Analysis of regulation of the ilvGMEDA operon by using leader-attenuator-galK gene fusions

Sustainable production of 4-hydroxyisoleucine with minimised carbon loss by simultaneously utilising glucose and xylose in engineered Escherichia coli

4-Hydroxyisoleucine is a promising drug for diabetes therapy; however, microbial production of 4-hydroxyisoleucine is not economically efficient because of the carbon loss in the form of CO₂. This study aims to achieve de novo synthesis of 4-hydroxyisoleucine with minimised carbon loss in engineered Escherichia coli. Initially, an L-isoleucine-producing strain, ILE-5, was established, and the 4-hydroxyisoleucine synthesis pathway was introduced. The flux toward α-ketoglutarate was enhanced by reinforcing the anaplerotic pathway and disrupting competitive pathways. Subsequently, the metabolic flux for 4-hydroxyisoleucine synthesis was redistributed by dynamically modulating the α-ketoglutarate dehydrogenase complex activity, achieving a 4-hydroxyisoleucine production of 16.53 g/L. Finally, carbon loss was minimised by employing the Weimberg pathway, resulting in a 24.5% decrease in sugar consumption and a 31.6% yield increase. The 4-hydroxyisoleucine production by strain IEOH-11 reached 29.16 g/L in a 5-L fermenter. The 4-hydroxyisoleucine yield (0.29 mol/mol sugar) and productivity (0.91 g/(L⋅h)) were higher than those previously reported.

Mechanisms of acetohydroxyacid synthases

Acetohydroxyacid synthases are thiamin diphosphate- (ThDP-) dependent biosynthetic enzymes found in all autotrophic organisms. Over the past 4-5 years, their mechanisms have been clarified and illuminated by protein crystallography, engineered mutagenesis and detailed single-step kinetic analysis. Pairs of catalytic subunits form an intimate dimer containing two active sites, each of which lies across a dimer interface and involves both monomers. The ThDP adducts of pyruvate, acetaldehyde and the product acetohydroxyacids can be detected quantitatively after rapid quenching. Determination of the distribution of intermediates by NMR then makes it possible to calculate individual forward unimolecular rate constants. The enzyme is the target of several herbicides and structures of inhibitor-enzyme complexes explain the herbicide-enzyme interaction.

Global gene expression profile of Yersinia pestis induced by streptomycin

Plague, caused by Y ersinia pestis, is one of the most dangerous diseases that impressed a horror onto human consciousness that persists to this day. Cases of plague can be normally controlled by timely antibiotic administration. Streptomycin is the first-line antibiotic for plague treatment. In this study, a DNA microarray was used to investigate the changes in the gene expression profile of Y. pestis upon exposure to streptomycin. A total of 345 genes were identified to be differentially regulated, 144 of which were up-regulated, and 201 down-regulated. Streptomycin-induced transcriptional changes occurred in genes responsible for heat shock response, drug/analogue sensitivity, biosynthesis of the branched-chain amino acids, chemotaxis and mobility and broad regulatory functions. A wide set of genes involved in energy metabolism, biosynthesis of small macromolecules, synthesis and modification of macromoclecules and degradation of small and macro molecules were among those down-regulated. The results reveal general changes in gene expression that are consistent with known mechanisms of action of streptomycin and many new genes that are likely to play important roles in the response to streptomycin treatment, providing useful candidates for investigating the specific mechanisms of streptomycin action.

Carbon source regulation of PIS1 gene expression in Saccharomyces cerevisiae involves the MCM1 gene and the two-component regulatory gene, SLN1

