A simple BLASTn-based approach generates novel insights into the regulation and biological function of type I toxin-antitoxins

ABSTRACT

Bacterial chromosomal type I toxin-antitoxin systems consist of a small protein, typically under 60 amino acids, and a small RNA (sRNA) that represses toxin translation. These gene pairs have gained attention over the last decade for their contribution to antibiotic persistence and phage tolerance in bacteria. However, biological functions for many remain elusive as gene deletions often fail to produce an observable phenotype. For many pairs, it is still unknown when the toxin and/or antitoxin gene are natively expressed within the bacterium. We examined sequence conservation of three type I toxin-antitoxin systems, tisB/istR-1, shoB/ohsC, and zor/orz, in over 2,000 Escherichia coli strains, including pathogenic and commensal isolates. Using our custom database, we found that these gene pairs are widespread across E. coli and have expression potential via BLASTn. We identified an alternative, dominant sequence variant of TisB and confirmed that it is toxic upon overproduction. Additionally, analyses revealed a highly conserved sequence in the zorO mRNA untranslated region that is required for full toxicity. We further noted that over 30% of E. coli genomes contain an orz antitoxin gene only and confirmed its expression in a representative strain: the first confirmed report of a type I antitoxin without its cognate toxin. Our results add to our understanding of these systems, and our methodology is applicable for other type I loci to identify critical regulatory and functional features.

IMPORTANCE

Chromosomal type I toxin-antitoxins are a class of genes that have gained increasing attention over the last decade for their roles in antibiotic persistence which may contribute to therapeutic failures. However, the control of many of these genes and when they function have remained elusive. We demonstrate that a simple genetic conservation-based approach utilizing free, publicly available data yields known and novel insights into the regulation and function of three chromosomal type I toxin-antitoxins in Escherichia coli. This study also provides a framework for how this approach could be applied to other genes of interest.

INTRODUCTION

Tolerance to environmental stress is key for bacterial survival. The production of toxins from chromosomal toxin-antitoxin systems has been implicated in a variety of stress tolerance mechanisms, including antibiotic persistence or resistance and phage exclusion (reviewed in reference 1)]. These gene pairs encode a toxin that, when overproduced, leads to cell death, and an antitoxin which represses this toxicity. Toxin-antitoxin systems are defined by the nature (protein or RNA) of the toxin and antitoxin and the mechanism of toxin repression, ranging from type I to type VIII, with type I and type II being the most well characterized (1). For the type I toxin-antitoxin systems, these encode a small (under 60 amino acids) toxic protein which induces cellular stasis or death upon overproduction and a small RNA (sRNA) that base pairs to the toxin mRNA, preventing its toxicity (2, 3).

Initially, type I toxin-antitoxin systems were described on plasmids where they serve a role in plasmid maintenance. Later, chromosomal pairs homologous to plasmid pairs as well as chromosomal systems with no homology to plasmid sequences were identified. For many chromosomal pairs that lack plasmid homology, their true biological function is unknown. Deletion of either the toxin or antitoxin encoding gene often has no observable phenotype. This is why, following confirmation of toxicity (and repression of toxicity) via overexpression, research toward a biological function can stall. For the best described chromosomally encoded type I toxin, TisB, unraveling its function was in part possible due to identification of a conserved LexA binding site in its promoter which led investigators to perform experiments demonstrating a role for TisB during the SOS response (4). Thus, regulation knowledge can aid in functional analysis of type I toxins.

While the regulation of the TisB toxin as it relates to function is well defined, this has not been the case for many other chromosomal type I systems (5–7). One reason for this is that attempts to identify novel regulatory mechanisms bioinformatically have had limited success. This is likely due to a combination of the limits of bioinformatic identification of regulatory sequences and the fact that only a single locus is used as a DNA sequence query for such approaches. To our knowledge, no one has examined the conservation of any type I toxin-antitoxin sequence across a single bacterial species. We hypothesized that, by using such a conservation-based approach, we could identify novel features of type I systems, including regions that may contribute to regulatory function or activity.

We therefore created a custom nucleotide database of complete Escherichia coli genomes from National Center for Biotechnology Information (NCBI) and used a BLASTn approach to examine sequence conservation of three chromosomal type I toxin-antitoxins from E. coli (tisB/istR-1, shoB/ohsC, and zor/orz) whose functions have been either directly or indirectly implicated in antibiotic persistence or resistance (8–10). Using this approach, we confirmed that the −35 and −10 promoter elements as well as ribosome binding sites (RBS) and other regulatory regions were highly conserved for the pairs examined. We also predicted and confirmed a regulatory element within the 5′ untranslated region (UTR) of the zor toxin mRNA that contributes to its toxicity. Additional analyses also indicated that tisB/istR-1 and zor/orz copy number correlates with intestinal disease isolates. Surprisingly, we identified that nearly a third of all E. coli possess an orz antitoxin gene without its cognate toxin gene: this provides impetus for future studies examining roles for antitoxins beyond just toxin repression.

RESULTS

Generation of a custom E. coli nucleotide database

To examine regions of high conservation as a means of identifying important regulatory sequences, we first created a custom database (Fig. 1A, Materials and Methods) from complete assembled genomes of E. coli available on NCBI (11). We designated each as an environmental or laboratory strain/isolate when possible. Environmental referred to strains isolated from known environments and included human/animal commensals or pathogenic variants. Laboratory isolates referred to strains used for cloning (e.g., K12 derivatives) or designated as laboratory/lab in their BioSample information. Following isolation source designation, we noted duplication of some specific isolates (e.g., E. coli MG1655) and therefore removed duplicates from all analyses, resulting in a total of 2,212 total genomes analyzed. Note that some isolates within the laboratory category were known or likely derivatives of E. coli MG1655 or E. coli B; however, we retained these derivatives for our analyses due to potential variation in the number of copies of the toxin-antitoxin systems analyzed. The breakdown of the distribution of these strains within our database, along with geographic and pathotype information (see below), can be found in Fig. 1B. Overall, the custom database used in this study represented E. coli with diversity in isolation location, source, and pathotype.

Fig 1.

Details of custom E. coli nucleotide database utilized in this study. (A) Outline of custom database construction and (B) isolation location, sources, and pathotype of E. coli genome assemblies included in the final custom database.

