A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli.

Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YcaN, YbhD, YgfI, YiaU, YneJ. We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

Introduction

Recently, the roles of uncharacterized LysR-type transcription factors (LTFs) have been identified via multiple approaches, including transcriptome analysis of uncharacterized TF (yTF)-deleted mutants (machine-learning-based), gene clustering, and the detection of DNA-binding sites[1]. The predicted yTF targets annotated as transporters and enzymes define the TF physiological role. A combination of the knowledge from EcoCyc, Fitness Browser, and iModulonDB with TF DNA-binding data provided hypotheses for the putative physiological functions of yTFs under different growth conditions[2]. Indeed, as an example, the function of one TF, PunR, was recently discovered to be an activator for punC, purine transporter important for adenosine utilization as a nitrogen source. Recently novel regulators for csgD were found by the promoter-specific screening of the 198 purified TFs including yTFs: YbiH, YdcI, YhjC, YiaU, YjgJ and YjiR. Two regulators for csgD: repressor YiaJ and activator YhjC (renamed RcdB) were found[3]. The SELEX method for the detection of the YbiH DNA-binding sites and antibiotics sensitivity for the yTF deletion mutant were used to predict the function for the CecR(YbiH)[4].

The RNA-seq data for the TF deletion mutants under specific growth conditions provide information about transcription affected by mutation (Fig. 1). In Escherichia coli, LTFs are regulators for amino acids (AAs), purine, and dicarboxylate metabolism, nitrogen assimilation (NAC), antibiotic resistance, and virulence. LTF regulatory proteins protect 50–60 bp regions with TA-rich regulatory binding sites and activation binding sites (ABS) and regulate different metabolic pathways. LTFs are known to regulate conserved gene clusters that are adjacent to the genes encoding the regulator[5], but additionally, LTF autoregulation is a common property. As one of the largest families of HTH-type regulators, LTFs contain an N-terminal helix-turn-helix DNA-binding domain and C-terminal co-inducer binding domain (Fig. S1). Given the broad conservation of LTFs, it is possible that they regulate a wide variety of target genes with diverse physiological functions using common regulatory features.

Figure 1

Systems approach for the prediction of transcription factor’s function. A systematic approach to identify LysR family unknown transcriptional factors physiological function in E. coli.

LTFs account for 16.7% (47 out of 280) of the total number of transcription factors in Escherichia coli K-12[6]. Out of the 47 LTFs, 26 (AbgR, AllS, ArgP, Cbl, CynR, CysB, Dan, DmlR, DsdC, GcvA, HcaR, HdfR, IlvY, LeuO, LrhA, LysR, MetR, Nac, NhaR, OxyR, PerR, PgrR, QseA, QseD, TdcA, XapR) have known functions and the majority were shown to regulate adjacent genes[7]. However, there are still many uncharacterized TFs belonging to the LysR-type family, which require further studies to determine their regulatory functions. This effort is also important for the reconstruction of the transcriptional regulatory network (TRN). The set of the six yTFs from LysR family (YbdO, YbeF, YcaN, YbhD, YgfI, YiaU) upregulated in the presence of l-threonine as supplement (iModulonDB, PRECISE) to minimal growth medium and YneJ, transcriptional analysis for the regulation of putrescine/l-glutamate utilization in minimal medium were characterized in our research.

Escherichia coli is a representative of the commensal mammalian intestinal microbiota and is the best characterized model gram-negative bacterium. Nutrient starvation conditions are important for the gut microbiome bacterial community as they cause stress, activating different survival mechanisms[8], and TRNs rewire the metabolism under different conditions. iModulonDB is a collection of E. coli MG1655 transcriptomics data for different growth medium and stress conditions[9]. Machine-learning based ICA data analysis (iModulonDB), RNA-seq data for the TF knockout, and ChIP-exo data (in vivo DNA-binding sites) are useful resources for LTF characterization. Recently, the ChIP-exo results for verified uncharacterized TFs in E. coli MG1655 was published[1]. The gene expression profiling for LTFs under multiple growth conditions in iModulonDB provides important information for predicting the growth conditions to verification of function for the yTFs[9].

We performed systems analysis for the prediction of LTF functional role using data combined from previously published chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) detected LTF DNA-binding sites, transcriptome data from iModulonDB (Fig. 1), RNA-seq analysis for LTF deletion mutants (experimental data), and genome cluster analysis using the bioinformatics tools (Fig. 1). We generated RNA-seq data for seven LTF mutants (ybdO, ybeF, ycaN, ybhD, ygfI, yiaU, and yneJ), analyzed the conserved genome clustering with LTF genes, and detected conserved genes that were differentially expressed in the LTF knockout. Accordingly, we generated a hypothesis about the possible regulatory targets of three LTFs and their physiological functions in response to the high l-threonine concentration in minimal medium (Fig. 1). The LTF regulation in response to the imbalance of Thr and catabolism for energy has been studied. The LTF deletion effect on the regulation of biochemical pathways of the Thr utilization and metabolism of glycerol, citrate, and formate (Fig. 1) had been investigated in E. coli BW25113.

Here, using a transcriptomic analysis systems approach, we identify the LTFs, YbdO, YgfI, YcaN, YbhD, important for Thr utilization pathway in minimal medium and regulating catabolism of citrate, pyruvate, formate or malate, and YiaU, YbeF important for liposaccharide modification and flagella biosynthesis and YneJ (PtrR), that directly controls sad gene expression in response to GABA, an intermediate of the Ptr utilization pathway.

For the detailed analysis, we investigated the effect of the YneJ transcriptional response in minimal medium under nitrogen starvation conditions. The yneJ-sad cluster is conserved in enterobacterial genomes, and Sad is involved in putrescine utilization as nitrogen source[10]. Many bacterial species, including E. coli, can simultaneously utilize l-glutamate (Glu) and the polyamine putrescine (Ptr) under carbon/nitrogen starvation conditions. Glu is also essential for tetrahydrofolate polyglutamylation[11]. Ptr is important for bacterial growth and for efficient DNA replication, transcription, and translation[12,13] and plays an important role in maintaining compact conformations of negatively charged nucleic acids[14]. Ptr is also involved in multiple antibiotic resistance mechanisms under stress conditions[15]. The puuA, puuD, puuE, and puuP genes in E. coli are induced by Ptr and regulated at the transcriptional level by the Ptr-responsive repressor PuuR[16,17]. The expression of sad (yneI) is induced by the addition of Ptr to the medium[18]; however, it is not regulated by PuuR, and a transcriptional regulator for sad had not been described before this work.

The predicted PtrR binding site in the sad promoter region was confirmed via an in vitro binding assay with the purified PtrR protein and using the ChIP-exo assay. We further compared the whole genome transcriptional response of the ptrR knockout and wild type E. coli strains to carbon/nitrogen starvation in the presence of Ptr and l-glutamate using RNA-Seq analyses, and the PtrR DNA-binding site was predicted for fnrS, encoding small regulatory RNA. The physiological roles of PtrR regulation and antibiotic resistance are discussed.

Results

An integrated systems-approach uncovers LysR-type transcription factors in E. coli K-12

Previously, we generated a list of candidate transcriptional factors (TFs) from uncharacterized genes (“y-genes”) using a homology-based algorithm[19]. Among these TFs, it was predicted that YeiE, YfeR, YidZ, YafC, YahB, YbdO, YbeF, YbhD, YcaN, YdcI, YdhB, YeeY, YfiE, YgfI, YhaJ, YhjC, YiaU, YneJ, and YnfL belong to the LTF based on Hidden Markov Model. YdhB (re-named PunR) function had been shown to be an activator for the purine transporter, PunC[1,2]. Recently YdcI (Salmonella enterica) function was shown related to biofilm formation[20]. We further chose 7 uncharacterized LysR-type TFs (yLTFs), which have transcriptional responses (increased mRNAs) to the presence of a l-threonine (Thr) in M9 medium (iModulonDB, PRECISE2). l-threonine is an important source for l-serine, l-glycine, branched-chain amino acid biosynthesis, and formate, which is important for anaerobic respiration. To elucidate roles of each yLTF and genome-wide target genes, we performed gene expression profiling via RNA-Seq and ChIP-exo detection of the LTF DNA-binding and growth phenotyping. The overall workflow is shown in Fig. 1.

