H-NS | |||||||||
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Identifiers | |||||||||
Symbol | H-NS | ||||||||
Pfam | PF00816 | ||||||||
InterPro | IPR001801 | ||||||||
CATH | [ P0ACF8] | ||||||||
SCOP2 | 1hns / SCOPe / SUPFAM | ||||||||
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Histone-like nucleoid-structuring protein (H-NS), is one of twelve nucleoid-associated proteins (NAPs) [1] whose main function is the organization of genetic material, including the regulation of gene expression via xenogeneic silencing. [2] H-NS is characterized by an N-terminal domain (NTD) consisting of two dimerization sites, a linker region that is unstructured and a C-terminal domain (CTD) that is responsible for DNA-binding. [2] Though it is a small protein (15 kDa), [3] it provides essential nucleoid compaction and regulation of genes (mainly silencing) [2] and is highly expressed, functioning as a dimer or multimer. [3] Change in temperature causes H-NS to be dissociated from the DNA duplex, allowing for transcription by RNA polymerase, and in specific regions lead to pathogenic cascades in enterobacteria such as Escherichia coli and the four Shigella species. [3]
H-NS has a specific topology that allows it to condense bacterial DNA into a superhelical structure based on evidence from X-ray crystallography. [2] The condensed superhelical structure has implicated H-NS in gene repression caused by the formation of oligomers. These oligomers form due to dimerization of two sites in the N-terminal domain of H-NS. [2] For example, in bacterial species like Salmonella typhimurium , the NTD of H-NS contains dimerization sites in helices alpha 1, alpha 2 and alpha 3. Alpha helices 3 and 4 are then responsible for creating the superhelical structure of H-NS-DNA interactions by head to head association (Figure 2). [2] [5] H-NS also contains an unstructured linker region, also known as a Q-linker. [2] The C-Terminal domain, also known as the DNA Binding Domain (DBD), shows high affinity for regions in DNA that are rich in Adenine and Thymine and present in a hook-like motif in a minor groove. [2] The base stacking present in this AT rich region of the DNA allows for minor widening of the minor groove that is preferential for binding. [2] Common DBD's include AACTA and TACTA regions which can appear hundreds of times throughout the genome. [2] Within these AT-rich regions, the minor groove has a width of 3.5 Å, [3] which is preferential for H-NS binding. In E. coli, it was observed that H-NS restructures the genome into microdomains in vivo. [2] While the bacterial genome is split into four different macrodomains including Ori and Ter (macrodomain of E. coli and Shigella spp. in which H-NS is encoded), [3] it is thought that H-NS plays a role in the formation of these small 10 kb microdomains throughout the genome. [2]
A major function of H-NS is to influence DNA topology (Figure 2). H-NS is responsible for formation of nucleofilaments along the DNA and DNA-DNA bridges. H-NS is known as a passive DNA bridger, meaning that it binds two distant segments of DNA and remains stationary, forming a loop. This DNA loop formation allows H-NS to control gene expression. [2] Relief of suppression by H-NS can be achieved by the binding of another protein, or by changes in DNA topology which can occur due to changes in temperature and osmolarity, for example. [6] The CTD binds to the bacterial DNA in such a way that inhibits the function of RNA polymerase. This is a common feature seen in horizontally acquired genes. [7] Structural studies of H-NS use bacterial species such as E. coli and Shigella spp. because the C-Terminal Domain is completely conserved. [3]
The process for formation of H-NS-DNA complexes begins with the CTD binding to a preferential site in the genome. This may be the result of the large amount of positively charged amino acid residues located within the linker region that causes the CTD to search for a binding site with high affinity. [2] Once the CTD is bound to its preferential region, TpA step, the NTD's can oligomerize and form rigid nucleofilaments that, if favorable conditions exist, will more freely bind to one another to form DNA-bridges. This form of bridging is known as "passive bridging" and may not allow RNAP to proceed with transcription. [2] The experiments used to support this method of DNA binding and gene silencing come from Atomic Force Microscopy and single-molecule studies in vitro. [2]
All bacteria must be sensitive to changes in their physical environment to survive. These mechanisms allow for turning genes on or off depending on its extracellular environment. [3] Many researchers believe that H-NS contributes to these sensory functions. H-NS has been observed to control around 60% of the temperature regulated genes and can dissociate from the DNA duplex at 37 °C. [2] This particular sensitivity seen in H-NS allows for pathogenesis and is the main focus of study. Outside of a host, the temperature of 32 °C prevents dissociation of H-NS from the virulence plasmid in Shigella spp. in order to conserve energy for energetically costly production of proteins involved in pathogenesis. [8] The presence of magnesium ions (Mg2+) has been shown to allow H-NS to form a slightly open to completely open conformational change in structure that will ultimately alter the interaction between the negatively charged NTD and positively charged CTD. [2] Magnesium concentrations below 2 mM, allows for the formation of rigid nucleoprotein filaments and high concentrations promote the formation of H-NS DNA bridges. [9] The charges seen in the NTD and CTD may explain how H-NS remains sensitive to changes in temperature and osmolarity (pH below 7.4). [3] H-NS can also interact with other proteins and influence their function, for example it can interact with the flagellar motor protein FliG to increase its activity. [6]
