# Gene transcriptions/Boxes/Furs

Notation: Let Fur stand for ferric uptake regulation.
"The Fur protein [...] acts as a transcriptional repressor of iron-regulated promoters by virtue of its Fe$^{2+}$-dependent DNA binding activity (5, 25, 32, 33)."

## Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans) is a gram-negative, facultative anaerobe, non-motile bacterium that is often found in association with localized aggressive periodontitis, a severe infection of the periodontium, also suspected to be involved in chronic periodontitis.
The species has attracted attention because of its association with localized aggressive periodontitis.
There is a phylogenetic similarity of A. actinomycetemcomitans and Haemophilus aphrophilus, H. paraphrophilus, and H. segnis, which suggests the new genus Aggregatibacter for them.
It is one of the bacteria that might be implicated in destructive periodontal disease, although it has been found more frequently in localized aggressive periodontitis. It has also been isolated from actinomycotic lesions (mixed infection with certain Actinomyces species, in particular A. israelii), possesses certain virulence factors that enable it to invade tissues, such as the pore-forming toxin leukotoxin A (LtxA), isolated from women with bacterial vaginosis and as an etiologic agent in endocarditis. The pore-forming toxin LtxA of A. actinomycetemcomitans may be a trigger of the autoimmune disease rheumatoid arthritis due to its ability to stimulate protein citrullination, a post-translational protein modification targeted by autoantibodies in this disease.

## Small non-coding RNAs

Four small non-coding RNAs containing a ferric uptake regulator (fur), or Fur box-like sequence identified by bioinformatics analysis in Aggregatibacter actinomycetemcomitans HK1651 called JA01-JA04 where the transcription of sRNAs was confirmed by Northern blot with fur binding demonstrated to each sRNA promoter, transcription of the sRNAs decreased in the presence of iron, increased by iron limitation anf JA03 may have the ability to regulate biofilm formation. JA01 is conserved only among A. actinomycetemcomitans. JA02 is present in both A. actinomycetemcomitans and P. multocida. JA03 and JA04 are most widely conserved and have orthologues across many Pasteurellaceae. HrrF RNA is another Fur-regulated sRNA conserved among the Pasteurcellaceae.