YbdO (CitR) regulatory effects are involved in citrate utilization and YbeF is involved in the flagella biosynthesis

The physiological function for LTFs CitR and YbeF was previously unknown. The YbdO (CitR) ChIP-exo result detected the peak for DNA-binding upstream of citR-ybdNM (Fig. 2A,B), that further was confirmed by the transcriptional analysis. The other ChiP-exo detected peaks for possible suggested genes regulation were not found in DEGs for citR deletion mutant strain. The citR (regulated by HNS) and ybdNM operons are conserved adjacent genes in Enterobacteriaceae (Fig. 2D) and the ybdN promoter was predicted to be regulated by FNR (EcoCyc). Further, gene expression profiling showed that citR deletion leads to strong upregulation of the ybdNM operon and the adjacent genes citCDEF. Interestingly that genome context analysis evolved that citR is conserved with the citrate lyase encoding genes cluster citCDEF. (Fig. 2C). Therefore, this result confirmed autoregulation of citR-ybdNM, and regulation for citrate lyase which is involved in anaerobic metabolism. From PRECISE2, upregulation of citC was detected when E. coli MG1655 strain was grown in M9 medium supplemented with Thr, suggesting that citrate utilization is important for the catabolizm of Thr. The YbdM has been predicted as yTF (Uniprot) and probably related to cit operon regulation. The DNA-binding site upstream of the citR gene was predicted by the phylogenetic footprinting method (Fig. S2), suggesting CitR is an autoregulator and ybdMN regulation.

Figure 2

The systems approach for YbdO and YbeF transcriptional factors function prediction. (A) The genome-wide binding of YbdO. (B) The zoom-in of the binding site at the promoter of the gene ybdO. (C) Transcriptomic data for citC (citrate transporter) (D) citCDEFXGT (citrate lyase encoding) genes clustering with ybdO-ybdMN, and ybeF, the analysis across the closely related bacteria. dcuC-anaerobic dicarboxylate transporter, lipA- lipoyl synthase (E) The growth measurement of the ybdO mutant compared to the wild type BW25113 strain of E. coli in 96-well plates microaerobically in M9 glucose supplemented by 30 mM citrate at pH 7.5 (orange and grey line) or glycerol as carbon source (blue and yellow line). (F) Growth was measured in 96-well plates (M9 with glycerol) as the carbon source, supplemented by 30 mM citrate at pH 6.5 (WT-orange and ybdO mutant strain-blue line).

To test the regulation of the citrate lyase encoding gene cluster (citEFG), the phenotype for growth in the M9 medium supplemented with citrate at low pH (pH 6.5) showed an effect of citR deletion on citrate utilization, suggesting artificial de-repression of citrate lyase (Fig. 2E-F), but no difference for the growth in M9 medium supplemented with citrate was found at pH 7.5. Additionally, citR mutation decreases the E. coli BW25113 fitness phenotype for motility in LB medium and affects growth using glycolate as carbon source (Fitness Browser, fit.genomics.lbl.gov) and microaerobic utilization of formate as carbon source (Fig. 7).

Figure 7

The systems approach for the phenotype detection of the transcription factors ybdO, ycaN and ygfI deletion mutants. The phenotype microarray (Biolog PM1 plate) (A. 12 h and B. 24 h growth) in M9 medium (95 carbon sources screening for ybdO and ygfI, ycaN deletion mutant strains compared to E. coli BW25113 (wild type, WT) strain. The carbon sources in PM1 plate: l-arabinose, N-acetyl-glucosamine, succinate, d-galactose, l-aspartate, l-proline, d-alanine, d-trehalose, d-mannose, d-serine, acetate, d-fructose, l-rhamnose, l-lactate, d-xylose, d-sorbitol, l-fucose, d-gluconate, d-glucuronate, d-glycerol-P, d-glucose, d-mellibiose, Lactose, maltose, uridine, l-glutamine, adenosine, l-glutamate, adenosine, l-serine, l-threonine, etc.

CitR and YbeF are paralogs (identity 30%), presented in conserved gene clusters in Enterobacterial genomes with citrate lyase operon cit (citCDEFXGT, Figs. 2C, S3). Interestingly the transcriptomic analysis of the citR and ybeF deletion mutants showed that the expression level of lrhA was substantially decreased (− 4.3-fold and − 3.5 -fold, respectively, Table 1, Supplementary data), likely indicating that YbeF and CitR has affected lrhA regulation (CitR/YbeF DNA-binding was not detected/predicted). The FlhDC iModulon includes FlhDC regulated genes that were upregulated in the ybeF and citR deletion mutants (Fig. S4B). LrhA is an LTF repressor for flhDC, flagellar biosynthesis genes responsible for motility and chemotaxis[21]. The deletion of ybeF showed downregulation of lrhA and upregulation of flhC. The iModulon FlhDC (Fig. S4) was substantially upregulated in ybeF mutant strain, suggesting connection for YbeF transcriptional regulation and flagella biosynthesis.

Table 1

Differentially expressed genes revealed by RNA-Seq ybdO deletion mutant strain and wild type E. coli strains during growth in M9 medium with glucose as the primary carbon source and 7 mM l-threonine as supplement.

