## 3 Modulators of RNAP  
Whatever the implicated type of transcriptional control, the central element of genetic regulation system is the multi-subunit RNAP holoenzyme, which not only transcribes genes adjusting the cellular metabolism to changing environmental conditions, but also receives numerous signals from the environment by interacting with regulatory proteins and other molecules providing various impacts according to the physiological state of the cell. These include factors involved in transcription initiation, elongation and termination, RNAP secondary channel modulators and small molecules, such as the purine nucleotide derivative alarmomes pppGpp and ppGpp that play a key role in stringent response as well as their putative opponent pppApp [38]. Ultimately, all these factors are involved in analog control by modifying and adjusting the RNAP composition and function to DNA topology and chromatin architecture [1; 39; 40]. Importantly, previous studies using various approaches made it increasingly clear, that in vivo the RNAP holoenzyme can be closely associated with DNA topoisomerases, ribosomal proteins and metabolic enzymes [41; 42; 43; 44; 45]. While the composition of such a multi-protein RNAP assembly, designated the RNAP supramolecular complex, critically depends on the applied isolation procedure, it was found to vary with growth phase [43; 46] and be alterable by mutations of NAP genes [45] (Figure 1; Supplementary Table S1). Despite variable composition, some of the RNAP-associated proteins such as the ribosomal proteins, DNA gyrase subunits and certain metabolic enzymes (e.g., inosine 5\({}^{\prime}\)-monophosphate dehydrogenase--IMPDH), have been identified repeatedly by different approaches. Detected ribosomal proteins most likely reflect the association of the transcribing RNAP with ribosomes in the expressome complex functionally coupling transcription with translation in _E. coli_ and _Mycoplasma_ but not in Gram positive model bacterium _B. subtilis_ and other Firmicutes, where most of the operons are translated without a closely trailing ribosome and where this \"runaway transcription\" creates different rules for cotranscriptional regulation [47; 48]. Interestingly, while about a third of the 30S ribosomal subunit proteins were found to be associated with RNAP supramolecular complex isolated by heparin column chromatography, none of the 50S subunit proteins were detected (Figure 1; SupplementaryTable S1), supporting the view that RNAP forms a complex with the 30S ribosomal subunit prior to expressome formation. The enzymes that co-purify with RNA polymerase, including those involved in tRNA processing, nucleotide metabolism, and energy biosynthesis, were proposed to be necessary for optimal transcription rates [43]. Notably, among the RNAP-associated metabolic enzymes, inositol monophosphate (SuhB) is an integral part of the ribosomal antitermination complex involved in rRNA maturation and ribosome assembly [49]. SuhB both interacts with RNA and competes with C-terminal domain of the RNAP \(\alpha\) subunit (\(\alpha\)CTD) for binding the antitermination protein NusA [50]. Another RNAP-associated enzyme, inositol monophosphate dehydrogenase (IMPDH), is encoded by _guaB_ gene conserved from prokaryotes to humans and catalyzes the NAD\({}^{+}\)-dependent oxidation of IMP to xanthosine monophosphate, thus controlling the guanine nucleotide pool size [51]. Notably, IMPDH binds single-stranded nucleic acids both in vivo and in vitro [52]. In _Drosophila_, IMPDH was shown to bind single-stranded CT-rich DNA, acting as a transcriptional repressor of an evolutionarily conserved gene regulatory network of nucleotide metabolic enzymes and thus, linking the metabolic state to cell proliferation [53]. Also the _E. coli_ IMPDH binds CT-rich single-stranded DNA via its Bateman domain and independent of its catalytic function, inhibits adenylate nucleotide biosynthesis [54].