| Cupriavidus necator | |
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| Species: | C. necator |
| Binomial name | |
| Cupriavidus necator (Davis 1969) Yabuuchi et al. 1996 | |
| Synonyms | |
Ralstonia eutropha | |
Cupriavidus necator is a Gram-negative soil bacterium of the class Betaproteobacteria. [1]
Cupriavidus necator has gone through a series of name changes. In the first half of the 20th century, many micro-organisms were isolated for their ability to use hydrogen. Hydrogen-metabolizing chemolithotrophic organisms were clustered into the group Hydrogenomonas. [2] C. necator was originally named Hydrogenomonas eutrophus because it fell under the Hydrogenomonas classification and was "well nourished and robust". [3] Some of the original H. eutrophus cultures isolated were by Bovell and Wilde. [4] [5] After characterizing cell morphology, metabolism and GC content, the Hydrogenomonas nomenclature was disbanded because it comprised many species of microorganisms. [2] H. eutrophus was then renamed Alcaligenes eutropha because it was a micro-organism with degenerated peritrichous flagellation. [3] [6] Investigating phenotype, lipid composition, fatty acid composition and 16S rRNA analysis, A. eutropha was found to belong to the genus Ralstonia and named Ralstonia eutropha. [1] Upon further study of the genus, Ralstonia was found to comprise two phenotypically distinct clusters. The new genus Wautersia was created from one of these clusters which included R. eutropha. In turn R. eutropha was renamed Wautersia eutropha. [7] Looking at DNA–DNA hybridization and phenotype comparison with Cupriavidus necator, W. eutropha was found to be the same species as previously described C. necator. Because C. necator was named in 1987 far before the name change to R. eutropha and W. eutropha, the name C. necator was assigned to R. eutropha according to Rule 23a of the International Code of Nomenclature of Bacteria. [8]
Cupriavidus necator is a hydrogen-oxidizing bacterium ("knallgas" bacterium) capable of growing at the interface of anaerobic and aerobic environments. It can easily adapt between heterotrophic and autotrophic lifestyles. Both organic compounds and hydrogen can be used as a source of energy [9] C. necator can perform aerobic or anaerobic respiration by denitrification of nitrate and/or nitrite to nitrogen gas. [10] When growing under autotrophic conditions, C. necator fixes carbon through the reductive pentose phosphate pathway. [11] It is known to produce and sequester polyhydroxyalkanoate (PHA) plastics when exposed to excess amounts of sugar substrate. PHA can accumulate to levels around 90% of the cell's dry weight. [12] To better characterize the lifestyle of C. necator, the genomes of two strains have been sequenced. [9] [13]
Cupriavidus necator can use hydrogen gas as a source of energy when growing under autotrophic conditions. It contains four different hydrogenases that have [Ni-Fe] active sites and all perform this reaction: [14] [15]
The hydrogenases of C. necator are like other typical [Ni-Fe] hydrogenases because they are made up of a large and a small subunit. The large subunit is where the [Ni-Fe] active site resides and the small subunit is composed of [Fe-S] clusters. [16] However, the hydrogenases of C. necator are different from typical [Ni-Fe] hydrogenases because they are tolerant to oxygen and are not inhibited by CO. [14] While the four hydrogenases perform the same reaction in the cell, each hydrogenase is linked to a different cellular process. The differences between the regulatory hydrogenase, membrane-bound hydrogenase, soluble hydrogenase and actinobacterial hydrogenase in C. necator are described below.
The first hydrogenase is a regulatory hydrogenase (RH) that signals to the cell hydrogen is present. The RH is a protein containing large and small [Ni-Fe] hydrogenase subunits attached to a histidine protein kinase subunit. [17] The hydrogen gas is oxidized at the [Ni-Fe] center in the large subunit and in turn reduces the [Fe-S] clusters in the small subunit. It is unknown whether the electrons are transferred from the [Fe-S] clusters to the protein kinase domain. [14] The histidine protein kinase activates a response regulator. The response regulator is active in the dephosphorylated form. The dephosphorylated response regulator promotes the transcription of the membrane bound hydrogenase and soluble hydrogenase. [18]
The membrane-bound hydrogenase (MBH) is linked to the respiratory chain through a specific cytochrome b-related protein in C. necator. [19] Hydrogen gas is oxidized at the [Ni-Fe] active site in the large subunit and the electrons are shuttled through the [Fe-S] clusters in the small subunit to the cytochrome b-like protein. [14] The MBH is located on the outer cytoplasmic membrane. It recovers energy for the cell by funneling electrons into the respiratory chain and by increasing the proton gradient. [19] The MBH in C. necator is not inhibited by CO and is tolerant to oxygen. [20]
The NAD+-reducing hydrogenase (soluble hydrogenase, SH) creates a NADH-reducing equivalence by oxidizing hydrogen gas. The SH is a heterohexameric protein [21] with two subunits making up the large and small subunits of the [Ni-Fe] hydrogenase and the other two subunits comprising a reductase module similar to the one of Complex I. [22] The [Ni-Fe] active site oxidized hydrogen gas which transfers electrons to a FMN-a cofactor, then to a [Fe-S] cluster relay of the small hydrogenase subunit and the reductase module, then to another FMN-b cofactor and finally to NAD+. [14] The reducing equivalences are then used for fixing carbon dioxide when C. necator is growing autotrophically.
