Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications

Large quantities of the potentially toxic compound styrene are produced and used annually by the petrochemical and polymer-processing industries. It is as a direct consequence of this that significant volumes of styrene are released into the environment in both the liquid and the gaseous forms. Styrene and its metabolites are known to have serious negative effects on human health and therefore, strategies to prevent its release, remove it from the environment, and understand its route of degradation were the subject of much research. There are a large number of microbial genera capable of metabolizing styrene as a sole source of carbon and energy and therefore, the possibility of applying these organisms to bioremediation strategies was extensively investigated. From the multitude of biodegradation studies, the application of styrene-degrading organisms or single enzymes for the synthesis of value-added products such as epoxides has emerged.     

Microbial degradation of furanic compounds: biochemistry,genetics, and impact

Microbial metabolism of furanic compounds, especially furfural and 5-hydroxymethylfurfural (HMF), is rapidly gaining interest in the scientific community. This interest can largely be attributed to the occurrence of toxic furanic aldehydes in lignocellulosic hydrolysates. However, these compounds are also widespread in nature and in human processed foods, and are produced in industry. Although several microorganisms are known to degrade furanic compounds, the variety of species is limited mostly to Gram-negative aerobic bacteria, with a few notable exceptions. Furanic aldehydes are highly toxic to microorganisms, which have evolved a wide variety of defense mechanisms, such as the oxidation and/or reduction to the furanic alcohol and acid forms. These oxidation/reduction reactions constitute the initial steps of the biological pathways for furfural and HMF degradation. Furfural degradation proceeds via 2-furoic acid, which is metabolized to the primary intermediate 2-oxoglutarate. HMF is converted, via 2,5-furandicarboxylic acid, into 2-furoic acid. The enzymes in these HMF/furfural degradation pathways are encoded by eight hmf genes, organized in two distinct clusters in Cupriavidus basilensis HMF14. The organization of the five genes of the furfural degradation cluster is highly conserved among microorganisms capable of degrading furfural, while the three genes constituting the initial HMF degradation route are organized in a highly diverse manner. The genetic and biochemical characterization of the microbial metabolism of furanic compounds holds great promises for industrial applications such as the biodetoxifcation of lignocellulosic hydrolysates and the production of value-added compounds such as 2,5-furandicarboxylic acid.     

Microbial biofilms: from ecology to molecular genetics.

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.     

苎麻雄性不育系生化代谢和育性遗传研究

用不同温度和日长处理盆栽材料,测试苎麻雄性不育系的温光反应;于雌雄性器官发育期取盆栽植株顶部展开叶往下数第7叶,分析不育系的生化代谢;根据杂交及自交后代育性分离情况,鉴定不育系的不育性遗传方式.结果如下高温加速营养生长,而短日促进生殖生长,短日高温明显加快不育系的发育进度,但高温的促进作用随日长增加而减弱,以至消失.不育系的叶片粗蛋白质、氨基酸含量比可育系减少,尤其是天门冬氨酸、谷氨酸、甘氨酸、胱氨酸、缬氨酸、苯丙氨酸和精氨酸减少明显,但游离脯氨酸含量增加.这些物质代谢的变化,可能是导致苎麻雄性不育的原因.不育系GS14-1、SS370、GSA-2、GS15-8和SS387等的不育性遗传与1对相对性状的遗传方式相符,已找到不育系的保持系和恢复系.     

Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.

This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail.     

