Hfq aptamer

•



Timeline

2010

The expression of BsHfq and A/G-repeat RNA complex, crys_x005f_x005f_x005f_x0002_tallization and preliminary X-ray study were reported[1]

2012

Describe RNA aptamers including fragment (AG)(3)A that are recognized by BsHfq and crystal structures of the BsHfq-(AG)(3)A complex at 2.2 Å[2]

2014

With an emphasis on Hfq, this review compares the RNA-binding properties of the various (L)Sm rings that were recently[4]

2023

The structures of Hfq were reviewed and biochemical data on interactions between Gram-negative and Gram-positive homologs were defined to highlight similarities and differences in interactions with RNA[5]

Description

In 2010, Seiki Baba et al. reported the expression, crystallization and preliminary X-ray studies of the complex of BsHfq(Bacillus subtilis Hfq) with A/G-repeat RNA. In 2012, Tatsuhiko Someya et al. described RNA aptamers including fragment (AG)3A that are recognized by BsHfq and crystal structures of the BsHfq-(AG)3A complex at 2.2 Å resolution[1,2].



SELEX

In 2012, Tatsuhiko Someya et al. isolated 47 sequences that bind to BsHfq-His through 9 rounds of selection. Sequencing the 47 clones isolated from the RNA pool after nine selection cycles showed that the 22 RNA aptamers possessed AG repeats, the other 25 RNA aptamers did not contain AG repeats[2].

Detailed information are accessible on SELEX page.



Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information. AGr aptamer is the truncated sequence from the full-length sequence m49f aptamer[2].

5'-AGAGAGA-3'

drawing

3D visualisation

Tatsuhiko Someya et al.sovled the crystal structure, at 2.8 Å resolution. The quaternary structure of BsHfq in these complexes was a homohexameric ring, the AGr bound to the distal site of BsHfq with a circular conformation. The PDB ID of this structure is 3HSB[2].
Additional available structures that have been solved and detailed information are accessible on Structures page.

(Clicking the "Settings/Controls info" to turn Spin off)      

drawing PDBe Molstar




Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 3HSB at 2.8 Å resolution. Hfq protein (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with Hfq protein.

drawing drawing


Ligand information

SELEX ligand

Tatsuhiko Someya et al. et al. used EMSA to analyze the relationship between AG repeat sequences and BsHfq binding ability. Nucleotides in lower-case letters indicate constant flanking sequences[2].

Name Sequence Ligand Affinity
m49f aptamer 5'-gggacacaauggacgUAGAGAGAGAUUAGAUCCUGUCCGCGGCUAuaacggccgacaugagag-3' Bacillus subtilis Hfq 10 nM
AG repeat sequence(AGr aptamer) 5'-UAGAGAGAGA-3' Bacillus subtilis Hfq 1 μM

Structure ligand

This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands.-----from Pfam

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
A0A7U4HWX3 PF17209 49.40 kDa
GGPYLQ ...... GAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSGAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSGAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSGAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSGAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSGAMAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS
1HK9 940073
drawing

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious.

RMSD: (Root Mean Square Deviation) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-score RMSD Description
1hk9-A 16.5 0 Original chain
6GWK-B 13.2 0.6 rna binding protein HFQ
3HFO-B 12.3 0.9 ssr3341 protein
6V4X-E 9.4 1.6 small nuclear ribonucleoprotein sm
6N7P-M 9.3 1.5 u1 small nuclear ribonucleoprotein
1M5Q-H 9.2 1.5 small nuclear ribonucleoprotein ho
6JIE-A 9.2 2 yaeo
1YCY-A 9.1 1 Conserved hypothesis protein
7UWY-A 9.1 1.7 de novo designed small beta-barrel
7UR7-A 8.8 2.3 17_bp_sh3


References

[1] Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA.
Baba, S., Someya, T., Kawai, G., Nakamura, K., & Kumasaka, T.
Acta crystallographica. Section F, Structural biology and crystallization communications, 66(Pt 5), 563–566. (2010)
[2] Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.
Someya, T., Baba, S., Fujimoto, M., Kawai, G., Kumasaka, T., & Nakamura, K.
Nucleic acids research, 40(4), 1856-1867. (2012)
[3] Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.
Horstmann, N., Orans, J., Valentin-Hansen, P., Shelburne, S. A., 3rd, & Brennan, R. G.
Nucleic acids research, 40(21), 11023–11035. (2012)
[4] RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation.
Weichenrieder O.
RNA biology, 11(5), 537–549. (2014)
[5] Models of Hfq interactions with small non-coding RNA in Gram-negative and Gram-positive bacteria.
Watkins, D., & Arya, D.
Frontiers in cellular and infection microbiology, 13, 1282258. (2023)