The Nif regulon is a set of seven operons used to regulate nitrogen fixation in the coliform bacterium Klebsiella pneumoniae under anaerobic and microaerophilic conditions. [1] It includes 17 nif genes, and is situated between the his and the Shi-A operon of the bacterium.
The nif regulon comprises 7 operons: nifRLA, nifJ, nifHDK, nifEN, nifUSVM, nifWF, nifBQ.
nifRLA operon: The tight expression regulation of the nitrogen fixation (nif) genes is mediated by the products of the nifRLA operon. NifA activates transcription of nif genes by the alternative form of RNA polymerase, s54-holoenzyme. NifL is a negative regulatory gene which inhibits the activation of other nif genes by nifA protein. NifR is a repressor binding site, between the promoter of the nifRLA operon and the nifL gene. No protein coded by nifR gene has been found. [2]
nifHDK operon: comprises three structural genes: nifK nifD and nifH. nifK encodes for B-subunit of Component 1 of nitrogenase. nifD encodes for alpha subunit of component 1 of nitrogenase. nifH encodes for component 2 of nitrogenase.
nifEN and nifBQ operons: This comprises nifE, nifN, nifB and nifQ genes which are responsible for formation of a functional Mo-Fe protein. (Mo-Fe-co catalytic site for nitrogenase.) nifQ is not absolutely essential.
nifJ operon:The nifJ gene encodes for the pyruvate-flavodoxin-oxidoreductase protein. This enzyme is involved in electron transfer to nitrogenase.
nifUSVM operon: The nifS, nifV and nifM genes encode for a protein that is required to process component II. Function of the nifU gene is undetermined.
nifWF operon: The function of nifW is undetermined. The nifF gene mediates electron transfer from nifJ protein to Fe protein of nitrogenase. [3]
The Nif regulon is regulated in response to a variety of environmental signals to ensure nitrogen-fixation only occurs when necessary:
The action site of O2 is the nifL protein which is basically a flavoprotein with FAD as the redox sensing cofactor. Fnr (fumarate nitrate reduction regulator) is the signal transduction molecule which transduces the oxygen status to the nifL protein. In the absence of oxygen, the nifL protein is in its reduced form (FADH2 as the cofactor ) and is unable to inhibit the action of nifA protein. In oxygen's presence, oxidized nifL (FAD as the cofactor) inhibits nifA protein and there by turns off all the other operons. [4]
The presence of ammonium ions in large amounts in the environment inhibits the transcription of nitrogenase and all the other nif genes. NH4+ acts as a co-repressor to the glutamine synthetase by modifying it covalently (adenylylation). This modified enzyme binds to the nifR region of the nifRLA operon and prevents the transcription of the genes, nifL and nifA. So, there is no initiation of transcription of the other genes by the σ-RNA polymerase. [4]
In the nitrogen limiting growth conditions, the inhibition of nifA protein by the nifL protein is prevented by the antagonizing action of Glnk protein on the nifL proteins. [2]
A homologue of the NifL-NifA regulatory gene system has not been found among the eukaryotes. However Entamoeba histolytica was found to possess a simplified and non-redundant NIF (nitrogen fixation)-like system for the Fe-S cluster formation, composed of only a catalytic component, NifS, and a scaffold component, NifU. EhNifS and EhNifU were found to be necessary and sufficient for Fe-S clusters of non-nitrogenase Fe-S proteins to form under anaerobic conditions. This is the first demonstration of the presence and biological significance of the NIF-like system in eukaryotes. [2]
Nitrogen fixation is a chemical process by which molecular nitrogen (N
2), which has a strong triple covalent bond, is converted into ammonia (NH
3) or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. The nitrogen in air is molecular dinitrogen, a relatively nonreactive molecule that is metabolically useless to all but a few microorganisms. Biological nitrogen fixation or diazotrophy is an important microbe-mediated process that converts dinitrogen (N2) gas to ammonia (NH3) using the nitrogenase protein complex (Nif).
In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.
Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia.
Nitrogenases are enzymes (EC 1.18.6.1EC 1.19.6.1) that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the reduction of nitrogen (N2) to ammonia (NH3). Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules (nucleotides, amino acids) that create plants, animals and other organisms. They are encoded by the Nif genes or homologs. They are related to protochlorophyllide reductase.
Ferredoxins are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum.
Azotobacter is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime. They are aerobic, free-living soil microbes that play an important role in the nitrogen cycle in nature, binding atmospheric nitrogen, which is inaccessible to plants, and releasing it in the form of ammonium ions into the soil. In addition to being a model organism for studying diazotrophs, it is used by humans for the production of biofertilizers, food additives, and some biopolymers. The first representative of the genus, Azotobacter chroococcum, was discovered and described in 1901 by Dutch microbiologist and botanist Martinus Beijerinck. Azotobacter species are Gram-negative bacteria found in neutral and alkaline soils, in water, and in association with some plants.
Azotobacter vinelandii is Gram-negative diazotroph that can fix nitrogen while grown aerobically. These bacteria are easily cultured and grown.
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.
Amino acid synthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids).
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.
The gal operon is a prokaryotic operon, which encodes enzymes necessary for galactose metabolism. Repression of gene expression for this operon works via binding of repressor molecules to two operators. These repressors dimerize, creating a loop in the DNA. The loop as well as hindrance from the external operator prevent RNA polymerase from binding to the promoter, and thus prevent transcription. Additionally, since the metabolism of galactose in the cell is involved in both anabolic and catabolic pathways, a novel regulatory system using two promoters for differential repression has been identified and characterized within the context of the gal operon.
