In molecular biology, the LuxR-type DNA-binding HTH domain is a

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

-binding,

helix-turn-helix Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two alpha helix, α helices, joined by a short strand of amino acids, that bind to the majo ...

(HTH)

domain A domain is a geographic area controlled by a single person or organization. Domain may also refer to: Law and human geography * Demesne, in English common law and other Medieval European contexts, lands directly managed by their holder rather ...

of about 65

amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the Proteinogenic amino acid, 22 α-amino acids incorporated into p ...

. It is present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after ''

Vibrio fischeri ''Aliivibrio fischeri'' (formerly ''Vibrio fischeri'') is a Gram-negative, rod-shaped bacterium found globally in marine environments. This bacterium grows most effectively in water with a salt concentration at around 20g/L, and at temperatures ...

'' luxR, a

transcriptional activator A transcriptional activator is a protein (transcription factor) 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 ...

for quorum-sensing control of

luminescence Luminescence is a spontaneous emission of radiation from an electronically or vibrationally excited species not in thermal equilibrium with its environment. A luminescent object emits ''cold light'' in contrast to incandescence, where an obje ...

. LuxR-type HTH domain

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s occur in a variety of

organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...

s. The DNA-binding HTH domain is usually located in the

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When t ...

region of the protein; the

N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...

region often containing an

autoinducer In biology, an autoinducer is a signaling molecule that enables detection and response to changes in the population density of bacterial cells. Synthesized when a bacterium reproduces, autoinducers pass outside the bacterium and into the surround ...

-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four- helical bundle

structure A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH

bind BIND () is a suite of software for interacting with the Domain Name System (DNS). Its most prominent component, named (pronounced ''name-dee'': , short for ''name Daemon (computing), daemon''), performs both of the main DNS server roles, acting ...

s DNA in the major groove, where the N-terminal part of the recognition

helix A helix (; ) is a shape like a cylindrical coil spring or the thread of a machine screw. It is a type of smooth space curve with tangent lines at a constant angle to a fixed axis. Helices are important in biology, as the DNA molecule is for ...

makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR.

Signalling A signal is both the process and the result of transmission of data over some media accomplished by embedding some variation. Signals are important in multiple subject fields including signal processing, information theory and biology. In ...

events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind

as multimers. LuxR-type HTH

s can be activated by one of four different mechanisms: 1. Regulators which belong to a two-component

sensory transduction In physiology, transduction is the translation of arriving stimulus into an action potential by a sensory receptor. It begins when stimulus changes the membrane potential of a sensory receptor. A sensory receptor converts the energy in a stimulu ...

system where the protein is activated by its

phosphorylation In biochemistry, phosphorylation is described as the "transfer of a phosphate group" from a donor to an acceptor. A common phosphorylating agent (phosphate donor) is ATP and a common family of acceptor are alcohols: : This equation can be writ ...

, generally on an

aspartate Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. The L-isomer of aspartic acid is one of the 22 proteinogenic amino acids, i.e., the building blocks of protein ...

residue, by a

transmembrane A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently u ...

kinase In biochemistry, a kinase () is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule don ...

. Some

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

that belong to this category are: * ''

Rhizobiaceae The Rhizobiaceae is a family of Pseudomonadota comprising multiple subgroups that enhance and hinder plant development. Some bacteria found in the family are used for plant nutrition and collectively make up the rhizobia. Other bacteria such as ' ...

'' fixJ (global regulator inducing expression of

nitrogen-fixation Nitrogen fixation is a chemical process by which molecular dinitrogen () is converted into ammonia (). It occurs both biologically and abiologically in chemical industries. Biological nitrogen fixation or ''diazotrophy'' is catalyzed by en ...

genes In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

in microaerobiosis) * ''

Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...

'' and ''

Salmonella typhimurium ''Salmonella enterica'' subsp. ''enterica'' is a subspecies of ''Salmonella enterica'', the rod-shaped, flagellated, aerobic, Gram-negative bacterium. Many of the pathogenic serovars of the ''S. enterica'' species are in this subspecies, includin ...

