 | This article may be too technical for most readers to understand.(December 2022) |
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Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). | |
Colanic acid is an exopolysaccharide synthesized by bacteria in the Enterobacteriaceae family. It is excreted by the cell to form a protective bacterial capsule, and it assists in the formation of biofilms.
Colanic acid is composed of polyanionic heteropolysaccharides with hexasaccharide repeating units, consisting of glucose, fucose, galactose, and glucuronic acid. [1] [2] It also consists of O-acetyl groups and pyruvate side chains attached to these sugar molecules. [3] It forms a protective capsule around cells, primarily Enterobacteriaceae . [4] Colanic acid's high molecular weight and branching structure contribute to its high viscosity, while the carboxylic acid groups in its structure are the primary contributors to its acidity. It is considered mildly toxic when injected intraperitoneally in mice, and its effect on mammals can be compared to the effects of low doses of endotoxin, [2] which can cause diarrhea and malaise.
E. coli colonies that produce colanic acid are said to be colicinogenic, and appear larger, smoother, and more opaque than those that do not. The colanic acid itself is observed as amorphous, white, and fibrous and is water-soluble as well as soluble in dilute salt solutions. [2]
The main function of colanic acid is to form a protective slimy capsule around the cell surface under stressful conditions to increase its chances of survival. [5] The stressful environment can come in the forms of desiccation, oxidative stress, and a low pH. Expression of colanic acid in E. coli has been shown to be required for the creation of normal E. coli biofilm architecture.
Colanic acid synthesis is up-regulated in biofilms, where acetylation plays a crucial role in modulating its structural conformation and physical and chemical properties. In E. coli, colanic acid plays an essential role in biofilm formation. However, it does not enhance bacterial adhesion, but instead blocks the establishment of specific binding between bacteria and the underlying substrate. [5]
Colanic acid begins to be synthesized and accumulate at 19 °C. Nutrients modulate the production of colanic acid with maximal production occurring when glucose and proline are used as carbon and nitrogen sources. E. coli, a member of the Enterobacteriaceae family, is commonly used to study the conditions and effects of colanic acid production. A study showed that E. coli K92 is able to produce colanic acid at temperatures ranging from 19 °C to 42 °C, but it predominates at around 20 °C. [6]
Colanic acid is typically produced at a low pH to protect bacteria from the acidic environment. A study was conducted to determine the minimal pH that E.coli could withstand. It was concluded that the production of colanic acid can range from a pH of 2 to a pH of 8; with the initial response to acidity occurring at a pH of 5.5. [7]
Colanic acid production in E. coli is dependent on both lipopolysaccharide structure and glucose availability, because important nucleotide-sugar precursors are needed and provided by both. [8]
At least two positive protein regulators, RcsA [9] and RcsB, [10] are involved in the transcription of the operon for capsule (cps) gene expression in E. coli. The activation of colanic acid is due to an initial response to an environmental stimulus such as osmotic shock. This stimulus is relayed to the MdoH gene [11] which is tied to the biosynthesis of MDOs. Unstable MDO levels due to changes within the environment, triggers the RcsC [12] sensor to directly or indirectly relay the signal to the RcsB gene, which is a main activator of cps expression. [13] The RcsA gene activates its own expression. [13]
The cps colanic acid operon can control the biosynthesis of colanic acid. [14] It is composed of one large transcriptional unit that contains a ugd gene right outside the cps operon. It has been shown that the transcriptional antiterminator rfaH promotes said cps transcription. It does so by mediating the cps operon and promoting ugd expression. [15]
A study was conducted to test whether RfaH was able to enhance cps colanic acid transcription for colanic acid production. E. coli K92 wild-type and rfaH mutant strains were grown and analyzed. It was observed that the deletion of rfaH had dramatically decreased colanic acid production in both. [15]
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 acetolactate synthase (ALS) enzyme is a protein found in plants and micro-organisms. ALS catalyzes the first step in the synthesis of the branched-chain amino acids.
fis is an E. coli gene encoding the 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.
RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur.
Spot 42 (spf) RNA is a regulatory non-coding bacterial small RNA encoded by the spf gene. Spf is found in gammaproteobacteria and the majority of experimental work on Spot42 has been performed in Escherichia coli and recently in Aliivibrio salmonicida. In the cell Spot42 plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex.
Leucine responsive protein, or Lrp, is a global regulator protein, meaning that it regulates the biosynthesis of leucine, as well as the other branched-chain amino acids, valine and isoleucine. In bacteria, it is encoded by the lrp gene.
The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis. The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates.