	Gene name	Gene function	p value	Base Mean	log2 Fold Change
b2289	lrhA	DNA-binding transcriptional dual regulator LrhA	3.89E−26	145	−4.3
b1496	yddA	ABC transporter family protein YddA	0.000511	13	−3.2
b4462	ygaQ	Putative uncharacterized protein YgaQ	4.66E−05	15	−3.0
b2368	emrK	Tripartite efflux pump membrane fusion protein EmrK	0.000211	16	−2.8
b2273	yfbN	Uncharacterized protein YfbN	0.000348	16	−2.5
b2845	yqeG	Putative transporter YqeG	2.13E−05	24	−2.5
b2373	oxc	Oxalyl-CoA decarboxylase	0.00095	11	−2.1
b4660_1	yhiL	Uncharacterized protein	0.000401	28	−2.0
b2310	argT	Lysine/arginine/ornithine ABC transporter periplasmic binding protein	0.000795	761	−1.8
b2349	intS	CPS-53 (KpLE1) prophage prophage CPS-53 integrase	0.000511	101	−1.6
b3043	ygiL	Putative fimbrial protein YgiL	0.00100	10	−1.6
b2309	hisJ	Histidine ABC transporter periplasmic binding protein	0.000348	216	−1.4
b1025	dgcT	Putative diguanylate cyclase DgcT	0.001038	122	−1.4
b0854	potF	Putrescine ABC transporter periplasmic binding protein	0.000346	400	−1.4
b2306	hisP	Lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit	4.90E−05	264	−1.4
b0287	yagU	Inner membrane protein that contributes to acid resistance	0.000166	870	−1.2
b0641	lptE	Lipopolysaccharide assembly protein LptE	0.000226	146	1.2
b4316	fimC	Type 1 fimbriae periplasmic chaperone	2.37E−05	168	1.2
b0605	ahpC	Alkyl hydroperoxide reductase AhpC component	5.59E−07	585	1.2
b4315	fimI	Putative fimbrial protein FimI	0.000279	291	1.3
b0622	pagP	Lipid IVA palmitoyltransferase	7.10E−05	45	1.6
b2013	yeeE	Inner membrane protein YeeE	0.000163	315	1.7
b1729	tcyP	Cystine/sulfocysteine:cation symporter	0.000397	655	1.8
b2423	cysW	Sulfate/thiosulfate ABC transporter inner membrane subunit CysW	5.00E−05	110	2.0
b2424	cysU	Sulfate/thiosulfate ABC transporter inner membrane subunit CysU	1.29E−05	245	2.0
b1950	fliR	Flagellar biosynthesis protein FliR	0.000674	20	2.3
b2751	cysN	Sulfate adenylyltransferase subunit 1	2.77E−08	297	2.4
b1879	flhA	Flagellar biosynthesis protein FlhA	1.37E−09	190	2.5
b2752	cysD	Sulfate adenylyltransferase subunit 2	2.03E−08	249	2.5
b0601	ybdM	ParB-like nuclease domain-containing protein YbdM	0.000248	20	2.5
b2764	cysJ	Sulfite reductase flavoprotein subunit	1.62E−08	381	2.6
b2750	cysC	Adenylyl-sulfate kinase	1.34E−08	162.1	2.6
b4110	yjcZ	Uncharacterized protein YjcZ	2.81E−08	351.3	2.7
b2422	cysA	Sulfate/thiosulfate ABC transporter ATP binding subunit	4.46E−08	296	2.7
b2763	cysI	Sulfite reductase hemoprotein subunit	3.02E−09	567	2.8
b1070	flgN	Flagellar biosynthesis protein FlgN	2.32E−06	338	2.9
b1880	flhB	Flagellar biosynthesis protein FlhB	4.53E−10	118	3.0
b1071	flgM	Anti-sigma factor for FliA (sigma(28))	7.52E−05	86	3.0
b1946	fliN	Flagellar motor switch protein FliN	1.42E−05	30	3.1
b1566	flxA	Qin prophage protein FlxA	8.91E−06	402	3.1
b2762	cysH	Phosphoadenosine phosphosulfate reductase	3.14E−09	145	3.2
b3525	pdeH	c-di-GMP phosphodiesterase PdeH	6.75E−11	176	3.3
b1072	flgA	Flagellar basal body P-ring formation protein FlgA	4.65E−13	225	3.3
b0615	citF	Citrate lyase alpha subunit	3.40E−08	20	3.3
b1941	fliI	Flagellum-specific ATP synthase FliI	1.66E−11	165	3.4
b1948	fliP	Flagellar biosynthesis protein FliP	2.90E−10	40	3.5
b1081	flgJ	Putative peptidoglycan hydrolase FlgJ	8.01E−15	126	3.5
b1943	fliK	Flagellar hook-length control protein	7.25E−10	87.3	3.7
b1083	flgL	Flagellar hook-filament junction protein 2	5.67E−16	3080	3.7
b1080	flgI	Flagellar P-ring protein	3.67E−17	263	3.7
b1942	fliJ	Flagellar biosynthesis protein FliJ	1.46E−05	27	3.7
b1939	fliG	Flagellar motor switch protein FliG	3.18E−13	213	3.8
b1940	fliH	Flagellar biosynthesis protein FliH	1.09E−12	73	3.8
b1938	fliF	Flagellar basal-body MS-ring and collar protein	1.44E−24	645	3.8
b1945	fliM	Flagellar motor switch protein FliM	3.39E−18	174	3.9
b1078	flgG	Flagellar basal-body rod protein FlgG	2.24E−17	209	3.9
b1882	cheY	Chemotaxis protein CheY	2.68E−11	232	4.0
b0618	citC	Citrate lyase synthetase	3.64E−07	12	4.0
b1922	fliA	RNA polymerase sigma 28 (sigma F) factor	8.52E−18	3038	4.0
b1074	flgC	Flagellar basal-body rod protein FlgC	1.73E−19	130	4.1
b1887	cheW	Chemotaxis protein CheW	1.74E−16	345	4.1
b1944	fliL	Flagellar protein FliL	2.57E−11	46	4.1
b1079	flgH	Flagellar L-ring protein	1.32E−16	115	4.2
b1925	fliS	Flagellar biosynthesis protein FliS	4.36E−07	134	4.2
b4355	tsr	Methyl-accepting chemotaxis protein Tsr	2.59E−21	2250	4.2
b1923	fliC	Flagellar filament structural protein	3.74E−19	18,478	4.2
b1073	flgB	Flagellar basal-body rod protein FlgB	2.75E−20	268	4.3
b1077	flgF	Flagellar basal-body rod protein FlgF	2.31E−23	532	4.3
b1881	cheZ	Chemotaxis protein CheZ	1.19E−26	381	4.3
b1082	flgK	Flagellar hook-filament junction protein 1	1.75E−21	1771	4.3
b1924	fliD	flagellar filament capping protein	1.63E−16	623	4.3
b1947	fliO	Flagellar biosynthesis protein FliO	7.05E−16	68	4.4
b0616	citE	Citrate lyase beta subunit	7.69E−07	9	4.4
b1884	cheR	Chemotaxis protein methyltransferase	1.17E−11	158	4.4
b1075	flgD	Flagellar biosynthesis initiation of hook assembly	1.13E−21	400	4.5
b1883	cheB	Protein-glutamate methylesterase/protein glutamine deamidase	1.04E−20	415	4.5
b1921	fliZ	DNA-binding transcriptional regulator FliZ	7.56E−15	155	4.6
b1076	flgE	Flagellar hook protein FlgE	1.14E−22	677	4.6
b1890	motA	Motility protein A	4.60E−21	267	4.6
b1885	tap	Methyl-accepting chemotaxis protein Tap	9.03E−23	1642	4.6
b1888	cheA	chemotaxis protein CheA	1.33E−27	679	4.8
b1889	motB	Motility protein B	5.67E−26	410	4.8
b1886	tar	Methyl-accepting chemotaxis protein Tar	7.76E−31	1507	4.9
b1926	fliT	Flagellar biosynthesis protein FliT	0.000596	21	5.3
b0602	ybdN	Putative PAPS reductase/DUF3440 domain-containing protein YbdN	1.86E−22	36	5.5

YcaN and YbhD regulators mutant characterization

The ybhD and ycaN mutant strains and WT were collected at the late-exponential phase after growth in the M9 medium supplemented with Thr. The conserved gene cluster ycaN-ycaK-ycaM with adjacent ycaC and ycaD genes was detected in the Escherichia coli K12 and Shigella boydii genomes. We noticed that in the ycaN deletion mutant strain differentially expressed genes ycaC (downregulated) and ycaD, focA (encoding formate channel) (upregulated) are genes adjacent to ycaN. It is interesting that ycaK, ycaC, and ycaD are predicted to be regulated by Nac (belonging to LTF), as Nac function is nitrogen assimilation, and ycaC and ycaD are probably nitrogen assimilation function related (EcoCyc). In ycaN deletion mutant highly DEGs are the tnaAB genes, encoding l-tryptophanase and a tryptophan transporter, l-arginine degradation, astCADBE, an autoinducer-2 transport system (lsrABCD, lsrR), and the HTH-type transcriptional regulator, galS, the genes were strongly downregulated (Supplementary Data 1). The genes encoding amino acid metabolism (l-valine biosynthesis (IlvB, IlvN), threonine dehydrogenase (Tdh), transcriptional activator (TdcA), and glycolate utilization pathway (GlcC, GlcD, GlcF)) were additionally downregulated in the ycaN mutant. The ycaN deletion mutant phenotype microarray applied for 95 carbon sources had evolved the negative phenotype for formate utilization specifically suggesting YcaN dependent focA regulation involved formate utilization (Fig. 7).

The ybhD gene is divergently oriented with respect to the conserved Enterobacterial gene cluster ybhHI and the putative hydrolase gene, ybhJ (Fig. S5A). YbhH is a 4-oxalomesaconate tautomerase homologous protein, and YbhI is a putative tricarboxylate transporter, homologous to 2-oxoglutarate/malate translocator, (id. 35%) (iModulonDB) (Fig. S5B). The YbhH encoding gene was strongly upregulated in a ybhD deletion mutant, as shown by transcriptomic analysis. ybhH and ybhI transcription is regulated by Nac (EcoCyc, iModulonDB) and the functional relation to nitrogen assimilation is suggested. The ybhD deletion strain growth phenotype in the M9 minimal medium with glycerol (carbon source), supplemented by l-malate was detected (Fig. S6).