'' uhpA (activates

hexose In chemistry, a hexose is a monosaccharide (simple sugar) with six carbon atoms. The chemical formula for all hexoses is , and their molecular weight is 180.156 g/mol. Hexoses exist in two forms, open-chain or cyclic, that easily convert into ...

phosphate

transport Transport (in British English) or transportation (in American English) is the intentional Motion, movement of humans, animals, and cargo, goods from one location to another. Mode of transport, Modes of transport include aviation, air, land tr ...

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

uhpT) *''E. coli'' narL and narP (activate

nitrate reductase Nitrate reductases are molybdoenzymes that reduce nitrate () to nitrite (). 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 ...

operon 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 splic ...

) *

Enterobacteria Enterobacteriaceae is a large family (biology), family of Gram-negative bacteria. It includes over 30 genera and more than 100 species. Its classification above the level of Family (taxonomy), family is still a subject of debate, but one class ...

rcsB (regulation of

exopolysaccharide Extracellular polymeric substances (EPS) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPS establish the functional and structural integrity of biofilms, and are considered the fundamental compo ...

biosynthesis Biosynthesis, i.e., chemical synthesis occurring in biological contexts, is a term most often referring to multi-step, enzyme-Catalysis, catalyzed processes where chemical substances absorbed as nutrients (or previously converted through biosynthe ...

enteric The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the digestive system that leads from the mouth to the anus. The tract is the largest of the body's systems, after the cardiovascular system. ...

and

plant Plants are the eukaryotes that form the Kingdom (biology), kingdom Plantae; they are predominantly Photosynthesis, photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with c ...

pathogenesis In pathology, pathogenesis is the process by which a disease or disorder develops. It can include factors which contribute not only to the onset of the disease or disorder, but also to its progression and maintenance. The word comes . Descript ...

) * ''

Bordetella pertussis ''Bordetella pertussis'' is a Gram-negative, aerobic, pathogenic, encapsulated coccobacillus bacterium of the genus ''Bordetella'', and the causative agent of pertussis or whooping cough. Its virulence factors include pertussis toxin, adenyla ...

'' bvgA (

virulence factor Virulence factors (preferably known as pathogenicity factors or effectors in botany) are cellular structures, molecules and regulatory systems that enable microbial pathogens (bacteria, viruses, fungi, and protozoa) to achieve the following: * c ...

) * ''

Bacillus subtilis ''Bacillus subtilis'' (), known also as the hay bacillus or grass bacillus, is a gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus ''Bacill ...

'' comA (involved in expression of late-expressing

competence Broad concept article: *Competence (polyseme), capacity or ability to perform effectively Competence or competency may also refer to: *Competence (human resources), ability of a person to do a job properly **Competence-based management, performa ...

genes) 2. Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as

quorum sensing In biology, quorum sensing or quorum signaling (QS) is the process of cell-to-cell communication that allows bacteria to detect and respond to cell population density by gene regulation, typically as a means of acclimating to environmental disadv ...

molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...

s in a variety of

Gram-negative bacteria Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelo ...

: *''Vibrio fischeri'' luxR (activates

bioluminescence Bioluminescence is the emission of light during a chemiluminescence reaction by living organisms. Bioluminescence occurs in multifarious organisms ranging from marine vertebrates and invertebrates, as well as in some Fungus, fungi, microorgani ...

operon) * ''

Agrobacterium tumefaciens ''Agrobacterium tumefaciens'' (also known as ''Rhizobium radiobacter'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are cause ...

'' traR (regulation of Ti

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and ...

transfer) * ''

Erwinia carotovora ''Pectobacterium carotovorum'' is a bacterium of the family Pectobacteriaceae; it used to be a member of the genus ''Erwinia''. The species is a plant pathogen with a diverse host range, including many agriculturally and scientifically impo ...

