Fis

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DNA-binding protein Fis
FisK36Ehomodimerstructure.jpg
Fis K36E homodimer structure
Identifiers
Organism E. coli
Symbolfis
UniProt P0A6R3
Search for
Structures Swiss-model
Domains InterPro

fis is an E. coli gene encoding the Fis (or FIS) protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.

Contents

History

Fis was first discovered for its role in stimulating Gin catalyzed inversion of the G segment of phage Mu genome. [1] Fis was originally identified as the factor for inversion stimulation of the homologous Hin and Gin site-specific DNA recombinases of Salmonella and phage Mu, respectively. This small, basic, DNA-bending protein has recently been shown to function in many other reactions including phage lambda site-specific recombination, transcriptional activation of rRNA and tRNA operons, repression of its own synthesis, and oriC-directed DNA replication. Cellular concentrations of Fis vary tremendously under different growth conditions which may have important regulatory implications for the physiological role of Fis in these different reactions. [2]

Structure

Fis protein structure Fisproteinstructure.gif
Fis protein structure

Structurally, Fis folds into four α-helices (A–D) and a β-hairpin. Helices A and B provide the contacts between Fis monomers, facilitating dimer formation, whereas the C and D helices form a helix-turn-helix motif that is essential for DNA binding. [3]

Properties and functions

Fis is a very important small nucleotide-associated protein which plays a role in affecting the bacterial chromosome structure and the initiation of DNA replication. [4] It is a nucleoid-associated protein in Escherichia coli that is abundant during early exponential growth in rich medium but is in short supply during stationary phase. [5] When stationary-phase cells are subcultured into a rich medium, Fis levels increase from less than 100 to over 50,000 copies per cell prior to the first cell division. As cells enter exponential growth, nascent synthesis is largely shut off, and intracellular Fis levels decrease as a function of cell division. Fis synthesis also transiently increases when exponentially growing cells are shifted to a richer medium. The magnitude of the peak of Fis synthesis appears to reflect the extent of the nutritional upshift. fis mRNA levels closely resemble the protein expression pattern, suggesting that regulation occurs largely at the transcriptional level. Two RNA polymerase-binding sites and at least six high-affinity Fis-binding sites are present in the fis promoter region. Expression of this fis operon is negatively regulated by Fis in vivo and purified Fis can prevent stable complex formation by RNA polymerase at the fis promoter in vitro. However, autoregulation only partially accounts for the expression pattern of Fis. Fluctuations in Fis levels have been shown to serve as an early signal of a nutritional upshift and is important in the physiological roles Fis plays in the cell. [6]

Fis regulation Fisregulation.jpg
Fis regulation
DNA negative supercoiling Dnanegativesupercoiling.jpg
DNA negative supercoiling

It is a global regulatory protein in Escherichia coli that activates ribosomal RNA (rRNA) transcription by binding to three upstream activation sites of the rRNA promoter and enhances transcription 5 to 10 fold in vivo. Fis overexpression results in different effects on cell growth depending on nutrient conditions. [7] The Fis nucleoid protein is differentiated by its fast increase in synthesis rates following nutrient upshifts and its abundance in rapidly growing E. coli cells. [8]

Fis has been known to activate ribosomal RNA transcription, as well other genes. It has a direct role in upstream activation of rRNA promoters. Fis binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. It has also been shown to prevent initiation of DNA replication from oriC. [9]

It has been shown that sequences from 32 to 94 nucleotides upstream of the fis AUG are responsible for increasing fis lacZ translation reporter activities over 100 fold. Within this region, an AU sequence element centered 35 nucleotides upstream of the fis AUG increases fis translation by as much as 15 fold. Formation of a supposed RNA secondary structure element beginning 50 nucleotides upstream of the AUG also positively affects fis translation by up to 10 fold. The fis gene is cotranscribed with the upstream dusB gene encoding a tRNA-modifying enzyme. DusB protein levels are very low even under conditions when there is high transcription of the operon and high levels of Fis protein. [10]

