The ''nif'' genes are

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s encoding enzymes involved in the fixation of atmospheric nitrogen into a form of

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...

available to living organisms. The primary enzyme encoded by the ''nif'' genes is the

nitrogenase Nitrogenases are enzymes () that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the Organic redox reaction, reduction of nitrogen (N2) to ammonia (NH3). Nitrog ...

complex which is in charge of converting atmospheric nitrogen (N₂) to other nitrogen forms such as

ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...

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 Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...

(nif) and for nodulation (nod) were cloned in the early 1980s by

Gary Ruvkun Gary Bruce Ruvkun (born March 1952, Berkeley, California) is an American molecular biologist at Massachusetts General Hospital and professor of genetics at Harvard Medical School in Boston. Ruvkun discovered the mechanism by which ''lin-4'', th ...

and

Sharon R. Long Sharon Rugel Long (born March 2, 1951) is an American plant biologist. She is the Steere-Pfizer Professor of Biological Science in the Department of Biology at Stanford University, and the Principal Investigator of the Long Laboratory at Stanford. ...

in Frederick M. Ausubel's laboratory.

Regulation

In most bacteria, regulation of ''nif'' genes transcription is done by the nitrogen sensitive NifA protein. When there isn't enough fixed nitrogen available for the organism's use, NtrC triggers NifA expression, and NifA activates the rest of the ''nif'' genes. If there is a sufficient amount of reduced nitrogen or oxygen is present, another protein is activated: NifL. NifL inhibits NifA activity resulting in the inhibition of nitrogenase formation. NifL is regulated by the products of ''glnD'' and ''glnK''. The ''nif'' genes can be found on bacterial

chromosomes A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...

, but in symbiotic bacteria they are often found on

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

s or symbiosis islands with other genes related to nitrogen fixation (such as the ''nod'' genes).

Examples in nature

The expression and regulation of ''nif'' genes, while sharing common features in all or most of the nitrogen-fixing organisms in nature, have distinct characters and qualities that differ from one diazotroph to another. Examples of ''nif'' gene structure and regulation in different diazotrophs include: ''

Klebsiella pneumoniae ''Klebsiella pneumoniae'' is a Gram-negative, non-motile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. It appears as a mucoid lactose fermenter on MacConkey agar. Although found in the normal flora of the mouth ...

''—a free-living anaerobic nitrogen-fixing bacterium. It contains a total of 20 ''nif'' genes located on the chromosome in a 24-Kb region. ''nifH'', ''nifD'', and ''nifK'' encode the nitrogenase subunits, while ''nifE'', ''nifN'', ''nifU'', ''nifS'', ''nifV'', ''nifW'', ''nifX'', ''nifB'', and ''nifQ'' encode proteins involved the assembly and incorporation of

iron Iron () is a chemical element with symbol Fe (from la, ferrum) and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, right in f ...

and

molybdenum Molybdenum is a chemical element with the symbol Mo and atomic number 42 which is located in period 5 and group 6. The name is from Neo-Latin ''molybdaenum'', which is based on Ancient Greek ', meaning lead, since its ores were confused with lea ...

atoms into the nitrogenase subunits. ''nifF'' and ''nifJ'' encode proteins related to electron transfer taking place in the reduction process and ''nifA'' and ''nifL'' are regulatory proteins in charge of regulating the expression of the other ''nif'' genes. Iwo Watanabe, "Biological Nitrogen Fixation and its Use in Agriculture (outline)"
/ref> ''

Rhodospirillum rubrum ''Rhodospirillum rubrum'' (''R. rubrum'') is a Gram-negative, pink-coloured bacterium, with a size of 800 to 1000 nanometers. It is a facultative anaerobe, thus capable of using oxygen for aerobic respiration under aerobic conditions, or an alte ...

''—a free-living anaerobic photosynthetic bacterium which, in addition to the transcriptional controls described above, regulates expression of the ''nif'' genes also in a metabolic way through a reversible

ADP-ribosylation ADP-ribosylation is the addition of one or more ADP-ribose moieties to a protein. It is a reversible post-translational modification that is involved in many cellular processes, including cell signaling, DNA repair, gene regulation and apoptosis. ...

of a specific

arginine Arginine is the amino acid with the formula (H2N)(HN)CN(H)(CH2)3CH(NH2)CO2H. The molecule features a guanidino group appended to a standard amino acid framework. At physiological pH, the carboxylic acid is deprotonated (−CO2−) and both the am ...

residue in the nitrogenase complex. The ribosylation takes place when reduced nitrogen is present and it causes a barrier in the electron transfer flow and thereby inactivates nitrogenase activity. The enzymes catalyzing the ribosylation are called DraG and DraT.Merrick MJ, Edwards RA (1995). Nitrogen control in bacteria. Microbiol Review 59(4):604-22 ''

Rhodobacter capsulatus ''Rhodobacter capsulatus'' is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus" ("with a chest", "encapsulated"), itself derived Latin noun " ...

''—a free-living anaerobic phototroph containing a transcriptional ''nif'' gene regulatory system. ''R. capsulatus'' regulates ''nif'' gene expression through ''nifA'' in the same manner described before, but it uses a different ''nifA'' activator which initiates the NtrC. NtrC activates a different expression of ''nifA'' and the other ''nif'' genes. ''

Rhizobium ''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants. The bacteria colonize plant cells ...

'' spp.—Gram-negative, symbiotic nitrogen fixing bacteria that usually form a symbiotic relationship with

legume A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock f ...

species. In some rhizobia, the ''nif'' genes are located on plasmids called 'sym plasmids' (sym = symbiosis) which contain genes related to nitrogen fixation and metabolism, while the chromosomes contain most of the housekeeping genes of the bacteria. Regulation of the ''nif'' genes is at the transcriptional level and is dependent on colonization of the plant host.

References

{{Reflist

External links

''nif'' gene—definition from Biology-Online.org
Prokaryote genes Molecular biology

Regulation

Examples in nature

See also

References

External links