Harnessing the power of enzymes for environmental stewardship

Enzymes are versatile catalysts with a growing number of applications in biotechnology. Their properties render them also attractive for waste/pollutant treatment processes and their use might be advantageous over conventional treatments. This review highlights enzymes that are suitable for waste treatment, with a focus on cell-free applications or processes with extracellular and immobilized enzymes. Biological wastes are treated with hydrolases, primarily to degrade biological polymers in a pre-treatment step. Oxidoreductases and lyases are used to biotransform specific pollutants of various nature. Examples from pulp and paper, textile, food and beverage as well as water and chemical industries illustrate the state of the art of enzymatic pollution treatment. Research directions in enzyme technology and their importance for future development in environmental biotechnology are elaborated. Beside biological and biochemical approaches, i.e. enzyme prospection and the design of enzymes, the review also covers efforts in adjacent research fields such as insolubilization of enzymes, reactor design and the use of additives. The effectiveness of enzymatic processes, especially when combined with established technologies, is evident. However, only a limited number of enzymatic field applications exist. Factors like cost and stability of biocatalysts need to be addressed and the collaboration and exchange between academia and industry should be further strengthened to achieve the goal of sustainability.     

Singlet oxygen production by biological systems

Singlet oxygen (1 delta g) is a highly reactive, short-lived intermediate which readily oxidizes a variety of biological molecules. The biochemical production of singlet oxygen has been proposed to contribute to the destructive effects seen in a number of biological processes. Several model biochemical systems have been shown to produce singlet oxygen. These systems include the peroxidase-catalyzed oxidations of halide ions, the peroxidase-catalyzed oxidations of indole-3-acetic acid, the lipoxygenase-catalyzed oxidation of unsaturated long chain fatty acids and the bleomycin-catalyzed decomposition of hydroperoxides. Results from these model systems should not be uncritically extrapolated to living systems. Recently, however, an intact cell, the human eosinophil, was shown to generate detectable amounts of singlet oxygen. This result suggests that singlet oxygen may be shown to be a significant biochemical intermediate in a few biological processes.     

The role of endogenous thiols in intrinsic radioprotection

Observations are reviewed from experiments performed to study the role of endogenous thiols in the radiation response of cells using a glutathione-deficient and a related glutathione-proficient cell strain. The effect of glutathione in the initial radical reactions was considered and the yield of single-strand DNA breaks was the end-point of the response. The rejoining of breaks and clonogenic survival were chosen as end-points when, in addition, the role of glutathione in the subsequent biochemical processes was studied. The results were interpreted to indicate that glutathione plays a role in both the radical and the biochemical reactions which follow irradiation. In the former case, it functions as a damage-restituting reactant, in general agreement with the 'competition model'. Some biochemical repair processes, in particular those concerned with the rejoining of breaks induced by radiation in the presence of oxygen or misonidazole, appear also to be critically dependent on glutathione. Due, probably, to its particular spatial distribution, endogenous glutathione is specific in the radical processes, and exogenous thiols cannot be substituted for it. No such specificity was indicated in the biochemical processes related to strand break rejoining.     

Steady state analysis of metabolic pathways using Petri nets

Computer assisted analysis and simulation of biochemical pathways can improve the understanding of the structure and the dynamics of cell processes considerably. The construction and quantitative analysis of kinetic models is often impeded by the lack of reliable data. However, as the topological structure of biochemical systems can be regarded to remain constant in time, a qualitative analysis of a pathway model was shown to be quite promising as it can render a lot of useful knowledge, e. g., about its structural invariants. The topic of this paper are pathways whose substances have reached a dynamic concentration equilibrium (steady state). It is argued that appreciated tools from biochemistry and also low-level Petri nets can yield only part of the desired results, whereas executable high-level net models lead to a number of valuable additional insights by combining symbolic analysis and simulation.     

Advances in somatic cell genetics of higher plants — the protoplast approach in basic studies on mutagenesis and isolation of biochemical mutants

Summary Selection strategies developed in microbial genetics were successfully extrapolated to in vitro cell culture systems of higher plants and are having a major impact in the elucidation of regulatory mechanisms of basic cellular processes in eukaryotes. Although an increasing number and wide spectrum of biochemical variants have been isolated in such cell culture systems, their routine selection, characterization, and manipulation have not yet been achieved. Methodological limitations are considered to be one of the major reasons. Suspension or callus cultures, so extensively employed during the last decade in mutation-selection experiments and so useful in demonstrating the potentialities of in vitro screening techniques in obtaining various biochemical markers, have inherent drawbacks which limit in our opinion their further contribution in this field. Protoplast cultures represent an ideal tool for mutation and selection experiments. It is the purpose of this review to show how, due to recent methodological advances in the manipulation of some model protoplast culture systems, essential aspects of mutagenesis and selection of biochemical mutants can be reconsidered. These systems are simple and efficient, and lend themselves to statistical interpretation. Genetic analysis of selected variants should help us to understand and define better the new set of problems and concepts revealed by the somatic cell genetics of higher plants; combined with biochemical analyses it should elucidate the basic relationship between control of biological processes at cellular and whole organism level.     