Fis has been deemed a bacterial chromatin architectural protein. [11] Besides modulating chromatin architecture, it is known to influence numerous promoters of E. coli and several other bacteria. Both in vivo and in vitro studies indicate that Fis acts as a transcriptional repressor of ''mom'' promoter. There is data that shows Fis mediates its repressive effect by denying access to RNA polymerase at the mom promoter. combined A repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. In addition to bringing about overall downregulation of the Mu genome, it also ensures silencing of the advantageous but potentially lethal mom gene. [12]

Fis as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial species such as P. multocida, Enteroaggregative Escherichia coli, [13] similar organisms. Some of these genes include important virulence factors. [14]

Role of Fis in bacterial motility

The role of fis is well studied in E. coli, but its role in pseudomonads has only been examined briefly. Recent studies in Enterobacteriaceae have shown that fis positively regulates the flagellar movement of bacteria. Observations in Pseudomonas putida demonstrate fis reduced the migration of P. putida onto the apices of barley roots and thereby the competitiveness of bacteria on the roots. It was also observed that the overexpression of fis drastically reducing swimming motility and facilitated the formation of P. putida biofilm. It is possible that the elevated expression of Fis is important in the adaptation of P. putida during colonization of plant roots by promoting biofilm formation when the migration of bacteria is no longer advantageous. [15]

It was demonstrated that Fis is essential for the stability of the linear plasmid pDSIUDi and affects the motility of S. Typhi. [16]

Fis buffers decrease of negative supercoiling in tyrT and rrnA expression. The upstream FIS binding site of rrnA is required for this and it's probable that FIS enables local DNA curvature. See Travers and Muskhelishvili 2005 for more detail.

Related Research Articles

<span class="mw-page-title-main">Lambda phage</span> Bacteriophage that infects Escherichia coli

Enterobacteria phage λ is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

<span class="mw-page-title-main">Promoter (genetics)</span> Region of DNA encouraging transcription

In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.

In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology.

<span class="mw-page-title-main">DnaA</span> Protein

DnaA is a protein that activates initiation of DNA replication in bacteria. Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. It is a replication initiation factor which promotes the unwinding of DNA at oriC. The DnaA proteins found in all bacteria engage with the DnaA boxes to start chromosomal replication. The onset of the initiation phase of DNA replication is determined by the concentration of DnaA. DnaA accumulates during growth and then triggers the initiation of replication. Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to loop in preparation for melting open by the helicase DnaB.

A transcriptional activator is a protein that increases transcription of a gene or set of genes. Activators are considered to have positive control over gene expression, as they function to promote gene transcription and, in some cases, are required for the transcription of genes to occur. Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements. The DNA site bound by the activator is referred to as an "activator-binding site". The part of the activator that makes protein–protein interactions with the general transcription machinery is referred to as an "activating region" or "activation domain".

<span class="mw-page-title-main">Nucleoid</span> Region within a prokaryotic cell containing genetic material

The nucleoid is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies and a cell may contain multiple copies of it.

<span class="mw-page-title-main">Silencer (genetics)</span> Type of DNA sequence

In genetics, a silencer is a DNA sequence capable of binding transcription regulation factors, called repressors. DNA contains genes and provides the template to produce messenger RNA (mRNA). That mRNA is then translated into proteins. When a repressor protein binds to the silencer region of DNA, RNA polymerase is prevented from transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA into proteins is impossible. Thus, silencers prevent genes from being expressed as proteins.

<i>trp</i> operon Operon that codes for the components for production of tryptophan

The trp operon is a group of genes that are transcribed together, encoding the enzymes that produce the amino acid tryptophan in bacteria. The trp operon was first characterized in Escherichia coli, and it has since been discovered in many other bacteria. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are repressed.

The gene rpoS encodes the sigma factor sigma-38, a 37.8 kD protein in Escherichia coli. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. rpoS is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The rpoS gene most likely originated in the gammaproteobacteria.

The L-arabinose operon, also called the ara or araBAD operon, is an operon required for the breakdown of the five-carbon sugar L-arabinose in Escherichia coli. The L-arabinose operon contains three structural genes: araB, araA, araD, which encode for three metabolic enzymes that are required for the metabolism of L-arabinose. AraB (ribulokinase), AraA, and AraD produced by these genes catalyse conversion of L-arabinose to an intermediate of the pentose phosphate pathway, D-xylulose-5-phosphate.

cAMP receptor protein Regulatory protein in bacteria

cAMP receptor protein is a regulatory protein in bacteria.

