Regulation of Indole Signalling during the Transition of E. coli from Exponential to Stationary Phase

Auxin biosynthesis by Microbacterium testaceum Y411 associated with orchid aerial roots and their efficacy in micropropagation

Root-associated bacteria strongly affect plant growth and development by synthesizing growth regulators and stress-relieving metabolites. The present study is mainly focused on assessing aerial root-associated bacteria of Rhynchostylis retusa (L.) Blume is an endemic epiphytic orchid responsible for auxin production and influencing plant growth. A bacterial isolate, Microbacterium testaceum Y411, was found to be the most active producer of indole-3-acetic acid (IAA). The maximum IAA production (170µg/mL) was recorded with the bacterium at optimum process parameters such as pH 7, temperature 30°C, and tryptophan 1000 µg/mL in a culture medium for 48 h. The extracted auxin was purified and analyzed by FT-IR, HPLC, and HR-MS, indicating bacterial auxin has a similar mass value to 4-chloroindole-3-acetic acid auxin. Furthermore, the bacterial auxin was tested on in vitro propagation of orchid, Cymbidium aloifolium, and 90% seed germination was recorded in Murashige and Skoog's medium supplemented with bacterial auxin. The novel results obtained in this study are used for agricultural applications and the Microbacterium testaceum Y411 is a valuable biotechnological resource for a natural auxin.

Production of indole and hydrogen sulfide by the oxygen-tolerant mutant strain Clostridium sp. Aeroto-AUH-JLC108 contributes to form a hypoxic microenvironment

In this study, the oxygen-tolerant mutant strain Clostridium sp. Aeroto-AUH-JLC108 was found to produce indole when grown aerobically. The tnaA gene coding for tryptophanase responsible for the production of indole was cloned. The tnaA gene from Aeroto-AUH-JLC108 is 1677 bp and has one point mutation (C36G) compared to the original anaerobic strain AUH-JLC108. Phylogenetic analyses based on the amino acid sequence showed significant homology to that of TnaA from Flavonifractor. Furthermore, we found that the tnaA gene also exhibited cysteine desulfhydrase activity. The production of hydrogen sulfide (H₂S) was accompanied by decrease in the amount of the dissolved oxygen in the culture medium. Similarly, the amount of indole produced by strain Aeroto-AUH-JLC108 obviously decreased the oxidation-reduction potential (ORP) in BHI liquid medium. The results demonstrated that production of indole and H₂S helped to form a hypoxic microenvironment for strain Aeroto-AUH-JLC108 when grown aerobically.

Detection of Bioactive Metabolites in Escherichia Coli Cultures Using Surface-Enhanced Raman Spectroscopy

Detection of bioactive metabolites produced by bacteria is important for identifying biomarkers for infectious diseases. In this study, a surface-enhanced Raman spectroscopy (SERS)-based technique was developed for the detection of bioactive metabolite indole produced by Escherichia coli (E. coli) in biological media. The use of highly sensitive Au@Ag core-shell nanoparticles resulted in the detection of indole concentration as low as 0.0886 mM in standard solution. The supplementation of growth media with 5 mM of exogenous tryptophan resulted in the production of a maximum yield of indole of 3.139 mM by E. coli O157:H7 at 37 °C. The growth of bacterial cells was reduced from 47.73 × 10⁸ to 1.033 × 10⁶ CFU/mL when the cells were grown in 0 and 10 mM exogenous tryptophan, respectively. The amount of indole in the Luria-Bertani (LB) media had an inverse correlation with the growth of cells, which resulted in a three-log reduction in the colony-forming unit when the indole concentration in the media was 20 times higher than normal. This work demonstrates that SERS is an effective and highly sensitive method for rapid detection of bioactive metabolites in biological matrix.

Indole Facilitates Antimicrobial Uptake in Bacteria

Indole signaling in bacteria plays an important role in antibiotic resistance, persistence, and tolerance. Here, we used the nonlinear optical technique, second-harmonic light scattering (SHS), to examine the influence of exogenous indole on the bacterial uptake of the antimicrobial quaternary ammonium cation (qac), malachite green. The transport rates of the antimicrobial qac across the individual membranes of Escherichia coli and Pseudomonas aeruginosa, as well as liposomes composed of the polar lipid extract of E. coli, were directly measured using time-resolved SHS. Whereas exogenous indole was shown to induce a 2-fold increase in the transport rate of the qac across the cytoplasmic membranes of the wild-type bacteria, it had no influence on a knockout strain of E. coli lacking the tryptophan-specific transport protein (Δmtr). Likewise, indole did not affect the transport rate of the qac diffusing across the liposome membrane. Our findings suggest that indole increases the bacterial uptake of antimicrobials through an interaction with the Mtr permease.

