Histone-like nucleoid-structuring protein

Last updated
H-NS
PDB 1lr1 EBI.jpg
Solution structure of the N-terminal domain (oligomerization domain) of the bacterial nucleoid structuring protein, H-NS.
Identifiers
SymbolH-NS
Pfam PF00816
InterPro IPR001801
CATH [ P0ACF8]
SCOP2 1hns / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

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]

Contents

Figure 1: The C-terminal domain (CTD) is also known as the DNA-binding domain. H-NS NTD's oligomerize with each other while the CTD binds to specific regions of DNA containing a specific topology called a TpA step. Aromatic amino acid residues are labelled in gray, negatively charged particles are displayed in red, and positively charged particles are labelled in teal. H-bond lengths are displayed in magenta. C-Terminal Domain of H-NS.png
Figure 1: The C-terminal domain (CTD) is also known as the DNA-binding domain. H-NS NTD's oligomerize with each other while the CTD binds to specific regions of DNA containing a specific topology called a TpA step. Aromatic amino acid residues are labelled in gray, negatively charged particles are displayed in red, and positively charged particles are labelled in teal. H-bond lengths are displayed in magenta.

Structure

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]

Figure 2: This figure portrays the oligomerization occurring in the alpha helices of the NTD in H-NS (and homologues) forming what is known as a "handshake topology" and an estimated view of how the CTD binds to DNA. Fold Topology and Oligomerization States of H-NS.jpg
Figure 2: This figure portrays the oligomerization occurring in the alpha helices of the NTD in H-NS (and homologues) forming what is known as a "handshake topology" and an estimated view of how the CTD binds to DNA.

Function

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]

Clinical Significance

Figure 3: (A) Illustration of the association of H-NS to S. flexneri DNA at 32degC and then when temperature reaches 37degC, H-NS dissociates from the DNA, allowing for the transcription of virF. (B) Further down the DNA duplex, the expression of VirB causes a disruption in silencing of icsB by H-NS and the cascade can continue causing wide-spread infection. VirF Cascade Facilitated by H-NS.png
Figure 3: (A) Illustration of the association of H-NS to S. flexneri DNA at 32°C and then when temperature reaches 37°C, H-NS dissociates from the DNA, allowing for the transcription of virF.(B) Further down the DNA duplex, the expression of VirB causes a disruption in silencing of icsB by H-NS and the cascade can continue causing wide-spread infection.

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]

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References

  1. ↑ Winardhi RS, Yan J, Kenney LJ (October 2015). "H-NS Regulates Gene Expression and Compacts the Nucleoid: Insights from Single-Molecule Experiments". Biophysical Journal. 109 (7): 1321–1329. Bibcode:2015BpJ...109.1321W. doi:10.1016/j.bpj.2015.08.016. PMC   4601063 . PMID   26445432.
  2. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Qin L, Erkelens AM, Ben Bdira F, Dame RT (December 2019). "The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins". Open Biology. 9 (12): 190223. doi:10.1098/rsob.190223. PMC   6936261 . PMID   31795918.
  3. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Picker MA, Wing HJ (December 2016). "H-NS, Its Family Members and Their Regulation of Virulence Genes in Shigella Species". Genes. 7 (12): 112. doi: 10.3390/genes7120112 . PMC   5192488 . PMID   27916940.
  4. ↑ Shindo H, Iwaki T, Ieda R, Kurumizaka H, Ueguchi C, Mizuno T, et al. (February 1995). "Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli". FEBS Letters. 360 (2): 125–131. doi: 10.1016/0014-5793(95)00079-o . PMID   7875316. S2CID   44479751.
  5. ↑ Bloch V, Yang Y, Margeat E, Chavanieu A, Augé MT, Robert B, et al. (March 2003). "The H-NS dimerization domain defines a new fold contributing to DNA recognition". Nature Structural Biology. 10 (3): 212–218. doi:10.1038/nsb904. PMID   12592399. S2CID   25761309.
  6. 1 2 Donato GM, Kawula TH (September 1998). "Enhanced binding of altered H-NS protein to flagellar rotor protein FliG causes increased flagellar rotational speed and hypermotility in Escherichia coli". The Journal of Biological Chemistry. 273 (37): 24030–24036. doi: 10.1074/jbc.273.37.24030 . PMID   9727020.
  7. ↑ Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JC (August 2006). "H-NS mediates the silencing of laterally acquired genes in bacteria". PLOS Pathogens. 2 (8): e81. doi: 10.1371/journal.ppat.0020081 . PMC   1550270 . PMID   16933988.
  8. ↑ Dorman CJ (September 2014). "H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria". Plasmid. 75: 1–11. doi:10.1016/j.plasmid.2014.06.004. PMID   24998344.
  9. ↑ Verma SC, Qian Z, Adhya SL (December 2019). "Architecture of the Escherichia coli nucleoid". PLOS Genetics. 15 (12): e1008456. doi: 10.1371/journal.pgen.1008456 . PMC   6907758 . PMID   31830036.
  10. ↑ Picker MA, Wing HJ (December 2016). "H-NS, Its Family Members and Their Regulation of Virulence Genes in Shigella Species". Genes. 7 (12): E112. doi: 10.3390/genes7120112 . PMC   5192488 . PMID   27916940.
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