The ''nif'' genes are

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

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

nitrogen Nitrogen is a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...

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 Ammonia is an inorganic chemical compound of nitrogen and hydrogen with the chemical formula, formula . A Binary compounds of hydrogen, stable binary hydride and the simplest pnictogen hydride, ammonia is a colourless gas with a distinctive pu ...

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 dinitrogen () is converted into ammonia (). It occurs both biologically and abiological nitrogen fixation, abiologically in chemical industry, chemical industries. Biological nitrogen ...

(nif) and for nodulation (nod) were cloned in the early 1980s by Gary Ruvkun and Sharon R. Long 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 package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most importa ...

, 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 and ...

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''—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; it has symbol Fe () 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, forming much of Earth's o ...

and

molybdenum Molybdenum is a chemical element; it has Symbol (chemistry), symbol Mo (from Neo-Latin ''molybdaenum'') and atomic number 42. The name derived from Ancient Greek ', meaning lead, since its ores were confused with lead ores. Molybdenum minerals hav ...

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''—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 of a specific

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

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''—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 ce ...

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

legume Legumes are plants in the pea family Fabaceae (or Leguminosae), or the fruit or seeds of such plants. When used as a dry grain for human consumption, the seeds are also called pulses. Legumes are grown agriculturally, primarily for human consum ...

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

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External links

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

Regulation

Examples in nature

See also

References

External links