<span class="mw-page-title-main">GcvB RNA</span>

The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. A deletion of GcvB RNA from Y. pestis changed colony shape as well as reducing growth. It has been shown by gene deletion that GcvB is a regulator of acid resistance in E. coli. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. A polymeric form of GcvB has recently been identified. Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of its target genes.

In biology, phase variation is a method for dealing with rapidly varying environments without requiring random mutation. It involves the variation of protein expression, frequently in an on-off fashion, within different parts of a bacterial population. As such the phenotype can switch at frequencies that are much higher than classical mutation rates. Phase variation contributes to virulence by generating heterogeneity. Although it has been most commonly studied in the context of immune evasion, it is observed in many other areas as well and is employed by various types of bacteria, including Salmonella species.

The gal operon is a prokaryotic operon, which encodes enzymes necessary for galactose metabolism. Repression of gene expression for this operon works via binding of repressor molecules to two operators. These repressors dimerize, creating a loop in the DNA. The loop as well as hindrance from the external operator prevent RNA polymerase from binding to the promoter, and thus prevent transcription. Additionally, since the metabolism of galactose in the cell is involved in both anabolic and catabolic pathways, a novel regulatory system using two promoters for differential repression has been identified and characterized within the context of the gal operon.

<span class="mw-page-title-main">Bacterial DNA binding protein</span>

In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. They are commonly referred to as histone-like and have many similar traits with the eukaryotic histone proteins. Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of bacteria and archaea, and are also encoded in the chloroplast genome of some algae. The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R.

The fnr gene of Escherichia coli encodes a transcriptional activator (FNR) which is required for the expression of a number of genes involved in anaerobic respiratory pathways. The FNR protein of E. coli is an oxygen – responsive transcriptional regulator required for the switch from aerobic to anaerobic metabolism.

"Type III mutants, originally frdB, were designated fnr because they were defective in fumarate and nitrate reduction and impaired in their ability to produce gas." - Lambden and Guest, 1976 Journal of General Microbiology97, 145-160

The gua operon is responsible for regulating the synthesis of guanosine mono phosphate (GMP), a purine nucleotide, from inosine monophosphate. It consists of two structural genes guaB (encodes for IMP dehydrogenase or and guaA apart from the promoter and operator region.

The gene rpoN encodes the sigma factor sigma-54, a protein in Escherichia coli and other species of bacteria. RpoN antagonizes RpoS sigma factors.

The locus of enterocyte effacement-encoded regulator (Ler) is a regulatory protein that controls bacterial pathogenicity of enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic Escherichia coli (EHEC). More specifically, Ler regulates the locus of enterocyte effacement (LEE) pathogenicity island genes, which are responsible for creating intestinal attachment and effacing lesions and subsequent diarrhea: LEE1, LEE2, and LEE3. LEE1, 2, and 3 carry the information necessary for a type III secretion system. The transcript encoding the Ler protein is the open reading frame 1 on the LEE1 operon.

