Organization of Enzymes in the Polyaromatic Synthetic Pathway: Separability in Bacteria

ULTRACENTRIFUGATION IN SUCROSE DENSITY GRADIENTS WAS EMPLOYED TO ESTIMATE THE MOLECULAR WEIGHTS AND TO DETERMINE POSSIBLE PHYSICAL AGGREGATION OF THE FIVE ENZYMES CATALYZING STEPS TWO TO SIX IN THE PRECHORISMIC ACID PORTION OF THE POLYAROMATIC SYNTHETIC PATHWAY IN SIX SPECIES OF BACTERIA: Escherichia coli, Salmonella typhimurium, Aerobacter aerogenes, Bacillus subtilis, Pseudomonas aeruginosa, and Streptomyces coelicolor. The five enzymes were not aggregated in extracts of any of the species examined, nor are the genes encoding these enzymes clustered in those bacterial species for which genetic evidence exists. (An initial examination of the blue-green alga Anabaena variabilis indicates nonaggregation in this species also.) This situation in bacteria is in marked contrast to that found in Neurospora crassa and other fungi in which the same five enzymes are associated as an aggregate encoded (at least in the case of N. crassa) by a cluster of five genes. In addition, also in contrast to N. crassa, no evidence was obtained for more than one kind of dehydroquinase activity in any of the bacteria examined. These comparative results are discussed in relation to the origin, evolution, and functional significance of the gene-enzyme relationships existing in the early steps of aromatic biosynthesis in bacteria and fungi.     

Enzymes of the Tryptophan Synthetic Pathway in Pseudomonas putida

The first four enzymatic activities of the tryptophan synthetic pathway in Pseudomonas putida were found on separate molecules. Gel filtration and density gradient centrifugation experiments did not disclose any associations or aggregations among them. These findings contrast with the situation found in the enteric bacteria, where the first two activities are found in an aggregate and the third and fourth are catalyzed by a single enzyme. Tryptophan synthetase, the last enzyme of the pathway, consists of two dissociable components. The affinity of these components is less in P. putida than is the case in Escherichia coli.     

Organization of the Tryptophan Pathway: a Phylogenetic Study of the Fungi

The enzymes involved in tryptophan biosynthesis have been analyzed in a variety of fungal strains and a few other microorganisms. The same five biosynthetic reactions occur in all organisms tested, but differences have been found in the stability requirements for the enzymes, in their differential precipitation with ammonium sulfate, and in their sedimentation pattern after zone centrifugation. Based on the sedimentation behavior of anthranilate synthetase, phosphoribosyl-transferase, N-(5′-phosphoribosyl)-anthranilate isomerase, and indole-3-glycerophosphate synthetase, five different patterns of enzyme association could be recognized. The distribution of these patterns was used to evaluate several specific features of proposed phylogenetic relationships in the fungi. A closer relationship between Chytridiales and Aspergillales is postulated, eliminating the Zygomycetes and the Endomycetales as probable intermediates; the latter groups are considered to be sidelines. The data support the idea of a polyphyletic origin of the phycomycetes and suggest that anascosporogenous yeasts tested are related to the heterobasidiomycetes rather than to the Endomycetales. A possible sequence of changes leading to the various patterns of organization of the tryptophan pathway during the course of evolution is also proposed.     

Enzymes of the Isoleucine-Valine Pathway in Acinetobacter

Regulation of four of the enzymes required for isoleucine and valine biosynthesis in Acinetobacter was studied. A three- to fourfold derepression of acetohydroxyacid synthetase was routinely observed in two different wild-type strains when grown in minimal medium relative to cells grown in minimal medium supplemented with leucine, valine, and isoleucine. A similar degree of synthetase derepression was observed in appropriately grown isoleucine or leucine auxotrophs. No significant derepression of threonine deaminase or transaminase B occurred in either wild-type or mutant cells grown under a variety of conditions. Three amino acid analogues were tested with wild-type cells; except for a two- to threefold derepression of dihydroxyacid dehydrase when high concentrations of aminobutyric acid were added to the medium, essentially the same results were obtained. Experiments showed that threonine deaminase is subject to feedback inhibition by isoleucine and that valine reverses this inhibition. Cooperative effects in threonine deaminase were demonstrated with crude extracts. The data indicate that the synthesis of isoleucine and valine in Acinetobacter is regulated by repression control of acetohydroxyacid synthetase and feedback inhibition of threonine deaminase and acetohydroxyacid synthetase.     

Common Element in the Repression Control of Enzymes of Histidine and Aromatic Amino Acid Biosynthesis in Bacillus subtilus

Single-step mutants of Bacillus subtilis derepressed for enzymes of both aromatic amino acid and histidine biosynthesis were isolated. These mutants occur at a frequency of 10(-6) per cell per generation. All histidine enzymes as well as all enzymes of aromatic acid synthesis which were examined are maximally derepressed. This level cannot be repressed by growth on either histidine or tyrosine. Some of the structural genes which specify the derepressed enzymes are linked to the aromatic cluster; others are unlinked. The significance of these nonrepressible strains is discussed in terms of the mechanism of repression.     

