kinase , but calcium activates these enzymes in allosteric regulation , often binding to these enzymes in

305-453: A complex with calmodulin . Calcium is, therefore, a cell signaling molecule, and not usually considered a cofactor of the enzymes it regulates. Other organisms require additional metals as enzyme cofactors, such as vanadium in the nitrogenase of the nitrogen-fixing bacteria of the genus Azotobacter , tungsten in the aldehyde ferredoxin oxidoreductase of the thermophilic archaean Pyrococcus furiosus , and even cadmium in

366-405: A diameter of approximately 400 nm , and have a very short and compact DNA sequence with the entire genome containing only 490,885 base pairs . While they have the genetic code to carry out processing and repair, they cannot carry out certain biosynthetic and metabolic processes such as lipid, amino-acid, cofactor , or nucleotide synthesis. Due to its limited machinery, it is an obligate parasite,

427-530: A different cofactor. This process of adapting a pre-evolved structure for a novel use is known as exaptation . Prebiotic origin of coenzymes . Like amino acids and nucleotides , certain vitamins and thus coenzymes can be created under early earth conditions. For instance, vitamin B3 can be synthesized with electric discharges applied to ethylene and ammonia . Similarly, pantetheine (a vitamin B5 derivative),

488-406: A few basic types of reactions that involve the transfer of functional groups . This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes . Each class of group-transfer reaction is carried out by a particular cofactor, which

549-482: A level of the Linnean hierarchy without referring to (evolutionary) relatedness is unsatisfactory, but a phenetic definition is useful when addressing questions of a morphological nature—such as how successful different body plans were. The most important objective measure in the above definitions is the "certain degree" that defines how different organisms need to be members of different phyla. The minimal requirement

610-435: A low-molecular-weight, non-protein organic compound that is loosely attached, participating in enzymatic reactions as a dissociable carrier of chemical groups or electrons; a prosthetic group is defined as a tightly bound, nonpolypeptide unit in a protein that is regenerated in each enzymatic turnover. Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at

671-443: A molecular mass less than 1000 Da) that can be either loosely or tightly bound to the enzyme and directly participate in the reaction. In the latter case, when it is difficult to remove without denaturing the enzyme, it can be called a prosthetic group . There is no sharp division between loosely and tightly bound cofactors. Many such as NAD can be tightly bound in some enzymes, while it is loosely bound in others. Another example

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732-406: A part of the protein sequence. This often replaces the need for an external binding factor, such as a metal ion, for protein function. Potential modifications could be oxidation of aromatic residues, binding between residues, cleavage or ring-forming. These alterations are distinct from other post-translation protein modifications , such as phosphorylation , methylation , or glycosylation in that

793-422: A phylum may have been lost by some members. Also, this definition is based on an arbitrary point of time: the present. However, as it is character based, it is easy to apply to the fossil record. A greater problem is that it relies on a subjective decision about which groups of organisms should be considered as phyla. The approach is useful because it makes it easy to classify extinct organisms as " stem groups " to

854-706: A phylum, other phylum-level ranks appear, such as the case of Bacillariophyta (diatoms) within Ochrophyta . These differences became irrelevant after the adoption of a cladistic approach by the ISP, where taxonomic ranks are excluded from the classifications after being considered superfluous and unstable. Many authors prefer this usage, which lead to the Chromista-Protozoa scheme becoming obsolete. Currently there are 40 bacterial phyla (not including " Cyanobacteria ") that have been validly published according to

915-512: A precursor of coenzyme A and thioester-dependent synthesis, can be formed spontaneously under evaporative conditions. Other coenzymes may have existed early on Earth, such as pterins (a derivative of vitamin B9 ), flavins ( FAD , flavin mononucleotide = FMN), and riboflavin (vitamin B2). Changes in coenzymes . A computational method, IPRO, recently predicted mutations that experimentally switched

976-423: A protein at some point, and then rebind later. Both prosthetic groups and cosubstrates have the same function, which is to facilitate the reaction of enzymes and proteins. An inactive enzyme without the cofactor is called an apoenzyme , while the complete enzyme with cofactor is called a holoenzyme . The International Union of Pure and Applied Chemistry (IUPAC) defines "coenzyme" a little differently, namely as

