Acinetobacter baumannii K106 and K112: Two Structurally and Genetically Related 6-Deoxy-l-talose-Containing Capsular Polysaccharides.

Whole genome sequences of two Acinetobacter baumannii clinical isolates, 48-1789 and MAR24, revealed that they carry the KL106 and KL112 capsular polysaccharide (CPS) biosynthesis gene clusters, respectively, at the chromosomal K locus. The KL106 and KL112 gene clusters are related to the previously described KL11 and KL83 gene clusters, sharing genes for the synthesis of l-rhamnose (l-Rhap) and 6-deoxy-l-talose (l-6dTalp). CPS material isolated from 48-1789 and MAR24 was studied by sugar analysis and Smith degradation along with one- and two-dimensional 1H and 13C NMR spectroscopy. The structures of K106 and K112 oligosaccharide repeats (K units) l-6dTalp-(1→3)-D-GlcpNAc tetrasaccharide fragment share the responsible genes in the respective gene clusters. The K106 and K83 CPSs also have the same linkage between K units. The KL112 cluster includes an additional glycosyltransferase gene, Gtr183, and the K112 unit includes α l-Rhap side chain that is not found in the K106 structure. K112 further differs in the linkage between K units formed by the Wzy polymerase, and a different wzy gene is found in KL112. However, though both KL106 and KL112 share the atr8 acetyltransferase gene with KL83, only K83 is acetylated.

Development and characterisation of chondroitin sulfate- and hyaluronic acid-incorporated sorbitan ester nanoparticles as gene delivery systems.

Glycosaminoglycans (GAGs) are natural polymers that are broadly used in gene delivery systems to increase stability as well as decrease toxicity and nonspecific interactions, thereby increasing transfection efficiency. In this work, we propose sorbitan ester-based lipid nanoparticles (SENS) functionalised with the GAGs chondroitin sulfate (CS) and hyaluronic acid (HA) as gene delivery systems. For this purpose, we describe the design and evaluation of these nanosystems loaded with plasmid DNA, including an evaluation of their physicochemical characteristics, stability properties, ability to protect and efficiently transfect cells with Enhanced Green Fluorescent Protein plasmid (pEGFP) in vitro, and biocompatibility both in vitro and in vivo. We confirm that molecules with high biological value and targeting potential, such as HA and CS, can be successfully incorporated into our recently developed sorbitan ester-based nanoparticles (SENS) and that this incorporation leads to effective stabilisation of both nanosystems as well as protects plasmid DNA. We demonstrated that the aforementioned incorporation of HA and CS enables long-term stability of the nanosystems in both liquid and lyophilised states, which is a remarkable property that can aid in their transfer to industry. The ability of these functionalised nanosystems to transfect the A549 cell line without compromising cell viability was also shown, as well as their innocuous safety profile in vivo. Thus, we provide valuable evidence of the suitable properties and potential of these hybrid nanoparticles as gene delivery systems.

Cloning, expression and purification of d-tagatose 3-epimerase gene from Escherichia coli JM109.

An unknown d-tagatose 3-epimerase (DTE) containing a IoIE domain was identified and cloned from Escherichia coli. This gene was subcloned into the prokaryotic expression vector pET-15b, and induced by IPTG in E. coli BL21 expression system. Through His-select gel column purification and fast-protein liquid chromatography, highly purified and stable DTE protein was produced. The molecular weight of the DTE protein was estimated to be 29.8kDa. The latest 83 DTE sequences from public database were selected and analyzed by molecular clustering, multi-sequence alignment. DTEs were roughly divided into five categories.

[Transcript profile of converting xylose and glucose to ethanol by Candida shehatae].