Primary sex determination: genetics and biochemistry

Summary On the basis of widespread phylogenetic conservatism, it has been propose'd that serologically-defined H-Y antigen is the inducer of primary sex differentiation in mammals, causing the initially indifferent gonad to become a testis rather than an ovary. The proposal has withstood extensive testing in a variety of biological circumstances: XX males have testes and are H-Y⁺ and fertile XY females lack testicular tissue and are H-Y; soluble H-Y antigen induces testicular organogenesis in XX indifferent gonads of the fetal calf in culture; H-Y antibody blocks tubular reaggregation of dispersed XY testicular cells, causing them to organize follicular clusters.There is a gonadal receptor for H-Y antigen: fetal ovarian cells that have been exposed to soluble H-Y (released for example by testicular Sertoli cells) take up the molecule and acquire the H-Y⁺ phenotype; they absorb H-Y antibody in serological tests. Specific uptake of soluble H-Y does not occur in the extra-gonadal tissues.It may be inferred that H-Y antigen is disseminated during embryogenesis and bound by specific receptors in cells of the primordial gonad, and that reaction of H-Y and its receptor signals a program of testicular differentiation, regardless of karyotype. The several anomalies of primary sexual differentiation manifest in such conditions as the XX male, the XX true hermaphrodite, and the XY female can thus reasonably be viewed as specific errors of synthesis, dissemination, and binding of H-Y antigen.H-Y is secreted by Daudi cells, cultured from a human XY Burkitt lymphoma. The Daudi-secreted moiety is a single hydrophobic protein of 18,000 molecular weight. Early attempts to characterize H-Y secreted by testicular Sertoli cells have yielded two molecules, one of 16,500 MW (corresponding to the Daudi-secreted 18,000 MW protein), and one of 31,000 MW. It remains to be ascertained whether both are in fact H-Y antigens, and if so, whether one is a polymer of the other, or whether each represents the product of genes with discrete testis-determining functions.     

Three fundamental contributions of molecular genetics to avian ecology and evolution

Studies in molecular genetics are having revisionary impact in at least three broad areas of avian ecology and evolution: mating systems, geographic population structure and gene flow, and phylogenetic relationships among species and higher taxa. With regard to mating systems, genetic analyses of maternity and paternity have revealed unexpectedly high frequencies of extra-pair fertilization and intraspecific brood parasitism in numerous avian species (including those thought to be socially monogamous), and these discoveries are prompting a fundamental reshaping of mating system theory for birds. With regard to genetic structure, molecular markers have uncovered a great variety of depths and patterns in the phylogeographic histories of conspecific populations, and these findings provide novel perspectives on historical gene flow regimes and species concepts. With regard to evolutionary relationships among higher avian taxa, molecular findings have suggested several phylogenetic realignments, thus prompting renewed interest in the cross-comparative aspects of molecular and morphological evolution as well as of alternative procedures for molecular analysis.     

Three fundamental contributions of molecular genetics to avian ecology and evolution

Studies in molecular genetics are having revisionary impact in at least three broad areas of avian ecology and evolution: mating systems, geographic population structure and gene flow, and phylogenetic relationships among species and higher taxa. With regard to mating systems, genetic analyses of maternity and paternity have revealed unexpectedly high frequencies of extra-pair fertilization and intraspecific brood parasitism in numerous avian species (including those thought to be socially monogamous), and these discoveries are prompting a fundamental reshaping of mating system theory for birds. With regard to genetic structure, molecular markers have uncovered a great variety of depths and patterns in the phylogeographic histories of conspecific populations, and these findings provide novel perspectives on historical gene flow regimes and species concepts. With regard to evolutionary relationships among higher avian taxa, molecular findings have suggested several phylogenetic realignments, thus prompting renewed interest in the cross-comparative aspects of molecular and morphological evolution as well as of alternative procedures for molecular analysis.     

Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize.

Nucleic acids fractions were isolated from pre-Columbian maize seeds and characterized using different approaches such as polyacrylamide gel electrophoresis, anti-DNA antibody binding, HPLC fractionation, molecular hybridization with cloned genes, and DNA amplification by the polymerase chain reaction. The nucleic acids were found to be very depolymerized (less than or equal to 140 base pairs in length) and composed mainly of ribosomal RNA. Despite the very low amount and degree of polymerization of seed DNA, specific maize nuclear Mu1, Mu4, Mu8 and, possibly, Mu5 element components could be detected, thanks to the use of amplification systems as short as 90 bp. The results suggest that evaluation of the relative proportions of Mu-type element components and, possibly, other maize genomic components in single mummified kernels, may offer a new key to the study of ancient maize populations.     