The active site of the SH of C. necator H16 has been extensively studied because C. necator H16 can be produced in large amounts, can be genetically manipulated, and can be analyzed with spectrographic techniques. However, no crystal structure is currently available for the C. necator H16 soluble hydrogenase in the presence of oxygen to determine the interactions of the active site with the rest of the protein. [14]
The [Ni-Fe] hydrogenase from Desulfovibrio vulgaris and D. gigas have similar protein structures to each other and represent typical [Ni-Fe] hydrogenases. [14] [23] [24] [25] The large subunit contains the [Ni-Fe] active site buried deep in the core of the protein and the small subunit contains [Fe-S] clusters. The Ni atom is coordinated to the Desulfovibrio hydrogenase by 4 cysteine ligands. Two of these same cysteine ligands also bridge the Fe of the [Ni-Fe] active site. [23] [24] The Fe atom also contains three ligands, one CO and two CN that complete the active site. [26] These additional ligands might contribute to the reactivity or help stabilize the Fe atom in the low spin +2 oxidation state. [23] Typical [NiFe] hydrogenases like those of D. vulgaris and D. gigas are poisoned by oxygen because an oxygen atom binds strongly to the NiFe active site. [20]
The SH in C. necator are unique for other organisms because it is oxygen tolerant. [27] The active site of the SH has been studied to learn why this protein is tolerant to oxygen. A recent study showed that oxygen tolerance as implemented in the SH is based on a continuous catalytically driven detoxification of O2 [Ref missing]. The genes encoding this SH can be up-regulated under heterotrophic growth condition using glycerol in the growth media [28] and this enables aerobic production and purification of the same enzyme. [29]
The oxygen-tolerant hydrogenases of C. necator have been studied for diverse purposes. C. necator was studied as an attractive organism to help support life in space. It can fix carbon dioxide as a carbon source, use the urea in urine as a nitrogen source, and use hydrogen as an energy source to create dense cultures that could be used as a source of protein. [30] [31]
Electrolysis of water is one way of creating oxygenic atmosphere in space and C. necator was investigated to recycle the hydrogen produced during this process. [32]
Oxygen-tolerant hydrogenases are being used to investigate biofuels. Hydrogenases from C. necator have been used to coat electrode surfaces to create hydrogen fuel cells tolerant to oxygen and carbon monoxide [20] and to design hydrogen-producing light complexes. [33] In addition, the hydrogenases from C. necator have been used to create hydrogen sensors. [34] Genetically modified C. necator can produce isobutanol from CO
2 that can directly substitute or blend with gasoline. The organism emits the isobutanol without having to be destroyed to obtain it. [35]
Researchers at UCLA have genetically modified a strain of the species C. necator (formerly known as R. eutropha H16) to produce isobutanol from CO2 feedstock using electricity produced by a solar cell. The project, funded by the U.S. Dept. of Energy, is a potential high energy-density electrofuel that could use existing infrastructure to replace oil as a transportation fuel. [36]
Chemical and biomolecular engineers at Korea Advanced Institute of Science and Technology has presented a scalable way to convert CO2 in the air into a polyester by means of the C. necator. [37]
Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.
A hydrogenase is an enzyme that catalyses the reversible oxidation of molecular hydrogen (H2), as shown below:
Aquifex is a bacterial genus, belonging to phylum Aquificota. There is one species of Aquifex with a validly published name – A. pyrophilus – but "A. aeolicus" is sometimes considered as species though it has no standing as a name given it has not been validly or effectively published. Aquifex spp. are extreme thermophiles, growing best at temperature of 85 °C to 95 °C. They are members of the Bacteria as opposed to the other inhabitants of extreme environments, the Archaea.
