New Intracellular Shikimic Acid Biosensor for Monitoring Shikimate Synthesis in Corynebacterium glutamicum.

The quantitative monitoring of intracellular metabolites with in vivo biosensors provides an efficient means of identifying high-yield strains and observing product accumulation in real time. In this study, a shikimic acid (SA) biosensor was constructed from a LysR-type transcriptional regulator (ShiR) of Corynebacterium glutamicum. The SA biosensor specifically responded to the increase of intracellular SA concentration over a linear range of 19.5 ± 3.6 to 120.9 ± 1.2 fmole at the single-cell level. This new SA biosensor was successfully used to (1) monitor the SA production of different C. glutamicum strains; (2) develop a novel result-oriented high-throughput ribosome binding site screening and sorting strategy that was used for engineering high-yield shikimate-producing strains; and (3) engineer a whole-cell biosensor through the coexpression of the SA sensor and a shikimate transporter shiA gene in C. glutamicum RES167. This work demonstrated that a new intracellular SA biosensor is a valuable tool facilitating the fast development of microbial SA producer.

Saturation mutagenesis of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase R308 site confirms its role in controlling substrate specificity.

Deacetoxy/deacetylcephalosporin C synthase (acDAOC/DACS) from Acremonium chrysogenum is a bifunctional enzyme that catalyzes both the ring-expansion of penicillin N to deacetoxycephalosporin C and the hydroxylation of the latter to deacetylcephalosporin C. The R308 residue located in close proximity to the C-terminus of acDAOC/DACS was mutated to the other 19 amino acids. In the resulting mutant pool, R308L, R308I, R308T and R308V showed significant improvement in their ability to convert penicillin analogs, thus confirming the role of R308 in controlling substrate selectivity, the four amino acids all possess short aliphatic sidechains that may improve hydrophobic interactions with the substrates. The mutant R308I showed the highest reactivity for penicillin G, with 3-fold increase in k(cat)/K(m) ratio and 7-fold increase in relative activity.

Application of a double-reporter-guided mutant selection method to improve clavulanic acid production in Streptomyces clavuligerus.

A reporter-guided mutant selection (RGMS) method has been developed wherein reporters are used to facilitate selection of target over-expressing mutants. It was applied to improve clavulanic acid (CA) production in Streptomyces clavuligerus. In a single-reporter design, the transcriptional activator ccaR of CA biosynthesis was chosen as the over-expressing target, and neo (resistance to kanamycin) as the reporter; 51% of the selected mutants produced higher CA titer than the starting strain. To reduce the high false positive rate of single-reporter method, a double-reporter RGMS vector was configured, in which an xylE-neo double-reporter cassette was used to monitor ccaR expression; 90% of mutants selected by the modified method showed improvement in CA titer. Double-reporter RGMS is the most efficient tool for mutant selection reported to date and is also an alternative method for target over-expression. The mutants obtained by RGMS showed great genetic diversity that could be further exploited in inverse metabolic engineering.

Jadomycin B, an Aurora-B kinase inhibitor discovered through virtual screening.

Aurora kinases have emerged as promising targets for cancer therapy because of their critical role in mitosis. These kinases are well-conserved in all eukaryotes, and IPL1 gene encodes the single Aurora kinase in budding yeast. In a virtual screening attempt, 22 compounds were identified from nearly 15,000 microbial natural products as potential small-molecular inhibitors of human Aurora-B kinase. One compound, Jadomycin B, inhibits the growth of ipl1-321 temperature-sensitive mutant more dramatically than wild-type yeast cells, raising the possibility that this compound is an Aurora kinase inhibitor. Further in vitro biochemical assay using purified recombinant human Aurora-B kinase shows that Jadomycin B inhibits Aurora-B activity in a dose-dependent manner. Our results also indicate that Jadomycin B competes with ATP for the kinase domain, which is consistent with our docking prediction. Like other Aurora kinase inhibitors, Jadomycin B blocks the phosphorylation of histone H3 on Ser10 in vivo. We also present evidence suggesting that Jadomycin B induces apoptosis in tumor cells without obvious effects on cell cycle. All the results indicate that Jadomycin B is a new Aurora-B kinase inhibitor worthy of further investigation.