MG1655 TisB is not the dominant protein variant

As proof of concept, we first examined conservation of tisB/istR-1 as it is the best described chromosomally encoded type I toxin-antitoxin system in E. coli. Transcription of the toxin gene tisB is repressed by LexA such that expression occurs in response to DNA damage (4); the small RNA IstR-1 can base pair to the tisB mRNA and prevent its translation. Base pairing of IstR-1 blocks a standby ribosome binding site, which is needed for translation of tisB (12). If the toxin escapes mRNA repression, production of TisB results in the formation of highly tolerant cells (persister cells) to specific antibiotics (8, 13, 14). The locus also possesses tisA, which encodes an open reading frame (ORF) upstream of the tisB ORF, and encodes IstR-2, an elongated version of IstR-1 that is only transcribed during SOS response and does not repress tisB translation (4, 15).

The full locus from MG1655 containing the entire intergenic region between tisB and istR-1 and all transcribed regions was used as a query for BLASTn (16), depicted in Fig. 2A [includes tisA and istR-2 in the region (4); for simplicity, referred to herein as tis/istR]. Raw and summarized results can be found in Table 1 and Tables S1 and S2.

Fig 2.

Conservation of the tis/istR locus across E. coli. (A) Genomic organization of tis/istR MG1655, (B) nucleotide sequence conservation of full tis/istR loci, (C) amino acid sequence conservation of TisB, and (D) amino acid sequence conservation of TisA. SD refers to the Shine-Dalgarno sequence. Note that the MG1655 amino acid sequence for TisB contains an asparagine (N) at the second position. For amino acid logos, positively charged/basic residues are in blue, negatively charged/acidic residues are in red, non-charged polar residues are in green, and hydrophobic residues are in black with neutral residues in purple.

TABLE 1.

Tis/IstR sequence conservation summary for full matches compared to E. coli MG1655

	TisB (toxin)	IstR-1 (antitoxin)	TisA (ORF)	IstR-2 (RNA)	Regulation
−35	N/Aa	99.8% (TTGCGC)	N/A	94.5% (TGGACA)	Transcription
−10	99.8% (TATAAT)	100% (TATACT)	99.8% (TATAAT)	99.8% (GATACT)	Transcription
LexA (from MG1655)	93.5%				Transcription
RSS	99.9% (see Fig. 2)	N/A	N/A	N/A	Translation
RBS	100% (AGGAGA)	N/A	N/A	N/A	Translation
ORF	99.9% (29 aa)	N/A	99.6% (37 aa)	N/A	Translation

^a N/A, not applicable.

We found that, across all tis/istR loci, promoter elements were highly conserved (Table 1; Fig. 2B), with 94% containing the annotated LexA binding site and −10 and −35 promoter sequences for tisAB, istR-1, and istR-2 found in MG1655. The predicted ribosome standby site (RSS) and RBS for tisB were >99% conserved. However, the consensus TisB protein sequence (85%) contained a serine at the second position which is different from the asparagine found in MG1655 (Fig. 2C). Overproduction of this consensus TisB (tisB-N2S) from an arabinose-inducible promoter on a multicopy plasmid revealed that tisB-N2S was more toxic than the MG155 tisB when induced at lower arabinose levels (0.0005%). Induction at high levels of arabinose (0.2%) resulted in equivalent toxicity between TisB and TisB N2S (Fig. 3A through D). There was no difference in cell survival over a 6-h exposure to ciprofloxacin when tis/istR from MG1655 with TisB or TisB N2S was present on a multicopy plasmid (Fig. 3E), suggesting the increased toxicity did not impact persister cell formation.

Fig 3.

Differential toxicity between the MG1655 TisB and the consensus TisB. (A–D) E. coli UTK007 ∆tis/istR harboring either pAZ3-tisB (solid lines) or pAZ3-tisB-N2S (dotted lines, encoding the consensus TisB) was grown to OD₆₀₀ ~0.25, split into two cultures as indicated by the arrow, with arabinose added to a final concentration of 0.0005% or 0.2% (induced). Note A and B represent OD₆₀₀ values over time while C and D are the log ratios of surviving colonies over time. (E) E. coli UTK007 ∆tis/istR harboring either pBR322-tis/istRmg (solid lines) or pAZ3-tis/istRmg-tisB-N2S (dotted lines, encoding the consensus TisB) was grown to OD₆₀₀ ~0.25, split into two cultures (T = 0 h), with ciprofloxacin added to a final concentration of 1 µg/mL as indicated. Shown are the averages and standard deviations for N = 3. * indicates a difference between induced and uninduced or treated vs untreated controls at a P < 0.05 calculated via multiple paired t-tests. (F) TisB consensus for lab strains and (G) non-lab strains.

We further examined whether TisB from MG1655 is a lab strain-specific protein variant by examining conservation of TisB in lab vs non-lab strains. Lab strains from the K-12 lineage contain TisB while those from the B lineage contain TisB N2S (Fig. 3F through G; Table S2). These data suggest that when the lab strains were originally isolated from their environmental host (see references 17–19 for lab strain ancestry), they contained one of the naturally occurring TisB variants.

Despite no experimental evidence that the tisA ORF is translated, >99% of E. coli containing a tis/istR locus encoded the 37 amino acid ORF with high protein sequence conservation (Fig. 2D). The biological implications of this are currently unknown.

High conservation of predicted regulatory elements of the shoB/ohsC locus across E. coli

Given the strong conservation observed for the LexA binding site above, we examined whether known transcription factor binding sites were conserved in another type I toxin-antitoxin locus. The chromosomal type I toxin-antitoxin shoB/ohsC (20, 21) has been indirectly implicated in the ability of E. coli to survive the antibiotic colistin (10). Like tis/istR, this locus contains a type I toxin gene, shoB, and an antitoxin gene, ohsC. The transcription factor CpxR was found to regulate shoB and ohsC at two proposed binding sites, named Cpx binding (CB1) and CB2 (22). However, it is not known whether binding of CpxR to one or both CB sites regulates shoB and/or ohsC in vivo. We used the shoB/ohsC sequence from MG1655 as our query (Fig. 4A), to examine the presence of CB site (20, 23), the results of which can be found in Table 2 ; Tables S3 and S4.