The Saccharomyces cerevisiae PIS1 gene encodes phosphatidylinositol synthase. The amount of phosphatidylinositol synthase is not affected by the presence of inositol and choline in the growth medium. This is unusual because the amounts and/or activities of other phospholipid biosynthetic enzymes are affected by these precursors, and the promoter of the PIS1 gene contains a sequence resembling the regulatory element that coordinates the inositol-mediated regulation (UASINO). We found that transcription of the PIS1 gene was insensitive to inositol and choline and did not require the putative UASINO regulatory sequence or the cognate regulatory genes (INO2 and OPI1). The PIS1 promoter includes sequences (MCEs) that bind the Mcm1 protein. Because the Mcm1 protein interacts with both the Sln1 and the Gal11 regulatory proteins, we examined the effect of mutant alleles of the MCM1 and SLN1 genes and carbon source on expression of the PIS1 gene. We found that expression of the PIS1 gene was reduced when cells were grown in a medium containing glycerol and increased when grown in a medium containing galactose relative to cells grown in a glucose medium. The glycerol-mediated repression of PIS1 gene expression required both the MCM1 gene and the MCEs, whereas the SLN1 gene was required for full galactose-mediated induction of a PIS1-lacZ reporter gene. Thus, PIS1 gene expression is unique among the phospholipid biosynthetic structural genes because it is uncoupled from the inositol response and regulated in response to the carbon source. This is the first example in yeast of a complete circuit linking a stimulus (carbon source) to gene regulation (PIS1) using a two-component regulator (SLN1).

Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus

The ilvR gene was located upstream of and transcribed divergently from the ilvD gene of Caulobacter crescentus. DNA nucleotide analysis determined that the ilvR and ilvD translation initiation codons are 98 bp apart. The promoter activity of the DNA region containing the divergent promoters was analyzed by using transcriptional fusions to promoterless reporter genes and immunoblot assays. The results indicate that the ilvR gene product positively regulates the expression of the ilvD gene while negatively autoregulating its own expression. The ilvR gene codes for a protein of 296 amino acid residues (M(r), 37,212). The N-terminal amino acid sequence of the IlvR protein contains a helix-turn-helix motif, suggesting that it is involved in protein-DNA interactions. Protein extracts from both wild-type and merodiploid strains showed specific DNA binding to a 227-bp DNA fragment spanning the ilvD-ilvR promoter region, while no protein-DNA complexes were observed in cell extracts from an ilvR mutant strain. Amino acid sequence comparison revealed that the IlvR protein is a member of the LysR family of transcriptional regulators.

Specificity of attenuation control in the ilvGMEDA operon of Escherichia coli K-12

Three different approaches were used to examine the regulatory effects of the amino acids specified by the peptide-coding region of the leader transcript of the ilvGMEDA operon of Escherichia coli K-12. Gene expression was examined in strains carrying an ilvGMED'-lac operon fusion. In one approach, auxotrophic derivatives were starved of single amino acids for brief periods, and the burst of beta-galactosidase synthesis upon adding the missing amino acid was determined. Auxotrophic derivatives were also grown for brief periods with a limited supply of one amino acid (derepression experiments). Finally, prototrophic strains were grown in minimal medium supplemented with single and multiple supplements of the chosen amino acids. Although codons for arginine, serine, and proline are interspersed among the codons for the three branched-chain (regulatory) amino acids, they appeared to have no effect when added in excess to prototrophs or when supplied in restricted amounts to auxotrophs. Deletions removing the terminator stem from the leader removed all ilv-specific control, indicating that the attenuation mechanism is the sole mechanism for ilv-specific control.

Mutations replacing the leucine codons or altering the length of the amino acid-coding portion of the ilvGMEDA leader region of Escherichia coli

The specificity of regulation by attenuation of the ilvGMEDA operon of Escherichia coli was examined by making alterations in the peptide-coding portion of the leader region. The effects of the alterations on attenuation control were monitored by operon fusions with the lacZ or cat gene. Substitution of the tandem leucine codons with arginine codons did not result in arginine control of attenuation even though the altered leader transcripts contained three consecutive arginine codons. Substitution of the single leucine codon with a proline codon at position 10 of the putative peptide, which had been shown to be important in the regulation of the Serratia marcescens ilv operon, did not result in control of attenuation by proline. Since the formation of neither proline nor arginine biosynthetic enzymes is regulated by attenuation control, the effect of tandem phenylalanine codons in place of the tandem leucine codons was examined and found not to result in control by phenylalanine supply. The latter failure may have been due to a configuration in the secondary structure of the protector stem of the leader transcript different from that of the wild-type transcript. The results of the study favored the idea that the lead ribosome does not initiate translation of the leader transcript until after the RNA polymerase has reached the pause site (117 bases into the leader region).