1037-486: A reduced genome and limited respiration, members of the Nanoarchaeota have unusual metabolic features. For example, N. equitans has a complex and highly developed intercellular communication system. The phylogeny of the Nanoarchaeota is anchored by its only cultured representative, Nanoarchaeum equitans , which clusters in a separate evolutionary group than other archaea, which have recently been reclassified. Further analysis has shown that N. equitans diverged early on in

1098-601: A structural property. Different sources give slightly different definitions of coenzymes, cofactors, and prosthetic groups. Some consider tightly bound organic molecules as prosthetic groups and not as coenzymes, while others define all non-protein organic molecules needed for enzyme activity as coenzymes, and classify those that are tightly bound as coenzyme prosthetic groups. These terms are often used loosely. A 1980 letter in Trends in Biochemistry Sciences noted

1159-422: A subsequent reaction catalyzed by a different enzyme. In the latter case, the cofactor can also be considered a substrate or cosubstrate. Vitamins can serve as precursors to many organic cofactors (e.g., vitamins B 1 , B 2 , B 6 , B 12 , niacin , folic acid ) or as coenzymes themselves (e.g., vitamin C ). However, vitamins do have other functions in the body. Many organic cofactors also contain

1220-418: Is thiamine pyrophosphate (TPP), which is tightly bound in transketolase or pyruvate decarboxylase , while it is less tightly bound in pyruvate dehydrogenase . Other coenzymes, flavin adenine dinucleotide (FAD), biotin , and lipoamide , for instance, are tightly bound. Tightly bound cofactors are, in general, regenerated during the same reaction cycle, while loosely bound cofactors can be regenerated in

1281-474: Is a paraphyletic taxon, which is less acceptable to present-day biologists than in the past. Proposals have been made to divide it among several new kingdoms, such as Protozoa and Chromista in the Cavalier-Smith system . Protist taxonomy has long been unstable, with different approaches and definitions resulting in many competing classification schemes. Many of the phyla listed below are used by

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1342-463: Is compatible with a host dependent lifestyle. Certain nanaoarchaeotes still have genes for the CRISPR-Cas systems, archaeal flagella , and the gluconeogenesis pathway. Nanoarchaeotes are obligate symbionts that grow attached to an archaeal host known as Ignicoccus . Both terrestrial hot springs and underwater hydrothermal vents have yielded isolates in the genus Nanoarchaeum . However, there

1403-563: Is conducted using X-ray crystallography and mass spectroscopy ; structural data is necessary because sequencing does not readily identify the altered sites. The term is used in other areas of biology to refer more broadly to non-protein (or even protein) molecules that either activate, inhibit, or are required for the protein to function. For example, ligands such as hormones that bind to and activate receptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors. One such example

1464-469: Is evidence that nanoarcheotes reside in a variety of habitats outside of marine thermal vents.  Genetic evidence for members of the Nanoarchaeota has been discovered to be pervasive in terrestrial hot springs and mesophilic hypersaline habitats using primers created based on the sequence of the 16S rRNA gene of Nanoarchaeum equitans . In addition, the discovery of ribosomal sequences in photic-zone water samples taken distant from hydrothermal vents raises

1525-481: Is generally included in kingdom Fungi, though its exact relations remain uncertain, and it is considered a protozoan by the International Society of Protistologists (see Protista , below). Molecular analysis of Zygomycota has found it to be polyphyletic (its members do not share an immediate ancestor), which is considered undesirable by many biologists. Accordingly, there is a proposal to abolish

1586-459: Is that all organisms in a phylum should be clearly more closely related to one another than to any other group. Even this is problematic because the requirement depends on knowledge of organisms' relationships: as more data become available, particularly from molecular studies, we are better able to determine the relationships between groups. So phyla can be merged or split if it becomes apparent that they are related to one another or not. For example,

1647-542: Is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NAD ) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates. Therefore, these cofactors are continuously recycled as part of metabolism . As an example,

