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.