BAH1 an E3 Ligase from Arabidopsis thaliana Stabilizes Heat Shock Factor σ32 of Escherichia coli by Interacting with DnaK/DnaJ Chaperone Team.

In Escherichia coli, the DnaK/DnaJ chaperone can control the stability and activity of σ32, which is the key factor in heat shock response. Heterologous expression of eukaryotic molecular chaperones protects E. coli from heat stress. Here, we show that BAH1, an E3 ligase from plant that has a similar zinc finger domain to DnaJ, can perform block the effect of DnaK on σ32 in Escherichia coli. By constructing a chimeric DnaJ protein, with the J-domain of DnaJ fused to BAH1, we found BAH1 could partially compensate for the DnaJ' zinc finger domain in vivo, and that it was dependent on the zinc finger domain of BAH1. Furthermore, BAH1 could interact with both σ32 and DnaK to increase the level of HSPs, such as GroEL, DnaK, and σ32. These results suggested that the zinc finger domain was conserved during evolution.

Plant E3 ligases ubiquitinate Escherichia coli σ32in vitro.

Ubiquitin-like proteins (UBLs) are extremely well-conserved among eukaryotes and prokaryotes allowing interactions between proteins from different organisms. For example, the prokaryotic ubiquitin-like proteins (Pups) and the Proteasome accessory factor A (PafA) of Mycobacterium tuberculosis are sufficient to pupylate at least 51 Escherichia coli proteins. This work shows that the plant E3 ligases BnTR1 and AT1G02860 can ubiquitinate E. coli σ32, but not Hsp70 DnaK in vitro. Molecular biology and biochemical studies confirm that the RING finger domain of BnTR1 and AT1G02860 is essential for their function. These results suggest that the substrates of plant E3 ligases can be prokaryotic protein and therefore the plant ubiquitylation system may have evolved from prokaryote.

Analysis of pupylation of Streptomyces hygroscopicus 5008 in vitro.

Prokaryotic ubiquitin-like protein (Pup) is a post-translational modifier that can be attached to substrate proteins in Actinobacteria. The modification process is defined as pupylation and is associated with proteasome-mediated protein degradation in mycobacteria and streptomycetes. Here, we report the pupylation of Streptomyces hygroscopicus 5008 in vitro. Each component of the Pup system was expressed in Escherichia coli and poly-Pup chains were observed by western blot analysis. Though only one potential Pup substrate (SHJG_3659) was identified using MS/MS, we verified this candidate and other predicted substrates by a reconstituted Pup system in E. coli. In addition, we discuss the depupylation activity of Dop (a Pup activation enzyme). The results presented here show that pupylation exists in S. hygroscopicus and that a reconstituted Pup system can function in vitro in a heterologous host.

Heat shock transcription factor δ³² is targeted for degradation via an ubiquitin-like protein ThiS in Escherichia coli.

The posttranslational modification of proteins with ubiquitin and ubiquitin-like proteins (UBLs) plays an important role in eukaryote biology, through which substrate proteins are targeted for degradation by the proteasome. Prokaryotes have been thought to degrade proteins by an ubiquitin independent pathway. Here, we show that ThiS, an ubiquitin-like protein, is covalently attached to δ(32) and at least 27 other proteins, leading to their subsequent degradation by proteases, in a similar manner to the ubiquitin-proteasome system (UPS) in eukaryotes. Molecular biology and biochemical studies confirm that specific lysine sites in δ(32) can be modified by ThiS. The results presented here establish a new model for δ(32) degradation and show that Escherichia coli uses a small-protein modifier to control protein stability.

MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding.

