4 RNA-BINDING PROTEINS
Interactions between proteins and RNA are indispensable for virtually
all processes in any living cell. From the biosynthesis of RNA molecules
to their degradation, the entire life cycle of RNA is associated to
RNA-binding proteins (RBP). RBPs are significantly more conserved across
evolution than non-RNA-binding proteins and comprise about 3-11% of the
proteome in all domains of life (Gerstberger et al., 2014). The
interplay of protein and RNA has traditionally been viewed as the
formation of highly dynamic ribonucleoprotein complexes that facilitate
multiple regulatory functions including RNA processing, modification,
translation or regulation (Dreyfuss et al., 2002; Babitzke et al.,
2019). Such ‘canonical’ RBPs bind RNA specifically via structurally
defined RNA-binding domains such as hnRNP homology (KH) domains
(Valverde et al., 2008), the S1 domain (Suryanarayana & Subramanian,
1984), RNA recognition motifs (RRM) (Cléry et al., 2008), the
RNA-binding domain of transcriptional antiterminators (Stülke, 2002) or
DEAD box helicase domains (Linder and Jankowsky, 2011).
The investigation of protein-RNA interactions is typically based on the
premise that specific protein domains can bind RNA. This view, however,
neglects the ability of RNA adopt highly diverse structures that in
principle can be able to bind any molecule. Strikingly, a study aimed at
identifying novel RBPs by crosslinking coupled to high resolution mass
spectrometry identified proteins crosslinked to RNA that lack any known
canonical RNA-binding domain. The discovery of those non-canonical RNA
binders such as the phosphoglycerate kinase, revealed a fundamentally
new group of proteins of both known and unknown function to be potential
RBPs (Schmidt et al., 2012; Kramer et al., 2014). The existence and
identification of those unconventional RBPs harboring unconventional
RBDs proposes novel mechanisms of protein-RNA interaction with new
biological functions (Hentze et al., 2018). Interestingly, several of
the poorly studied but highly expressed proteins of B. subtilisthat are thought to bind to RNA and/ or the ribosome do not possess
known RNA-binding domains. These proteins are YlbN, YlxR, YrzB as well
as the poorly studied RNA-binding SpoVG protein (see Table 1, Burke &
Portnoy, 2016). It is tempting to speculate that these proteins will
define novel RNA-binding domains.
One particularly important open question in the investigation of
RNA-binding proteins in B. subtilis and other Gram-positive
bacteria is related to the base-pairing of small regulatory RNAs with
mRNAs. As in other bacteria, small cis- and trans-acting RNA molecules
bind to partially complementary mRNAs to control their stability and
translation (Ul Haq et al., 2020; Mars et al., 2016). In E. coli ,
the Hfq protein acts as a chaperone that facilitates the base-pairing
between only rather short complementary sequences in the two RNA
molecules (Vogel and Luisi, 2011). In B. subtilis , a shorter Hfq
protein is present; however, despite all attempts so far, there is no
indication that Hfq also has this function in B. subtilis(Dambach et al., 2013; Hämmerle et al., 2014; Rochat et al., 2015). It
has recently been proposed that the lack of 5’-3’ exonucleolytic RNases
in E. coli and related bacteria results in the accumulation of
mRNA 3’ UTR. This may have provided a larger pool of unconstrained RNA
sequences that has stimulated the evolution of Hfq function and small
RNA (sRNA) regulation. In contrast, the presence of the 5’-3’
exoribonuclease RNase J prevents the accumulation of 3’ UTR sRNAs inB. subtilis . As a consequence, there was no selective pressure on
Hfq to evolve to become a mediator of RNA-RNA interactions (Mediati et
al., 2021). Since the physical conditions in the B. subtilis cell
are certainly similar to those in cells of E. coli , it seems
unlikely that regulation exerted by base-pairing of RNA molecules works
without a chaperone. The identification of the protein that takes over
this function is a major challenge in the future research on RNA-binding
proteins in B. subtilis .
Taken together, to understand both basic and complex processes of the
cell, extensive research on RNA-protein interactions is required. Even
though numerous conventional RBPs have been identified over the past
decades, some still remain to be characterized. With the discovery of
unconventional RBPs harboring non-canonical RNA-binding domains, the
field of understudied RBPs has dramatically increased.