Fig 4.

Conservation of the shoB/ohsC locus across E. coli. (A) Genomic organization of shoB/ohsC MG1655, (B) nucleotide sequence conservation of full shoB/ohsC loci and (C) amino acid sequence conservation of ShoB. For amino acid logos, positively charged/basic residues are in blue, negatively charged/acidic residues are in red, non-charged polar residues are in green, and hydrophobic residues are in black with neutral residues in purple.

TABLE 2.

ShoB/OhsC sequence conservation summary compared to E. coli MG1655

	ShoB (toxin)	OhsC (antitoxin)	Regulation
−35	99.9% (GTGACC)	66.8% (TTGTAA), 33.1% (TTGTAC)	Transcription
−10	99.6% (TAAAAT)	100% (CATAAT)	Transcription
CB1 (from MG1655)	91.3%		Transcription
CB2 (from MG1655)	52.2%		Transcription
RBS (AAGGAA)	100%	N/A	Translation
ORF (26 aa)	>99.9%	N/A	Translation

Conservation of CB1 across strains was high with 91% having the identical sequence of MG1655 (Table 2; Fig. 4B). In contrast, only 52% of loci had the same CB2 as MG1655 with the region encompassing CB2 being highly variable. Additionally, except for the −35 of ohsC which overlaps with CB2, >99% of shoB/ohsC had the identical promoter elements, RBS, and ORF length for shoB and ohsC as MG1655. The consensus ShoB amino acid sequence can be found in Fig. 4C.

High conservation of type I toxin-antitoxin zor/orz reveals a novel sequence that controls ZorO-induced toxicity

Finally, we wanted to examine whether this approach could be used in a system not identified in E. coli MG1655 but possessed in a pathogenic variant, E. coli O157:H7 EDL933 (referred to herein as EDL933). The zor/orz locus was initially identified in 2010 as two tandemly encoded, highly similar toxin-antitoxin pairs, zorO/orzO and zorP/orzP, with a zor gene encoding a 29 amino acid toxin protein and an orz gene encoding the antitoxin (21, 24). Translation of zorO is repressed by its own 5′ UTR (25). Processing of the 5′ UTR results in a single-stranded open region (termed EAP, for “exposed after processing,”) far upstream of the ribosome binding site. This EAP region is required for robust translation but is also where the OrzO antitoxin binds. Multiple copies of the zor-orz locus from EDL933 or just the zorO-orzO pair increased the minimum inhibitory concentration of aminoglycoside antibiotics and reduced lag in sublethal levels of kanamycin, though the mechanism is unknown (9, 26). We initially examined zor/orz sequence conservation with zorO/orzO from EDL933 as a query (depicted in Fig. 5A). Follow-up queries are described in Materials and Methods.

Fig 5.

Conservation of the zor/orz locus across E. coli. (A) Genomic organization of zor/orz EDL933, (B) nucleotide sequence conservation of full zor/orz loci (includes all copies in strains containing more than one zor/orz copy), and (C) amino acid sequence conservation of Zor. For amino acid logos, positively charged/basic residues are in blue, negatively charged/acidic residues are in red, non-charged polar residues are in green, and hydrophobic residues are in black with neutral residues in purple.

Across all zor/orz, promoter elements were highly conserved with 99% or more loci containing the same −10 and −35 promoter sequences as found in EDL933 (Table 3; Tables S5 to S10; Fig. 5B). ZorO, the product of the zorO gene from EDL933 (21), was the dominant protein sequence identified from 72.5% of all zor ORFs. Major protein variants identified also included ZorP and ZorQ with amino acid differences relative to ZorO of T3S and A20S, respectively (Fig. 5C). In this case, ZorP refers to the product of the zorP gene from EDL933 (21), while ZorQ represents a common protein variant of a third locus type, zorQ/orzQ (see Materials and Methods).

TABLE 3.

Zor/Orz sequence conservation summary for full matches to zor/orz or orz-only loci compared to EDL933^a

	Zor (toxin)	Orz (antitoxin)	Regulation
Full zor/orz loci
−35 (TTGCAA)	99.4%	99.4%	Transcription
−10 (TATAAT)	100%	99.8%	Transcription
Base-pairing potential (based on Wen et al. [24])	99.8%		Post-transcription
RBS (AAGGAG)	99.8%	n/a	Translation
ORF (29 aa)	99.5%	n/a	Translation
orz-only loci
−35 (TTGCAA)	99.7%	99.7%	Transcription
−10 (TATAAT)	100%	98.9%	Transcription

^a A total of 2,439 full zor/orz were analyzed and 656 orz-only loci were analyzed.

The region of base pairing between the zor mRNA and Orz sRNA was quite variable. This variation may prevent crosstalk between zor/orz loci in multicopy strains as is the case for zor-orz from EDL933 (24). We previously demonstrated that either 15 nucleotides of continuous base pairing or 17 nucleotides of discontinuous base pairing with one internal mismatch was sufficient for OrzO to repress ZorO-induced toxicity (24). Using these as requirements for repressive activity, we determined that 99.8% of Orz in full zor/orz have the potential to repress their cognate zor (Table S11).

The EAP region of zorO was hypothesized to contain a ribosome standby site similar to the tisB mRNA that allows for increased ribosomal interaction and translation of the toxin (2, 12, 27, 28). While ribosomal binding to the EAP of zorO has not been demonstrated, removal of a portion of the EAP sequence did reduce translation efficiency (25). We noted that, within the zor/orz EAP consensus, there was a conserved “GGAGTG/AG” sequence that resembled a ribosome binding site (Fig. 6A). We mutated the GAG of this sequence to CTC in a plasmid that overproduces the toxic-processed (Δ28zorO) variant from EDL933 and compared its overproduction to the wild-type sequence. As shown in Fig. 6B and C, mutation of these residues reduced toxicity compared to the parental plasmid.

Fig 6.

