R. B. Cain

Abstract: SUMMARY: The metabolic control of the protocatechuate branch of the 3-oxoadipate pathway in Rhodotorula mucilaginosa was examined and the specific inducers identified using appropriately blocked mutants. Three successive inductive events permitted the synthesis of the five enzymes converting p-hydroxybenzoate to 3-oxoadipyl-CoA: the independent induction of 4-hydroxybenzoate 3-mono-oxygenase by its own specific substrate, the independent induction of protocatechuate 3,4-dioxygenase by either protocatechuate or p-hydroxybenzoate, and finally the co-ordinate induction of 3-carboxymuconate cyclase, 3-carboxymucono-lactone hydrolase and 3-oxoadipate CoA-transferase by cither protocatechuate or p-hydroxybenzoate. Evidence is presented which suggests that R. mucilaginosa is unable to metabolize catechol or its usual precursors, and the significance of this is discussed in relation to control of the protocatechuate branch and the differing control mechanisms governing the synthesis of enzymes of the 3-oxoadipate pathway in other fungi and bacteria.

Abstract: The beta-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to beta-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the beta-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic beta-ketoadipate pathway. In the face of enzyme conservation, the beta-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to beta-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by beta-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the beta-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.

Abstract: Lignin is a major component of lignocellulosic biomass and as such, it is processed in enormous amounts in the pulp and paper industry worldwide. In such industry it mainly serves the purpose of a fuel to provide process steam and electricity, and to a minor extent to provide low grade heat for external purposes. Also from other biorefinery concepts, including 2nd generation ethanol, increasing amounts of lignin will be generated. Other uses for lignin – apart from fuel production – are of increasing interest not least in these new biorefinery concepts. These new uses can broadly be divided into application of the polymer as such, native or modified, or the use of lignin as a feedstock for the production of chemicals. The present review focuses on the latter and in particular the advances in the biological routes for chemicals production from lignin. Such a biological route will likely involve an initial depolymerization, which is followed by biological conversion of the obtained smaller lignin fragments. The conversion can be either a short catalytic conversion into desired chemicals, or a longer metabolic conversion. In this review, we give a brief summary of sources of lignin, methods of depolymerization, biological pathways for conversion of the lignin monomers and the analytical tools necessary for characterizing and evaluating key lignin attributes.

Abstract: A literature review is given on growth of yeasts on benzene compounds and on the catabolic pathways involved. Additionally, a yeast collection was screened for assimilation of phenol and 3-hydroxybenzoic acid. Fifteen ascomycetous and thirteen basidiomycetous yeast species were selected and were tested for growth on 84 benzene compounds. It appeared that 63 of these compounds supported growth of one or more yeast species. The black yeast Exophiala jeanselmei assimilated 54 of these compounds. The catechol branch of the 3-oxoadipate pathway and its hydroxyhydroquinone variant were involved in phenol and resorcinol catabolism of ascomycetes as well as of basidiomycetes. However, these two groups of yeasts showed characteristic differences in hydroxybenzoate catabolism. In the yeastlike fungus E. jeanselmei and in basidiomycetes of the genera Cryptococcus, Leucosporidium and Rhodotorula, the protocatechuate branch of the 3-oxoadipate pathway was induced by growth on 3- and 4-hydroxybenzoic acids. In three Trichosporon species and in all ascomycetous yeasts tested, 4-hydroxybenzoic acid was catabolyzed via protocatechuate and hydroxyhydroquinone. These yeasts were unable to cleave protocatechuate. 3-Hydroxybenzoic and 3-hydroxycinnamic acids were catabolized in ascomycetous yeasts via the gentisate pathway, but in basidiomycetes via protocatechuate. Incomplete oxidation of phenol, some chlorophenols, cresols and xylenols was observed in cultures of Candida parapsilosis growing on hydroquinone. Most compounds transformed by the growing culture were also converted by the phenol monooxygenase present in cell-free extracts of this yeast. They did not support growth. The relationship between the ability of ascomycetous yeasts to assimilate n-alkanes, amines and benzene compounds, and the presence of Coenzyme Q9 is discussed.

Abstract: Lignin valorization offers significant potential to enhance the economic viability of lignocellulosic biorefineries. However, because of its heterogeneous and recalcitrant nature, conversion of lignin to value-added coproducts remains a considerable technical challenge. In this study, we employ base-catalyzed depolymerization (BCD) using a process-relevant solid lignin stream produced via deacetylation, mechanical refining, and enzymatic hydrolysis to enable biological lignin conversion. BCD was conducted with the solid lignin substrate over a range of temperatures at two NaOH concentrations, and the results demonstrate that the lignin can be partially extracted and saponified at temperatures as low as 60 °C. At 120 °C and 2% NaOH, the high extent of lignin solubility was accompanied by a considerable decrease in the lignin average molecular weight and the release of lignin-derived monomers including hydroxycinnamic acids. BCD liquors were tested for microbial growth using seven aromatic-catabolizing bact...

Abstract: Pseudomonas aeruginosa (Pa) and Burkholderia cepacia complex (Bcc) lung infections are responsible for much of the mortality in cystic fibrosis (CF). However, little is known about the ecological interactions between these two, often co-infecting, species. This study provides what is believed to be the first report of the intra- and interspecies bacteriocin-like inhibition potential of Pa and Bcc strains recovered from CF patients. A total of 66 strains were screened, and shown to possess bacteriocin-like inhibitory activity (97 % of Pa strains and 68 % of Bcc strains showed inhibitory activity), much of which acted across species boundaries. Further phenotypic and molecular-based assays revealed that the source of this inhibition differs for the two species. In Pa, much of the inhibitory activity is due to the well-known S and RF pyocins. In contrast, Bcc inhibition is due to unknown mechanisms, although RF-like toxins were implicated in some strains. These data suggest that bacteriocin-based inhibition may play a role in governing Pa and Bcc interactions in the CF lung and may, therefore, offer a novel approach to mediating these often fatal infections.