Localization of the ActIII actinorhodin polyketide ketoreductase to the cell wall.

Structurally diverse polyketides provide a rich reservoir of bioactive molecules. Actinorhodin, a model aromatic polyketide, is synthesized by minimal type II polyketide synthase and tailoring enzymes. The ActIII actinorhodin ketoreductase is a key tailoring enzyme in actinorhodin biosynthesis. With purified antibodies against actinorhodin polyketide synthase alpha subunit (KSalpha) and ketoreductase, we conducted systematic localization experiments of the two proteins in Streptomyces coelicolor subproteomes. The results support the membrane location of KSalpha and cell-wall location of ketoreductase. Considering previous evidence that some other tailoring enzymes of actinorhodin biosynthesis may be located outside the cytoplasm, a picture is emerging of an extensive role for extracellular biochemistry in the synthesis of type II polyketide antibiotic.

CabC, an EF-hand calcium-binding protein, is involved in Ca2+-mediated regulation of spore germination and aerial hypha formation in Streptomyces coelicolor.

Ca(2+) was reported to regulate spore germination and aerial hypha formation in streptomycetes; the underlying mechanism of this regulation is not known. cabC, a gene encoding an EF-hand calcium-binding protein, was disrupted or overexpressed in Streptomyces coelicolor M145. On R5- agar, the disruption of cabC resulted in denser aerial hyphae with more short branches, swollen hyphal tips, and early-germinating spores on the spore chain, while cabC overexpression significantly delayed development. Manipulation of the Ca(2+) concentration in R5- agar could reverse the phenotypes of cabC disruption or overexpression mutants and mimic mutant phenotypes with M145, suggesting that the mutant phenotypes were due to changes in the intracellular Ca(2+) concentration. CabC expression was strongly activated in aerial hyphae, as determined by Western blotting against CabC and confocal laser scanning microscopy detection of CabC::enhanced green fluorescent protein (EGFP). CabC::EGFP fusion proteins were evenly distributed in substrate mycelia, aerial mycelia, and spores. Taken together, these results demonstrate that CabC is involved in Ca(2+)-mediated regulation of spore germination and aerial hypha formation in S. coelicolor. CabC most likely acts as a Ca(2+) buffer and exerts its regulatory effects by controlling the intracellular Ca(2+) concentration.

Engineering a regulatory region of jadomycin gene cluster to improve jadomycin B production in Streptomyces venezuelae.

Streptomyces venezuelae ISP5230 produces a group of jadomycin congeners with cytotoxic activities. To improve jadomycin fermentation process, a genetic engineering strategy was designed to replace a 3.4-kb regulatory region of jad gene cluster that contains four regulatory genes (3' end 272 bp of jadW2, jadW3, jadR2, and jadR1) and the native promoter upstream of jadJ (P(J)) with the ermEp* promoter sequence so that ermEp* drives the expression of the jadomycin biosynthetic genes from jadJ in the engineered strain. As expected, the mutant strain produced jadomycin B without ethanol treatment, and the yield increased to about twofold that of the stressed wild-type. These results indicated that manipulation of the regulation of a biosynthetic gene cluster is an effective strategy to increase product yield.

Sample preparation for two-dimensional blue native/SDS polyacrylamide gel electrophoresis in the identification of Streptomyces coelicolor cytoplasmic protein complexes.

Ammonium sulfate precipitation was tested as a sample preparation step for BN-PAGE analyses of S. coelicolor cytoplasmic protein complexes. A procedure of sample preparation compatible with two-dimensional BN/SDS-PAGE was established and used to visualize protein complexes. To validate the sample preparation procedure, representative protein complexes were identified. Several previously characterized protein complexes were rediscovered and their reported oligomeric states reconfirmed. In addition, we identified new but plausible interactions that have never been reported before. Our work provides useful reference for the wide application of BN-PAGE in protein interaction study.

Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring.