Theoretical studies on identity SN2 reactions of lithium halide and methyl halide: A microhydration model

Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase halogen-exchange S_N2 reactions. These water molecules coordinated with the center metal lithium ion, and also interacted with entering and leaving halogen anion via hydrogen bond in complexes and transition state, which to some extent compensated hydration of halogen anion. At 298 K the reaction profiles all involve central barriers ΔE _cent which are found to decrease in the order F > Cl > Br > I. The same trend is also found for the overall barriers (ΔE _ovr ) of the title reaction. In the S_N2 reaction of sodium iodide and methyl iodide, the activation energy agrees well with the aqueous conductometric investigation.     

Glucosinolates – biochemistry, genetics and biological activity

This paper provides a brief overview of the biochemistry, genetics andbiological activity of glucosinolates and their degradation products.These compounds are found in vegetative and reproductive tissues of16 plant families, but are most well known as the major secondarymetabolites in the Brassicaceae. Following tissue disruption, theyare hydrolysed to a variety of products of which isothiocyanates(`mustard oils') are the most prominent. The majority of geneticstudies have concentrated on reducing the levels of these compoundsin the seeds of oilseed Brassica crops due to antinutritionalfactors associated with 2-hydroxy-3-butenyl glucosinolate. However,current interest is concerned with the anticarcinogenic activity ofisothiocyanates derived from cruciferous vegetables and salad crops.     

Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495

Aminobacter lissarensis CC495 is an aerobic facultative methylotroph capable of growth on glucose, glycerol, pyruvate and methylamine as well as the methyl halides methyl chloride and methyl bromide. Previously, cells grown on methyl chloride have been shown to express two polypeptides with apparent molecular masses of 67 and 29 kDa. The 67 kDa protein was purified and identified as a halomethane:bisulfide/halide ion methyltransferase. This study describes a single gene cluster in A. lissarensis CC495 containing the methyl halide utilisation genes cmuB, cmuA, cmuC, orf 188, paaE and hutI. The genes correspond to the same order and have a high similarity to a gene cluster found in Aminobacter ciceronei IMB-1 and Hyphomicrobium chloromethanicum strain CM2 indicating that genes encoding methyl halide degradation are highly conserved in these strains.     

Protein prenylation in eukaryotic microorganisms: genetics, biology and biochemistry

Modrfication of proteins at C-terminal cysteine residue(s) by the isoprenoids farnesyl (C15) and geranylgeranyl (C20) is essential for the biological function of a number of eukaryotic proteins including fungal mating factors and the small, GTP-binding proteins of the Ras superfamily. Three distinct enzymes, conserved between yeast and mammals, have been identified that prenylate proteins: farnesyl protein transferase, geranylgeranyl protein transferase type I and geranylgeranyl protein transferase type II. Each prenyl protein transferase has its own protein substrate specificity. Much has been learned about the biology, genetics and biochemistry of protein prenylation and prenyl protein transferases through studies of eukaryotic microorganisms, particularly Saccharo-myces cerevisiae. The functional Importance of protein prenylation was first demonstrated with fungal mating factors. The initial genetic analysis of prenyl protein transferases was in S. cerewisiae with the isolation and subsequent characterization of mutations in the RAM1, RAM2, CDC43 and BET2 genes, each of which encodes a prenyl protein transferase subunit. We review here these and other studies on protein prenylation in eukaryotic microbes and how they relate to and have contributed to our knowledge about protein prenylation in all eukaryotic cells.     

Integrated cell biology/biochemistry/molecular genetics laboratories: the cytoplasmic genome projects

This paper describes an integrated laboratory project for intermediate to advanced undergraduate students. The project spans an entire academic quarter (10 weeks) and involves a series of operations that give students experience with fundamental techniques in cell biology, molecular biology, biochemistry, genomics, and bioinformatics. In the process, the student learning community is strengthened, students gain increasing confidence in their abilities in the laboratory, and data are collected toward the eventual sequencing of a cytoplasmic genome. The culmination of the project is the preparation by students of a paper written in the format of a particularly accessible online journal. Journal of Industrial Microbiology & Biotechnology (2000) 24, 339–344. Received 02 April 1999/ Accepted in revised form 22 November 1999