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.     

A review of bacterial methyl halide degradation: biochemistry,genetics and molecular ecology

Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the alpha-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.     

Microbial degradation of organophosphorus compounds

Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.     

Microbial degradation of synthetic recalcitrant compounds

Synthetic compounds, particularly highly chlorinated aromatics, comprise the bulk of the environmental pollutants that somehow must be removed from the environment. Microbial degradation of such compounds is usually very slow, making them highly persistent in nature. Some synthetic compounds, with a lower degree of chlorination are, however, biodegradable; biochemical, genetic, and molecular studies demonstrate the evolution of new plasmid-encoded enzymatic activities specifically designed for the chlorinated substrates. Nucleotide sequences of many of the genes encoding such enzymatic activities demonstrate considerable homology either near the active sites or throughout the molecules with the chromosomal genes encoding enzymes catalyzing analogous reactions. In some cases, unique repeated sequences, reminiscent of prokaryotic insertion sequence elements, are present at or near the newly evolved genes. This suggests gene duplication and divergence as well as recombinational events mediated by transposable type elements as key ingredients in the evolution of new degradative functions. An understanding of such evolutionary processes is an essential feature for the development of genetically-improved bacteria capable of utilizing and thereby removing highly chlorinated environmental pollutants from our environment.     

环境激素类有机污染物的微生物降解和药物类化合物的残留问题

合成有机物在环境中的残留和危害已不仅仅局限于其毒性、富集、致畸和致突变,同时还能干扰包括人类在内的生物的内分泌调节作用.近年来发达国家已开始逐渐有了环境方面的条例,限制和控制这类化合物在水及食物链中的含量.现已清楚地知道,部分除草剂和杀虫剂(如阿特拉津、DDT),塑料的添加增塑剂均有内分泌激素活性,从而对生物的正常生长发育造成不良的影响.而这些化合物不但广泛存在于环境中,在特定的环境中其含量更是非常之高.以增塑剂邻苯二甲酸和邻苯二甲酸二甲酯为例,它们在填埋渗出液中的含量可高达10g·L^-1.在我们研究这类化合物的微生物降解时发现,从活性污泥和红树林中富集到的好氧微生物能将这类化合物完全矿化,且反应速度很快.同时也发现,在降解邻苯二甲酸二甲酯时,单一的纯菌不能完全降解这类化合物,而二种或三种组合的纯菌可以在一周内将500mg·L^-1的底物完全矿化.我们已分离、鉴定出中间产物,建立起了降解途径.研究的结果证实,邻苯二甲酸二甲酯类环境激素是能够在排放前通过微生物的作用达到完全矿化的.另一方面,药物类化合物的残留问题也是一个逐渐显现出的环境问题,这方面的研究应引起更多的关注和重视.     

Microbial degradation of recalcitrant compounds and synthetic aromatic polymers

The evolution of microbial catabolic enzymes cannot keep pace with the rapid introduction of novel compounds into the environment. These new synthetic compounds that are slowly biodegradable or non-biodegradable are known as recalcitrant compounds, and range from simple halogenated hydrocarbons to complex polymers. Recalcitrant compounds can be made biodegradable by developing microorganisms capable of degrading the compound and by treating the compound to make it more conducive to mirobial attack. Many factors contribute to recalcitrance. The organism may lack the necessary genetic information. The organism can acquire this information by plasmid transfer or de novo enzyme synthesis. Plasmids have been characterized that degrade or transform antibiotics, pesticides, and hydrocarbons. By the use of chemostat techniques or chemical mutagens, organisms have been shown to synthesize de novo enzymes. The compound may be too large to enter the cell, or a transport system may not exist to transport it across the membrane. The compound may be insoluble, either as a solid or a liquid, and the microorganism may lack the proper nutrients. Recalcitrant compounds can be oxygenated prior to degradation, in the presence of a readily assimilable carbon source. In the absence of the assimilable carbon source, the recalcitrant compound is not degraded, or only very slowly. Examples of such co-oxidative metabolism are alkane and lignin degradation. Polymers, particularly synthetic ones, are prime examples of difficult-to-degrade compounds. The initial rate of polymer degradation follows a Freundlich or modified Langmuir isotherm rather than Michaelis-Menten kinetics. Microorganisms can irreversibly bind to solid surfaces by various methods. Soil microorganisms have been found to degrade styrene monomers and dimers. Polystyrene has been shown to be biodegradable by ¹⁴CO₂ evolution but at a very slow rate. In car tyres, styrene as a copolymer of butadiene is co-metabolized in the presence of other assimilable carbon sources.     

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.     

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.     

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.     