Mycobacterium tuberculosis, the bacterium responsible for human tuberculosis, has a genome encoding a remarkably high number of toxin-antitoxin systems of largely unknown function. We have recently shown that the M. tuberculosis genome encodes four of a widespread, MenAT family of nucleotidyltransferase toxin-antitoxin systems. In this study we characterize MenAT1, using tRNA sequencing to demonstrate MenT1 tRNA modification activity. MenT1 activity is blocked by MenA1, a short protein antitoxin unrelated to the MenA3 kinase. X-ray crystallographic analysis shows blockage of the conserved MenT fold by asymmetric binding of MenA1 across two MenT1 protomers, forming a heterotrimeric toxin-antitoxin complex. Finally, we also demonstrate tRNA modification by toxin MenT4, indicating conserved activity across the MenT family. Our study highlights variation in tRNA target preferences by MenT toxins, selective use of nucleotide substrates, and diverse modes of MenA antitoxin activity.

Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis.

Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of Mycobacterium tuberculosis, whose inhibition requires the concerted action of the antitoxin and its dedicated SecB-like chaperone. We show that the TAC toxin is a bona fide ribonuclease and identify exact cleavage sites in mRNA targets on a transcriptome-wide scale in vivo. mRNA cleavage by the toxin occurs after the second nucleotide of the ribosomal A-site codon during translation, with a strong preference for CCA codons in vivo. Finally, we report the cryo-EM structure of the ribosome-bound TAC toxin in the presence of native M. tuberculosis cspA mRNA, revealing the specific mechanism by which the TAC toxin interacts with the ribosome and the tRNA in the P-site to cleave its mRNA target.

ClpXP-mediated Degradation of the TAC Antitoxin is Neutralized by the SecB-like Chaperone in Mycobacterium tuberculosis.

Bacterial toxin-antitoxin (TA) systems are composed of a deleterious toxin and its antagonistic antitoxin. They are widespread in bacterial genomes and mobile genetic elements, and their functions remain largely unknown. Some TA systems, known as TAC modules, include a cognate SecB-like chaperone that assists the antitoxin in toxin inhibition. Here, we have investigated the involvement of proteases in the activation cycle of the TAC system of the human pathogen Mycobacterium tuberculosis. We show that the deletion of endogenous AAA+ proteases significantly bypasses the need for a dedicated chaperone and identify the mycobacterial ClpXP1P2 complex as the main protease involved in TAC antitoxin degradation. In addition, we show that the ClpXP1P2 degron is located at the extreme C-terminal end of the chaperone addiction (ChAD) region of the antitoxin, demonstrating that ChAD functions as a hub for both chaperone binding and recognition by proteases.

The ubiquitin-like modification by ThiS and ThiF in Escherichia coli.

Escherichia coli, one of the most well-studied gram-negative bacterial species, encodes two ubiquitin-like proteins (UBLs), ThiS and MoaD. The studies on prokaryotic UBLs such as Pup, and small archaeal modifier protein have revealed the function of UBLs. However, in gram-negative bacteria, the functions of UBLs in protein modification are still poorly understood to date. Here, we report that ThiS, which has a ß-grasp fold and carboxy-terminal diglycine motif similar to ubiquitin, is able to form protein conjugates in vivo and in vitro. We also constructed in vitro ThiS conjugation (thisylation) system and identified the modified lysine sites by MS/MS, this provides an essential platform for studying the UBLs thisylation system in E. coli. The modification system is dependent on lysine 83 (ATPase activity site) and cysteine 169 (zinc binding site) in ThiF and three important substrates, GroEL, PriC, FtsA, were found to be covalently modified by this system in vitro. Taken together, this study provided evidence that the protein conjugation function of ß-grasp fold UBLs is conserved in the three major evolutionary lineages of life.

DBP alteration from NOM and model compounds after UV/persulfate treatment with post chlorination.