'' carR (control of

carbapenem Carbapenems are a class of very effective antibiotic agents most commonly used for treatment of severe bacterial infections. This class of antibiotics is usually reserved for known or suspected multidrug-resistant (MDR) bacterial infections. Si ...

antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy ...

) *''E. carotovora'' expR (virulence factor for soft rot disease; activates plant tissue macerating

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

genes) * ''

Pseudomonas aeruginosa ''Pseudomonas aeruginosa'' is a common Bacterial capsule, encapsulated, Gram-negative bacteria, Gram-negative, Aerobic organism, aerobic–facultative anaerobe, facultatively anaerobic, Bacillus (shape), rod-shaped bacteria, bacterium that can c ...

'' lasR (activates

elastase In molecular biology, elastase is an enzyme from the class of proteases (peptidases) that break down proteins, specifically one that can break down elastin. In other words, the name only refers to the substrate specificity (i.e. what proteins i ...

gene lasB) * ''

Erwinia chrysanthemi ''Dickeya dadantii'' is a Gram-negative Bacillus (shape), bacillus that belongs to the family Pectobacteriaceae. It was formerly known as ''Erwinia chrysanthemi'' but was reassigned as ''Dickeya dadantii'' in 2005. Members of this family are facu ...

'' echR and '' Erwinia stewartii'' esaR * ''

Pseudomonas chlororaphis ''Pseudomonas chlororaphis'' is a bacterium used as a soil inoculant in agriculture and horticulture. It can act as a biocontrol agent against certain fungal plant pathogens via production of phenazine-type antibiotics. Based on 16S rRNA analysi ...

'' phzR (positive regulator of

phenazine Phenazine is an organic compound with the formula (C6H4)2N2. It is a dibenzo annulation, annulated pyrazine, and the parent substance of many dyestuffs, such as the toluylene red, indulines, and safranines (and the closely related eurhodines). Phe ...

antibiotic production) * ''Pseudomonas aeruginosa'' rhlR (activates rhlAB

and lasB gene) * ''

Acinetobacter baumannii ''Acinetobacter baumannii'' is a typically short, almost round, rod-shaped (coccobacillus) Gram-negative bacterium. It is named after the bacteriologist Paul Baumann. It can be an opportunistic pathogen in humans, affecting people with compromis ...

'' abaR (activates operon for production of surfactant-like lipopeptide acinetin-505)Pérez-Varela M, Tierney ARP, Kim JS, Vazquez-Torres A, Rather P. Characterization of RelA in Acinetobacter baumannii ublished online ahead of print, 2020 Mar 30 J Bacteriol. 2020;JB.00045-20. doi:10.1128/JB.00045-20 3. Autonomous

effector Effector may refer to: *Effector (biology), a molecule that binds to a protein and thereby alters the activity of that protein * ''Effector'' (album), a music album by the Experimental Techno group Download * ''EFFector'', a publication of the El ...

domain regulators, without a regulatory domain, represented by gerE. *''B. subtilis'' gerE (transcription activator and

repressor In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor blocks the attachment of RNA polymerase to the ...

for the

regulation Regulation is the management of complex systems according to a set of rules and trends. In systems theory, these types of rules exist in various fields of biology and society, but the term has slightly different meanings according to context. Fo ...

spore In biology, a spore is a unit of sexual reproduction, sexual (in fungi) or asexual reproduction that may be adapted for biological dispersal, dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores fo ...

formation) 4. Multiple ligand-binding regulators, exemplified by malT. *''E. coli'' malT (activates

maltose } Maltose ( or ), also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α(1→4) bond. In the isomer isomaltose, the two glucose molecules are joined with an α(1→6) bond. Maltose is the tw ...

operon; MalT binds ATP and

maltotriose Maltotriose is a trisaccharide (three-part sugar) consisting of three glucose molecules linked with α-1,4 glycosidic bonds. It is most commonly produced by the digestive enzyme alpha-amylase (a common enzyme in human saliva) on amylose in star ...

)

References

{{InterPro content, IPR000792 Protein domains