Discovering functional relationships: biochemistry versus genetics

Biochemists and geneticists, represented by Doug and Bill in classic essays, have long debated the merits of their methods. We revisited this issue using genomic data from the budding yeast, Saccharomyces cerevisiae, and found that genetic interactions outperformed protein interactions in predicting functional relationships between genes. However, when combined, these interaction types yielded superior performance, convincing Doug and Bill to call a truce.     

Protein bodies of seeds: Ultrastructure,biochemistry, biosynthesis and degradation

Typical organelles for protein storage occur in seeds, protein bodies are found in haploid, diploid or triploid tissues and are single membrane bound. In some plants, they exhibit inclusions (globoid and crystalloid), but not in Gramineae endosperm or in Leguminosae cotyledons. A relationship between species and protein body ultrastructure can be put forward. The chemical composition is based mainly on storage proteins and phytic acid but, hydrolytic enzymes(protease and phytase), cations and ribonucleic acids are also present. Other minor biochemical components include oxalic acid, carbohydrates (excluding starch) and lipids. The locations of the storage proteins, enzymes and phytin are described. Protein body ontogeny during seed maturation has given rise to much controversy: are they plastidic or vacuolar? Recent studies on the location of proteosynthesis show that protein bodies are probably synthesized in endoplasmic reticulum lumen and that the Golgi apparatus plays an important role in storage protein synthesis. During germination protein bodies swell and fuse, giving rise to the cell central vacuole, while the integrity of the membrane is maintained. Protein bodies may be considered as being an example of tonoplast origin from endo-plasmic reticulum.     

The response of Pseudomonas aeruginosa to iron: genetics, biochemistry and virulence

During the past decade significant progress has been made towards identifying some of the schemes that Pseudomonas aeruginosa uses to obtain iron and towards cataloguing and characterizing many of the genes and gene products that are likely to play a role in these processes. This review will largely recount what we have learned in the past few years about how P. aeruginosa regulates its acquisition, intake and, to some extent, trafficking of iron, and the role of iron acquisition systems in the virulence of this remarkable opportunistic pathogen. More specifically, the genetics, biochemistry and biology of an essential regulator (Ferric uptake regulator - Fur) and a Fur-regulated alternative sigma factor (PvdS), which are central to these processes, will be discussed. These regulatory proteins directly or indirectly regulate a substantial number of other genes encoding proteins with remarkably diverse functions. These genes include: (i) other regulatory genes, (ii) genes involved in basic metabolic processes (e.g. Krebs cycle), (iii) genes required to survive oxidative stress (e.g. superoxide dismutase), (iv) genes necessary for scavenging iron (e.g. siderophores and their cognate receptors) or genes that contribute to the virulence (e.g. exotoxin A) of this opportunistic pathogen. Despite this recent expansion of knowledge about the response of P. aeruginosa to iron, many significant biological issues surrounding iron acquisition still need to be addressed. Virtually nothing is known about which of the distinct iron acquisition mechanisms P. aeruginosa brings to bear on these questions outside the laboratory, whether it be in soil, in a pipeline, on plants or in the lungs of cystic fibrosis patients.     

Gelsolin amyloidosis: genetics,biochemistry, pathology and possible strategies for therapeutic intervention

Protein misassembly into aggregate structures, including cross-β-sheet amyloid fibrils, is linked to diseases characterized by the degeneration of post-mitotic tissue. While amyloid fibril deposition in the extracellular space certainly disrupts cellular and tissue architecture late in the course of amyloid diseases, strong genetic, pathological and pharmacologic evidence suggests that the process of amyloid fibril formation itself, known as amyloidogenesis, likely causes these maladies. It seems that the formation of oligomeric aggregates during the amyloidogenesis process causes the proteotoxicity and cytotoxicity characteristic of these disorders. Herein, we review what is known about the genetics, biochemistry and pathology of familial amyloidosis of Finnish type (FAF) or gelsolin amyloidosis. Briefly, autosomal dominant D187N or D187Y mutations compromise Ca²⁺ binding in domain 2 of gelsolin, allowing domain 2 to sample unfolded conformations. When domain 2 is unfolded, gelsolin is subject to aberrant furin endoproteolysis as it passes through the Golgi on its way to the extracellular space. The resulting C-terminal 68 kDa fragment (C68) is susceptible to extracellular endoproteolytic events, possibly mediated by a matrix metalloprotease, affording 8 and 5 kDa amyloidogenic fragments of gelsolin. These amyloidogenic fragments deposit systemically, causing a variety of symptoms including corneal lattice dystrophy and neurodegeneration. The first murine model of the disease recapitulates the aberrant processing of mutant plasma gelsolin, amyloid deposition, and the degenerative phenotype. We use what we have learned from our biochemical studies, as well as insight from mouse and human pathology to propose therapeutic strategies that may halt the progression of FAF.