FnrS RNA is a family of
Hfq
The Hfq protein (also known as HF-I protein) encoded by the ''hfq'' gene was discovered in 1968 as an ''Escherichia coli'' host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RN ...
-binding small
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
whose
expression is upregulated in response to
anaerobic conditions. It is named FnrS because its expression is strongly dependent on
fumarate
Fumaric acid is an organic compound with the formula HO2CCH=CHCO2H. A white solid, fumaric acid occurs widely in nature. It has a fruit-like taste and has been used as a food additive. Its E number is E297.
The salts and esters are known as f ...
and
nitrate reductase
Nitrate reductases are molybdoenzymes that reduce nitrate (NO) to nitrite (NO). This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.
Types
Euka ...
regulator (FNR), a direct
oxygen
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as wel ...
availability sensor.
A conserved intergenic region between genes ''ydaN'' and ''dbpA'' was predicted to encode an sRNA, adjacent to where another
non-coding RNA (
C0343) has been identified. However,
northern blot
The northern blot, or RNA blot,Gilbert, S. F. (2000) Developmental Biology, 6th Ed. Sunderland MA, Sinauer Associates. is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.K ...
analysis of this 477
bp sequence yielded no results. A subsequent
tiling array analysis sequencing Hfq-binding sRNA found that the Watson strand did indeed encode an sRNA.
Gene regulation
FnrS has been shown to downregulate 32 different
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
s in ''
Enterobacteria
Enterobacteriaceae is a large family of Gram-negative bacteria. It was first proposed by Rahn in 1936, and now includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but on ...
'', in 15 of these cases it does so by
base-pairing
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
with the mRNA
transcript.
The majority of genes downregulated by FnrS are required for
aerobic metabolism
Cellular respiration is the process by which biological fuels are oxidised in the presence of an inorganic electron acceptor such as oxygen to produce large amounts of energy, to drive the bulk production of ATP. Cellular respiration may be des ...
or the
oxidative stress response.
Some of the genes downregulated by FnrS are:
*''adhP'' - an
alcohol dehydrogenase involved in metabolism
*''cydD'' - zinc sensitive
ATP
ATP may refer to:
Companies and organizations
* Association of Tennis Professionals, men's professional tennis governing body
* American Technical Publishers, employee-owned publishing company
* ', a Danish pension
* Armenia Tree Project, non ...
-binding component of
cytochrome
Cytochromes are redox-active proteins containing a heme, with a central Fe atom at its core, as a cofactor. They are involved in electron transport chain and redox catalysis. They are classified according to the type of heme and its mode of bin ...
-related transport
*''mqo'' - membrane associated malate:quinone oxidoreductase which operates in the
citric acid cycle
The citric acid cycle (CAC)—also known as the Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of chemical reactions to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins ...
*''sodB/A'' - a superoxide dismutase which aids with oxygen stress resistance
*''ygiW'' - a hypothetical
outer membrane protein
A study incorporating comparative target prediction and subsequent experimental verification of selected predictions, suggests that FnrS might be a more global regulator in ''
Escherichia coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
''. It is predicted to control several transcription factors. These include the verified targets ''marA'' and ''IscR''.
MarA activates genes involved in the resistance to superoxide,
which might not be necessary at the anaerobic conditions where FnrS is expressed. IscR regulates genes for iron-sulfur-cluster containing or biogenesis proteins.
FnrS might be involved in the observed O
2 dependent expression of the IscR regulon.
Further targets of FnrS are ''nagZ'' and ''sdhA''.
There is also evidence to suggest that the expression of FnrS is regulated by the RcsCDB signalling system in ''
Salmonella enterica
''Salmonella enterica'' (formerly ''Salmonella choleraesuis'') is a rod-headed, flagellate, facultative anaerobic, Gram-negative bacterium and a species of the genus '' Salmonella''. A number of its serovars are serious human pathogens.
Epidem ...
''.
References
Further reading
*
*
External links
* {{Rfam, id=RF01796, name=Fumarate/nitrate reductase regulator sRNA
Non-coding RNA