H-NS has a conserved role in the pathogenicity of gram-negative bacteria including Shigella spp., Escherichia coli, Salmonella spp., and many others. It is implicated in the transcription of the virF gene causing what is known as the virF leading to bacillary dysentery, a disease affecting children mainly seen in developing countries. These two bacterial species contain a virulence plasmid that is responsible for invasion of host cells and is regulated by H-NS. [10] Interestingly, almost 70% of the open reading frames (ORF) of the specialized virulence plasmid in Shigella spp. is AT-rich, allowing for long term regulation of this plasmid by H-NS. [3]
Aforementioned, studies show that temperature sensitive H-NS will dissociate from bacterial DNA at 37 °C, triggering RNA polymerase to transcribe virF, the gene responsible for the expression of VirF. VirF is the main regulator of the virulence cascade and is expressed due to the temperature sensitive "hinge" region of the virF promoter changing conformation so that is no longer favorable for DNA-bridging by H-NS (Figure 3). [3] Once VirF is expressed, it up regulates the production of icsA, functions to promote motility, and virB, encodes the next regulation protein in the Shigella cascade. As soon as VirB is expressed, it will disrupt H-NS for the rest of the virulence plasmid. [3]
Shigella spp. contain "molecular backups", or paralogues, to H-NS that have been studied in detail due to their apparent assistance in organization of the virulence plasmid. [3] StpA is a paralogue of H-NS that is conserved across the species but the other, Sfh is expressed solely in the S. flexneri mutant strain 2457T. [3] This mutant strain is of much interest to researchers because it acts as a replacement for H-NS since 2457T does not contain the hns gene. The correlation between H-NS and its paralogues is poorly understood at this time. [3] Due to importance of these paralogues in the absence of H-NS in the mutant, further research and focus on these paralogues could lead to promising antibacterial treatments. [3]
Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacteria.
Escherichia coli ( ESH-ə-RIK-ee-ə KOH-ly) is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes such as EPEC, and ETEC are pathogenic and can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains are part of the normal microbiota of the gut and are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of E. coli benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between E. coli and humans are a type of mutualistic biological relationship — where both the humans and the E. coli are benefitting each other. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for three days, but its numbers decline slowly afterwards.
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DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase and is a subclass of Type II topoisomerases that reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase or by helicase in front of the progressing replication fork. It is the only known enzyme to actively contribute negative supercoiling to DNA, while it also is capable of relaxing positive supercoils. It does so by looping the template to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break, changing the linking number by two in each enzymatic step. This process occurs in bacteria, whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each other to form supercoils. Gyrase is also found in eukaryotic plastids: it has been found in the apicoplast of the malarial parasite Plasmodium falciparum and in chloroplasts of several plants. Bacterial DNA gyrase is the target of many antibiotics, including nalidixic acid, novobiocin, albicidin, and ciprofloxacin.
A tumour inducing (Ti) plasmid is a plasmid found in pathogenic species of Agrobacterium, including A. tumefaciens, A. rhizogenes, A. rubi and A. vitis.
Shigella flexneri is a species of Gram-negative bacteria in the genus Shigella that can cause diarrhea in humans. Several different serogroups of Shigella are described; S. flexneri belongs to group B. S. flexneri infections can usually be treated with antibiotics, although some strains have become resistant. Less severe cases are not usually treated because they become more resistant in the future. Shigella are closely related to Escherichia coli, but can be differentiated from E.coli based on pathogenicity, physiology and serology.
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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.
In DNA repair, the Ada regulon is a set of genes whose expression is essential to adaptive response, which is triggered in prokaryotic cells by exposure to sub-lethal doses of alkylating agents. This allows the cells to tolerate the effects of such agents, which are otherwise toxic and mutagenic.
In molecular biology, the haemolysin expression modulating protein family is a family of proteins. This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of this family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer. The HHA family of proteins display striking similarity to the oligomerisation domain of the H-NS proteins.
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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.