## Iron boxes

"In high G + C Gram-positive bacteria, the control of the expression of genes involved in iron metabolism is exerted by a DmdR [divalent (bivalent) metal-dependent regulatory] protein, previously named DtxR (diphtheria toxin repressor), in the presence of Fe$^{2+}$ or other bivalent ions. This system was first reported in Corynebacterium diphtheriae, and controls the expression of the diphtheriae toxin (tox) gene [1]. Expression of the tox gene, located in the integrated corynephage β DNA, is controlled by the DtxR protein in presence of Fe$^{2+}$. The tox gene promoter region contains a 27 bp palindrome, which overlaps the − 10 region of the promoter [2–4]. The minimal consensus sequence for binding of the DtxR protein was confirmed by Tao and Murphy [5] by the CAST (cyclic amplification and selection of targets) technique."
"An analysis of the 28 kDa DtxR protein [1] showed that it binds to the tox palindromic sequence as a dimer (56 kDa form) [6,7], which was confirmed by cross-linking studies [8]. A bivalent metal (Fe$^{2+}$, Co$^{2+}$, Ni$^{2+}$ or Cd$^{2+}$) is required for binding of the DtxR protein to the palindrome sequence in the DNA [5,6,9]."
"The nucleotide sequence of iron boxes of the desA and tox promoters have 14 nt in common, including the inverted repeat."
"Electrophoretic mobility-shift assays showed that both [divalent (bivalent) metal-dependent regulatory protein] DmdR1 and DmdR2 bind to the 19-nt tox and desA iron boxes forming two different complexes in each case."
"Ten different iron boxes were found in a search for iron boxes in the genome of S. coelicolor. Most of them correspond to putative genes involved in siderophore biosynthesis. [The] nucleotide sequence of these ten boxes is identical (or slightly different)".
"Iron box sequences (CD1–CD10) found in the genome of S. coelicolor by searching with the desA box of S. pilosus (TTAGGTTAGGCTCACCTAA).
* CD 1 TTAGGTTAGGCTCACCTAA 63 nt ATG pyridoxyl-dependent decarboxylase
* CD 2 TTAGGTTAGGCTCACCTAA 20 nt GTG antibiotic hydrolase (ABP) / 45 nt ATG ABC transporter ATP-binding protein
* CD 3 TTAGGTTAGGCTCgCCTAA 48 nt ATG esterase (cchJ) / 19 nt ATG hypothetical protein
* CD 4 TgAGGgTAGGCTtACCTcA 33 nt ATG iron-siderophore binding lipoprotein (cchF)
* CD 5 cTcGaTTAGGCTCgCCTtA 8 nt GTG iron-siderophore ABC transporter ATP-binding protein (cchE)
* CD 6 TTAGcTTAGGCTCACCTAA 131 nt ATG formyltransferase (cchA) / 24 nt ATG peptide monoxygenase (cchB)
* CD 7 TTAGGTaAGGCTCACCTAA 21 nt ATG hypothetical protein
* CD 8 TTAGGTTAGGCTaACCTtc 5 nt GTG ABC-transport protein ATP-binding component
* CD 9 TcAGGTTAGGCTCACCTct 1 nt GTG hypothetical protein
* CD 10 actcGTTAGGCTCACCTAA 69 nt ATG integral membrane protein
DmdR consense t 9 t 7 a 8 g 9 g 8 t 9 t 9 A 10 G 10 G 10 C 10 T 10 c 8 a 8 C 10 C 10 T 10 a 7 a 8
The distance in nucleotides of the iron boxes to the ATG-translation start codon is indicated. The consensus iron box sequence and the percentage of conservation is indicated in the [number next to the nucleotide]. Capital letters indicate full conservation of the nucleotides [10, conservation in the ten CD sequences (100 %); 9, 90 % conservation; 8, 80 % conservation; 7, 70 % conservation]. The designation of the genes and the putative proteins encoded by them are indicated on the right-hand side [...]."
"Several putative iron boxes were found upstream of ten different open reading frames in the genome of S. coelicolor. This allowed us to define a consensus iron box for Streptomyces species (TTAGGTTAGGCTCACCTAA; see the above table)."

## Transcription inhibitors

"Under iron-rich conditions Fur binds the divalent ion, acquires a configuration able to bind target DNA sequences (generally known as Fur boxes or iron boxes, [...]), and inhibits transcription from virtually all the genes and operons repressed by the metal."

## Siderophores

Def. Any "medium-sized molecule that has a high specificity for binding or chelating iron; they are employed by microorganisms to obtain iron from the environment" is called a siderophore.
When "iron is scarce, the equilibrium is displaced to release Fe$^{2+}$, the RNA polymerase accesses cognate promoters, and the genes for the biosynthesis of siderophores and other iron-related functions are expressed (41, 55)."

## Consensus sequences

The "sequence 5′-GATAATGATAATCATTATC-3′ [is] the functional target of the Fur protein."
Many "iron-regulated promoters appear to have not just one Fur box but multiple, sometimes overlapping, boxes (42, 53, 87)"
The "same 19-bp sequence [5′-GATAATGATAATCATTATC-3′] can be viewed as a combination of three adjacent repeats, 5′-NATA/TAT-3′."
Consensus is 3'-NAT(A/T)AT-5', but three of them as 3'-NAT(A/T)ATNAT(A/T)ATNAT(A/T)AT-5'.

## Hypotheses

* A1BG is not transcribed by a Fur box.

## Orthologs

A ferric iron uptake transcriptional regulator occurs in Providencia stuartii MRSN 2154, but no orthologs exist for Homo sapiens.