Transketolase activity modulates glycerol-3-phosphate levels inEscherichia coli

Metabolic Mechanism of Bacillus sp. LM24 under Abamectin Stress

Abamectin (ABM) has been recently widely used in aquaculture. However, few studies have examined its metabolic mechanism and ecotoxicity in microorganisms. This study investigated the molecular metabolic mechanism and ecotoxicity of Bacillus sp. LM24 (B. sp LM24) under ABM stress using intracellular metabolomics. The differential metabolites most affected by the bacteria were lipids and lipid metabolites. The main significant metabolic pathways of B. sp LM24 in response to ABM stress were glycerolipid; glycine, serine, and threonine; and glycerophospholipid, and sphingolipid. The bacteria improved cell membrane fluidity and maintained cellular activity by enhancing the interconversion pathway of certain phospholipids and sn-3-phosphoglycerol. It obtained more extracellular oxygen and nutrients to adjust the lipid metabolism pathway, mitigate the impact of sugar metabolism, produce acetyl coenzyme A to enter the tricarboxylic acid (TCA) cycle, maintain sufficient anabolic energy, and use some amino acid precursors produced during the TCA cycle to express ABM efflux protein and degradative enzymes. It produced antioxidants, including hydroxyanigorufone, D-erythroascorbic acid 1'-a-D-xylopyranoside, and 3-methylcyclopentadecanone, to alleviate ABM-induced cellular and oxidative damage. However, prolonged stress can cause metabolic disturbances in the metabolic pathways of glycine, serine, threonine, and sphingolipid; reduce acetylcholine production; and increase quinolinic acid synthesis.

Static Magnetic Field Inhibits Growth of Escherichia coli Colonies via Restriction of Carbon Source Utilization

Magnetobiological effects on growth and virulence have been widely reported in Escherichia coli (E. coli). However, published results are quite varied and sometimes conflicting because the underlying mechanism remains unknown. Here, we reported that the application of 250 mT static magnetic field (SMF) significantly reduces the diameter of E. coli colony-forming units (CFUs) but has no impact on the number of CFUs. Transcriptomic analysis revealed that the inhibitory effect of SMF is attributed to differentially expressed genes (DEGs) primarily involved in carbon source utilization. Consistently, the addition of glycolate or glyoxylate to the culture media successfully restores the bacterial phenotype in SMF, and knockout mutants lacking glycolate oxidase are no longer sensitive to SMF. These results suggest that SMF treatment results in a decrease in glycolate oxidase activity. In addition, metabolomic assay showed that long-chain fatty acids (LCFA) accumulate while phosphatidylglycerol and middle-chain fatty acids decrease in the SMF-treated bacteria, suggesting that SMF inhibits LCFA degradation. Based on the published evidence together with ours derived from this study, we propose a model showing that free radicals generated by LCFA degradation are the primary target of SMF action, which triggers the bacterial oxidative stress response and ultimately leads to growth inhibition.

Designing next generation recombinant protein expression platforms by modulating the cellular stress response in Escherichia coli

BACKGROUND

A cellular stress response (CSR) is triggered upon recombinant protein synthesis which acts as a global feedback regulator of protein expression. To remove this key regulatory bottleneck, we had previously proposed that genes that are up-regulated post induction could be part of the signaling pathways which activate the CSR. Knocking out some of these genes which were non-essential and belonged to the bottom of the E. coli regulatory network had provided higher expression of GFP and L-asparaginase.

RESULTS

We chose the best performing double knockout E. coli BW25113ΔelaAΔcysW and demonstrated its ability to enhance the expression of the toxic Rubella E1 glycoprotein by 2.5-fold by tagging it with sfGFP at the C-terminal end to better quantify expression levels. Transcriptomic analysis of this hyper-expressing mutant showed that a significantly lower proportion of genes got down-regulated post induction, which included genes for transcription, translation, protein folding and sorting, ribosome biogenesis, carbon metabolism, amino acid and ATP synthesis. This down-regulation which is a typical feature of the CSR was clearly blocked in the double knockout strain leading to its enhanced expression capability. Finally, we supplemented the expression of substrate uptake genes glpK and glpD whose down-regulation was not prevented in the double knockout, thus ameliorating almost all the negative effects of the CSR and obtained a further doubling in recombinant protein yields.

CONCLUSION

The study validated the hypothesis that these up-regulated genes act as signaling messengers which activate the CSR and thus, despite having no casual connection with recombinant protein synthesis, can improve cellular health and protein expression capabilities. Combining gene knockouts with supplementing the expression of key down-regulated genes can counter the harmful effects of CSR and help in the design of a truly superior host platform for recombinant protein expression.