Identification of critical residues for toxicity in the 5´ UTR of zor. (A) DNA consensus from all zor/orz for the EAP region originally identified in zorO from strain EDL933. Nucleotides 245–250 represent a possible ribosome standby site. GAG (boxed) indicates sequence mutated to CTC in pAZ3-Δ28zorO-CTC. (B) E. coli UTK007 harboring either pAZ3-Δ28zorO or pAZ3-Δ28zorO-CTC was grown to OD₆₀₀ 0.25, split into two cultures as indicated by the arrow, and arabinose was added to a final concentration of 0.0001% (induced). Shown are the averages and standard deviations for n = 3. * indicates a difference between induced and uninduced controls at a P < 0.05 calculated via multiple paired t-tests.

Copy number analysis reveals presence of widespread orz antitoxin-only strains

It was previously suggested that copy number of toxin-antitoxins may correlate with pathotype, but given a limited number of complete E. coli genomes at the time, a thorough investigation was not performed (21). To test the hypothesis that copy number varies by pathotype, we first quantified the variability in copy number across all E. coli in our database.

Eighty-two percent of E. coli had one full match to tis/istR, 3% had an interrupted match, and 15% had no match to tis/istR. For shoB/ohsC, E. coli contained either a full (98%), interrupted (1%), or no match (<1%) to shoB/ohsC. In addition, two antitoxin-only strains were identified for shoB/ohsC. Copy number designations and evidence of insertion or deletion events for interrupted and antitoxin-only strains were noted in Tables S2, S4, and S10.

For zor/orz, we found that 3% of the 2,212 assemblies contained no match to zor/orz, 25% had one full match to zor/orz (i.e., a single toxin-antitoxin pair), 42% had two full matches to zor/orz, and <0.1% had a disrupted locus (Fig. 7A; Table S10). A minority of genomes were unusual in their copy number for zor/orz. Sixteen had three full zor/orz loci, six had one full locus with an additional orz (1.5 copies), and an isolate from a human patient contained four copies of zor/orz on its chromosome. Unlike for tis/istR1 and shoB/ohsC, we did identify a two-copy zor/orz locus on a plasmid (p11A_p2) from a hospitalized patient, though these were identical to the chromosomal copies (Table S10).

Fig 7.

Evidence of antitoxin-only strains. (A) Copy number variation for zor/orz in lab and environmental strains of E. coli detected via BLASTn. Copy number of 0.5 refers to containing one orz-only locus; a copy number of 1 has one zor/orz locus; a copy number of 1.5 has one zor/orz locus and an additional orz-only locus, etc. (B) Nucleotide sequence conservation of orz loci in orzP-only strains. (C) OrzPmg detection in MG1655. Northern blot of total RNA from strain MG1655 or the ΔorzPmg derivative isolated from cells grown to OD₆₀₀ 0.3 and 24 h post-inoculation. Shown is a representative of three biological replicates.

Surprisingly, approximately 30% of genomes lacked an intact zor toxin gene but possessed solely an antitoxin (orz) gene. In >99% of these orz-only assemblies, 27–29 nucleotides of the zor 5′ UTR was still present as determined via an alignment to zorP from EDL933. Since these fragments of the zor UTR did not contain the toxin open reading frame nor did they possess the base-pairing region for Orz interaction, these strains were considered to be “orz-only” (antitoxin only; 0.5 copies). In 96% of cases, these orz-only loci share highest similarity to orzP from strain EDL933 and were highly similar to each other (Fig. 7B).

Given this finding, we wanted to determine if an orphan orzP was expressed. We examined dRNA-Seq of MG1655 published previously and noted a possible transcript in this region of MG1655 (an orz-only variant [29, 30]). We confirmed this via northern analysis in MG1655 and a derivative deleted for the gene (Fig. 7C). Given that the sequence in MG1655 was 100% identical to the previously identified OrzP antitoxin from EDL933, we named this sRNA OrzPmg.

We also detected 18 partial matches on plasmids to a ~113 nucleotide segment of the zor 5′ UTR, but this segment, which ranged from 71% to 74% identity to the analogous zor sequence, was ~35 nucleotides upstream of a dinQ toxin ORF, suggesting that this was in fact part of a potential dinQ 5′ UTR and not a zor 5′ UTR (Table S6). To our knowledge, no evolutionary relationship has been proposed between the zor/orz and the dinQ/agrB toxin-antitoxin families.

Metadata analysis of zor/orz and tis/istR provides potential link between copy number and pathotype

Given that we detected notable variation in copy number for tis/istR and zor/orz but minimal variation for shoB/ohsC, we sought to determine whether copy number would vary by general pathotype for tis/istR and zor/orz. We indeed found that pathotype correlated with differences in copy number variation for tis/istR and zor/orz (Fig. 8). Post hoc analysis using a Monte Carlo Tukey test indicated that differences in copy number among pathotypes were driven by the intestinal disease-causing isolate group: intestinal disease-causing isolates were both more likely to have tis/istR (P < 0.05 for all comparisons; n = 605, 10⁴ resampling iterations) and to have more copies of zor/orz (P < 0.05 for all comparisons, n = 605, 10⁴ resampling iterations) than the other pathotype groups analyzed. We found that there may be a correlation in zor-orz copy number distribution dependent upon geographical isolation, but these differences were modest (Materials and Methods).

Fig 8.

Copy number variation in environmental E. coli strains by pathotype for (A) tis/istR and (B) zor/orz. For pathotype designation, the category refers to the disease the sample can cause in humans (see Materials and Methods). Healthy samples came from human stool, rectal, or other gastrointestinal sources that were designated as being from a healthy host.

BLASTn identifies zor/orz genes that PSI-BLAST and tBLASTn do not

We also compared the BLASTn-based method employed in this study to the most commonly used bioinformatic approaches to identify type I toxin-antitoxin loci, i.e., PSI-BLAST and tBLASTn, which use only toxin amino acid sequences as the query. We found that, while tBLASTn was able to detect most Zor ORFs (seven were undetected; see Materials and Methods for settings), PSI-BLAST failed to detect the majority of Zor ORFs (Tables S12 to S15). This is likely because PSI-BLAST relies on prior annotation of ORFs which, when performed automatically, often miss small ORFs. Neither could detect orz-only loci as these loci did not contain an ORF. It is important to note that PSI-BLAST and tBLASTn did not detect zor toxin genes that were not also detected via BLASTn. Together, a BLASTn may be a more sensitive approach to identifying both type I toxin and antitoxin genes in a single species of interest.

