Nif gene

The nif gene is the gene responsible for the coding of proteins related and associated with the fixation of atmospheric nitrogen into a form of nitrogen available to plants. These genes are found in nitrogen fixing bacteria and cyanobacteria.

Nif genes have both positive and negative regulators. Some of nf genes are: Nif A, D, L,K, F,H S,U,Y,W,Z

The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen. 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 plant 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 in 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).

Regulation

In most plants, activation of nif genes transcription is done by the nitrogen sensitive NifA protein. When there isn't enough fixed nitrogen factor for available for the plant's use, NtrC which is a RNApolymerase triggers NifA's expression, and NifA activates the rest of the nif genes transcription. If there is a sufficient amount of reduced nitrogen or oxygen is present, another protein is activated – NifL, and NifL inhibits NifA activity resulting in the inhibition of nitrogenase forming. NifL is regulated by glnD and glnK gene products. The nif genes can be found on bacteria's chromosomes, but a lot of the times they are found on bacteria's plasmids 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 differed from one diazotroph to another. Examples of nif genes structure and regulation in different diazotrophs:

Klebsiella pneumoniae – a free living anaerobic nitrogen fixing bacteria. It contains a total of 20 nif genes located on the bacteria's chromosome in a 24kb region. nifH, nifK and nifD encode the nitrogenase's subunits, while nifE, nifN, nifU, nifS, nifV, nifW, nifX, nifB and nifQ encode proteins involved the assembly and incorporation of the Fe and Mo into the nitrogenase's subunits. nifF and nifJ encode proteins related to electron transfer taking place in the reduction process and nifA is a regulatory protein in-charge of regulating the nif genes expression. Regulation of the nif genes expression is done through nifA and nifL.^[1][2]

Rhodospirillum rubrum – a free living anaerobic photosynthetic bacteria which in addition to the transcriptional control described before, regulates expression of the nif genes also in a metabolic way through a reversible ADP-ribosylation of a specific arginine 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 by so, inactivates nitrogenase's activity. The enzymes catalyzing the ribosylation are called DRAG and DRAT.^[2][3]

Rhodobacter capsulatus - free living anaerobic phototroph containing a transcriptional nif genes regulatory system. R. capsulatus regulates nif genes expression through nifA in the same manner described before, but it uses a different nifA activator called factor which initiates the RcNtrC. RcNtrC activates a different Expression of nifA and the- nif genes.^[2][3].

Rhizobium spp. - Gram negative, symbiotic nitrogen fixing bacteria. It usually forms symbiotic relationship with Legum species. In some Rhizobia, the nif genes are located on plasmids called the sym plasmids (sym = symbiosis) which contain genes related to nitrogen fixing and some housekeeping genes, while the chromosomes contain most of the housekeeping genes of the bacteria. Regulation of the nif genes expression is done at the transcription level inside the symbiotic plant.^[2][3].

References

• Nif gene - definition from Biology-Online.org

1. ^ [1]
2. ^ ^{a b c d} Iwo Watanabe, "Biological Nitrogen Fixation and its Use in Agriculture (outline)"
3. ^ ^{a b c} Merrick MJ, Edwards RA (1995). Nitrogen control in bacteria. Microbiol Review 59(4):604-22