The molecular effects of ultrasound on the expression of cellular proteome

High frequency and low intensity, diagnostic ultrasound methods are recognized to be safe in epidemiology and pathology but the bioeffects of these methods on molecular and proteomic levels are unknown. As a representative organism that can directly reflect the molecular response to stresses, Escherichia coli was selected for exposure to ultrasound probes C1-5, M5s and 9 L for 10 min and 20 min. ITRAQ was used to measure the expression of the cellular proteome. The results showed that both the frequency and time of exposure to ultrasound affected the proteome expression. Fifty biological processes were affected and nineteen metabolic processes, including carbohydrate metabolism, asparagine metabolism and phosphate import were differentially regulated. Lower frequency ultrasound caused copper export and iron‑sulfur cluster biosynthesis upregulation. Nine proteins (GlpD, AsnB, TdcB, CopA, IscR, IscU, IscS, IscA, RecA) were key for the adaption to ultrasound. Accordingly, the results of the potential risks based on the calculation of the orthologous genome clarified that relevant pathways and potentially sensitive individuals were worthy of further study. These findings offer insights into reveal the bioeffects of ultrasound at the metabolic network and proteomic levels.

Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E

RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5′-sensor pocket that renders enzyme activity maximal on 5′-monophosphorylated RNAs. The protein's non-catalytic C-terminal half (CTH) harbours RNA-binding motifs and serves as scaffold for a multiprotein degradosome complex, but is dispensable for viability. Here, we provide evidence that a full-length hetero-tetramer, composed of a mixture of wild-type and (recessive lethal) active-site mutant subunits, exhibits identical activity in vivo as the wild-type homo-tetramer itself (‘recessive resurrection’). When all of the cognate polypeptides lacked the CTH, the active-site mutant subunits were dominant negative. A pair of C-terminally truncated polypeptides, which were individually inactive because of additional mutations in their active site and 5′-sensor pocket respectively, exhibited catalytic function in combination, both in vivo and in vitro (i.e. intragenic or allelic complementation). Our results indicate that adjacent subunits within an oligomer are separately responsible for 5′-sensing and cleavage, and that RNA binding facilitates oligomerization. We propose also that the CTH mediates a rate-determining initial step for enzyme function, which is likely the binding and channelling of substrate for NTH’s endonucleolytic action.

Functional analysis of Salmonella Typhi adaptation to survival in water

Contaminated water is a major risk factor associated with the transmission of Salmonella enterica serovar Typhi (S. Typhi), the aetiological agent of human typhoid. However, little is known about how this pathogen adapts to living in the aqueous environment. We used transcriptome analysis (RNA‐seq) and transposon mutagenesis (TraDIS) to characterize these adaptive changes and identify multiple genes that contribute to survival. Over half of the genes in the S. Typhi genome altered expression level within the first 24 h following transfer from broth culture to water, although relatively few did so in the first 30 min. Genes linked to central metabolism, stress associated with arrested proton motive force and respiratory chain factors changed expression levels. Additionally, motility and chemotaxis genes increased expression, consistent with a scavenging lifestyle. The viaB‐associated gene tviC encoding a glcNAc epimerase that is required for Vi polysaccharide biosynthesis was, along with several other genes, shown to contribute to survival in water. Thus, we define regulatory adaptation operating in S. Typhi that facilitates survival in water.

Direct inhibition of transcription in vitro by the isolated N-terminal domain of the Escherichia coli nucleoid-associated protein H-NS and by its paralogue Hha

H-NS is an abundant nucleoid-associated protein in the enterobacteria that mediates both chromatin compaction and transcriptional silencing of numerous genes, especially those that have been acquired by horizontal transfer or that are involved in virulence functions. With two dimerization domains (N-terminal and central) and a C-terminal DNA-binding domain, the 15 kDa H-NS polypeptide can assemble as long polymeric filaments on DNA, and mutations in any of the three domains confer a dominant-negative phenotype in vivo by a subunit-poisoning mechanism. Here we confirm that several of these mutants [L26P, I119T and a truncation beyond residue 92(Δ93)] are also dominant-negative in vitro, in that they reverse the inhibition imposed by native H-NS in two different transcription assay formats (initiation+elongation, or elongation alone). On the other hand, another dominant-negative truncation mutant Δ64 (which possesses only the protein's N-terminal domain) per se completely and unexpectedly inhibited transcription in both assay formats. The Hha protein, which is a paralogue of H-NS and resembles its isolated N-terminal domain, also behaved like Δ64 as an inhibitor of transcription in vitro. We propose that under certain growth conditions, Escherichia coli RNA polymerase may be the direct inhibitory target of Hha, and that this effect is experimentally mimicked by the isolated N-terminal domain of H-NS.