OBJECTIVE: We detected and analyzed transcript profile differences between hexose and pentose fermentation by Candida shehatae, a typical xylose fermenting yeast strain. On this basis, the encoding genes of key enzymes and functional protein were screened for discovering candidates of metabolism and regulation. METHODS: To discover the key genes of xylose metabolism and ethanol fermentation in Candida shehatae, we performed a new high throughout de novo transcriptome sequencing technology on Roche 454 GS FLX Titanium platform. Two cDNA libraries were constructed and sequenced for xylose and glucose fermentation for comparison of its expressed sequence tags differences. RESULTS: Second sequencing run resulted in 600000 reads with the average length of 400bp for each cDNA library. We got 7250 and 7168 contigs by assembly, and annotated 2412 and 2456 unique genes by BLAST and Gene Ontology analysis for xylose and glucose respectively. By comparison, we identified 158 genes as different expression genes candidates at p < 0.05 for xylose metabolism and ethanol fermentation in Candida shehatae. CONCLUSIONS: The group genes for xylose metabolism and ethanol fermentation in Candida shehatae was discovered by using transcript profile sequencing and comparison. It will provide fundamental data for the relative research on molecular biology and metabolic regulation.

Gene expression and biochemical changes of carbohydrate metabolism in in vitro micro-propagated apple plantlets infected by 'Candidatus Phytoplasma mali'.

'Candidatus Phytoplasma mali' (Ca. P. mali) is the disease agent causing apple proliferation (AP), which has detrimental effects on production in many apple growing areas of Central and Southern Europe. The present study investigated transcriptional and biochemical changes related to the sugar metabolism as well as expression of pathogenesis-related (PR) protein genes in in vitro micro-propagated AP-infected and healthy control plantlets with the aim of shedding light on host plant response to 'Ca. P. mali' infection. Expression changes between infected and control plantlets were detected by quantitative real-time PCR analysis. The most significant transcriptional changes were observed for genes coding for pathogenesis-related proteins and for heat shock protein 70, as well as for some genes related to the sugar metabolism, such as a sorbitol transporter (SOT5), hexokinase, sucrose-phosphate synthase or granule bound starch synthase. Furthermore, biochemical analyses revealed that infected plantlets were characterized by a significant accumulation of starch and sucrose, while hexoses, such as glucose and fructose, and sorbitol were present at lower concentrations. In summary, the present analysis provides an overview of a gene set that is involved in response to phytoplasma infection and, therefore, it may help for a better understanding of the molecular mechanisms involved in phytoplasma-host plant interaction in apple.

A pathway closely related to the (D)-tagatose pathway of gram-negative enterobacteria identified in the gram-positive bacterium Bacillus licheniformis.

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production.

Interest in thermophilic bacteria as live-cell catalysts in biofuel and biochemical industry has surged in recent years, due to their tolerance of high temperature and wide spectrum of carbon-sources that include cellulose. However their direct employment as microbial cellular factories in the highly demanding industrial conditions has been hindered by uncompetitive biofuel productivity, relatively low tolerance to solvent and osmic stresses, and limitation in genome engineering tools. In this work we review recent advances in dissecting and engineering the metabolic and regulatory networks of thermophilic bacteria for improving the traits of key interest in biofuel industry: cellulose degradation, pentose-hexose co-utilization, and tolerance of thermal, osmotic, and solvent stresses. Moreover, new technologies enabling more efficient genetic engineering of thermophiles were discussed, such as improved electroporation, ultrasound-mediated DNA delivery, as well as thermo-stable plasmids and functional selection systems. Expanded applications of such technological advancements in thermophilic microbes promise to substantiate a synthetic biology perspective, where functional parts, module, chassis, cells and consortia were modularly designed and rationally assembled for the many missions at industry and nature that demand the extraordinary talents of these extremophiles.

Sugar partitioning in sprouting lateral bud and shoot development of sugarcane.