YgfI (DhfA) regulation and glycerol and formate utilization

ChIP-exo assays previously detected DhfA binding upstream of the dhaKLM operon encoding the dihydroxyacetone phosphotransferase (DHAK) (Fig. 3A-B). The transcriptional activation of DhaKLM is important for glycerol utilization and M9 supplemented by Thr or l-tryptophan (Fig. 3B) (iModulonDB). DHAK in the E. coli MG1655 strain is involved in glycerol utilization (Uniprot). Accordingly, we decided to test the effect of the dhfA deletion on the growth on glucose (Fig. 3C-D) and glycerol (Fig. 3E). The resulting deficiency in growth on glycerol is potentially explained by dhaKLM as well as pflB, hycBCD, hycEFG, and adhB transcriptional DhfA activation, as shown by RNA-seq (Table 2), and the DhfA binding site was predicted upstream of those genes (Table S1). The DEGs detected by RNA-seq showed substantial downregulation of formate fermentation related genes (Fig. 3F) encoding pyruvate-formate lyase (pflB), fumarate reductase (frdABCD), formate hydrogenlyase (hycBCD, hycEFG), and the regulator (hycA), as well as hydrogenase encoding genes (hybABC, hybEF, and hybO) and the gene encoding protein involved in maturation of all hydrogenases isozymes (hypB) (Fig. 3F) and the dhaKLM operon (Table 2, Supplementary Data). dhfA deletion had little effect on growth using glucose as the carbon source (Fig. 3C) and with Thr supplement (Fig. 3D) aerobically, but the dhfA strain had a low growth rate microaerobically without Thr supplement in minimal medium (Fig. S7).

Figure 3

The systems approach for YgfI transcriptional factor function prediction. (A-B) The genome-wide binding of YgfI and the zoom-in for the dhaK binding site. Transcriptomic profile for the YgfI regulated dhaK gene. (D-E) The YgfI function was assessed based on the growth phenotype under different conditions. The growth measurement of the ygfI mutant (orange line) compared to the wild type BW25113 strain of E. coli was measured in 96-well plates in M9 medium or the same medium supplemented with 7 mM l-threonine (C) or M9 medium with glycerol as the carbon source (F) The glycerol utilization pathway – glycerol kinase (GK, glpK), glycerol-3phosphate dehydrogenase (G3PDH, glpD), glycerol dehydrogenase (GlyDH, gldA), dihydroacetone kinase (DHAK, dhaKLM). RNA-seq differentially expressed genes are marked by a red arrow. Transcriptomic data analysis for the ygfI mutant compared to the wild type BW25113 strain of E. coli shows the glycerol and l-threonine utilization pathway genes (the DEGs are marked by arrows, predicted YgfI binding site marked by red stars) regulation. (G) The concentration (mM) for the formate (orange line) and acetate (blue line) produced by E. coli BW25113 WT (circles) and ygfI deletion mutant (triangles) strains in M9 glucose medium supplemented by 7 mM Thr (microaerobic conditions).

Table 2

Differentially expressed genes revealed by RNA-Seq ygfI deletion mutant strain and wild type E. coli strains during growth in M9 medium with glucose as the primary carbon source and 7 mM l-threonine as supplement.

	Gene name	Gene function	Base mean	log2 fold change
b2724	hycB	Formate hydrogenlyase subunit HycB	29.3	− 9.0
b1557	cspB	Qin prophage cold shock-like protein CspB	48.8	− 8.3
b1937	fliE	Flagellar basal-body protein FliE	66.8	7.7
b0990	cspG	cold shock protein CspG	10.2	− 7.6
b2727	hypB	Hydrogenase isoenzymes nickel incorporation protein HypB	53.6	− 7.5
b2921	ygfI	Putative LysR-type transcriptional regulator	21.6	− 7.3
b1922	fliA	RNA polymerase sigma 28 (sigma F) factor	3038.3	7.2
b3556	cspA	cold shock protein CspA	247.8	− 7.2
b0572	cusC	Copper/silver export system outer membrane channel	1017.0	7.1
b2720	hycF	Formate hydrogenlyase subunit HycF	37.7	− 7.1
b4335	yjiM	Putative dehydratase subunit	228.8	− 6.9
b1904	yecR	Lipoprotein YecR	6.0	6.6
b1938	fliF	flagellar basal-body MS-ring and collar protein	645.3	6.5
b1939	fliG	flagellar motor switch protein FliG	213.0	6.5
b2721	hycE	Formate hydrogenlyase subunit HycE	154.6	− 6.4
b1729	tcyP	Cystine/sulfocysteine:cation symporter	654.8	6.3
b4037	malM	Maltose regulon periplasmic protein	110.6	− 6.2
b1409	ynbB	Putative CDP-diglyceride synthase	2.4	− 6.1
b1674	ydhY	Putative 4Fe-4S ferredoxin-type protein	80.9	− 6.1
b2728	hypC	Hydrogenase 3 maturation protein HypC	5.7	− 6.1
b1072	flgA	Flagellar basal body P-ring formation protein FlgA	225.3	6.0
b1886	tar	Methyl-accepting chemotaxis protein Tar	1507.2	6.0
b1258	yciF	DUF892 domain-containing protein YciF	27.2	6.0
b1566	flxA	Qin prophage protein FlxA	402.2	6.0
b1887	cheW	Chemotaxis protein CheW	345.4	6.0
b2378	lpxP	Palmitoleoyl acyltransferase	422.4	− 5.9
b1073	flgB	Flagellar basal-body rod protein FlgB	267.6	5.9
b1375	ynaE	Rac prophage uncharacterized protein YnaE	4.5	− 5.9
b1923	fliC	Flagellar filament structural protein	18,478.4	5.8
b1880	flhB	Flagellar biosynthesis protein FlhB	118.3	5.8
b1942	fliJ	Flagellar biosynthesis protein FliJ	27.2	5.8
b2971	yghG	Lipoprotein YghG	3.4	5.8
b4380	yjjI	DUF3029 domain-containing protein YjjI	128.5	− 5.7
b4034	malE	Maltose ABC transporter periplasmic binding protein	402.0	− 5.7
b2997	hybO	Hydrogenase 2 small subunit	245.6	− 5.7
b1241	adhE	aldehyde-alcohol dehydrogenase	8441.5	− 5.7
b1925	fliS	Flagellar biosynthesis protein FliS	134.0	5.6
b1587	ynfE	Putative selenate reductase YnfE	250.8	− 5.6
b1083	flgL	Flagellar hook-filament junction protein 2	3080.4	5.6
b1552	cspI	Qin prophage cold shock protein CspI	6.3	− 5.6
b3370	frlA	Fructoselysine/psicoselysine transporter	2.1	− 5.5
b1589	ynfG	Putative oxidoreductase YnfG	87.0	− 5.5
b1890	motA	Motility protein A	267.0	5.4
b1940	fliH	Flagellar biosynthesis protein FliH	73.1	5.4
b0903	pflB	Pyruvate formate-lyase	23,055.8	− 5.4
b4355	tsr	Methyl-accepting chemotaxis protein Tsr	2250.0	5.4
b0849	grxA	Reduced glutaredoxin 1	8.0	5.4
b2995	hybB	Hydrogenase 2 membrane subunit	157.1	− 5.4
b2723	hycC	Formate hydrogenlyase subunit HycC	118.9	− 5.4
b0894	dmsA	Dimethyl sulfoxide reductase subunit A	454.5	− 5.4
b2722	hycD	Formate hydrogenlyase subunit HycD	50.9	− 5.4
b1944	fliL	Flagellar protein FliL	46.2	5.4
b4334	yjiL	Putative ATPase activator of (R)-hydroxyglutaryl-CoA dehdratase	50.6	− 5.3
b1946	fliN	Flagellar motor switch protein FliN	30.4	5.3
b4036	lamB	Maltose outer membrane channel/phage lambda receptor protein	191.8	− 5.3
b1757	ynjE	Molybdopterin synthase sulfurtransferase	335.9	− 5.3
b1531	marA	DNA-binding transcriptional dual regulator MarA	33.0	5.3
b2021	hisC	Histidinol-phosphate aminotransferase	960.3	− 5.3
b1751	ydjY	4Fe-4S ferredoxin-type domain-containing protein YdjY	133.1	− 5.2
b1926	fliT	Flagellar biosynthesis protein FliT	21.2	5.2
b4307	yjhQ	KpLE2 phage-like element putative acetyltransferase TopAI antitoxin YjhQ	2.1	− 5.2
b2024	hisA	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase	608.7	− 5.2
b1889	motB	Motility protein B	409.8	5.2
b4154	frdA	Fumarate reductase flavoprotein subunit	2376.0	− 5.2
b1112	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA	3.5	5.2
b0621	dcuC	Anaerobic C4-dicarboxylate transporter DcuC	120.9	− 5.1
b1878	flhE	Flagellar protein	27.4	5.1
b2020	hisD	Histidinal/histidinol dehydrogenase	1390.9	− 5.1
b1945	fliM	Flagellar motor switch protein FliM	174.1	5.1
b1885	tap	Methyl-accepting chemotaxis protein Tap	1641.7	5.0
b2022	hisB	Imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase	950.7	− 5.0
b0297	eaeH	Putative porin domain-containing protein EaeH	1.9	− 5.0
b3476	nikA	Ni2(+) ABC transporter periplasmic binding protein	126.7	− 5.0
b1080	flgI	Flagellar P-ring protein	263.1	5.0
b1742	ves	HutD family protein Ves	111.3	4.9
b1200	dhaK	Dihydroxyacetone kinase subunit K	127.4	− 1.4
b3634	coaD	Pantetheine-phosphate adenylyltransferase	40.9	2.6
b2025	hisF	Imidazole glycerol phosphate synthase subunit HisF	1087.6	− 4.9

