The xpt and pbuX genes from Bacillus subtilis were cloned, and their nucleotide sequences were determined. The xpt gene encodes a specific xanthine phosphoribosyltransferase, and the pbuX gene encodes a xanthinespecific purine permease. The genes have overlapping coding regions, and Northern (RNA) blot analysis indicated an operon organization. The translation of the second gene, pbuX, was strongly dependent on the translation of the first gene, xpt. Expression of the operon was repressed by purines, and the effector molecules appear to be hypoxanthine and guanine. When hypoxanthine and guanine were added together, a 160-fold repression was observed. The regulation of expression was at the level of transcription, and we propose that a transcription termination-antitermination control mechanism similar to the one suggested for the regulation of the purine biosynthesis operon exists. The expression of the xpt-pbuX operon was reduced when hypoxanthine served as the sole nitrogen source. Under these conditions, the level of the hypoxanthine-and xanthinedegrading enzyme, xanthine dehydrogenase, was induced more than 80-fold. The xanthine dehydrogenase level was completely derepressed in a glnA (glutamine synthetase) genetic background. Although the regulation of the expression of the xpt-pbuX operon was found to be affected by the nitrogen source, it was normal in a glnA mutant strain. This result suggests the existence of different signalling pathways for repression of the transcription of the xpt-pbuX operon and the induction of xanthine dehydrogenase.

Microscopic examination of cross sections of dorsal and ventral sutures of soybean pods ( Glycine max cv. TGx1835-2E) at two different stages of maturity revealed that the dehiscence zone of soybean pods is functionally equivalent to the dehiscence zone known from crucifers. Enzymatic assays demonstrated the presence of endo-1,4-β β β β -glucanases and endopolygalacturonases, the activity of which accumulated in the dehiscence zone and peaked during maturation. A single partial cDNA encoding an endopolygalacturonase was isolated by polymerase chain reaction and this clone was used to isolate the complete gene encoding the endopolygalacturonase in question. Approximately 1·2 kb of 5 ′ ′ ′ ′ upstream sequence was cloned in the plant transformation vector pCAMBIA1301 in front of the uidA (GUS) gene and transformed into Arabidopsis thaliana . Expression analysis of the soybean endopolygalacturonase transcript revealed that the endopolygalacturonase is primarily found in dehiscence-related tissue and is presumably involved in the breakdown of the middle lamella prior to dehiscence. This result was corroborated by GUS stainings of the transgenic Arabidopsis lines

Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono-and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium Colwellia echini A3 T is a potent enzyme producer since it completely hydrolyzes agar and -carrageenan. Here, we report that the genome of C. echini A3 T harbors two large gene clusters for the degradation of carrageenan and agar, respectively. Phylogenetical and functional studies combined with transcriptomics and in silico structural modeling revealed that the carrageenolytic cluster encodes furcellaranases, a new class of glycoside hydrolase family 16 (GH16) enzymes that are key enzymes for hydrolysis of furcellaran, a hybrid carrageenan containing both ␤and -carrageenan motifs. We show that furcellaranases degrade furcellaran into neocarratetraose-43-O-monosulfate [DA-(␣1,3)-G4S-(␤1,4)-DA-(␣1,3)-G], and we propose a molecular model of furcellaranases and compare the active site architectures of furcellaranases, -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, C. echini A3 T was shown to encode -carrageenases, -carrageenases, and members of a new class of enzymes, active only on hybrid ␤/-carrageenan tetrasaccharides. On the basis of our genomic, transcriptomic, and functional analyses of the carrageenolytic enzyme repertoire, we propose a new model for how C. echini A3 T degrades complex sulfated marine polysaccharides such as furcellaran, -carrageenan, and -carrageenan. IMPORTANCE Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on -carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of -carrageenan and agar, respectively. As the first, we report on the structure/ function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated ␤/-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 ␤-galactosidases and show that this new class of enzymes is active only on hybrid ␤/-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize ␤/-, -, and -carrageenan.

Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less abundant GH96 α-agarases harbored in the agar specific polysaccharide utilization locus (PUL) of Colwellia echini A3T facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the α-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that α-agarases of C. echini A3T create a novel auxiliary pathway. α-Agarases convert even-numbered neoagarooligosaccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genome analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution while the essential core agarolytic gene set was conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of α-agarase, promote metabolic versatility by channeling agar metabolism through different routes. Importance Colwellia echini A3T is an example of how the gene gain can lead to the evolutionary expansion of agar specific polysaccharide utilization loci (PUL). C. echini A3T encodes two α-agarases in addition to the core β-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few α-agarases have been biochemically characterized. The molecular and biological functions of two α-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete α-agarolytic pathway in C. echini A3T. The addition of α-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility.

Pseudomonas fluorescens In5 synthesizes the antifungal cyclic lipopeptides (CLPs) nunamycin and nunapeptin, which are similar in structure and genetic organization to the pseudomonas-derived phytotoxins syringomycin and syringopeptin. Regulation of syringomycin and syringopeptin is dependent on the two-component global regulatory system GacS/GacA, and the SalA, SyrF, and SyrG transcription factors, which activate syringomycin synthesis in response to plant signalling molecules. Previously, we demonstrated that a specific transcription factor, NunF, positively regulates the synthesis of nunamycin and nunapeptin in P. fluorescens In5 and that the nunF gene is upregulated by fungal-associated molecules. This study focusses on further unravelling the complex regulation governing CLP synthesis in P. fluorescens In5. Promoter fusions were used to show that the specific activator NunF is dependent on the global regulator of secondary metabolism GacA and is regulated by fungal-associated molecules and low temperatures. In contrast, GacA is stimulated by plant signalling molecules leading to the hypothesis that P. fluorescens is a hyphosphere-associated bacterium encoding transcription factor genes that respond to signals indicating the presence of fungi and oomycetes. Based on these findings, we present a model for how synthesis of nunamycin and nunapeptin is regulated by fungal- and oomycete-associated molecules. Importance: Cyclic lipopeptide (CLP) synthesis gene clusters in pseudomonads display a high degree of synteny and the structure of the peptides synthesized is very similar. Accordingly, the genomic island encoding the synthesis of syringomycin and syringopeptin in P. syringae pv. syringae closely resembles that of P. fluorescens In5, which code for synthesis of the antifungal and anti-oomycete peptides nunamycin and nunapeptin, respectively. However, the regulation of syringomycin and syringopeptin synthesis is different from that of nunamycin and nunapeptin synthesis. While CLP synthesis in the plant pathogenic P. syringae pv. syringae is induced by plant signalling molecules, such compounds do not significantly influence synthesis of nunamycin and nunapeptin in P. fluorescens In5. Instead, fungal-associated molecules positively regulate anti-fungal peptide synthesis in P. fluorescens In5 while the synthesis of the global regulator GacA in P. fluorescens In5 is positively regulated by plant signal molecules but not fungal-associated molecules.