Sugarcane is a leading energy crop of the world due to its ability to capitulate high sucrose. To understand the mechanism associated with shoot establishment from the lateral bud of sugarcane setts, at the time of germination, we established shoots and these shoots were incubated in total darkness and dark/light regime. The concentration of sugars (sucrose and hexoses) and activities of sugar metabolizing enzymes were measured from 0 to 21 days with 7 days intervals during shoot establishment using sugarcane cultivar CoS 97264. A decrease in sucrose concentration and increase in hexoses level was observed in intermodal tissues whereas in the shoots, the level of both sucrose and hexoses increased continuously during shoot establishment. During 0-21 days shooting period, the dry mass of internodes declined by 20 and 25% in plants incubated in dark/light and darkness respectively. All invertases, soluble acid invertase, neutral invertase and cell wall bound invertase were expressed with almost similar pattern in both the intermodal tissues and the shoots. The activity of enzyme sucrose synthase, measured within first 10 days of shooting in both types of tissues, appeared to be higher particularly in sugar breakdown direction. In the shoots, slight increase in sucrose synthase activity in sucrose synthesis direction was observed throughout shooting period in the shoots. The results suggest that sucrose is the main substrate used during shoot establishment and that shoot establishment period is characterized by increased activities of invertases and sucrose synthase and increased level of hexoses in the shoots.

Genetic analysis of the O-antigen gene clusters of Yersinia pseudotuberculosis O:6 and O:7.

Among the 21 O-polysaccharide (OPS) O-antigen-based serotypes described for Yersinia pseudotuberculosis, those of O:6 and O:7 are unusual in that both contain colitose (4-keto-3,6-dideoxy-d-mannose or 4-keto-3,6-dideoxy-l-xylo-hexose), which has not otherwise been reported for this species, and the O:6 OPS also contains yersiniose A (4-C[(R)-1-hydroxyethyl]-3,6-dideoxy-d-xylo-hexose), another unusual dideoxyhexose sugar. In Y. pseudotuberculosis, the genes for OPS synthesis generally cluster together between the hemH and gsk loci. Here, we present the sequences of the OPS gene clusters of Y. pseudotuberculosis O:6 and O:7, and the location of the genes required for synthesis of these OPSs, except that there is still ambiguity regarding allocation of some of the glycosyltransferase functions. The O:6 and O:7 gene clusters have much in common with each other, but differ substantially from the group of 13 gene clusters already sequenced, which share several features and sequence similarities. We also present a possible sequence of events for the derivation of the O:6 and O:7 gene clusters from the most closely related set of 13 sequenced previously.

Mitochondrial and nuclear genomic responses to loss of LRPPRC expression.

Rapid advances in genotyping and sequencing technology have dramatically accelerated the discovery of genes underlying human disease. Elucidating the function of such genes and understanding their role in pathogenesis, however, remain challenging. Here, we introduce a genomic strategy to characterize such genes functionally, and we apply it to LRPPRC, a poorly studied gene that is mutated in Leigh syndrome, French-Canadian type (LSFC). We utilize RNA interference to engineer an allelic series of cellular models in which LRPPRC has been stably silenced to different levels of knockdown efficiency. We then combine genome-wide expression profiling with gene set enrichment analysis to identify cellular responses that correlate with the loss of LRPPRC. Using this strategy, we discovered a specific role for LRPPRC in the expression of all mitochondrial DNA-encoded mRNAs, but not the rRNAs, providing mechanistic insights into the enzymatic defects observed in the disease. Our analysis shows that nuclear genes encoding mitochondrial proteins are not collectively affected by the loss of LRPPRC. We do observe altered expression of genes related to hexose metabolism, prostaglandin synthesis, and glycosphingolipid biology that may either play an adaptive role in cell survival or contribute to pathogenesis. The combination of genetic perturbation, genomic profiling, and pathway analysis represents a generic strategy for understanding disease pathogenesis.

Bioassay-guided evolution of glycosylated macrolide antibiotics in Escherichia coli.

Macrolide antibiotics such as erythromycin are clinically important polyketide natural products. We have engineered a recombinant strain of Escherichia coli that produces small but measurable quantities of the bioactive macrolide 6-deoxyerythromycin D. Bioassay-guided evolution of this strain led to the identification of an antibiotic-overproducing mutation in the mycarose biosynthesis and transfer pathway that was detectable via a colony-based screening assay. This high-throughput assay was then used to evolve second-generation mutants capable of enhanced precursor-directed biosynthesis of macrolide antibiotics. The availability of a screen for macrolide biosynthesis in E. coli offers a fundamentally new approach in dissecting modular megasynthase mechanisms as well as engineering antibiotics with novel pharmacological properties.