1708-626: The Bacteriological Code Currently there are 2 phyla that have been validly published according to the Bacteriological Code Other phyla that have been proposed, but not validly named, include: Coenzymes Cofactors can be classified into two types: inorganic ions and complex organic molecules called coenzymes . Coenzymes are mostly derived from vitamins and other organic essential nutrients in small amounts. (Some scientists limit

1769-565: The Catalogue of Life , and correspond to the Protozoa-Chromista scheme, with updates from the latest (2022) publication by Cavalier-Smith . Other phyla are used commonly by other authors, and are adapted from the system used by the International Society of Protistologists (ISP). Some of the descriptions are based on the 2019 revision of eukaryotes by the ISP. The number of protist phyla varies greatly from one classification to

1830-465: The bearded worms were described as a new phylum (the Pogonophora) in the middle of the 20th century, but molecular work almost half a century later found them to be a group of annelids , so the phyla were merged (the bearded worms are now an annelid family ). On the other hand, the highly parasitic phylum Mesozoa was divided into two phyla ( Orthonectida and Rhombozoa ) when it was discovered

1891-559: The carbonic anhydrase from the marine diatom Thalassiosira weissflogii . In many cases, the cofactor includes both an inorganic and organic component. One diverse set of examples is the heme proteins, which consist of a porphyrin ring coordinated to iron . Iron–sulfur clusters are complexes of iron and sulfur atoms held within proteins by cysteinyl residues. They play both structural and functional roles, including electron transfer, redox sensing, and as structural modules. Organic cofactors are small organic molecules (typically

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1952-564: The last universal ancestor , which lived about 4 billion years ago. Organic cofactors may have been present even earlier in the history of life on Earth. The nucleotide adenosine is a cofactor for many basic metabolic enzymes such as transferases. It may be a remnant of the RNA world . Adenosine-based cofactors may have acted as adaptors that allowed enzymes and ribozymes to bind new cofactors through small modifications in existing adenosine-binding domains , which had originally evolved to bind

2013-618: The nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP , coenzyme A , FAD , and NAD . This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world . It has been suggested that the AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two major groups: organic cofactors , such as flavin or heme ; and inorganic cofactors , such as

2074-499: The Greek phylon ( φῦλον , "race, stock"), related to phyle ( φυλή , "tribe, clan"). Haeckel noted that species constantly evolved into new species that seemed to retain few consistent features among themselves and therefore few features that distinguished them as a group ("a self-contained unity"): "perhaps such a real and completely self-contained unity is the aggregate of all species which have gradually evolved from one and

2135-521: The Orthonectida are probably deuterostomes and the Rhombozoa protostomes . This changeability of phyla has led some biologists to call for the concept of a phylum to be abandoned in favour of placing taxa in clades without any formal ranking of group size. A definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen (as Haeckel had done

2196-497: The Zygomycota phylum. Its members would be divided between phylum Glomeromycota and four new subphyla incertae sedis (of uncertain placement): Entomophthoromycotina , Kickxellomycotina , Mucoromycotina , and Zoopagomycotina . Kingdom Protista (or Protoctista) is included in the traditional five- or six-kingdom model, where it can be defined as containing all eukaryotes that are not plants, animals, or fungi. Protista

2257-524: The amino acids typically acquire new functions. This increases the functionality of the protein; unmodified amino acids are typically limited to acid-base reactions, and the alteration of resides can give the protein electrophilic sites or the ability to stabilize free radicals. Examples of cofactor production include tryptophan tryptophylquinone (TTQ), derived from two tryptophan side chains, and 4-methylidene-imidazole-5-one (MIO), derived from an Ala-Ser-Gly motif. Characterization of protein-derived cofactors

2318-586: The author could not arrive at a single all-encompassing definition of a "coenzyme" and proposed that this term be dropped from use in the literature. Metal ions are common cofactors. The study of these cofactors falls under the area of bioinorganic chemistry . In nutrition , the list of essential trace elements reflects their role as cofactors. In humans this list commonly includes iron , magnesium , manganese , cobalt , copper , zinc , and molybdenum . Although chromium deficiency causes impaired glucose tolerance , no human enzyme that uses this metal as