DISCUSSION

The initial goal of our study was to investigate whether nucleotide conservation of type I toxin-antitoxins could identify novel sequences related to the regulation and possible function of these loci. By using a custom genomic database for over 2,000 E. coli strains, we identified conserved sequences and features for three chromosomally encoded type I toxin-antitoxin systems. We were able to correlate copy number of tis/istR and zor/orz to intestinal disease-causing isolates, as well as uncovered the widespread presence of an antitoxin-only locus (orz-only) that is conserved across environmental and laboratory strains of E. coli. We validated expression of this antitoxin via northern analysis in an orz-only strain.

The results of this study highlight the power of BLASTn-based conservation approaches for identifying known type I toxin-antitoxin loci within a single species of interest. For example, BLASTn detected genes from these loci that had not been detected previously, such as for orz antitoxins in orz-only strains that were not detected via PSI-BLAST or tBLASTn. This nucleotide-based conservation approach generated hypotheses for previously described toxin-antitoxin pairs. While it was proposed that the zor 5′ UTR contained a ribosome standby site (25), it was not testable until the consensus generated in this approach revealed a sequence reminiscent of an RBS. This observation allowed for targeted disruption of that sequence to identify its impact on toxicity (Fig. 6C). Therefore, the use of simple bioinformatics approaches can provide needed insight into regulatory features of a type I toxin-antitoxin pair.

We were surprised to note that, often, >99% of −35 and −10 promoter elements for these toxin-antitoxin genes across the strains in our database were identical to the reference query genome (MG1655 or EDL933). To our knowledge, no one has examined sequence conservation of these specific elements for a gene across a single species. We used our BLASTn approach for three other non-essential σ⁷⁰-controlled genes (sodA, araC, ompC) in MG1655 and compared their −10 and −35 sequences across the isolates in our database (see Materials and Methods). We found that for the matches obtained, 100% had the exact same −10 and −35 promoter elements (Tables S16 to S19). Thus, the high levels of conservation for the type I toxin-antitoxins examined was not outside the norm for σ⁷⁰-controlled, non-essential genes. It should be noted that, even though these three genes were considered to be non-essential for E. coli (31), 99.1%–99.8% of the strains within our database contained at least one full match to each after identification via BLASTn. Therefore, it is possible that these genes conferred a fitness advantage in nature which could impact conservation estimates.

While several questions relating to the regulation of these three toxin-antitoxin systems in E. coli were addressed by the results of this study, what perhaps was more impactful was the new questions this study generated. One is whether a type I antitoxin could be performing a function in the absence of a type I toxin. A significant portion of genomes analyzed contained only an orz antitoxin sequence fully intact. We noted as well that a large portion of lab strains are orz only. When examining the history of E. coli lab strain variants, it appears that most are derived from a few (possibly only one or two) original isolates (17–19). Thus, this enrichment is likely due to chance as some non-lab E. coli strains possess only orz.

In orz-only strains, both the transcriptional regulatory sequences and the transcribed region itself are highly conserved. In E. coli MG1655, the promoter sequence and transcribed region for orzPmg are 100% identical to the orzP gene found in pathogenic E. coli. We confirmed the presence of this RNA both via direct northern analysis and noted its detection by others via dRNA-Seq (29, 30). No evidence in the literature suggests type I antitoxins may function beyond toxin repression. However, NikS in Helicobacter pylori is a small RNA that regulates major virulence factors; it is also proposed to be a type I antitoxin to aapB (32, 33). Combined with OrzPmg, it suggests that at least some antitoxins have functions beyond toxin repression. We note that several other antitoxins are readily detected under laboratory conditions, even when their toxin mRNAs are not easily detectable (5, 23).

It is not surprising that we see evidence of antitoxin-only strains but not toxin-only strains. In the absence of a toxin gene, antitoxin presence would theoretically cause no negative effects on the cell. However, if there is only a toxin gene without its cognate antitoxin, this deregulation of the toxin could result in increased levels of toxin production, resulting in potential growth inhibition or cellular death. This has even been experimentally validated for some chromosomal type I toxin-antitoxins. For example, under constitutive SOS-inducing conditions, deletion of the chromosomally encoded istR antitoxin was nonviable unless istR was also present on a plasmid (4). For the ratA/txpA type I toxin-antitoxin in Bacillus subtilis, deletion of the ratA antitoxin resulted in a lysis phenotype during late stages of colony growth while deletion of txpA with ratA gave no lysis phenotype (34).

Using this approach, we noted widespread conservation for the three toxin-antitoxin systems across E. coli lab and environmental strains. Past analyses of hok/sok copies found in E. coli chromosomes indicated variation in their potential for expression given various insertional elements within the copies and differences in regulatory features (35–37). The high degree of regulatory feature (and protein) conservation for tis/istR, shoB/ohsC, and zor/orz suggests that these systems may possess a true biological function. Furthermore, we noted that, for the minimal lab strains present in our studies, there does not appear to be “loss” of gene expression potential, at least in the time since laboratory domestication. However, more systematic biological analyses of environmental and lab species are needed.

We do appreciate the limitations of our analysis. As our analyses are focused upon sequence conservation, we may be missing new insights into toxin-antitoxin biology given regions of high-degree sequence variation. For example, there is large variation in the regions of base pairing for shoB-ohsC (Fig. 4B) and for zor-orz (Fig. 5B). As there was experimental evidence for the requirements of zor-orz base pairing (24), we were able to validate that for an individual zor-orz, the majority possess enough pairing potential for successful regulation. The same cannot yet be said for shoB-ohsC. Another important limitation is that the sequences deposited within NCBI may be biased in favor of strains that cause disease and some projects may have sequenced multiple E. coli isolates from related populations. Additionally, since not all strain designations were included in the BioSample metadata information, it is possible that not all duplicate sequences were removed. Therefore, one must be careful about trying to apply conservation estimates obtained this way to the entire population of E. coli. However, our BLASTn approach provides a framework for capturing major trends.