The eps-Associated RNA element is a conserved RNA motif associated with exopolysaccharide (eps) or capsule biosynthesis genes in a subset of bacteria classified within the order Bacillales. It was initially discovered in Bacillus subtilis, located between the second and third gene in the eps operon. Deletion of the EAR element impairs biofilm formation.
In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. It is present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region of the protein; the N-terminal region often containing an autoinducer-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 capsule biosynthesis, or CPS operon, is a section of the genome present in some Escherichia coli, of which regulates the production of polysaccharides making up the bacterial capsule. These polysaccharides help protect the bacteria from harsh environments, toxic chemicals, and bacteriophages.
The gab operon is responsible for the conversion of γ-aminobutyrate (GABA) to succinate. The gab operon comprises three structural genes – gabD, gabT and gabP – that encode for a succinate semialdehyde dehydrogenase, GABA transaminase and a GABA permease respectively. There is a regulatory gene csiR, downstream of the operon, that codes for a putative transcriptional repressor and is activated when nitrogen is limiting.
D-glycero-beta-D-manno-heptose-7-phosphate kinase is an enzyme with systematic name ATP:D-glycero-beta-D-manno-heptose 7-phosphate 1-phosphotransferase. This enzyme catalyses the following chemical reaction
D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase is an enzyme with systematic name ATP:D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase. This enzyme catalyses the following chemical reaction
The glnALG operon is an operon that regulates the nitrogen content of a cell. It codes for the structural gene glnA the two regulatory genes glnL and glnG. glnA encodes glutamine synthetase, an enzyme which catalyzes the conversion of glutamate and ammonia to glutamine, thereby controlling the nitrogen level in the cell. glnG encodes NRI which regulates the expression of the glnALG operon at three promoters, which are glnAp1, glnAp2 located upstream of glnA) and glnLp. glnL encodes NRII which regulates the activity of NRI. No significant homology is found in Eukaryotes.
The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily is a group of integral membrane protein families. The MOP flippase superfamily includes twelve distantly related families, six for which functional data are available:
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.
CsgD is a transcription and response regulator protein referenced to as the master modulator of bacterial biofilm development. In E. coli cells, CsgD is tasked with aiding the transition from planktonic cell motility to the stationary phase of biofilm formation, in response to environmental growth factors. A transcription analysis assay illustrated a heightened decrease in CsgD's DNA-binding capacity when phosphorylated at A.A. D59 of the protein's primary sequence. Therefore, in the protein's active form (unphosphorylated), CsgD is capable of carrying out its normal functions of regulating curli proteins (fimbria) and producing ECM polysaccharides (cellulose). Following a promoter-lacZ fusion assay of CsgD binding to specific target sites on E. coli's genome, two classes of binding targets were identified: group I genes and group II genes. The group I genes, akin to fliE and yhbT, exhibit repressed transcription following their interaction with CsgD, whilst group II genes, including yccT and adrA, illustrated active functionality. Other group I operons that illustrate repressed transcription include fliE and fliEFGH, for motile flagellum formation. Other group II genes, imperative to the transition towards stationary biofilm development, include csgBA, encoding for curli fimbriae, and adrA, encoding for the synthesis of cyclic diguanylate. In this context, c-di-GMP functions as a bacterial secondary messenger, enhancing the production of extracellular cellulose and impeding flagellum production and rotation.
The Curli protein is a type of amyloid fiber produced by certain strains of enterobacteria. They are extracellular fibers located on bacteria such as E. coli and Salmonella spp. These fibers serve to promote cell community behavior through biofilm formation in the extracellular matrix. Amyloids are associated with several human neurodegenerative diseases such as Alzheimer's disease, Huntington's disease, Parkinson's disease, and prion diseases. The study of curli may help to understand human diseases thought to arise from improper amyloid fiber formation. The curli pili are generally assembled through the extracellular nucleation precipitation pathway.
The Phosphate (Pho) regulon is a regulatory mechanism used for the conservation and management of inorganic phosphate within the cell. It was first discovered in Escherichia coli as an operating system for the bacterial strain, and was later identified in other species. The Pho system is composed of various components including extracellular enzymes and transporters that are capable of phosphate assimilation in addition to extracting inorganic phosphate from organic sources. This is an essential process since phosphate plays an important role in cellular membranes, genetic expression, and metabolism within the cell. Under low nutrient availability, the Pho regulon helps the cell survive and thrive despite a depletion of phosphate within the environment. When this occurs, phosphate starvation-inducible (psi) genes activate other proteins that aid in the transport of inorganic phosphate.
Escherichia coli K-12 substr. MG1655