2379-550: The cofactor specificity of Candida boidinii xylose reductase from NADPH to NADH. Evolution of enzymes without coenzymes . If enzymes require a co-enzyme, how does the coenzyme evolve? The most likely scenario is that enzymes can function initially without their coenzymes and later recruit the coenzyme, even if the catalyzed reaction may not be as efficient or as fast. Examples are Alcohol Dehydrogenase (coenzyme: NAD⁺ ), Lactate Dehydrogenase (NAD⁺), Glutathione Reductase ( NADPH ). The first organic cofactor to be discovered

2440-415: The confusion in the literature and the essentially arbitrary distinction made between prosthetic groups and coenzymes group and proposed the following scheme. Here, cofactors were defined as an additional substance apart from protein and substrate that is required for enzyme activity and a prosthetic group as a substance that undergoes its whole catalytic cycle attached to a single enzyme molecule. However,

2501-420: The course of the day. This means that each ATP molecule is recycled 1000 to 1500 times daily. Organic cofactors, such as ATP and NADH , are present in all known forms of life and form a core part of metabolism . Such universal conservation indicates that these molecules evolved very early in the development of living things. At least some of the current set of cofactors may, therefore, have been present in

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2562-533: The creation of monomers like amino acids, nucleotides, and coenzymes , lack recognizable genes in this organism. Phylum (biology) In biology , a phylum ( / ˈ f aɪ l əm / ; pl. : phyla ) is a level of classification or taxonomic rank below kingdom and above class . Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts

2623-407: The early 20th century, with ATP being isolated in 1929 by Karl Lohmann, and coenzyme A being discovered in 1945 by Fritz Albert Lipmann . The functions of these molecules were at first mysterious, but, in 1936, Otto Heinrich Warburg identified the function of NAD in hydride transfer. This discovery was followed in the early 1940s by the work of Herman Kalckar , who established the link between

2684-848: The evolution of Archaea, as indicated by the 16S rRNA sequence. This suggests that they occupy a deeply branching position within this group. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the National Center for Biotechnology Information (NCBI). " Ca. Tiddalikarchaeum anstoanum " " Ca. Acidifodinimicrobium mancum " " Ca. P. acidiphilum" " Ca. P. paracidiphilum" "Pacearchaeales" "Woesearchaeales" " Nanoarchaeum equitans " " Ca. Nanoclepta minuta " Nanobdella aerobiophila " Ca. N. acidilobi" " Ca. N. stetteri" Cells of N. equitans are spherical with

2745-507: The first publication of the APG system in 1998, which proposed a classification of angiosperms up to the level of orders , many sources have preferred to treat ranks higher than orders as informal clades. Where formal ranks have been provided, the traditional divisions listed below have been reduced to a very much lower level, e.g. subclasses . Wolf plants Hepatophyta Liver plants Coniferophyta Cone-bearing plant Phylum Microsporidia

2806-468: The four embranchements of Georges Cuvier . Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan . At its most basic, a phylum can be defined in two ways: as a group of organisms with a certain degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition). Attempting to define

2867-536: The idea that each of the phyla represents a distinct body plan. A classification using this definition may be strongly affected by the chance survival of rare groups, which can make a phylum much more diverse than it would be otherwise. Total numbers are estimates; figures from different authors vary wildly, not least because some are based on described species, some on extrapolations to numbers of undescribed species. For instance, around 25,000–27,000 species of nematodes have been described, while published estimates of

2928-709: The influential (though contentious) Cavalier-Smith system in equating "Plantae" with Archaeplastida , a group containing Viridiplantae and the algal Rhodophyta and Glaucophyta divisions. The definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years. Thus some sources place horsetails in division Arthrophyta and ferns in division Monilophyta, while others place them both in Monilophyta, as shown below. The division Pinophyta may be used for all gymnosperms (i.e. including cycads, ginkgos and gnetophytes), or for conifers alone as below. Since

2989-404: The junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), cosubstrates nicotinamide adenine dinucleotide (NAD ) and coenzyme A (CoA), and a metal ion (Mg ). Organic cofactors are often vitamins or made from vitamins. Many contain