Rieske proteins are iron–sulfur protein (ISP) components of cytochrome bc1 complexes and cytochrome b6f complexes and are responsible for electron transfer in some biological systems. John S. Rieske and co-workers first discovered the protein and in 1964 isolated an acetylated form of the bovine mitochondrial protein. In 1979 Trumpower's lab isolated the "oxidation factor" from bovine mitochondria and showed it was a reconstitutively-active form of the Rieske iron-sulfur protein
It is a unique [2Fe-2S] cluster in that one of the two Fe atoms is coordinated by two histidine residues rather than two cysteine residues. They have since been found in plants, animals, and bacteria with widely ranging electron reduction potentials from -150 to +400 mV.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
Biohydrogen is H2 that is produced biologically. Interest is high in this technology because H2 is a clean fuel and can be readily produced from certain kinds of biomass, including biological waste. Furthermore some photosynthetic microorganisms are capable to produce H2 directly from water splitting using light as energy source.
Hydrogen-oxidizing bacteria are a group of facultative autotrophs that can use hydrogen as an electron donor. They can be divided into aerobes and anaerobes. The former use hydrogen as an electron donor and oxygen as an acceptor while the latter use sulphate or nitrogen dioxide as electron acceptors. Species of both types have been isolated from a variety of environments, including fresh waters, sediments, soils, activated sludge, hot springs, hydrothermal vents and percolating water.
A hydrogenase mimic or bio-mimetic is an enzyme mimic of hydrogenases.
In enzymology, ferredoxin hydrogenase, also referred to as [Fe-Fe]hydrogenase, H2 oxidizing hydrogenase, H2 producing hydrogenase, bidirectional hydrogenase, hydrogenase (ferredoxin), hydrogenlyase, and uptake hydrogenase, is found in Clostridium pasteurianum, Clostridium acetobutylicum,Chlamydomonas reinhardtii, and other organisms. The systematic name of this enzyme is hydrogen:ferredoxin oxidoreductase
In enzymology, a hydrogen:quinone oxidoreductase (EC 1.12.5.1) is an enzyme that catalyzes the chemical reaction
An enzymatic biofuel cell is a specific type of fuel cell that uses enzymes as a catalyst to oxidize its fuel, rather than precious metals. Enzymatic biofuel cells, while currently confined to research facilities, are widely prized for the promise they hold in terms of their relatively inexpensive components and fuels, as well as a potential power source for bionic implants.
Cupriavidus metallidurans is a non-spore-forming, Gram-negative bacterium which is adapted to survive several forms of heavy metal stress.
Iron–nickel (Fe–Ni) clusters are metal clusters consisting of iron and nickel, i.e. Fe–Ni structures displaying polyhedral frameworks held together by two or more metal–metal bonds per metal atom, where the metal atoms are located at the vertices of closed, triangulated polyhedra.
Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium and those lacking nickel.
In molecular biology, the hydrogenase maturation protease family is a family of aspartic endopeptidases belonging to MEROPS family A31.
[NiFe] hydrogenase is a type of hydrogenase, which is an oxidative enzyme that reversibly converts molecular hydrogen in prokaryotes including Bacteria and Archaea. The catalytic site on the enzyme provides simple hydrogen-metabolizing microorganisms a redox mechanism by which to store and utilize energy via the reaction
Cupriavidus gilardii is a Gram-negative, aerobic, motile, oxidase-positive bacterium from the genus Cupriavidus and the family Burkholderiaceae. It is motil by a single polar flagellum. It is named after G. L. Gilardi, an American microbiologist. The organism was initially identified as Ralstonia gilardii in 1999, renamed Wautersiella gilardii, and most recently moved into the genus Cupriavidus after 16S rRNA gene sequencing revealed it to be most closely related to Cupriavidus necator. Notably, species of this genus are not inhibited by copper due to the production of chelation factors, and may actually be stimulated by the presence of copper.
The 4-Toluene Sulfonate Uptake Permease (TSUP) family is also referred to as the TauE/SafE/YfcA/DUF81 Family.
Wolfgang Lubitz is a German chemist and biophysicist. He is currently a director emeritus at the Max Planck Institute for Chemical Energy Conversion. He is well known for his work on bacterial photosynthetic reaction centres, hydrogenase enzymes, and the oxygen-evolving complex using a variety of biophysical techniques. He has been recognized by a Festschrift for his contributions to electron paramagnetic resonance (EPR) and its applications to chemical and biological systems.
ChoKyun Rha was a Korean-born American food technologist, inventor, and professor of biomaterials science and engineering at the Massachusetts Institute of Technology (MIT). She was the first Asian woman awarded tenure at MIT.