The Identity of the Constriction Region of the Ribosomal Exit Tunnel Is Important to Maintain Gene Expression in Escherichia coli

Mutational changes in bacterial ribosomes often affect gene expression and consequently cellular fitness. Understanding how mutant ribosomes disrupt global gene expression is critical to determining key genetic factors that affect bacterial survival. Here, we describe gene expression and phenotypic changes presented in Escherichia coli cells carrying an uL22(K90D) mutant ribosomal protein, which displayed alterations during growth. Ribosome profiling analyses revealed reduced expression of operons involved in catabolism, indole production, and lysine-dependent acid resistance. In general, translation initiation of proximal genes in several of these affected operons was substantially reduced. These reductions in expression were accompanied by increases in the expression of acid-induced membrane proteins and chaperones, the glutamate-decarboxylase regulon, and the autoinducer-2 metabolic regulon. In agreement with these changes, uL22(K90D) mutant cells had higher glutamate decarboxylase activity, survived better in extremely acidic conditions, and generated more biofilm in static cultures compared to their parental strain. Our work demonstrates that a single mutation in a non-conserved residue of a ribosomal protein affects a substantial number of genes to alter pH resistance and the formation of biofilms. IMPORTANCE All newly synthesized proteins must pass through a channel in the ribosome named the exit tunnel before emerging into the cytoplasm, membrane, and other compartments. The structural characteristics of the tunnel could govern protein folding and gene expression in a species-specific manner but how the identity of tunnel elements influences gene expression is less well-understood. Our global transcriptomics and translatome profiling demonstrate that a single substitution in a non-conserved amino acid of the E. coli tunnel protein uL22 has a profound impact on catabolism, cellular signaling, and acid resistance systems. Consequently, cells bearing the uL22 mutant ribosomes had an increased ability to survive acidic conditions and form biofilms. This work reveals a previously unrecognized link between tunnel identity and bacterial stress adaptation involving pH response and biofilm formation.

Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production

As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.

Metabolic Engineering of Escherichia coli for Production of α-Santalene, a Precursor of Sandalwood Oil

α-Santalene belongs to a class of natural compounds with many physiological functions and medical applications. Advances in metabolic engineering enable non-native hosts (e.g., Escherichia coli) to produce α-santalene, the precursor of sandalwood oil. However, imbalances in enzymatic activity often result in a metabolic burden on hosts and repress the synthetic capacity of the desired product. In this work, we manipulated ribosome binding sites (RBSs) to optimize an α-santalene synthetic operon in E. coli, and the best engineered E. coli NA-IS_3D strain could produce α-santalene at a titer of 412 mg·L^-1. Concerning the observation of the inverse correlation between indole synthesis and α-santalene production, this study speculated that indole-associated amino acid metabolism would be competitive to the synthesis of α-santalene rather than indole toxicity itself. The deletion of tnaA could lead to a 1.5-fold increase in α-santalene production to a titer of 599 mg·L^-1 in E. coli tnaA^- NA-IS_3D. Our results suggested that the optimization of RBS sets of the synthetic module and attenuation of the competitive pathway are promising approaches for improving the production of terpenoids including α-santalene.

Bacterial fermentation and isotope labelling optimized for amyloidogenic proteins

We developed a cost sensitive isotope labelling procedure using a fed-batch fermentation method and tested its efficiency producing the 15 N-, 13 C- and 15 N/13 C-labelled variants of an amyloidogenic miniprotein (E5: EEEAVRLYIQWLKEGGPSSGRPPPS). E5 is a surface active protein, which forms amyloids in solution. Here, we confirm, using both PM-IRRAS and AFM measurements, that the air-water interface triggers structural rearrangement and promotes the amyloid formation of E5, and thus it is a suitable test protein to work out efficient isotope labelling schemes even for such difficult sequences. E. coli cells expressing the recombinant, ubiquitin-fused miniprotein were grown in minimal media containing either unlabelled nutrients, or 15 N-NH4 Cl and/or 13 C-D-Glc. The consumption rates of NH4 Cl and D-Glc were quantitatively monitored during fermentation and their ratio was established to be 1:5 (for NH4 Cl: D-Glc). One- and two-step feeding schemes were custom-optimized to enhance isotope incorporation expressing five different E5 miniprotein variants. With the currently optimized protocols we could achieve a 1.5- to 5-fold increase of yields of several miniproteins coupled to a similar magnitude of cost reduction as compared to flask labelling protocols.

Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings

An endophytic Escherichia coli USML2 originally isolated from the inner part of an oil palm (Elaeis guineensis Jacq.) leaf tissue was inoculated to rice seedlings to investigate its ability in colonising plant inner tissues and promoting growth. Infection of E. coli USML2 was initiated by colonisation on the root surface, invasion of the interior root system followed by endophytic spreading. Inoculation of E. coli USML2 in the rice rhizosphere zone resulted in a significant increase in leaf numbers (33.3%), chlorophyll content (33.3%), shoot height (34.8%) and plant dry weight (90.4%) of 42 days old rice seedlings as compared to the control. These findings also demonstrated the ability of E. coli USML2 to spread endophytically which serves as a beneficial strategy for the bacterium to colonise the host plant and gain protection against adverse soil conditions. The genome of E. coli USML2 had also revealed predicted genes essential for endophytic bacterial colonisation and plant growth promotion which further proven potentials of E. coli USML2 as Plant Growth Promoting Endophyte (PGPE).

Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters

Persisters are a sub-population of genetically sensitive bacteria that survive antibiotic treatment by entering a dormant state. The emergence of persisters from dormancy after antibiotic withdrawal leads to recurrent infection. Indole is an aromatic molecule with diverse signalling roles, including a role in persister formation. Here we demonstrate that indole stimulates the formation of Escherichia coli persisters against quinolone antibiotics which target the GyrA subunit of DNA gyrase. However, indole has no effect on the formation of E. coli persisters against an aminocoumarin, novobiocin, which targets the GyrB subunit of DNA gyrase. Two modes of indole signalling have been described: persistent and pulse. The latter refers to the brief but intense elevation of intracellular indole during stationary phase entry. We show that the stimulation of quinolone persisters is due to indole pulse, rather than persistent, signalling. In silico docking of indole on DNA gyrase predicts that indole docks perfectly to the ATP binding site of the GyrB subunit. We propose that the inhibition of indole production offers a potential route to enhance the activity of quinolones against E. coli persisters.

The Signaling Molecule Indole Inhibits Induction of the AR2 Acid Resistance System in Escherichia coli

Induction of the AR2 acid response system of Escherichia coli occurs at a moderately low pH (pH 5.5) and leads to high levels of resistance to pH levels below 2.5 in the presence of glutamate. Induction is mediated in part by the EvgAS two component system. Here, we show that the bacterial signaling molecule indole inhibits the induction of key promoters in the AR2 system and blocks the development of glutamate-dependent acid resistance. The addition of tryptophan, the precursor for indole biosynthesis, had the same effects, and this block was relieved in a tnaA mutant, which is unable to synthesize indole. Expression of a constitutively active EvgS protein was able to relieve the inhibition caused by indole, consistent with EvgS being inhibited directly or indirectly by indole. Indole had no effect on autophosphorylation of the isolated cytoplasmic domain of EvgS. This is consistent with a model where indole directly or indirectly affects the ability of EvgS to detect its inducing signal or to transduce this information across the cytoplasmic membrane. The inhibitory activity of indole on the AR2 system is not related to its ability to act as an ionophore, and, conversely, the ionophore CCCP had no effect on acid-induced AR2 promoter activity, showing that the proton motive force is unlikely to be a signal for induction of the AR2 system.

Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner

Bacterial cells are critically dependent upon pH regulation. Here we demonstrate that indole plays a critical role in the regulation of the cytoplasmic pH of Escherichia coli. Indole is an aromatic molecule with diverse signalling roles. Two modes of indole signalling have been described: persistent and pulse signalling. The latter is illustrated by the brief but intense elevation of intracellular indole during stationary phase entry. We show that under conditions permitting indole production, cells maintain their cytoplasmic pH at 7.2. In contrast, under conditions where no indole is produced, the cytoplasmic pH is near 7.8. We demonstrate that pH regulation results from pulse, rather than persistent, indole signalling. Furthermore, we illustrate that the relevant property of indole in this context is its ability to conduct protons across the cytoplasmic membrane. Additionally, we show that the effect of the indole pulse that occurs normally during stationary phase entry in rich medium remains as a "memory" to maintain the cytoplasmic pH until entry into the next stationary phase. The indole-mediated reduction in cytoplasmic pH may explain why indole provides E. coli with a degree of protection against stresses, including some bactericidal antibiotics.

The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli

Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.

Indole at low concentration helps exponentially growing Escherichia coli survive at high temperature

A culture of stationary phase Escherichia coli cells has been reported to produce copious indole when exposed to high temperature (50°C), and this response has been proposed to aid survival. We reinvestigated this phenomenon and found that indole production under these conditions is probably not a direct response to heat stress. Rather, E. coli produces indole when growth is prevented, irrespective of whether this is due to heat stress, antibiotic treatment or the removal of nutrients. Moreover, 300μM indole produced at 50°C does not improve the viability of heat stressed cells. Interestingly, a much lower concentration of indole (20 μM) improves the survival of an indole-negative strain (ΔtnaA) when heat stressed during exponential growth. In addition we have shown that the distribution of tryptophanase, the enzyme responsible for indole synthesis, is highly heterogeneous among cells in a population, except during the transition between exponential and stationary phases. The observation that, despite the presence of the tryptophanase, very little indole is produced during early exponential phase suggests that there is post-translational regulation of the enzyme.