A new gene encoding a thermostable Fe-superoxide dismutase (tcSOD) was identified from a metagenomic library prepared from a hot spring sample. The open reading frame of tcSOD encoded a 211 amino acid protein. The recombinant protein was overexpressed in Escherichia coli and confirmed to be a Fe-SOD with a specific activity of 1,890 U/mg using the pyrogallol method. The enzyme was highly stable at 80 degrees C and retained 50% activity after heat treatment at 95 degrees C for 2 h. It showed striking stability across a wide pH span from 4 to 11. The native form of the enzyme was determined as a homotetramer by analytical ultracentrifugation and gradient native polyacrylamide gel electrophoresis. Fe(2+) was found to be important to SOD activity and to the stability of tcSOD dimer. Comparative modeling analyses of tcSOD tetramer indicate that its high thermostability is mainly due to the presence of a large number of intersubunit ion pairs and hydrogen bonds and to a decrease in solvent accessible hydrophobic surfaces.

TPR repeats and ELTR pattern: length variation as a function evolution mechanism.

TPR repeat was originally defined as a 34 amino acid structural repeat (TPR-34). Equal length tandem repeats (ELTR) was proposed to represent the ancestral repeat pattern. Length polymorphism of TPR repeats was analyzed using PATTINPROT, two new versions of TPR repeat of 40 and 42 amino acids were identified. These 'long' TPRs endow new functional capacities to the resulting proteins. A strong correlation between varied lengths and new functions supports the hypothesis that length variation is an underlying mechanism for the function evolution of repeat containing proteins.

[Construction and analysis of a metagenomic library from Tengchong hot spring soil in Yunnan Province].

By a combination of freezing/thawing/ proteinase K-based method and SDS/high-salt/heating treatment, the mixed environmental genomic DNA was isolated directly from a hot spring soil in Tengchong, Yunnan, China. With this method, The DNA yield was up to 1 - 2 microg/g soil. After purification with the Wizard DNA clean up system (Promega, Madison, Wis), the mixed genomic DNA was partially digested with restriction enzyme Pst I. Digested DNA fragments of 3 - 8 kb were recovered from agrose gel and ligated to the pSK (+) vector. The ligation mixture was transformed into DH10B strain, resulting in the construction of a metagenomic library with about 2.5 x 10(4) clones. Restriction enzyme analysis revealed that the average insert is about 4.6 kb. Some novel sequences were identified via sequencing and gene annotation analysis of 30 clones randomly chosen from this library.

[Functional analyses of TcrA-a TPR-containing regulatory protein in Streptomyces coelicolor A3(2)].

In Streptomyces coelicolor A3(2), SCO5433 encodes a TPR domain containing protein designated TcrA (TPR containing regulator A). TcrA is similar in amino acid sequence to AfsR, a well-characterized global regulatory protein in S. coelicolor A3(2). Disruption of tcrA enhanced the production of spore pigment on MM containing glucose or mannitol and also resulted in more diffusible pigment production on MM containing mannitol or MS agar medium, but no significant effects on morphological differentiation were observed. Complementation of tcrA mutation restored the phenotype of tcrA mutant to that of the wild-type strain. These results suggest that tcrA is involved in the regulation of secondary metabolism under defined conditions. In S. coelicolor A3(2), the AfsK/AfsR system positively regulates the production of secondary metabolites while the results of our work suggest that there might be a TcrA-dependent pathway that negatively regulates secondary metabolism.

[Analyses of Streptomyces coelicolor inner membrane proteome by multidimentional protein identification technology].

Streptomyces coelicolor is the model species among streptomycetes. Until now, proteomic analyses of S. coelicolor have been conducted using two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry method, few integral membrane proteins were identified due to the hydrophobic and low-abundance nature of these proteins. In this work, 154 possible inner membrane proteins from S. coelicolor were identified using high pH-proteinase K sample preparation method and multidimensional protein identification technology, among them 44 are integral membrane proteins containing at least one transmembrane domain, most peptides and their corresponding proteins were identified experimentally for the first time.

Cytotoxic activities of new jadomycin derivatives.