The UV/persulfate process is an effective advanced oxidation process (AOP) for the abatement of a variety of micropollutants via producing sulfate radicals (SO4•-). However, when this technology is used to reduce target pollutants, the precursors of disinfection byproducts (DBPs), such as natural organic matter (NOM) and organic nitrogen compounds, can be altered. This study systematically investigated the DBP formation from NOM and five model compounds after UV/H2O2 and UV/persulfate treatments followed with 24 h chlorination. Compared to chlorination alone, the yields of trichloromethane (TCM) and dichloroacetonitrile (DCAN) from NOM decreased by 50% and 54%, respectively, after UV/persulfate treatment followed with chlorination, whereas those of chloral hydrate (CH), 1,1,1-trichloropropanone (1,1,1-TCP) and trichloronitromethane (TCNM) increased by 217%, 136%, and 153%, respectively. The effect of UV/H2O2 treatment on DBP formation shared a similar trend to that of UV/persulfate treatment, but the DBP formation was higher from the former. As the UV/persulfate treatment time prolonged or the persulfate dosage increased, the formation of TCM and DCAN continuously decreased, while that of CH, 1,1,1-TCP and TCNM presented an increasing and then decreasing pattern. SO4•- activated benzoic acid (BA) to form phenolic compounds that enhanced the formation of TCM and CH, while it deactivated resorcinol to decrease the formation of TCM. SO4•- reacted with aliphatic amines such as methylamine (MA) and dimethylamine (DMA) to form nitro groups, which significantly increased the formation of TCNM in post chlorination, and the rate was determined to be higher than that of HO•. This study illuminated the diverse impacts of the structures of the precursors on DBP formation after UV/persulfate treatment, and DBP alteration depended on the reactivity between SO4•- and specific precursor.

Feasibility of the solar/chlorine treatment for lipid regulator degradation in simulated and real waters: The oxidation chemistry and affecting factors.

This work investigated the feasibility and mechanisms of solar/chlorine process in the removal of a kind of emerging contaminants, lipid regulators (gemfibrozil (GFRZ), benzafibrate (BZF), and clofibric acid (CA)), in simulated and real waters. These lipid regulators could be effectively removed by solar/chlorine treatment, and their corresponding pseudo-first-order rate constants (k') increased with increasing chlorine dosage. The degradation of GFRZ and BZF was primarily ascribed to reactive chlorine species (RCS) and ozone, while that of CA was mainly attributable to hydroxyl radical (HO) and ozone. As pH rose from 5.0 to 8.4, kozone' of GFRZ and BZF increased, while kHO' decreased. However, kRCS' of GFRZ increased by 130%, while that of BZF decreased by 43.3%. These changes resulted in slight changes in the overall k's with increasing pH. k's of GFRZ, BZF, and CA by solar/chorine treatment were inhibited by natural organic matter (NOM) while the presence of bromide enhanced the degradation of GFRZ by solar/chlorine process. The degradation of lipid regulators was still effective in a secondary wastewater effluent sample and a sand-filtered water sample, although that was inhibited due to the dissolve organic matter (DOM) contained in real waters. The acute toxicity during the degradation of GFRZ by solar/chlorine treatment was comparable to that by treatment with chlorine alone. This study demonstrated that RCS played an important role in the degradation of micropollutants by the solar/chlorine treatment and the feasibility of solar/chlorine process in the application for the degradation of organic compounds in real waters.

A novel plant E3 ligase stabilizes Escherichia coli heat shock factor σ32.

The heat shock response is crucial for organisms against heat-damaged proteins and maintaining homeostasis at a high temperature. Heterologous expression of eukaryotic molecular chaperones protects Escherichia coli from heat stress. Here we report that expression of the plant E3 ligase BnTR1 significantly increases the thermotolerance of E. coli. Different from eukaryotic chaperones, BnTR1 expression induces the accumulation of heat shock factor σ32 and heat shock proteins. The active site of BnTR1 in E. coli is the zinc fingers of the RING domain, which interacts with DnaK resulting in stabilizing σ32. Our findings indicate the expression of BnTR1 confers thermoprotective effects on E. coli cells, and it may provide useful clues to engineer thermophilic bacterial strains.