LtuCAD1 Is a Cinnamyl Alcohol Dehydrogenase Ortholog Involved in Lignin Biosynthesis in Liriodendron tulipifera L., a Basal Angiosperm Timber Species

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis and catalyzes the final step in the synthesis of monolignols. Seven CAD homologs (LtuCAD1 to LtuCAD7) have been previously identified from a basal angiosperm species Liriodendron tulipifera L., which is an important timber tree species with significant ecological and economic values. The phylogenetic analysis indicates that LtuCAD1 is the only Liriodendron CAD grouped with the bona fide CADs, the primary CAD genes involved in lignification. In this study, the predicted protein sequence of LtuCAD1 was found to have conserved domains and the same key determinant site with the bona fide CADs in other plant species. Additionally, LtuCAD1 had the highest expression level in xylem as revealed by quantitative RT-PCR analysis. The expression of beta-glucuronidase (GUS) driven by the LtuCAD1 promoter was largely localized in vascular tissues in Arabidopsis. In stem cross sections, GUS staining was found exclusively in xylem and phloem. When expressed in the Arabidopsis cad4 cad5 double mutant, LtuCAD1 was able to restore the total lignin content and decrease the S/G lignin ratio. Our data indicate that LtuCAD1 is a CAD ortholog involved in lignin biosynthesis in Liriodendron.     

Predicting thymine dimerization yields from molecular dynamics simulations

It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)₁₈ are fully formed in <1 ps after ultraviolet excitation. The speed and low quantum yield of this reaction suggest that only a small fraction of the conformers of this structurally disordered oligonucleotide are in a position to react at the instant of photon absorption. In this work, we explore the hypothesis that conventional molecular dynamics simulations can be used to predict the yield of cyclobutane pyrimidine dimers in DNA. Conformations obtained from simulations of thymidylyl-(3′-5′)-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22°.     

Involvement of exo5 in production of surface polysaccharides in Rhizobium leguminosarum and its role in nodulation of Vicia sativa subsp. nigra

Analysis of two exopolysaccharide-deficient mutants of Rhizobium leguminosarum, RBL5808 and RBL5812, revealed independent Tn5 transposon integrations in a single gene, designated exo5. As judged from structural and functional homology, this gene encodes a UDP-glucose dehydrogenase responsible for the oxidation of UDP-glucose to UDP-glucuronic acid. A mutation in exo5 affects all glucuronic acid-containing polysaccharides and, consequently, all galacturonic acid-containing polysaccharides. Exo5-deficient rhizobia do not produce extracellular polysaccharide (EPS) or capsular polysaccharide (CPS), both of which contain glucuronic acid. Carbohydrate composition analysis and nuclear magnetic resonance studies demonstrated that EPS and CPS from the parent strain have very similar structures. Lipopolysaccharide (LPS) molecules produced by the mutant strains are deficient in galacturonic acid, which is normally present in the core and lipid A portions of the LPS. The sensitivity of exo5 mutant rhizobia to hydrophobic compounds shows the involvement of the galacturonic acid residues in the outer membrane structure. Nodulation studies with Vicia sativa subsp. nigra showed that exo5 mutant rhizobia are impaired in successful infection thread colonization. This is caused by strong agglutination of EPS-deficient bacteria in the root hair curl. Root infection could be restored by simultaneous inoculation with a Nod factor-defective strain which retained the ability to produce EPS and CPS. However, in this case colonization of the nodule tissue was impaired.     

Glycosylation Variants of a β-Glucosidase Secreted by a Taiwanese Fungus,Chaetomella raphigera,Exhibit Variant-Specific Catalytic and Biochemical Properties

Cellulosic biomass is an abundant and promising energy source. To make cellulosic biofuels competitive against conventional fuels, conversion of rigid plant materials into sugars must become efficient and cost-effective. During cellulose degradation, cellulolytic enzymes generate cellobiose (β-(1→4)-glucose dimer) molecules, which in turn inhibit such enzymes by negative feedback. β-Glucosidases (BGLs) cleave cellobiose into glucose monomers, assisting overall cellulolytic activities. Therefore, BGLs are essential for efficient conversion of cellulosic biomass into biofuels, and it is important to characterize newly isolated BGLs for useful traits. Here, we report our discovery that the indigenous Taiwanese fungus Chaetomella raphigera strain D2 produces two molecular weight variants of a single BGL, D2-BGL (shortened to “D2”), which differ in O-glycosylation. The more extensively O-glycosylated form of native D2 (nD2L) has increased activity toward the natural substrate, cellobiose, compared to the less O-glycosylated form (nD2S). nD2L is more stable at 60°C, in acidic pH, and in the presence of the ionic detergent sodium dodecyl sulfate than nD2S. Furthermore, unlike nD2S, nD2L does not display substrate inhibition by an artificial substrate p-nitrophenyl glucopyranoside (pNPG), and the glucose feedback inhibition kinetics of nD2L is competitive (while it is non-competitive for nD2S), suggesting that these two glycovariants of D2 bind substrates differently. Interestingly, D2 produced in a heterologous system, Pichia pastoris, closely mimics properties of nD2S. Our studies suggest that O-glycosylation of D2 is important in determining its catalytic and biochemical properties.     

The Lewis x epitope is a major non-reducing structure in the sulphated N-glycans attached to Asn-65 of bovine pro-opiomelanocortin

The N-terminal glycopeptide of pro-opiomelanocortin (POMC),designated as the 16K fragment, is highly conserved throughoutvertebrates from amphibians to mammals and is likely thereforeto have an important functional role. In this paper, we reportthe first structural characterization of N-glycans attachedto asparagine-65 of a 16K glycopeptide. The 16K fragment wasisolated from bovine pituitaries and the N-glycans were analysedusing fast atom bombardment mass spectrometry together withsugar and linkage analysis. Sulphated-N-acetylgalactosamine-cappedantennae, typical of the pituitary glycohormones, were presentin the major acidic components. The POMC oligo-saccharides aredistinct from those of the pituitary glycohormones because thesulphate is exclusively located on the 3-arm of biantennarystructures and, in addition, a significant proportion of themolecules carry the Lewis x epitope. It is probable that thesedifferences reflect the absence of a tripeptide motif in POMCwhich fully conforms to the criteria previously defined forthe recognition sequence for the N-acetylgalactosamine transferasethat is specific for the pituitary glycohormones [Smith andBaenziger (1992) Proc. Natl. Acad. Sci. USA, 89, 329–333].It remains to be seen whether the Lewis x epitope is involvedin selectin-mediated events, but previous studies suggest thatthe sulphated moieties are unlikely to play a major role inclearance. The Lewis x epitope is also present in the neutralN-linked oligosaccharides, together with a variety of otherantennae including a rarely found fucosylated GalNAc-GlcNAcstructure. FAB-MS glycoprotein Lewis x POMC sulphated-GalNAc     

Identification of a Novel Triterpenoid Saponin from Pisum sativum as a Specific Inhibitor of the Diguanylate Cyclase of Acetobacter xylinum

A specific and highly potent inhibitor of diguanylate cyclase,the key regulatory enzyme of the cellulose synthesizing apparatusin the bacterium Acetobacter xylinum, was isolated from extractsof etiolated pea shoots (Pisum sativum). The inhibitor has beenpurified by a multistep procedure, and sufficient amounts ofhighly purified compound (3-8 mg) for spectral analysis wereobtained. The structure of this compound was established as3-O-a-L-rhamnopyranosyl-(l