3050-399: The metal ions Mg , Cu , Mn and iron–sulfur clusters . Organic cofactors are sometimes further divided into coenzymes and prosthetic groups . The term coenzyme refers specifically to enzymes and, as such, to the functional properties of a protein. On the other hand, "prosthetic group" emphasizes the nature of the binding of a cofactor to a protein (tight or covalent) and, thus, refers to

3111-411: The next. The Catalogue of Life includes Rhodophyta and Glaucophyta in kingdom Plantae, but other systems consider these phyla part of Protista. In addition, less popular classification schemes unite Ochrophyta and Pseudofungi under one phylum, Gyrista , and all alveolates except ciliates in one phylum Myzozoa , later lowered in rank and included in a paraphyletic phylum Miozoa . Even within

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3172-533: The only one known in the Archaea. Because of their unusual ss rRNA sequences, they are difficult to detect using standard polymerase chain reaction methods. Cells of N. equitans contain a normal S-layer with sixfold symmetry with a 15 nm lattice constant. Small cells between 100 and 400 nm in diameter and highly streamlined genomes of 0.491-0.606 Mbp characterize nanoarchaeotes. The genomes of described nanoarchaeotes demonstrate different degrees of reduction, which

3233-433: The oxidation of sugars and the generation of ATP. This confirmed the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941. Later, in 1949, Morris Friedkin and Albert L. Lehninger proved that NAD linked metabolic pathways such as the citric acid cycle and the synthesis of ATP. In a number of enzymes, the moiety that acts as a cofactor is formed by post-translational modification of

3294-436: The phyla with which they bear the most resemblance, based only on the taxonomically important similarities. However, proving that a fossil belongs to the crown group of a phylum is difficult, as it must display a character unique to a sub-set of the crown group. Furthermore, organisms in the stem group of a phylum can possess the "body plan" of the phylum without all the characteristics necessary to fall within it. This weakens

3355-420: The possibility that Nanoarchaeota are an ubiquitous and diversified group of Archaea that can live in habitats with a variety of temperatures and geochemical settings. Although much of the metabolism of members of the Nanoarchaeota is unknown, its host is an autotroph that grows on elemental sulphur as an electron acceptor and H 2 as an electron donor . The majority of recognized metabolic processes, such as

3416-411: The same common original form, as, for example, all vertebrates. We name this aggregate [a] Stamm [i.e., stock] ( Phylon )." In plant taxonomy , August W. Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi. The definitions of zoological phyla have changed from their origins in the six Linnaean classes and

3477-416: The terms as equivalent. Depending on definitions, the animal kingdom Animalia contains about 31 phyla, the plant kingdom Plantae contains about 14 phyla, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics is uncovering the relationships among phyla within larger clades like Ecdysozoa and Embryophyta . The term phylum was coined in 1866 by Ernst Haeckel from

3538-420: The total number of nematode species include 10,000–20,000; 500,000; 10 million; and 100 million. The kingdom Plantae is defined in various ways by different biologists (see Current definitions of Plantae ). All definitions include the living embryophytes (land plants), to which may be added the two green algae divisions, Chlorophyta and Charophyta , to form the clade Viridiplantae . The table below follows

3599-431: The total quantity of ATP in the human body is about 0.1  mole . This ATP is constantly being broken down into ADP, and then converted back into ATP. Thus, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over

3660-416: The use of the term "cofactor" for inorganic substances; both types are included here. ) Coenzymes are further divided into two types. The first is called a " prosthetic group ", which consists of a coenzyme that is tightly (or even covalently) and permanently bound to a protein. The second type of coenzymes are called "cosubstrates", and are transiently bound to the protein. Cosubstrates may be released from

3721-496: Was NAD , which was identified by Arthur Harden and William Young 1906. They noticed that adding boiled and filtered yeast extract greatly accelerated alcoholic fermentation in unboiled yeast extracts. They called the unidentified factor responsible for this effect a coferment . Through a long and difficult purification from yeast extracts, this heat-stable factor was identified as a nucleotide sugar phosphate by Hans von Euler-Chelpin . Other cofactors were identified throughout

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