Cytotoxic activities of jadomycin B and five new jadomycin derivatives against four cancer cell lines (HepG2, IM-9, IM-9/Bcl-2 and H460) were evaluated. Jadomycin S was most potent against HepG2, IM-9 and IM-9/Bcl-2 while jadomycin F was most potent against H460. Their potencies correlated with the degrees of apoptosis induced. Structure-activity-relationship analyses clearly demonstrate that the side chains of the oxazolone ring derived from the incorporated amino acids make a significant impact on biological activity. Therefore, jadomycin offers an ideal scaffold to manipulate structure and could be exploited to make many novel bioactive compounds with altered activities.

C-terminus mutations of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase with improved activity toward penicillin analogs.

Deacetoxy/deacetylcephalosporin C synthase (acDAOC/DACS) from Acremonium chrysogenum is a bifunctional enzyme that catalyzes both the ring-expansion of penicillin N to deacetoxycephalosporin C (DAOC) and the hydroxylation of the latter to deacetylcephalosporin C (DAC). Three residues N305, R307 and R308 located in close proximity to the C-terminus of acDAOC/DACS were each mutated to leucine. The N305L and R308L mutant acDAOC/DACSs showed significant improvement in their ability to convert penicillin analogs. R308 was identified for the first time as a critical residue for DAOC/DACS activity. Kinetic analyses of purified R308L enzyme indicated its improved catalytic efficiency is due to combined improvements of K(m) and k(cat). Comparative modeling of acDAOC/DACS supports the involvement of R308 in the formation of substrate-binding pocket.

Functional analyses of oxygenases in jadomycin biosynthesis and identification of JadH as a bifunctional oxygenase/dehydrase.

A novel angucycline metabolite, 2,3-dehydro-UWM6, was identified in a jadH mutant of Streptomyces venezuelae ISP5230. Both UWM6 and 2,3-dehydro-UWM6 could be converted to jadomycin A or B by a ketosynthase alpha (jadA) mutant of S. venezuelae. These angucycline intermediates were also converted to jadomycin A by transformant of the heterologous host Streptomyces lividans expressing the jadFGH oxygenases in vivo and by its cell-free extracts in vitro; thus the three gene products JadFGH are implicated in catalysis of the post-polyketide synthase biosynthetic reactions converting UWM6 to jadomycin aglycone. Genetic and biochemical analyses indicate that JadH possesses dehydrase activity, not previously associated with polyketide-modifying oxygenase. Since the formation of aromatic polyketides often requires multiple dehydration steps, bifunctionality of oxygenases modifying aromatic polyketides may be a general phenomenon.

[Construction and characterization of TetR and GFP fusion protein].

Tetracycline repressor gene (tetR) from E. coli transposon Tn10 was fused in frame with green fluorescent protein gene (gfp) from jellyfish Aequorea Victoria on an E. coli expression vector and the fusion protein (TR::GFP) was purified. The binding of TR::GFP with tetracycline (tc) was demonstrated by nitrocellulose filter binding assay. TR::GFP also maintained the fluorescence property of GFP. Most significantly, fluorescence emission intensity of TR::GFP increased by 2-fold in the presence of tc, from 1.132 to 2.214, while those of GFP and TetR showed little change under similar conditions. The results indicated TR::GFP possesses characteristics of a tetracycline biosensor.

[Construction of efficient conjugal plasmids between Escherichia coli and Streptomycetes].

Conjugal plasmid pGH112 has been developed based on the replicons of Streptomyces coelicolor plasmid SCP2 and E. coli ColE. The plasmid contains ampicilin resistance gene(amp) for selection in E. coli and thiostrepton resistance gene (tsr) for selection in Streptomycetes, and a 0.76 kb oriT fragment of (IncP) RK2. Conjugal transfer of pGH112 was performed from E. coli to S. coelicolor A3(2), S. avermitilis, S. lividans TK54, S. toxytricini NNRL15443, S. venezuelae ISP5230 and Sacc. erythraea by conjugation, results show that the plasmid was able to transfer efficenctly from E. coli to Streptomycetes, was stably inherited in the recipients. pGH113 was constructed from pGH112 by combining the constitutive ermE promoter with green fluorescent protein gene(gfp).