The detected DhfA binding upstream of dhaKLM and the defect for the growth on glycerol (Fig. 3E) for the dhfA mutant confirm the DhfA-dependent transcriptional activation of DHAK, as DHAK is involved in glycerol utilization[22]. We suggest re-naming YgfI to DhfA—dihydroxyacteone/formate utilization activator. The fermentation products during microaerobic growth on M9 glucose were detected in the Thr supplemented M9 medium. The analysis evolved the higher efflux of formate and acetate for the dhfAmutant strain (Fig. 3G), suggesting that DhfA is important for formate utilization. The DhfA dependent activation of hyc and hyb operons was important the formate utilization microaerobically as was shown by the phenotype microarray analysis (Fig. 7).

YiaU (LpsR) regulatory network and yiaU mutant growth phenotype

ChIP-exo results show the LpsR binding for the regulation of waaP (encoding lipopolysaccharide (LPS) biosynthesis glycero-d-manno-heptose kinase) (Fig. 4A). The results suggest that LpsR is important for LPS biosynthesis at specific conditions and the majority of DEGs encode the proteins involved in cell wall/membrane/envelope biogenesis, carbohydrate transport, energy production, and amino acid metabolism (Fig. 4B). Accordingly, gene expression for the lpsR mutant was lower for the genes from the operon waaPSBOJYZU, suggesting that LpsR is the LPS biosynthesis operon activator (Table 3); previously the regulator for waa operon was not known (ecocyc.org). Additionally, ChIP-exo detected binding for the genes encoding adenine transporter, adeP, suggests transcriptional regulation, and they were detected as DEGs for the yiaU mutant (Fig. 4D). We suggest re-name YiaU to LpsR—LPS biosynthesis regulator. The Biolog plates with the antibiotics were tested microaerobically in RPMI10LB medium for the possible LTF waa operon activation in response to the stress. LpsR was found essential for survival at high concentration of oxacillin microaerobically (Fig. 4C) in RPMI_10LB medium. WaaZ and WaaY were shown to be essential for survival with nafcillin in E. coli[23]. The difference for the growth in exponential/log phase for the lpsR mutant strain had not been detected (Fig. 4D), although LpsR regulation had affected final OD600 (stationary phase) in the M9 glucose medium. The phenotype (log phase) for the mutant in M9 with 0.3 M NaCl added was additionally detected (Fig. 4D).

Figure 4

The systems approach for the function of the transcription factor YiaU. (A). The genome-wide binding of YiaU across the genome. (B). Clusters of Orthologous Groups (COGs) were enriched among the differentially expressed genes between the wild type BW25113 and yiaU mutant strains. (C). The phenotypes of the E. coli BW25113 and yiaU knockout strains in the Biolog plate PM12B, measured in RPMI_10LB medium for oxacillin at 4 different doubling concentrations. yiaU mutant strain (left panel) had a negative phenotype at the highest oxacillin concentration (8X) PM12B microarray (yellow line). The other antibiotics tested at 4 different concentrations are penicillin G, tetracycline, carbenicillin, penimepicycline, polymyxin B, paromomycin, vancomycin, d,l-serine hydroxamate, sisomycin, sulfamethazine, novobiocin, 2,4-diamino-6,7-dilsopropyl-pteridine, sulfadiazine, benzethonium chloride, tobramycin, 5-fluoroorotate, spectinomycin, l-aspartic-b-hydroxamate, spiramycin, rifampicin, dodecyl trimethyl ammonium bromide. (D). The growth measurement of the wild type and yiaU mutant strains under different conditions. Left panel: M9 glucose with l-threonine. Right panel: M9 glucose with l-threonine and 0.3 M NaCl. (E) Predicted structure and YiaU regulation of waa operon, yiaT and adeP in E.coli BW25113. The differentially expressed genes are shown by a red arrow. The waa and gltBD operon promoters are shown by a black arrow.

Table 3

Differentially expressed genes revealed by RNA-Seq of a yiaU knockout and wild type E. coli strains during growth in M9 medium supplemented with 7 mM l-threonine.

Locus tag	Gene name	P value	Base mean	log2 fold change
b3584	yiaT	9.32E−07	26	2.8
b1787	yeaK	6.57E−10	57	− 4.4
b2036	glf	1.01E−09	2378	− 2.6
b2035	wbbH	1.63E−07	694	− 1.9
b3714	adeP	7.68E−05	357	− 1.32
b3213	gltD	0.000187	3158	− 1.27
b2028	ugd	0.005533	74	− 1.27
b3624	waaZ	5.06E−05	121	− 1.79
b3625	waaY	2.08E−05	178	− 1.77
b3622	waaL	3.53E−08	352	− 2.81
b3623	waaU	3.98E−05	129	− 1.72
b3629	waaS	1.84E−08	263	− 2.57
b3631	waaG	8.90E−05	140	− 1.61
b3630	waaP	0.001681	99	− 1.44
b3627	waaO	0.003191	199	− 1.22
b3628	waaB	3.78E−05	168	− 1.76

The LysR family representatives are known to regulate adjacent genes, and lpsR-yiaT are conserved in the bacterial genomes (Fig. 4E). The RNA-seq results for the lpsR deletion mutant strain showed upregulation of the yiaT gene, encoding a predicted outer membrane protein membrane anchor for the surface display for the proteins, homologue of MipA. MipA is an MltA (murein-degrading enzyme) interacting protein.

YneJ (PtrR) regulatory effects for sad and fnrS transcription and putrescine utilization

Two distinct Ptr utilization pathways are known for E. coli (Fig. 5A). The first is catalyzed by the PuuA, PuuB, PuuC, and PuuD enzymes encoded by the puuP, puuA, puuDR, puuCB, puuE gene cluster and involves degradation of Ptr to γ-aminobutyric acid (GABA) via γ-glutamylated intermediates. The alternative pathway of Ptr degradation to GABA consists of PatA (Ptr aminotransferase) and PatD (γ-aminobutyraldehyde dehydrogenase)[24]. The PuuABCDE pathway is essential for Ptr utilization in E. coli using PuuP as the major Ptr transporter[25]. GABA is further utilized by two alternative 4-aminobutyrate aminotransferases (GABA-AT) encoded by gabT and puuE, and also two succinate semialdehyde dehydrogenases (SSADH) encoded by gabD and sad[26,27].

