1) Introduction
Regulation of gene expression occurs in all domains of life at different
molecular levels. Although the transcriptional level with transcription
factors has been extensively studied, other largely underestimated
regulatory mechanisms also play an important role. One such mechanism is
the relationship between DNA organisation and gene expression (Le Berreet al. , 2022). Chromosomal DNA forms a structure in the bacterial
cell called the nucleoid. DNA compaction is achieved by a combination of
mechanisms, including DNA supercoiling, DNA bridging, DNA bending, DNA
wrapping, and self-assembly of nucleoid proteins. The proteins involved
in this compaction are known as nucleoid-associated proteins (NAPs),
which also regulate the transcription of a significant portion of the
bacterial chromosome (Amemiya, Schroeder and Freddolino, 2021; Schwab
and Dame, 2024). A dozen NAPs have been identified in Escherichia
coli and most Gram-negative bacteria, and their architectural and
regulatory activities have been relatively well characterised: H-NS, HU,
IHF, Fis, and Lrp (Azam and Ishihama, 1999). Although they are highly
abundant proteins, their cellular concentration can vary depending on
the physiological state of the cell, indicating that the production of
NAPs is regulated (Ali Azam et al. , 1999; Talukder and Ishihama,
2015).
In recent decades, there has also been a growing interest in
post-transcriptional regulation by RNAs, highlighting the crucial role
of such regulation in global regulatory networks (Papenfort and Melamed,
2023). In bacteria, post-transcriptional regulation by RNAs is carried
out by small non-coding RNAs (sRNAs), which range in size from 50 to 500
nucleotides (nt) and typically do not encode peptides (Storz, Vogel and
Wassarman, 2011). While some regulatory RNAs can be longer and encode
peptides or proteins, the mechanism of action involves repression or
activation of target genes through complementary base pairing with
target mRNAs. This interaction affects mRNA stability or translation by
modifying the secondary structure of the RNA and affecting the
accessibility of RNAses to cleavage sites or ribosomes to the ribosome
binding site (RBS) (Storz, Vogel and Wassarman, 2011; Papenfort and
Melamed, 2023) Antisense RNAs are a category of regulatory RNAs that are
transcribed from the opposite DNA strand of their target gene, they have
relatively long and precise base pairings with their RNA target, and
each antisense RNA targets only one mRNA (Georg and Hess, 2011). The
second category of regulatory RNA is called trans- acting RNA,
which usually has multiple target mRNAs. In this case, the RNA-RNA
binding is short (around 10 nt) and has imperfect base complementarity
(Holmqvist et al. , 2018; Melamed et al. , 2020). Thesetrans- acting sRNAs work in concert with RNA chaperones, such as
Hfq and ProQ, which increase sRNA stability and facilitate base pairing
with trans -encoded transcripts (Quendera et al. , 2020). It
is worth noting that Hfq is also referred to as a NAP (Amemiya,
Schroeder and Freddolino, 2021). In addition, one of the earliest
examples of non-coding RNA regulation was the regulation of hns mRNA by the sRNA DsrA (Lease, Cusick and Belfort, 1998). Since then,
several other examples have been studied, underscoring the interplay
between NAPs and post-transcriptional RNA regulation.
The purpose of this review is to examine the cross-talk between NAPs and
non-coding RNAs. Our focus is primarily on E. coli , as most
research has been conducted in this model strain. This review will first
provide a summary of the current knowledge base regarding the major
NAPs, focusing on the specific role played by Hfq. We will then present
examples of the regulation of NAPs by RNAs and the regulation of sRNAs
by NAPs, illustrating the complexity of regulatory networks. The role of
sRNAs in nucleoid structuring will also be discussed.