References

  1. ↑ Koch C, Kahmann R (November 1986). "Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu". The Journal of Biological Chemistry. 261 (33): 15673–15678. doi: 10.1016/S0021-9258(18)66770-5 . PMID   3536909.
  2. ↑ Finkel SE, Johnson RC (November 1992). "The Fis protein: it's not just for DNA inversion anymore". Molecular Microbiology. 6 (22): 3257–65. doi:10.1111/j.1365-2958.1992.tb02193.x. PMID   1484481. S2CID   43009781.
  3. ↑ Steen JA, Steen JA, Harrison P, Seemann T, Wilkie I, Harper M, et al. (February 2010). "Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors". PLOS Pathogens. 6 (2): e1000750. doi: 10.1371/journal.ppat.1000750 . PMC   2816674 . PMID   20140235.
  4. ↑ Wold S, Crooke E, Skarstad K (September 1996). "The Escherichia coli Fis protein prevents initiation of DNA replication from oriC in vitro". Nucleic Acids Research. 24 (18): 3527–3532. doi: 10.1093/nar/24.18.3527 . PMC   146119 . PMID   8836178.
  5. ↑ Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (September 2007). "Effects of Fis on Escherichia coli gene expression during different growth stages". Microbiology. 153 (Pt 9): 2922–2940. doi: 10.1099/mic.0.2007/008565-0 . PMID   17768236.
  6. ↑ Ball CA, Osuna R, Ferguson KC, Johnson RC (December 1992). "Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli". Journal of Bacteriology. 174 (24): 8043–8056. doi: 10.1128/jb.174.24.8043-8056.1992 . PMC   207543 . PMID   1459953.
  7. ↑ Choe LH, Chen W, Lee KH (1999). "Proteome analysis of factor for inversion stimulation (Fis) overproduction in Escherichia coli". Electrophoresis. 20 (4–5): 798–805. doi:10.1002/(SICI)1522-2683(19990101)20:4/5<798::AID-ELPS798>3.0.CO;2-F. PMID   10344250. S2CID   96418560.
  8. ↑ Nafissi M, Chau J, Xu J, Johnson RC (May 2012). "Robust translation of the nucleoid protein Fis requires a remote upstream AU element and is enhanced by RNA secondary structure". Journal of Bacteriology. 194 (10): 2458–2469. doi: 10.1128/jb.00053-12 . PMC   3347164 . PMID   22389479.
  9. ↑ Ross W, Thompson JF, Newlands JT, Gourse RL (November 1990). "E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo". The EMBO Journal. 9 (11): 3733–3742. doi:10.1002/j.1460-2075.1990.tb07586.x. PMC   552129 . PMID   2209559.
  10. ↑ Nafissi M, Chau J, Xu J, Johnson RC (May 2012). "Robust translation of the nucleoid protein Fis requires a remote upstream AU element and is enhanced by RNA secondary structure". Journal of Bacteriology. 194 (10): 2458–2469. doi: 10.1128/jb.00053-12 . PMC   3347164 . PMID   22389479.
  11. ↑ Travers A, Schneider R, Muskhelishvili G (February 2001). "DNA supercoiling and transcription in Escherichia coli: The FIS connection". Biochimie. 83 (2): 213–217. doi:10.1016/S0300-9084(00)01217-7. PMID   11278071.
  12. ↑ Karambelkar S, Swapna G, Nagaraja V (May 2012). "Silencing of toxic gene expression by Fis". Nucleic Acids Research. 40 (10): 4358–4367. doi: 10.1093/nar/gks037 . PMC   3378877 . PMID   22287621.
  13. ↑ Rossiter AE, Browning DF, Leyton DL, Johnson MD, Godfrey RE, Wardius CA, et al. (July 2011). "Transcription of the plasmid-encoded toxin gene from enteroaggregative Escherichia coli is regulated by a novel co-activation mechanism involving CRP and Fis". Molecular Microbiology. 81 (1): 179–191. doi: 10.1111/j.1365-2958.2011.07685.x . PMID   21542864. S2CID   205369787.
  14. ↑ Steen JA, Steen JA, Harrison P, Seemann T, Wilkie I, Harper M, et al. (February 2010). "Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors". PLOS Pathogens. 6 (2): e1000750. doi: 10.1371/journal.ppat.1000750 . PMC   2816674 . PMID   20140235.
  15. ↑ Jakovleva J, Teppo A, Velts A, Saumaa S, Moor H, Kivisaar M, Teras R (March 2012). "Fis regulates the competitiveness of Pseudomonas putida on barley roots by inducing biofilm formation". Microbiology. 158 (Pt 3): 708–720. doi: 10.1099/mic.0.053355-0 . PMID   22222498.
  16. ↑ Zhang H, Ni B, Zhao X, Dadzie I, Du H, Wang Q, et al. (2012). "Fis is essential for the stability of linear plasmid pBSSB1 and affects the motility of Salmonella enterica serovar Typhi". PLOS ONE. 7 (7): e37462. Bibcode:2012PLoSO...737462Z. doi: 10.1371/journal.pone.0037462 . PMC   3402438 . PMID   22911678.
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