Enzymes of the Tryptophan Pathway in Acinetobacter calco-aceticus

All enzymes of the tryptophan synthetic pathway were detectable in extracts from wild-type Acinetobacter calco-aceticus. The levels of these enzymes were determined in extracts from a number of auxotrophs grown under limiting tryptophan. In each case only anthranilate synthetase was found to be present in increased amounts, whereas the specific activities of the remaining enzymes remained unchanged and unaffected by the tryptophan concentration. Derepression of anthranilate synthetase was found to occur as the concentration of tryptophan became limiting. Anthranilate synthetase and phosphoribosyl transferase activities are both feedback-inhibited by tryptophan. Molecular weight determination carried out by gel filtration and zonal centrifugation in sucrose revealed that all the enzymes are less than 100,000, and no molecular aggregates of these enzymes were detected. The data indicate that tryptophan synthesis in Acinetobacter is regulated both by feedback inhibition of the first two enzymes of the pathway and by repression control of anthranilate synthetase.     

Fine-Mapping the HOXB Region Detects Common Variants Tagging a Rare Coding Allele: Evidence for Synthetic Association in Prostate Cancer

The HOXB13 gene has been implicated in prostate cancer (PrCa) susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of 3195 SNPs in 20,440 PrCa cases and 21,469 controls in The PRACTICAL consortium. We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk, described by rs117576373 (OR 1.30, P = 2.62×10⁻¹⁴). Additional genotyping, conditional regression and haplotype analyses indicated that the newly identified common variants tag a rare, partially correlated coding variant in the HOXB13 gene (G84E, rs138213197), which has been identified recently as a moderate penetrance PrCa susceptibility allele. The potential for GWAS associations detected through common SNPs to be driven by rare causal variants with higher relative risks has long been proposed; however, to our knowledge this is the first experimental evidence for this phenomenon of synthetic association contributing to cancer susceptibility.     

Fungi in the Canopy: How Soil Fungi and Extracellular Enzymes Differ Between Canopy and Ground Soils

Ecosystems - Tropical montane cloud forests contain a large abundance and diversity of canopy epiphytes, which depend on canopy soil to retain water and nutrients. We lack an in depth understanding...     

Alcohol Selectivity in a Synthetic Thermophilic n-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes

n-Butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. A synthetic pathway for n-butanol production from acetyl coenzyme A (acetyl-CoA) that functioned at 70°C was assembled in vitro from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. Recombinant versions of eight thermophilic enzymes (β-ketothiolase [Thl], 3-hydroxybutyryl-CoA dehydrogenase [Hbd], and 3-hydroxybutyryl-CoA dehydratase [Crt] from Caldanaerobacter subterraneus subsp. tengcongensis; trans-2-enoyl-CoA reductase [Ter] from Spirochaeta thermophila; bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase [AdhE] from Clostridium thermocellum; and AdhE, aldehyde dehydrogenase [Bad], and butanol dehydrogenase [Bdh] from Thermoanaerobacter sp. strain X514) were utilized to examine three possible pathways for n-butanol. These pathways differed in the two steps required to convert butyryl-CoA to n-butanol: Thl-Hbd-Crt-Ter-AdhE (C. thermocellum), Thl-Hbd-Crt-Ter-AdhE (Thermoanaerobacter X514), and Thl-Hbd-Crt-Ter-Bad-Bdh. n-Butanol was produced at 70°C, but with different amounts of ethanol as a coproduct, because of the broad substrate specificities of AdhE, Bad, and Bdh. A reaction kinetics model, validated via comparison to in vitro experiments, was used to determine relative enzyme ratios needed to maximize n-butanol production. By using large relative amounts of Thl and Hbd and small amounts of Bad and Bdh, >70% conversion to n-butanol was observed in vitro, but with a 60% decrease in the predicted pathway flux. With more-selective hypothetical versions of Bad and Bdh, >70% conversion to n-butanol is predicted, with a 19% increase in pathway flux. Thus, more-selective thermophilic versions of Bad, Bdh, and AdhE are needed to fully exploit biocatalytic n-butanol production at elevated temperatures.     

Engineered Synthetic Pathway for Isopropanol Production in Escherichia coli

A synthetic pathway was engineered in Escherichia coli to produce isopropanol by expressing various combinations of genes from Clostridium acetobutylicum ATCC 824, E. coli K-12 MG1655, Clostridium beijerinckii NRRL B593, and Thermoanaerobacter brockii HTD4. The strain with the combination of C. acetobutylicum thl (acetyl-coenzyme A [CoA] acetyltransferase), E. coli atoAD (acetoacetyl-CoA transferase), C. acetobutylicum adc (acetoacetate decarboxylase), and C. beijerinckii adh (secondary alcohol dehydrogenase) achieved the highest titer. This strain produced 81.6 mM isopropanol in shake flasks with a yield of 43.5% (mol/mol) in the production phase. To our knowledge, this work is the first to produce isopropanol in E. coli, and the titer exceeded that from the native producers.     