Production of D-tagatose at high temperatures using immobilized Escherichia coli cells expressing L-arabinose isomerase from Thermotoga neapolitana.

Escherichia coli cells expressing L-arabinose isomerase from Thermotoga neapolitana (TNAI) were immobilized in calcium alginate beads. The resulting cell reactor (2.4 U, t (1/2) = 43 days at 70 degrees C) in a continuous recycling mode at 70 degrees C produced 49 and 38 g D-tagatose/l from 180 and 90 g D-galactose/l, respectively, within 12 h.

Tagatose production by immobilized recombinant Escherichia coli cells containing Geobacillus stearothermophilus l-arabinose isomerase mutant in a packed-bed bioreactor.

Using immobilized recombinant Escherichia coli cells containing Geobacillus stearothermophilus l-arabinose isomerase mutant (Gali 152), we found that the galactose isomerization reaction was maximal at 70 degrees C and pH 7.0. Manganese ion enhanced galactose isomerization to tagatose. The immobilized cells were most stable at 60 degrees C and pH 7.0. The cell and substrate concentrations and dilution rate were optimal at 34 g/L, 300 g/L, and 0.05 h(-1), respectively. Under the optimum conditions, the immobilized cell reactor with Mn2+ produced an average of 59 g/L tagatose with a productivity of 2.9 g/L.h and a conversion yield of 19.5% for the first 20 days. The operational stability of immobilized cells with Mn2+ was demonstrated, and their half-life for tagatose production was 34 days. Tagatose production was compared for free and immobilized enzymes and free and immobilized cells using the same mass of cells. Immobilized cells produced the highest tagatose concentration, indicating that cell immobilization was more efficient for tagatose production than enzyme immobilization.

Combining sugar biosynthesis genes for the generation of L- and D-amicetose and formation of two novel antitumor tetracenomycins.

L- and D-stereoisomers of amicetose were generated by combining sugar biosynthesis genes from four different antibiotic gene clusters and both sugars were transferred to the elloramycin aglycone by the sugar flexible ElmGT glycosyltransferase.

The mycarose-biosynthetic genes of Streptomyces fradiae, producer of tylosin.

The tylCK region of the Streptomyces fradiae genome was sequenced, revealing an incomplete set of five tylC genes encoding all-but-one of the enzymes involved in the biosynthesis of mycarose. The latter is a 6-deoxyhexose sugar required during production of the macrolide antibiotic, tylosin. The missing mycarose-biosynthetic gene, tylCVI, was found about 50 kb distant from its functional partners, on the other side of the tylG (polyketide synthase) gene complex. Mutational analysis, involving targeted gene transplacement, was employed to confirm the functions of specific genes, including tylCVI. Particularly interesting was the similarity between the tylosin-biosynthetic mycarosyltransferase enzyme, TylCV, and proteins of the macrolide glycosyltransferase (MGT) family that inactivate macrolides via glycosylation of attached sugar residues and are involved in resistance and/or antibiotic efflux. The arrangement of genes within the 'mycarose cluster' would allow their expression as two short operons with divergent, and perhaps co-regulated, promoters. Whether displacement of tylCVI relative to the other tylC genes provides additional regulatory opportunities remains to be established.

Mechanisms and pathways from recent deoxysugar biosynthesis research.

In the past few years, there have been many important advances in our understanding of the biosynthesis of deoxysugars. Mechanistic studies have shed light on how enzymes can cleave C-O bonds, epimerize the configuration of substituents and reduce keto groups to make deoxysugars. Exciting progress has also been made in our comprehension of the genetics of deoxysugar biosynthesis in antibiotics. All this information is important for potential medical and biotechnological applications, such as drug discovery based on combinatorial biology.