We also appreciate that other approaches could be applied to further probe conservation of these loci in our database. For example, the orz antitoxins (originally sRNA-1 and sRNA-2) were identified using RNA secondary structure prediction (21). For tis/istR and zor/orz, RNA structural analyses have been performed; however, we note that structure prediction software did not accurately predict the structure for the processed form of zor (25). While all three toxin mRNAs are processed in order to be effectively translated, it is still unknown what does the processing: an RNase, multiple RNases, or self-cleaving RNAs are all potential possibilities. Given these unknowns and that we wanted to create an approach that can be done with publicly accessible data by those with limited available tool sets, a nucleotide BLAST approach can still be informative.

Overall, we have demonstrated the benefits of utilizing a custom nucleotide database to detect type I toxin-antitoxin loci which are notoriously difficult to identify given the limitations of protein-based algorithms. From our approach, we identified a large portion of E. coli strains harboring the type I antitoxin gene orz without its cognate toxin gene, an observation that was missed in previous studies and represents the first known widespread finding of a solo type I antitoxin. This approach also allowed us to identify critical regulatory features and develop new hypotheses for these loci. Moving forward, combining multiple conservation approaches will likely expedite identification of loci and important features across bacteria.

MATERIALS AND METHODS

Custom E. coli nucleotide database construction and BioSample metadata

E. coli sequence assemblies were obtained by searching for “E. coli” in the NCBI Assembly database using filters for non-anomalous, non-partial, complete genomes on 31 August 2021 (11). These assemblies were then compiled into a custom database of complete E. coli using the makeblastdb utility of the NCBI BLAST toolkit (version 2.9.0+) run on Linux (Ubuntu 20.04.6 LTS). After further analysis, we removed one assembly (GCA_902141745) from our custom database because of its small size (170,000 bp), even though it was labeled as a complete genome.

Some common lab strains such as strain MG1655 were represented multiple times in the custom BLASTn database. Therefore, all assemblies with the same strain name were compared for tis/istR, shoB/ohsC, and zor/orz copy number. If all strains with the same name also had the same copy number for these toxin-antitoxins, one was labeled as “duplicate, keep” and maintained for analyses, while all others were labeled as “duplicate, remove” and not included in analyses (Table S20). In a single case, two assemblies with the same strain name had a difference in copy number. For the three DH5α strains, two assemblies had 0.5 copies of zor/orz (i.e., they harbor only orz) while one assembly had two copies, so one genome with 0.5 copies was retained and one genome with two copies was retained for analyses. See Table S1 notes section for duplicates removed. This resulted in a custom nucleotide database of 2,212 E. coli genome assemblies.

Metadata collection and analysis

Metadata information for each assembly in the custom database was collected by downloading all corresponding BioSample data from NCBI using utilizing GenBank accessions as queries for the Batch Entrez tool (11). BioSample data were organized and linked to the custom database nomenclature manually in each table. Each strain was then categorized as either environmental or laboratory based on isolation source and pathotype information and connected to its chromosomal GenBank code. We called strains “environmental” if isolated from humans, animals, water, food, plants, terrestrial, sediment, and air; note that this category included pathogens and commensals. “Laboratory” isolates included those with strain names of known laboratory strains (such as K12 derivatives) and those with “laboratory” in their metadata for isolation source. A full list of assemblies categorized as “lab isolates” can be found in Table S20. Assemblies with unknown isolation sources were categorized as unknown.

BLASTn query sequences and parameters

BLASTn methods were utilized throughout this study (16). All query sequences are included in Table S21. For tis/istR, the transcribed region of tisB from MG1655, with the shared intergenic region with istR through the istR transcribed region, was used as a query (4) (Fig. 2). For the shoB/ohsC locus, the sequence including the shoB ORF, the intergenic region between shoB and ohsC, and the ohsC transcribed region was used as a query (20) (Fig. 4). To perform BLASTn searches described for zor/orz, the “blastn” program from the NCBI BLAST toolkit was run using text files of the zorO/orzO, UTR-zorO, and orzO DNA sequences from EDL933 (24). Query “zorO/orzO” refers to the full zorO/orzO locus containing the predicted transcribed region of orzO through its shared intergenic region of zorO to the zorO stop codon (Fig. 5). The second query “UTR-zorO only” was from the mapped zorO transcriptional start site to its stop codon (9, 21). The third query, “orzO only,” contained the predicted transcribed region of orzO (21). After analysis of copy number was performed, the full zorP/orzP locus containing the predicted transcribed region of orzP through its shared intergenic region with zorP and to the zorP stop codon was used as query to confirm locus copy number. For BLASTn, queries were provided in FASTA format and the BLASTn setting was set to 10,000 max sequences (-max_target_seqs), much larger than the possible number of loci in each database, with task set to “blastn.” Additional default settings were used, including an E-value cutoff of 10.

Analysis of zor/orz, tis/istR, and shoB/ohsC loci for conservation and evidence of gene expression potential

The protein sequence for the toxin ORF was determined by translating the BLASTn results for each match using the Sequence Manipulation Suite Translate tool (38). Predicted −10 and −35 promoter boxes, RBS, RSS, and relevant transcription factor binding sites (LexA, CpxR [4, 22]) were determined using manual curation of BLASTn results with the assistance of Jalview as a user interface (39). The identification of these sites was based on previous annotation (4, 20, 22–25, 28) and were categorized as either the same as in MG1655 (for tis/istR and shoB/ohsC) or EDL933 (for zor/orz). Consensus sequence logos were constructed using WebLogo 3 (40). Base-pairing potential was determined manually with the assistance of Jalview as a user interface (39).

Analysis of BLASTn results for toxin-antitoxin copy number

tis/istR and shoB/ohsC copy number was determined via manual curation of the BLASTn results. BLASTn picked up additional short matches to the 3′ end of istR (~25 nucleotides in length) and ohsC (~51 nucleotides in length). When looking at a few of these examples in-depth, it was discovered that the short istR matches do not appear near any predicted small ORF and may represent a somewhat common sequence for transcriptional termination in E. coli. Follow-up analysis of the surrounding genomic region found no evidence that the short istR matches represented interrupted tis/istR loci or istR-only loci and were therefore not considered for conservation or copy number analysis. The short ohsC matches appeared to represent an almost palindromic region within the ohsC 3′ region, allowing for ohsC in the 5′ to 3′ direction to map to itself in the 3′ to 5′ direction; thus, these examples were excluded. Note that these short ohsC matches are found within the single copy of shoB/ohsC identified within a specific genome; thus, these genomes possess only one shoB/ohsC match.

