Sandbox 1: Difference between revisions
No edit summary |
No edit summary |
||
| Line 42: | Line 42: | ||
==RNA binding sites== | ==RNA binding sites== | ||
The ring-like architecture of the Hfq exposes two well | The ring-like architecture of the Hfq exposes two well characterized RNA binding sites referred to as “proximal”, representing the surface on which the amino (N)-terminal α-helix is exposed, and “distal” face, corresponding to the opposite surface of the proximal (Vogel & Luisi, 2011; Updegrove et al., 2016). In addition, recently studies have shown the presence of other two binding sites referred to as “lateral” or “rim” face, corresponding to the outer ring of the ring-like structure, and the carboxy (C)-terminal tail (Faner & Feig, 2014; Updegrove et al., 2016). | ||
Generally, the proximal face preferentially binds to U-rich RNA sequences, such as the poly(U) tracts that are preceded or followed by a hairpin structure present at the 3’ termini, at rho-independent terminator, of most sRNAs, or sometimes found in a central location of the sRNA (Faner & Feig, 2014; Schulz et al., 2017). The proximal face binds polyU sequences such that uridines are stacked adjacent to phenylalanine, in pockets between neighboring monomers around the central pore. This configuration is conserved in Hfq from Gram-negative and positive bacteria (Updegrove et al., 2016). | Generally, the proximal face preferentially binds to U-rich RNA sequences, such as the poly(U) tracts that are preceded or followed by a hairpin structure present at the 3’ termini, at rho-independent terminator, of most sRNAs, or sometimes found in a central location of the sRNA (Faner & Feig, 2014; Schulz et al., 2017). The proximal face binds polyU sequences such that uridines are stacked adjacent to phenylalanine, in pockets between neighboring monomers around the central pore. This configuration is conserved in Hfq from Gram-negative and positive bacteria (Updegrove et al., 2016). | ||
Generally, the distal face has high affinity to A-rich sequences, which are commonly found in the 5’ untranslated regions (UTR) of mRNAs (Schulz et al., 2017). RNA contacts of the distal face are more varied than those on the proximal face (Updegrove et al., 2016). It was observed that in E. coli the distal site of each Hfq subunit can accommodate a triplet of RNA nucleotides (ARN or AAN), where A-site binds specifically adenines, R-site can accommodate both adenine and guanine with preference for A, while the N-site can be any nucleotide as it points away from Hfq towards the solvent (Schulz et al., 2017). However, in Staphylococcus aureus the distal site binds a RL motif, where R is a purine specific and L is a non-specific linker (Faner & Feig, 2014). Also, studies have shown that some sRNAs also have A-rich sequences that allow them to bind the distal surface (Updegrove et al., 2016). | Generally, the distal face has high affinity to A-rich sequences, which are commonly found in the 5’ untranslated regions (UTR) of mRNAs (Schulz et al., 2017). RNA contacts of the distal face are more varied than those on the proximal face (Updegrove et al., 2016). It was observed that in E. coli the distal site of each Hfq subunit can accommodate a triplet of RNA nucleotides (ARN or AAN), where A-site binds specifically adenines, R-site can accommodate both adenine and guanine with preference for A, while the N-site can be any nucleotide as it points away from Hfq towards the solvent (Schulz et al., 2017). However, in Staphylococcus aureus the distal site binds a RL motif, where R is a purine specific and L is a non-specific linker (Faner & Feig, 2014). Also, studies have shown that some sRNAs also have A-rich sequences that allow them to bind the distal surface (Updegrove et al., 2016). | ||
| Line 48: | Line 48: | ||
The role of the C-terminal domain in RNA binding remains murky, but what studies suggest is that it may bind to longer RNA molecules and/or increase interaction specificity by recognizing additional motifs within a RNA (Faner & Feig, 2014). | The role of the C-terminal domain in RNA binding remains murky, but what studies suggest is that it may bind to longer RNA molecules and/or increase interaction specificity by recognizing additional motifs within a RNA (Faner & Feig, 2014). | ||
[[Image: | |||
[[Image:Hfq-RNA_binding.PNG]] | |||
| Line 65: | Line 66: | ||
The Sm and Lsm proteins are present in members of the Eukarya, Archaea and Bacteria domains, suggesting that this family may have evolved from a early ancestral (Schumacher et al., 2002; Wilusz & Wilusz, 2005). The Sm proteins contain two conserved regions termed the Sm1 and Sm2 motifs, which are separated by a not conserved region, neither in sequence nor in length, named variable region (Schumacher et al., 2002). There are two structures properties set Hfq apart from the others Sm proteins (Schumacher et al., 2002). First, the bacteria Hfq, unlike others described Sm proteins that usually form a heteroheptameric ring structure, oligomerizes to form a homohexameric structure (Wilusz & Wilusz, 2005). Secondly, Hfq variable region contains only a very short loop, whereas in other Sm proteins variable region consists of a long loop and also the β-strands β3 and β4 are extended to form a longer antiparallel sheet (Schumacher et al., 2002). | The Sm and Lsm proteins are present in members of the Eukarya, Archaea and Bacteria domains, suggesting that this family may have evolved from a early ancestral (Schumacher et al., 2002; Wilusz & Wilusz, 2005). The Sm proteins contain two conserved regions termed the Sm1 and Sm2 motifs, which are separated by a not conserved region, neither in sequence nor in length, named variable region (Schumacher et al., 2002). There are two structures properties set Hfq apart from the others Sm proteins (Schumacher et al., 2002). First, the bacteria Hfq, unlike others described Sm proteins that usually form a heteroheptameric ring structure, oligomerizes to form a homohexameric structure (Wilusz & Wilusz, 2005). Secondly, Hfq variable region contains only a very short loop, whereas in other Sm proteins variable region consists of a long loop and also the β-strands β3 and β4 are extended to form a longer antiparallel sheet (Schumacher et al., 2002). | ||
[[Image:Sm_proteins1.PNG]] | |||
[[Image:Sm proteins2.PNG]] | |||