Figure 5

The experimental validation of the transcription factor YneJ (PtrR). (A) Overview of two alternative pathways of putrescine utilization in E. coli. PtrR-regulated genes are shown in yellow boxes. Transporters are shown in blue. Abbreviations: GABAld – gamma-aminobutyraldehyde, PatA—putrescine aminotransferase, PatD—gamma-aminobutyraldehyde dehydrogenase, YneI (Sad)—succinate-semialdehyde dehydrogenase, YneH (GlsB)—glutaminase. GadAB- two glutamate decarboxylase isoforms, GabD, Sad (YneI)-succinate-semialdehyde dehydrogenase, GlsB (YneH), glutaminase. (B) The growth measurement of the ptrR, yneH mutants compared to the wild type BW25113 strain of E. coli. The cell cultures were grown in M9 medium with 10 mM Glu/10 mM Ptr, as nitrogen sources and 0.4% glycerol (v/v) as the primary carbon source or (C) M9 glucose medium. (D) Transcriptomic data for sad (yneJ) and glsB (yneH) at different growth conditions for E. coli MG1655 strain and adapted MG1655 derivatives (iModulonDB, PRECISE2). The activation of the sad and glsB promoter at the ptrR mutant strain was detected.

We decided to characterize in detail the YneJ (re-named PtrR) by analyzing the PtrR ChIP-exo detected binding sites[1]. The ptrR gene is located in a conserved gene cluster with the divergently transcribed sad (yneI) gene, which encodes succinate semialdehyde dehydrogenase and yneH (glsB) glutaminase (Fig. 6A and 6C), upregulated in the evolved yneJ mutant strain (iModulonDB)[28]. To identify and characterize DNA binding sites of PtrR in the E. coli genome we utilized a combined bioinformatics and experimental approach. First, we applied a comparative genomic approach of phylogenetic footprinting[27] to predict putative PtrR-binding sites in the common intergenic region of the ptrR and sad genes (Fig. 6C, Fig. S8). The ptrR/sad genes are conserved in several taxonomic groups including Escherichia/Salmonella/Shigella, Citrobacter, Enterobacter, and Klebsiella, as well as in Pseudomonas spp. In E. coli and closely related enterobacteria the sad gene belongs to the putative sad-yneH gene cluster, while in Enterobacter and Citrobacter the orthologous genes include an additional gene encoding the methyl-accepting chemotaxis protein I (serine chemoreceptor protein, Mcp) (Fig. 6C). The multiple sequence alignment of ptrR/sad upstream regions from E. coli and closely related enterobacteria (termed Group 1 species) contains a conserved 15-bp palindromic sequence with consensus TTCACnAATnGAGAA downstream predicted sigma-E dependent promoter (Fig. 6A). We also analyzed upstream regions of ptrR orthologs in other enterobacterial genomes (Group 2 species), where the sad gene ortholog is absent and ptrR is co-localized with an uncharacterized MFS-family transporter gene. Further, we predicted two conserved DNA sites with similar consensus sequences located in their common intergenic region (Fig. 6C).

Figure 6

The systems approach for the function of the transcription factor PtrR. (A) The zoom-in of the PtrR-binding site at the promoter region of the ptrR (yneJ) and sad genes. Location of sigma-H and sigma-E promoters is from the EcoCyc database. (B) Fluorescent polarization assay of PtrR binding to the predicted operator site at sad gene. PhrR protein from Halomonas was used as a negative control. (C) The phylogenetic tree of PtrR orthologous proteins and predicted PtrR-binding motifs in E. coli and related genomes of Enterobacteria and Pseudomonas spp. The maximum likelihood phylogenetic tree was constructed using RAxML. The distinct genomic context of ptrR genes from two major tree branches (groups of PtrR orthologs) is shown by arrows with the following colors: black (ptrR regulator), yellow (sad for succinate semialdehyde dehydrogenase), green (yneH for glutaminase), pink (mcp for methyl-accepting chemotaxis protein), and blue (mfs for putative MFS-family transporter), while the predicted PtrR-binding sites are shown by black dots. Sequence logos of predicted DNA binding sites of PtrR from each of the two groups of analyzed species were constructed using WebLogo 2.0.

We further confirmed the identified putative PtrR-binding site upstream of the sad genes in E. coli and conducted genome-wide mapping of other PtrR-binding sites using the ChIP-exo method. To identify in vivo PtrR binding sites, E. coli was grown under glucose as the carbon source in the M9 minimal media. A total of nine PtrR-binding sites were detected in these experiments. PtrR binds in the promoter regions of the fhuC, moeB, dhaK, fnrS, gltS/xanP, and ptrR/sad genes. The experimentally identified 50-bp PtrR-binding region at sad/ptrR genes contains the conserved palindromic DNA motif identified via phylogenetic footprinting (Fig. S8). Comparison of this DNA motif with eight other regions containing experimentally mapped PtrR-binding regions did not reveal significant sequence similarity except for the PtrR-binding area at fnrS, which shares a common consensus with the identified DNA motif at sad/ptrR. We created multiple alignments of the upstream DNA sequences of closely related species with the beginning of the E. coli gene for fnrS and these binding sites corresponded to the ChIP-exo protected areas. The binding sites TTCACGAATCGaGAA, TTCtCGATTCGTGAA, and TgaAtGcAaCGTcAA were predicted for ptrR, sad(yneI), and fnrS, respectively.

Experimental assessment of the computationally predicted PtrR DNA-binding site TTCtCGATTCGTGAA in the sad promoter region has been facilitated using a PtrR-binding fluorescent polarization (FP) assay (Fig. 6B). The recombinant overproduced PtrR was obtained using a strain from the ASKA collection. The PtrR purification procedure is described in Supplemental materials. The binding of the purified refolded PtrR protein to synthetic DNA fragments containing the predicted PtrR-binding site was assessed using FP in the assay mixture containing 10 mM urea (Fig. 6B). Specific binding of PtrR to the DNA (5′-GGGTTCTCGATTCGTGAAGGG-3′) was detected at 0.6 uM of PtrR in contrast to the negative control (PhrR)[29]. The fluorescent polarization assay showed binding for the PtrR to the predicted sad binding site and the addition of GABA leads to dissociation of PtrR from the fluorescently labeled DNA (Fig. 6B), suggesting a regulatory function for Ptr/GABA catabolism for energy. If the Ptr utilization pathway intermediate, GABA, accumulates, PtrR de-repress sad and fnrS. The upregulation for sad and glsB had been detected for the yneJ mutant strain for adapted E. coli MG1655 mutant (deletion menF-entC-ubiC) (Fig. 5D)[28].

An E. coli BW25113 (WT) and ptrR mutant strain growth phenotype on glutamate as the nitrogen source in minimal medium (glycerol as the carbon source) has been detected for the growth. Cells showed a growth phenotype when the ptrR gene was deleted under the starvation conditions (Fig. S9); a decrease in the growth rate was observed for the ptrR mutant. The mRNA level for sad was higher in the ptrR mutant at these conditions (Table S2, Table 4). The ptrR mutation led to the upregulation of 121 genes.

Table 4

Differentially expressed genes revealed by RNA-Seq of a ptrR knockout and wild type E. coli strains during growth in M9 medium with l-glutamate and putrescine as nitrogen sources and glycerol as the primary carbon source.