For the zor/orz locus, BLASTn results were used to identify strains with both a zor and an orz gene, a zor gene only, an orz gene only, or no detected zor/orz genes. This was done by first performing a BLASTn of the zorO/orzO locus followed by a BLASTn of either only zorO or only orzO (see BLASTn query sequences and parameters above). For these queries, results of the searches were compared using a series of Linux command line functions. Briefly, the “grep” function was used to condense all lines of the BLASTn results down to only those containing the symbol “>” which resulted in a list of each assembly, one per line, which matched in part to the query sequence. The two BLASTn results were combined using the “cat” function, alphabetized using the “sort” function, and lines with duplication, indicating the same assembly was matched in both BLASTn searches, were removed using the “uniq -u” function. The remaining assemblies listed after this were those with hits in only one of the BLASTn results. Assemblies that appeared in zorO/orzO BLASTn results but not orzO BLASTn results were annotated as “zor only” and assemblies that appeared in zorO/orzO BLASTn results but not in zorO BLASTn results were annotated as “orz only.” No assemblies were found to appear in zorO or orzO BLASTn and not zorO/orzO BLASTn results. These categorizations along with copy number per assembly were confirmed by manually comparing the initial categorization to the number of alignments and the length of the alignment in the BLASTn results for zorO/orzO and zorP/orzP. During confirmation of copy number with BLASTn, 15 short hits to ~40 nucleotides of the 3′ end of orzO were found. Some of which identified an additional orz that lacked a cognate zor (“orphan” antitoxins).

PSI-BLAST and tBLASTn

PSI-BLAST was performed for ZorO on 24 August 2022 on NCBI and tBLASTn on 29 April 2024 (11). tBLASTn was also performed on our custom E. coli database using the tBLASTn function. Parameters were set to be as close to those previously found to be optimal for detection of small toxin proteins (21). These included matrix = PAM70, word size = 2, PSI-BLAST inclusion threshold = 1 (for PSI-BLAST only), expect threshold = 100, low complexity filtering turned off, no composition-based statistics. For tBLASTn, the organism of interest was set to E. coli only. Gap cost was set to existence 8, extension 2. Following the initial PSI-BLAST, a follow-up PSI-BLAST with the less conserved Zor-translated ORF was performed to search for additional matches. The score cutoff for a match to Zor for tBLASTn was 39.

Translation of tBLASTn results was performed using the Sequence Manipulation Suite Translate tool (38). Translated ORF alignments were performed using Clustal Omega on EMBL-EBI (41), while consensus sequence logos were constructed using WebLogo 3 (40).

Identification of plasmid localization

To determine if plasmid sequences were identified, the grep function was used on the BLASTn results to identify lines with the word “plasmid” and “extrachromosomal.” Such hits were confirmed by manual observation.

Analysis of zor and orz locus for zorO/orzO, zorP/orzP, or zorQ/orzQ categorization

For categorization of zor/orz loci as zorO/orzO, zorP/orzP, or zorQ/orzQ, a bit score >650 via BLASTn was categorized as the query used because (i) there was no overlap between categorizations using it; (ii) there was a large decrease in bit score between the scores above and below this threshold (decrease for zorO-orzP = 163, zorP/orzP = 65, and zorQ/orzQ = 60); and (iii) all alignments above this cutoff had the highest level of percent identity to the main query over the others. For orzO in orz-only loci, a bit score cutoff of 280 was used while the cutoff for orzP was 250 using the same logic as above.

Statistical analyses

t-Tests were performed for analysis of toxicity and persistence assays using GraphPad Prism version 10.0.3 for Windows, GraphPad Software, Boston, MA, USA, https://www.graphpad.com/.

For analysis of pathotype correlations with copy number, pathotype was determined based on annotation (e.g., EHEC, STEC) or based on isolation source and host disease state (such as human blood or fecal sample and diarrheal disease). If not enough information was provided to categorize by pathotype (such as isolated from human stool but no information if a healthy host), they were excluded from this analysis.

Differences in distribution of gene frequencies among pathotypes for both zor/orz and tisB/istR pairs were tested via a one-way analysis of variance (ANOVA). Because the sample sizes among pathotypes were imbalanced and variance was not equal among pathotypes, we determined significance by comparing observed F-values to the distribution of F generated in a Monte Carlo sample of data with randomly shuffled labels, representing the null hypothesis, i.e., no difference in the mean copy number between the pathotypes (42). Ad hoc analysis included a Monte Carlo Tukey test to compare means within a pair-wise fashion. We also examined potential copy number distribution per geographical location for zor-orz. Our analysis indicated that there are small but significant differences (P < 0.03 via ANOVA) between copy number of zor-orz from North American isolates (strains were fewer copies) versus those in Asia and Europe details (https://github.com/adsteen/toxin-antitoxin/blob/main/monte-carlo.md, under the heading “zor region diffs”).

A notebook showing R code for all statistical analyses, run using R version 4.3.2, is available at https://githb/adsteen/toxin-antitoxin.

Bacterial strains

All bacterial strains and plasmids utilized in this work are listed in Table S22. The sequences of all oligonucleotides are listed in Table S23.

E. coli UTK007 (derivative of MG1655) Δtis/istR was constructed as described previously via recombineering (43). Briefly, the flippase recognition target (FRT)-flanked kanamycin resistance gene region of plasmid pKD4 (43) was amplified with external homology arms to the region of interest (see Table S22 through 23 for plasmids and primers). The tis/istR region in E. coli strain NM1100 was replaced with the kanamycin resistance cassette, followed by P1 transduction into E. coli UTK007. The kanamycin resistance cassette was then removed via transformation of pCP20 which harbors the FLP recombinase (44), generating E. coli Δtis/istR.