Two Feedback-Insensitive Enzymes of the Aspartate Pathway in Nicotiana sylvestris

Lysine and threonine overproducer mutants in Nicotiana sylvestris, characterized by an altered regulation of, respectively, dihydrodipicolinate synthase and aspartate kinase activities, were crossed to assess the effects of the simultaneous presence of these genes on the biosynthesis of aspartate-derived amino acids. The monogenic dominant behavior of both resistance traits was confirmed, and their loci were found to be unlinked. Study of the inhibition properties of dihydrodipicolinate synthase and aspartate kinase activities in RAEC-1 × RLT 70 confirmed the heterozygote state of both mutations, because only half of their lysine-sensitive activity could still be inhibited by this negative effector. Analysis of the free amino acid pool during the growth of the double mutant revealed a major free lysine overproduction reaching up to 50% of the total pool, whereas the other aspartate-derived amino acids remained equally or even less abundant than in the wild type. An abnormal phenotype was clearly associated with such high levels of lysine accumulation, which points out the possible role of this amino acid in the developmental features of the plant. Comparison of the amino acid content, free and total (free + protein-bound), between the wild type, the two mutants, and the double mutant obtained by crossing them brings new insights on the regulation of the aspartate pathway, and on its implications in relationship to plant nutritional value improvement.     

Evidence for Distinct Aggregation Factors and Receptors in Cells

SINCE the original observations by Wilson¹ that dissociated sponge cells could reassociate in vitro, cell aggregation (or reaggregation) has been widely used as an operational criterion for the study of intercellular adhesion². The introduction of rotation-mediated methods to promote cell aggregation^3,4 led to the possibility of obtaining reproducible quantitative data. In these methods, suspensions of dissociated single cells are shaken under defined conditions of speed and temperature and cell aggregation is measured by either the size of aggregates or the number of single cells. The aggregation of dissociated cells from sponges⁵, chick and mouse embryos⁴ and tissue culture cells⁶ has been investigated with this method. Cells maintained in vitro seemed particularly suitable for studying mechanisms of cell aggregation as they represent a histotypically homogeneous population.     

A Comparison of Isolation Methods for Black Fungi Degrading Aromatic Toxins

Mycopathologia - The prevalence of black fungi in the order Chaetothyriales has often been underestimated due to the difficulty of their isolation. In this study, three methods which are often used...     

植物细胞壁多糖合成酶系及真菌降解酶系

秸秆类植物细胞壁多糖高效降解转化对我国农业经济的绿色可持续发展具有重要意义,然而植物细胞壁在长期进化过程中形成了复杂结构限制了工业化酶解转化的过程。一方面从植物细胞壁多糖合成酶系的多样性、细胞壁多糖成分的复杂性、超分子结构的异质性等方面综述了形成植物细胞壁抗降解屏障的原因;另一方面从真菌降解植物细胞壁酶系的多样性、不同菌株降解酶组成差异性等分析降解转化植物细胞壁时发挥的不同作用,从而为工业转化合理复配真菌降解酶系,提高秸秆生物质的利用效率提供理论支持。     

Biological Reduction of Aromatic Nitroso Compounds: Evidence for the Involvement of Superoxide Anions

The in vitro formation of phenylhydronitroxide and 2-methylphenylhydronitroxide free radicals from nitrosobenzene (NB) and 2-nitrosotoluene (NT), respectively, in either red blood cells (RBC) or RBC hemolysates, was confirmed by electron spin resonance spectroscopy (ESR). Free radicals were generated nonenzymatically from reaction of the respective nitroso compounds with a number of biological reducing agents as corroborated by model studies of NB or NT with NAD(P)H. Under aerobic conditions, phenylhydronitroxide and 2-methylphenylhydronitroxide underwent a subsequent one-electron transfer to oxygen, which then resulted in the formation of superoxide anion (O₂^-). The latter product was confirmed by the superoxide dismutase (SOD)-inhibitable reduction of cytochrome c (cyt c). Apparently, oxygen is needed for continuous formation of the hydronitroxide radical derivatives. On the other hand, under anaerobic conditions, no phenylhydronitroxide radical was generated from NB in the presence of NADH, but the formation of phenylhydroxylamine from NB was detected by the absorption spectrometry. These results suggest that oxygen is a preferential electron acceptor for hydronitroxide radical derivatives.     

A Dynamic Study of Protein Secretion and Aggregation in the Secretory Pathway

Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.