Locus tag	Gene name	Gene function	P value	Base mean	log2 fold change
b0123	cueO	Blue copper oxidase CueO	1.53E−04	178	1.8
b0484	copA	Copper-exporting P-type ATPase	3.00E−05	521	1.8
b0570	cusS	Sensor histidine kinase CusS	4.39E−04	112	2.2
b0571	cusR	Transcriptional regulatory protein	2.97E−05	181	2.5
b0572	cusC	Cation efflux system protein CusC	1.42E−05	949	7.8
b0574	cusB	Cation efflux system protein CusB	3.81E−05	208	6.0
b0575	cusA	Cation efflux system protein CusA	6.52E−05	281	4.8
b0778	bioD1	ATP-dependent dethiobiotin synthetase BioD 1	1.11E−04	126	− 1.4
b1297	puuA	Gamma-glutamylputrescine synthetase	4.64E−07	706	1.9
b1298	puuD	Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD	6.21E−05	337	1.9
b1299	puuR	HTH-type transcriptional regulator PuuR	9.24E−05	113	1.3
b1302	puuE	4-aminobutyrate aminotransferase PuuE	3.16E−04	161	1.6
b1495	nuoK	NADH-quinone oxidoreductase subunit K	4.59E−07	73	− 1.9
b1496	yddA	Inner membrane ABC transporter ATP-binding protein YddA	1.25E−06	63	− 2.3
b1526	yneJ	Transcriptional regulator YneJ	9.41E−06	26	− 6.2
b1596	ynfM	Inner membrane transport protein YnfM	3.06E−04	221	− 1.5
b1656	sodB	Superoxide dismutase [Fe]	5.46E−05	323	4.8
b1717	rpmI	50S ribosomal protein L35	3.57E−05	55	2.4
b1886	tar	Methyl-accepting chemotaxis protein II	4.20E−05	298	1.4
b1889	motB	Motility protein B	3.08E−04	61	1.6
b2094	gatA	PTS system galactitol-specific EIIA component	6.09E−05	1719	− 1.4
b2106	rsnA	Nickel/cobalt efflux system RcnA	5.47E−07	323	− 1.5
b3858	yihD	Protein YihD	1.29E−06	42	2.6
b3938	metJ	Met repressor	3.84E−04	191	1.4
b4142	groS	10 kDa chaperonin	1.40E−04	197	1.9
b4207	fklB	FKBP-type peptidyl-prolyl cis–trans isomerase	2.03E−05	539	1.5
b4314	fimA	Type-1 fimbrial protein, A chain	3.46E−04	1118	1.4

The phenotype microarray using Biolog PM2A was tested under the microaerobic conditions for the ptrR mutant phenotype and the E. coli WT BW25113 strain. The phenotype using Glu as the energy/nitrogen source was minimal when D-glucosamine or dihydroxyacetone was the carbon source. The ptrR mutant defect in growth/respiration with glycine, l-ornithine, or gamma-hydroxybutyrate was observed using M9 medium with l-glutamate as the sole nitrogen source. Phenotypes for the ptrR mutant with d-tagatose, oxalomalic acid, gamma-hydroxybutyrate, glycine, and l-alaninamide were observed under the same conditions with Glu as a supplement (Fig. S10). The regulatory effect of PtrR during aerobic growth with putrescine/Glu as the nitrogen source was detected for M9 medium with glycerol as the primary carbon source. The growth of BW25113 (WT) as well as ptrR, yneH (glsB) null mutant strains are shown in Fig. 5B-C. The E. coli WT strain had a longer lag-phase compared to the ptrR mutant. A growth deficiency for a glsB mutant was observed under the same conditions, suggesting a functional relationship between GlsB (YneH) and Sad, encoding genes conserved in genome clusters with ptrR. The effect of a yneH deletion was substantial as cells approached the stationary phase.

PtrR-dependent regulation during growth with Ptr/Glu as nitrogen sources and antibiotic resistance

The E. coli WT and ptrR mutant were grown aerobically in M9 medium with 20 mM Glu and Ptr as nitrogen sources and 0.2% glycerol. To determine the effect of the ptrR deletion mutation, the cells were collected at the log-phase, and total mRNA was purified (see Materials and methods). PuuR and PuuADE, SodB, and two copper related transport systems’ mRNA levels increased in the ptrR mutant strain (Table 5). SodB (superoxide dismutase) mRNA was increased in ptrR mutant and SodB produced H2O2. The copA and cus operons are regulated by the CusSR and HprRS system. H2O2.is the effector for HprRS and likely has a transcriptional effect for the copA and cus system.

Table 5

Differentially expressed ptrR adjacent genes revealed by RNA-Seq ptrR(yneJ) deletion mutant strain and wild type E. coli strains during growth in M9 medium with glucose as the primary carbon source and 20 mM l-glutamate as nitrogen source.

Locus tag	Base mean	log2 fold change	p value	Gene name
b1525	222.2	1.32	0.022	sad
b1526	26.1	− 6.69	0.0003	yneJ
b1527	14.1	2.78	0.032	yneK

Antibiotic resistance induced by ptrR mutation in E. coli BW25113 was detected. We propose that PtrR negatively controls the FnrS small RNA, which is involved in regulation of MarA mRNA. MarA is a global regulator of E. coli genes involved in resistance to antibiotics, oxidative stress, organic solvents, and heavy metals[30]. We tested the ptrR mutant and wild type E. coli strains for antibiotic resistance using the Biolog plate 11C[31]. Since FnrS is under positive control of the global anaerobic regulator Fnr, E. coli was grown under microaerobic conditions. The ptrR mutant showed increased resistance to high concentrations of demeclocycline, a tetracycline group antibiotic, which survived after 42 h, in contrast to the wild type. We also detected the increased resistance of the ptrR mutant to chlorotetracycline (another tetracycline analog) (Fig. S11). However, with other antibiotics tested, no significant difference in growth of the mutant and wild type strains was observed.

Discussion

In this study, we applied a systems approach to characterize the transcriptional responses of seven putative LTFs: YbdO (CitR), YbeF, YbhD, YcaN, YiaU (LpsR), YgfI (DhfA), and YneJ (PtrR) (Table 6). The transcriptional response for the deletion of each LTF had been detected by RNAseq in M9 minimal medium supplemented by 7 mM l-threonine for all yTFs, except PtrR. The transcriptional analysis for the ptrR deletion mutant was detected in the M9 medium with Ptr and/or Glu as nitrogen source. For LTFs, conserved adjacent genes had been shown to be differentially expressed. For example, gene clusters encoding ybdNM and citrate utilization genes citCDEF (citrate lyase) were detected as transcriptionally regulated in the citR deletion mutant. The CitR DNA-binding site upstream of citR has been predicted and confirmed by ChIP-exo assay, suggesting autoregulation. CitR has been shown to be important for the growth in minimal medium supplemented by citrate at acidic conditions, suggesting citrate lyase regulation microaerobically. Additionally, flagella biosynthesis genes (FlhDC regulon) were differentially expressed in the mutant. The citR mutant in E. coli BW25113 fitness phenotype had been previously shown for motility in LB medium. Additionally, CitR is important for E. coli BW25113 fitness in minimal medium with glycolate as the carbon source (fit.genomics.lbl.gov), and D-glycine as the nitrogen source. The phenotype for formate and l-glutamate utilization citR deletion mutant was detected microaerobically (Fig. 7). YbeF is conserved in the gene cluster with citrate lyase encoding genes. The ybeF deletion leads to lrhA gene downregulation and upregulation of FlhDC regulated genes and, accordingly, the FlhDC iModulon.

Table 6

Summary of the yTFs newly characterized in this study. Abbreviation: LPS-lipopolysaccharide.

yTF gene name	Number of DEGs	DNA binding sites (ChIP-exo/DNA-binding predicted)	Predicted roles	Related references
YbdO	86	2/1 ybdO	Citrate utilization related, Flagella biosynthesis	2
YgfI	1402	2/9 dhaK, pflB, adhE, hycBCDEF, narZ	Dihydroxyacetone, glycerol or Thr utilization	2
YiaU	674	9/5 waaPSBOJYZU (operon), yjiT, adeP, yiaT, gltD	Membrane modification/ LPS biosynthesis	2
YcaN	702	6/2, ycaC, ycaD	unknown	2
YbhD	238	1/2, ybhH, ybhI	L-malate utilization related	2
YbeF	67	3/-	Flagella biosynthesis, putative citrate utilization related	2
YneJ	121	9/2, sad, fnrS	Putrescine utilization related	12–15, 17–19, 24–27

The YgfI (DhfA) DNA-binding site upstream of the dhaKLM operon for dihydroxyacetone phosphotransferase was detected by ChIP-exo. The transcriptome analysis shows that DhfA was important for regulation of dhaKLM, pflB, hycBCDEFG, narZYWV and adhB. The dhfA mutant growth phenotype using glycerol as a carbon source had been detected (Fig. 3C). The common DNA-binding motif upstream of the dhak, pflB, adhE, hycB, and narZ genes was found, but future experiments to confirm DhfA binding to the predicted DNA-binding sites are essential (Table 6). The PflB and hycBCDEFG encoded hydrogenlyase are involved in pyruvate and Thr utilization as energy source (Fig. 3F). The dhfA mutant growth deficiency on glucose as the carbon source in minimal medium at microaerobic conditions had been shown, but supplementation by Thr reduced the growth phenotype (Fig. S7), suggesting DhfA dependent pflB and hycBCDEFG activation important for anaerobic metabolism. dhfA deletion mutant phenotype had been detected in microaerobic conditions for formate utilization in minimal medium after incubation at 37 °C for 24 h (Fig. 7).