E. coli MG1655 ΔorzPmg was constructed as described previously via recombineering (43). Briefly, the FRT-flanked chloramphenicol resistance gene region of plasmid pKD3 (43) was amplified with external homology arms to the region of interest (see Table S22 to S23 for plasmids and primers). The ΔorzPmg gene deletion resulted in the loss of the orzPmg promoter and the first 34 nucleotides of orzPmg as well as all homology to the region that aligned to the zorP promoter and the zorP 5′ UTR. The region in E. coli strain NM1100 was first deleted, followed by P1 transduction into E. coli strain MG1655. The chloramphenicol resistance cassette was removed via transformation of pCP20 which harbors the FLP recombinase (44), generating MG1655 ΔorzPmg.

Plasmid construction

To generate pAZ3-tisB-N2S, site-directed mutagenesis was performed as described previously on pAZ3-tisB using oligonucleotides EF2051 and EF2052 (Table S22) (23, 24, 45). The reaction mixture was digested with DpnI (New England Biolabs), purified using Qiaquick PCR Purification Kit (Qiagen), and then transformed into E. coli TOP10 cells (ThermoFisher). Plasmid DNA was extracted via the QiaPrep Spin Miniprep Kit (Qiagen) and confirmed via sequencing.

To generate pBR322-tis/istRmg, Gibson assembly was performed as described previously (46). Briefly, the tis/istR sequence was amplified from E. coli strain MG1655 using oligonucleotides EF2080 and EF2081. Next, pBR322 vector backbone was amplified from pBR322 using oligonucleotides EF2082 and EF2083. These two products were then assembled using the NEB Gibson Assembly Master Mix. The assembled product was transformed into E. coli strain TOP10 and sequence verified.

To generate pBR322-tis/istRmg-tisB-N2S, site-directed mutagenesis was performed as described above on pBR322-tis/istRmg, using oligonucleotides EF2051 and EF2052 (Table S22) (23, 24, 45). To generate pAZ3-Δ28zorO-CTC, site-directed mutagenesis was also performed as described above on pAZ3-Δ28zorO (25) using oligonucleotides EF2022 and EF2023 (Table S22) (23, 24, 45).

Growth conditions

E. coli strains were grown at 37°C in lysogeny broth (per liter: 10 g NaCl, 10 g tryptone, 5 g yeast extract) (LB) medium with shaking. Antibiotics were added as warranted at the following concentration: 25 µg/mL chloramphenicol, 30 µg/mL kanamycin, 100 µg/mL ampicillin.

For toxicity assays, strain UTK007 (MG1655 derivative [24]) or UTK007 Δtis/istR was transformed with pAZ3-Δ28zorO (25), pAZ3-Δ28zorO-CTC, pAZ3-tisB, or pAZ3-tisB-N2S (23). For pAZ3 plasmids, cultures were grown overnight in LB media supplemented with 0.2% glucose to ensure repression of the P_BAD promoter (47). In the morning, cultures were diluted to a final OD₆₀₀ of 0.01. Upon reaching an OD₆₀₀ ~0.25, cultures were divided into two, one serving as a no arabinose control and the other receiving arabinose added to the indicated final concentration. Either OD₆₀₀ values were recorded over time or samples were taken, serial diluted, and plated on LB agar to enumerate colony foming units (CFU) per milliliter. Log ratio of survivors was calculated by taking the ratio of cell counts at each given timepoint to cell counts at timepoint 0 and performing a log transformation. Shown are the averages and standard deviations for n = 3.

For persistence assays, a modified persister assay was performed based on those previously described (8). UTK007 Δtis/istR was first transformed with pBR322, pBR322-tis/istRmg, or pBR322-tis/istR-tisB-N2S. Cultures were grown in Mueller Hinton media supplemented with 10 mg/L MgSO₄ and 20 mg/L CaCl₂ overnight and diluted to a final OD₆₀₀ of 0.01 the following morning in the same medium. Upon reaching an OD₆₀₀ ~0.25, cultures were divided into two, one serving as a no ciprofloxacin control and the other receiving ciprofloxacin added to a final concentration of 1 µg/mL. Samples were taken at the indicated timepoints, serially diluted, and plated on LB agar to enumerate CFU per milliliter. Log ratio of survivors was calculated as described above. Shown are the averages and standard deviations for n = 3.

RNA isolation

For detection of OrzPmg sRNA from E. coli, overnight cultures of MG1655 derived strains were grown overnight in LB broth and diluted the next morning to an OD₆₀₀ of 0.01. At an OD₆₀₀ of ~0.3 and 24 h post-dilution, cells (15 mL and 10 mL, respectively) were harvested for RNA isolation as previously described (48). RNA integrity was confirmed via gel electrophoresis.

Sample RNA (12 µg) and the Biotinylated sRNA Ladder (Kerafast) were separated on a denatured 8% polyacrylamide-urea gel for detection of OrzPmg and then transferred to a Zeta-Probe Genomic GT Membrane (Bio-Rad). Hybridization (ULTRAhyb Ultrasensitive Hybridization Solution, ThermoFisher) was performed as previously described (49) with the 5′-end labeled biotin-specific oligonucleotide probes listed in Table S22. Detection was based on the previous methodology of the Brightstar Biotect Kit (formerly of Ambion). Briefly, the blots were washed two times in 1× wash buffer (58 mM Na₂HPO₄, 17 mM NaH₂PO₄, 68 mM NaCl, 0.1% sodium dodecyl sulfate [SDS]), 5 min each. This was followed with three washes (2 for 5 min; final for 1 h) in 1× blocking buffer (58 mM Na₂HPO₄, 17 mM NaH₂PO₄, 68 mM NaCl, 0.3% casein, 2% SDS) and then incubated with streptavidin alkaline phosphatase conjugate (ThermoFisher; in 1× blocking buffer) for 30–60 min. The blot was then washed once for 10 min with 1× blocking buffer, and three times in 1× wash buffer for 15 min each. This was followed by two 2-min washes in 1× assay buffer (100 mM Tris, 100 mM NaCl, pH 9.5), and then incubation with CDP-STAR (ThermoFisher) for 5 min. Excess reagent was allowed to drip off and the blot was exposed to X-ray film.

DATA AVAILABILITY

The data underlying this article are available in the article and in its supplemental material.

SUPPLEMENTAL MATERIAL

The following material is available online at https://doi.org/10.1128/msystems.01204-23.

Tables S1 to S23. msystems.01204-23-s0001.xlsx.

Supplemental tables of raw and processed data.

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