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Nif genes

 

The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. They are found in nitrogen-fixing bacteria. 

They occur as an operon (a segment of DNA containing adjacent genes including structural genes, an operator gene and a regulatory gene; thus a functional unit of transcription and genetic regulation) in free-living anaerobic nitrogen-fixing bacteria such as Klebsiella pneumoniae, Rhodospirillum rubrum, and Rhodobacter capsulatus. These genes may also be found on plasmids in symbiotic bacteria, such as in Rhizobium inhabiting the roots of leguminous plants. 

Functions

nif genes encode an important enzyme, nitrogenase complex which is in charge of converting atmospheric nitrogen (N2 ) to usable form of nitrogen such as ammonia. Nitrogen fixation is important because many living organisms are unable to metabolize directly the atmospheric nitrogen and would require the nitrogen fixation capability of certain bacteria in order to produce a form of nitrogen that can be readily utilized.  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.


Nif gene

Product of nif gene and proposed function

J

Pyruvate oxidoreductase; generates electrons from pyruvate to reduce flavodoxin

H

Fe-protein subunit; required for active Fe protein and FeMo-cofactor biosynthesis

D

MoFe protein α-subunit; required for active MoFe protein

K

MoFe protein β-subunit; required for active MoFe protein

T,Y

Unknown

E,N

Two polypeptides that combine to form a template for FeMo-cofactor biosynthesis

X

A protein involved in FeMo-cofactor biosynthesis

U

A protein that likely supplies Fe for cluster biosynthesis

S

Cysteine desulfurase; supplies sulfur for cluster biosynthesis

V

Homocitrate synthase; makes homocitrate required for FeMo-cofactor

W,Z

Uncertain; but may be involved in FeMo-cofactor biosynthesis or insertion

M

Peptidyl prolyl isomerase; activates Fe protein

F

Flavodoxin; reduces the Fe protein

L

Negative regulatory protein; responds to O2, fixed-N and energy status

A

Positive regulator protein; activates transcription at nif promoters

B

NifB-cofactor; a FeMo-cofactor precursor

Q

A protein involved in Mo uptake for FeMo-cofactor biosynthesis

Regulation of nif genes

· 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 inhibits NifA activity resulting in the inhibition of nitrogenase formation. 

· In Klebsiella pneumoniae (Figure), nif genes are organized into a regulon of 17 genes consisting of seven or eight operons each of which is transcribed into a single, usually polycistronic mRNA. 

· Regulation of nif gene expression has two elements: an external system designated ntr (nitrogen regulatory) and an internal system mediated by nif A and nif L. 

· The ntr system responds to conditions of nitrogen starvation by activating genes that enable the organism to utilize ‘unusual’ nitrogen sources such as arginine, proline, and histidine as well as N2 itself. 

· The ntr A gene product (NtrA) is a-factor of RNA polymerase which recognize the nif and, other ntr – regulated genes. 

· These promoters have a structure different from that of typical bacterial promoters. 

· NtrA allows RNA polymerase to bind at the nif promoters and to initiate transcription. 

· The ntrB gene product (NtrB) is an enzyme that functions both as a protein kinase and as a phosphatase, the substrate of which is NtrC (the ntrC gene product). 

· Whether kinase or phosphatase activity predominates depends upon the nitrogen status of bacterium, and the consequence of this is that, under condition of starvation, NtrC-P acts as an activator of, nifL and nif A. 

·  The nif A product is an activator of transcription of other nif genes, whilst the nif L product, in the presence of either intermediate concentrations of fixed nitrogen or inactivate the nif A product, thereby preventing transcription of other nif genes.

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