We suggest re-name YiaU to LpsR, lipopolysaccharide biosynthesis regulator. ChIP-exo detected multiple LpsR DNA-binding sites (Fig. 4A). The RNAseq transcriptomic analysis and ChIP-Exo (LpsR DNA-binding) additionally detected direct regulation of the waaPSBOJYZU operon gltB and adeP genes, suggesting LpsR relationship to glutamate metabolism. lpsR deletion mutant transcriptomic analysis suggested the regulation of yiaT, the conserved adjacent gene to lpsR, which is divergently transcribed and yeaK, encoding deacylase for mischarged aminoacyl-tRNA (l-serine, l-threonine) (Table 3, Fig. 4D). Thr supplement in minimal medium could lead to mischarged tRNA and LpsR is important for the yeaK regulation in the presence of Thr. The lpsR deletion leads to increased sensitivity to oxacillin in RPMI_10LB medium microaerobically and LpsR was found to have the effect on the biofilm formation previously[3].

The ybhD adjacent gene ybhH conserved in enterobacterial genomes was upregulated in the ybhD deletion mutant. The ybhH, ybhI, and ybhD genes are conserved adjacent genes and potentially regulated by Nac (EcoCyc). YbhI is the putative tricarboxylate transporter, homologous to 2-oxoglutarate/malate translocator, (id. 35%) (Fig. S8)[32]. We detected the ybhD deletion strain growth phenotype in the M9 minimal medium with glycerol (carbon source), supplemented by l-malate (Fig. S9), but not in the absence of l-malate, suggesting that the de-repressed ybhI and ybhH genes are probably involved in l-malate utilization (Table 6).

We detected that PtrR (YneJ) is the transcriptional regulator for Sad and the small RNA, FnrS. PtrR was predicted to be a repressor of the fnrS gene, encoding a small regulatory RNA (Table 6). We demonstrated PtrR binding to the predicted DNA-binding site. According to RNA-Seq data, PtrR is a repressor for sad under the nutrient limitation-stress conditions. The ptrR gene deletion effect was shown by growth phenotype (aerobically) and phenotype microarray data (micro-aerobically).

PtrR-mediated regulation appears to be important for Ptr utilization as an energy source. A pleiotropic effect of the PtrR-dependent regulation of the sad gene under nitrogen/carbon starvation has been investigated and discussed. The known stress/starvation sigma σS-controlled csiD-ygaF-gabDTP region is related to GABA utilization, while Sad is important for Ptr utilization[25,33-35].

Extracellular Ptr alters the OmpF porin charge and pore size, resulting in partial pore closure and a consequent decrease in outer membrane permeability[15,36]. Our results demonstrated that PtrR is important for the growth of the E. coli BW25113 strain with Glu as the sole nitrogen source and glycerol as the carbon source and resistance to the tetracycline group of antibiotics (i.e., demeclocycline and chlortetracycline), but not to chloramphenicol, erythromycin, and other antibiotics. PtrR is potentially important for the regulation of the highly conserved, anaerobically induced small RNA- fnrS, which is likely important for regulation under anaerobic growth conditions[37]. Interestingly, a ptrR mutant was shown previously to be resistant to bacteriophage lambda infection[38] and we found that PtrR is potentially related to tetracycline resistance[39]. ChIP-exo and RNAseq results have been analyzed, providing a hypothesis for the physiological functions of YneJ (tentatively re-named PtrR, putrescine related regulator), YgfI (tentatively re-named DhfA, dihydroxyacetone phosphotransferase and formate utilization activator), and YbdO (tentatively re-named CtrR, citrate utilization related regulator).

The identification of the additional DNA-binding sites for YgfI, YcaN, YiaU, YbeF, YneJ by gSELEX (genomic SELEX) method in the presence of Thr in the minimal medium possibly will provide additional information about novel LTFs transcriptional regulatory network[6,40]. LTFs are not always expressed under laboratory growth conditions (for instance, see Ishihama et al. J. Bacteriol. 196, 2718–2727, 2014).

Taken together, the systems analysis of the E. coli BW25113 and MG1655 strains transcriptomic data, ChIP-exo DNA-binding data for LTF, and the regulated biochemical pathway reconstruction and fitness/phenotype of the LTF deletion mutants strains produce fruitful hypotheses for the yTF function prediction that is important for TRN reconstruction in E. coli.

Methods

RNA sequencing

The wild type BW25113 strain was grown as a control for the isogenic ptrR mutant strain. Pre-cultures were obtained by scraping frozen stocks and growing the cells in LB medium. Cells were washed twice with M9 medium and inoculated to an OD600 of 0.05. The cells were collected at an OD600 of 0.9 (only ycaN, yiaU, ybhD mutants and the WT control were collected at OD600 of 2.0; late-exponential phase) and were harvested using the Qiagen RNA-protect bacteria reagent according to the manufacturer’s specifications. Pelleted cells were stored at − 80 °C, and after cell resuspension and partial lysis, they were ruptured with a beat beater; the total RNA was extracted using a Qiagen RNA purification kit. After total RNA extraction and subsequent ribosomal RNA removal, the quality was assessed using an Aglient Bioanalyser using an RNA 6000 kit. The data processing is described in Supplemental materials.

Protein purification

The PrtR-producing strain was grown overnight, re-inoculated into 50 mL of the fresh medium, and induced with 0.6 mM IPTG after an OD600 of 0.6 was reached. The cells were harvested after 4 h and lysed, the cell pellet was resuspended in the lysis buffer. Rapid purification of recombinant proteins on Ni-nitrilotriacetic acid-agarose minicolumns was performed. The protein was refolded on a mini-column, and the buffer was changed to a buffer containing 0.1 M Tris–HCl, 0.1 M NaCl, 10 mM urea.

Fluorescent polarization assay

The purified PtrR protein and 10 nM fluorescently labeled DNA fragment (5′-gggTTCTCGATTCGTGAAggg-3′) were incubated in the assay mixture. The PtrR binding assay mixture (0.1 ml) contained Tris buffer, pH 7.5, 0.1 M NaCl, 10 mM MgSO4, 5 mg/ml sperm DNA and 1uM of the fluorescently labeled predicted PtrR binding DNA fragment as well as 0–0.6 mM GABA. Then the PtrR protein (0–1.5 uM) was added to the assay mixture, and it was incubated for 1 h at 30 °C in the presence or the absence of GABA.

Targeted high-performance liquid chromatography

For organic acid and carbohydrate detection, samples were collected after 4 h for every 30–45 min. The filtered samples were loaded onto a 1260 Infinity series (Agilent Technologies) high-performance liquid chromatography (HPLC) system with an Aminex HPX-87H column (Bio-Rad Laboratories) and a refractive index detector and HPLC was operated using ChemStation software. The HPLC was run with a single mobile phase composed of HPLC grade water buffered with 5 mM sulfuric acid (H2SO4). The flow rate was held at 0.5 mL/minute, the sample injection volume was 10 uL, and the column temperature was maintained at 45 °C. The identities of compounds were determined by retention time comparison to standard curves of acetate, ethanol, glucose, lactate, pyruvate, formate and succinate. The peak area integration and resulting chromatograms were generated within ChemStation and compared to that of the standard curves to determine the concentration of each compound in the samples.

Phenotype microarray

The E. coli BW25113 wild type and ybdO, ygfI, ptrR mutant strains were grown overnight in M9 glucose medium, washed with M9 medium (PM1, PM2) or RPMI with 10% LB (RPMI_LB) for PM12B and inoculated as recommended to the Omnolog plates PM1, PM2, PM11C or PM12B, for the antibiotic resistance measurements at 37 °C. The experiments were repeated two times.

Supplementary Information 1.

Supplementary Information 2.