Vanadium nitrogenase is a key enzyme for nitrogen fixation found in nitrogen-fixing bacteria, and is used as an alternative to molybdenum nitrogenase when molybdenum is unavailable. Vanadium nitrogenases are an important biological use of vanadium, which is uncommonly used by life. An important component of the nitrogen cycle, vanadium nitrogenase converts nitrogen gas to ammonia, thereby making otherwise inaccessible nitrogen available to plants. Unlike molybdenum nitrogenase, vanadium nitrogenase can also reduce carbon monoxide to ethylene, ethane and propane but both enzymes can reduce protons to hydrogen gas and acetylene to ethylene.
CandidatusAtelocyanobacterium thalassa, also referred to as UCYN-A, is a diazotrophic species of cyanobacteria commonly found in measurable quantities throughout the world's oceans and some seas. Members of A. thalassa are spheroid in shape and are 1-2µm in diameter, and provide nitrogen to ocean regions by fixing non biologically available atmospheric nitrogen into biologically available ammonium that other marine microorganisms can use. Unlike many other cyanobacteria, the genome of A. thalassa does not contain genes for RuBisCO, photosystem II, or the TCA cycle. Consequently, A. thalassa lacks the ability to fix carbon via photosynthesis. Some genes specific to the cyanobacteria group are also absent from the A. thalassa genome despite being an evolutionary descendant of this group. With the inability to fix their own carbon, A. thalassa are obligate symbionts that have been found within photosynthetic picoeukaryote algae. Most notably, the UCYN-A2 sublineage has been observed as an endosymbiont in the alga Braarudosphaera bigelowii with a minimum of 1-2 endosymbionts per host. A. thalassa fixes nitrogen for the algae, while the algae provide carbon for A. thalassa through photosynthesis. There are many sublineages of A. thalassa that are distributed across a wide range of marine environments and host organisms. It appears that some sublineages of A. thalassa have a preference for oligotrophic ocean waters while other sublineages prefer coastal waters. Much is still unknown about all of A. thalassa's hosts and host preferences.
RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the organization of the genes in transcription units, operons and regulons. A total of 120 sRNAs with 231 total interactions which all together regulate 192 genes are also included. RegulonDB was founded in 1998 and also contributes data to the EcoCyc database.
The gab operon is responsible for the conversion of γ-aminobutyrate (GABA) to succinate. The gab operon comprises three structural genes – gabD, gabT and gabP – that encode for a succinate semialdehyde dehydrogenase, GABA transaminase and a GABA permease respectively. There is a regulatory gene csiR, downstream of the operon, that codes for a putative transcriptional repressor and is activated when nitrogen is limiting.
John Raymond Postgate, FRS was an English microbiologist and writer, latterly Professor Emeritus of Microbiology at the University of Sussex. Postgate's research in microbiology investigated nitrogen fixation, microbial survival, and sulphate-reducing bacteria. He worked for the Agricultural Research Council's Unit of Nitrogen Fixation from 1963 until he retired, by then its Director, in 1987. In 2011, he was described as a "father figure of British microbiology".
In bacterial genetics, the mal regulon is a regulon - or group of genes under common regulation - associated with the catabolism of maltose and maltodextrins. The system is especially well characterized in the model organism Escherichia coli, where it is classically described as a group of ten genes in multiple operons whose expression is regulated by a single regulatory protein, malT. MalT binds to maltose or maltodextrin and undergoes a conformational change that allows it to bind DNA at sequences near the promoters of genes required for uptake and catabolism of these sugars. The maltose regulation system in E. coli is a classic example of positive regulation. malT is regulated by catabolite repression via the catabolite activator protein. Genes under the control of malT include ATP-binding cassette transporter components, maltoporin, maltose binding protein, and several enzymes. Other Gram-negative bacteria such as Klebsiella pneumoniae have additional genes under the control of malT.
FeMoco (FeMo cofactor) is the primary cofactor of nitrogenase. Nitrogenase is the enzyme that catalyzes the conversion of atmospheric nitrogen molecules N2 into ammonia (NH3) through the process known as nitrogen fixation. Studying FeMoco's role in the reaction mechanism for nitrogen fixation is a potential use case for quantum computers. Even limited quantum computers could enable better simulations of the reaction mechanism. Because it contains iron and molybdenum, the cofactor is called FeMoco. Its stoichiometry is Fe7MoS9C.
Cyanothece is a genus of unicellular, diazotrophic, oxygenic photosynthesizing cyanobacteria.
Crocosphaera watsonii is an isolate of a species of unicellular diazotrophic marine cyanobacteria which represent less than 0.1% of the marine microbial population. They thrive in offshore, open-ocean oligotrophic regions where the waters are warmer than 24 degrees Celsius. Crocosphaera watsonii cell density can exceed 1,000 cells per milliliter within the euphotic zone; however, their growth may be limited by the concentration of phosphorus. Crocosphaera watsonii are able to contribute to the oceanic carbon and nitrogen budgets in tropical oceans due to their size, abundance, and rapid growth rate. Crocosphaera watsonii are unicellular nitrogen fixers that fix atmospheric nitrogen to ammonia during the night and contribute to new nitrogen in the oceans. They are a major source of nitrogen to open-ocean systems. Nitrogen fixation is important in the oceans as it not only allows phytoplankton to continue growing when nitrogen and ammonium are in very low supply but it also replenishes other forms of nitrogen, thus fertilizing the ocean and allowing more phytoplankton growth.