Genetic organisation and evolution of Yersinia pseudotuberculosis 3,6-dideoxyhexose biosynthetic genes.

3,6-dideoxyhexose (DDH) sugars occur in some of the O antigens of Salmonella enterica and Yersinia pseudotuberculosis, but are otherwise rarely found in nature. Y. pseudotuberculosis DDH biosynthetic genes rfbS (encoding CDP-paratose synthetase) and rfbE (encoding CDP-tyvelose epimerase) were amplified and cloned, and their sequences determined. Comparisons with the equivalent genes of S. enterica show that the genetic arrangement of DDH genes is very similar; however, in Y. pseudotuberculosis there is no suggestion that paratose producing strains are derived from tyvelose-producing strains by inactivation of rfbE, which is the case in S. enterica. The previously determined DNA sequence of the rfb region of an abequose-producing strain was re-examined. It contains the remnants of an insertion sequence (IS) adjacent to a truncated and non-functional rfbE gene. This suggests that the IS was involved in recombination events contributing to O-antigen antigenic diversity in Y. pseudotuberculosis.

Molecular analysis of the 3,6-dideoxyhexose pathway genes of Yersinia pseudotuberculosis serogroup IIA.

Salmonella enterica and Yersinia pseudotuberculosis are the only examples in nature known to use a variety of 3,6-dideoxyhexose derivatives as O antigen constituents. To allow a comparison of the responsible biosynthetic genes of the two organisms, we have sequenced a section of the Y. pseudotuberculosis serogroup IIA rfb region that contained the genes for the abequose biosynthetic pathway. Comparison of the identified genes with the rfb region of S. enterica LT2 showed that the two dideoxyhexose pathway gene clusters are related. The arrangement of the genes was largely conserved, and the G + C compositions of the two DNA regions were strikingly similar; however, the degree of conservation of nucleotide and protein sequences suggested that the two gene clusters have been evolving independently for considerable time. Hybridization experiments showed that the dideoxyhexose pathway genes are widespread throughout the various serogroups of Y. pseudotuberculosis.

Molecular cloning and genetic characterization of the rfb region from Yersinia pseudotuberculosis serogroup IIA, which determines the formation of the 3,6-dideoxyhexose abequose.

The rfb region of Yersinia pseudotuberculosis serogroup IIA has been cloned and expression of O antigen in Escherichia coli K12 was demonstrated. Transposon mutagenesis analysis confined the DNA region required for O antigen expression to a 19.3 kb fragment, and the O antigen expressed was visualized by SDS-PAGE and silver staining. Southern hybridization analysis demonstrated significant levels of similarity between the Yersinia rfb region and the 3,6-dideoxyhexose pathway genes rfbF and rfbG, previously isolated from Salmonella enterica LT2, but no similarity to the abequose synthase gene rfbJ of the same strain or the paratose synthase gene rfbS isolated from S. enterica Ty2. The evolutionary relationship between the abequose biosynthetic genes of the two species of Salmonella and Yersinia is discussed.

Isolation of streptomycin-nonproducing mutants deficient in biosynthesis of the streptidine moiety or linkage between streptidine 6-phosphate and dihydrostreptose.

Eight streptidine idiotrophic mutants (SD20, SD81, SD141, SD189, SD245, SD261, SD263, and SD274) which required streptidine to produce streptomycin were derived from Streptomyces griseus ATCC 10137 by UV mutagenesis. By both the characterization of intermediates accumulated by the idiotrophs and the assay of enzymes involved in streptidine biosynthesis, the biochemical lesions of the mutants were deduced as follows: SD20 and SD263, transamination; SD81, SD261, and SD274, phosphorylation; SD141, transamidination; SD189, dehydrogenation; SD245, linkage between streptidine 6-phosphate and dihydrostreptose. An accumulation of streptidine 6-phosphate was found in SD245 to impair its aminotransferase activity. This finding suggests that aminotransferase activity might have been negatively controlled by the end product, streptidine 6-phosphate, of the streptidine biosynthetic pathway.