Diagnosis of damage to Norway spruce (Picea abies) through biochemical criteria

Bioindication can be carried out at different hierarchical levels, eg. cell, organism, and ecosystem. While the monitoring of damage by visible criteria (e.g. loss of needles) is connected with the organism as a whole, the monitoring of damage by biochemical indicators is above all connected with cell metabolism.
The degree of vitality of a tree can be ascertained through the integration of a number of biochemical parameters. Furthermore, a differential diagnosis of a particular stress pattern can be carried out because of the feedback pattern of several biochemical indicators. In order to describe and interpret biochemical or physiological changes that have been caused by a number of factors, multivariate statistical methods are being used more frequently. Apart from cluster and discriminant analysis, it is especially factor analysis which provides a helpful tool when dealing with problems in the field of environmental analysis. Factor analysis can be used for an integrating as well as a differentiating assessment.
Within the framework of forest damage research, numerous changes at the level of cell metabolism have been detected to which a bioindicative character can be attached. A number of physiological and biochemical parameters with bioindicative character concerning Norway spruce are presented.     

Depression, antidepressants, and peripheral blood components

The biological attributes of affective disorders and factors which are able to predict a response to treatment with antidepressants have not been identified sufficiently. A number of biochemical variables in peripheral blood constituents have been tested for this purpose, as a consequence of the lack of availability of human brain tissue. At first, the biological attributes of mental disorders were sought at the level of concentrations of neurotransmitters and their metabolites or precursors. Later on, attention shifted to receptor systems. Since the 1990s, intracellular processes influenced by an illness or its treatment with psychopharmaceuticals have been at the forefront of interest. Interest in biological predictors of treatment with antidepressants has reappeared in recent years, thanks to new laboratory techniques which make it possible to monitor cellular processes associated with the transmission of nerve signals in the brain. These processes can also be studied in plasma and blood elements, especially lymphocytes and platelets. The selection of the qualities to which attention is paid can be derived from today's most widely discussed biochemical hypotheses of affective disorders, especially the monoamine hypothesis and the molecular and cellular theory of depression. Mitochondrial enzymes can also play an important role in the pathophysiology of depression and the effects of antidepressants. In this paper, we sum up the cellular, neurochemical, neuroendocrine, genetic, and neuroimmunological qualities which can be measured in peripheral blood and which appear to be indicators of affective disorders, or parameters which make it possible to predict therapeutic responses to antidepressant administration.     

Constraints on microbial metabolism drive evolutionary diversification in homogeneous environments

Understanding the evolution of microbial diversity is an important and current problem in evolutionary ecology. In this paper, we investigated the role of two established biochemical trade-offs in microbial diversification using a model that connects ecological and evolutionary processes with fundamental aspects of biochemistry. The trade-offs that we investigated are as follows:(1) a trade-off between the rate and affinity of substrate transport; and (2) a trade-off between the rate and yield of ATP production. Our model shows that these biochemical trade-offs can drive evolutionary diversification under the simplest possible ecological conditions: a homogeneous environment containing a single limiting resource. We argue that the results of a number of microbial selection experiments are consistent with the predictions of our model.     

Functional arginine-containing amino acid sequences in peptides and proteins

L-Arginine is a source of nitrogen oxide and plays a great role in a number of other biochemical processes. Functions and prospects for practical application of five groups of arginine-containing amino acid sequences and synthetic polyarginine sequences are considered. The physiological characteristics of well-known arginine-containing peptides, such as RGD containing, kyotorphin, and tuftsin, are described in detail.     

Cell division: Biochemically controlled mechanics

Technical advances are providing new insights into the mechanical properties of cells. Now, by combining genetic and biochemical studies with high-resolution mechanical measurements from atomic force microscopy, the biochemical bases of mechanical processes such as cytokinesis should be discernible.     

Metabolic specialization and the assembly of microbial communities

Metabolic specialization is a general biological principle that shapes the assembly of microbial communities. Individual cell types rarely metabolize a wide range of substrates within their environment. Instead, different cell types often specialize at metabolizing only subsets of the available substrates. What is the advantage of metabolizing subsets of the available substrates rather than all of them? In this perspective piece, we argue that biochemical conflicts between different metabolic processes can promote metabolic specialization and that a better understanding of these conflicts is therefore important for revealing the general principles and rules that govern the assembly of microbial communities. We first discuss three types of biochemical conflicts that could promote metabolic specialization. Next, we demonstrate how knowledge about the consequences of biochemical conflicts can be used to predict whether different metabolic processes are likely to be performed by the same cell type or by different cell types. We then discuss the major challenges in identifying and assessing biochemical conflicts between different metabolic processes and propose several approaches for their measurement. Finally, we argue that a deeper understanding of the biochemical causes of metabolic specialization could serve as a foundation for the field of synthetic ecology, where the objective would be to rationally engineer the assembly of a microbial community to perform a desired biotransformation.     

Paraquat toxicity

Paraquat (1,1'-dimethyl-4,4'-bipyridylium dichloride) is marketed as a contact herbicide. Although it has proved safe in use there have been a number of cases of poisoning after the intentional swallowing of the commercial product. The most characteristic feature of poisoning is lung damage, which causes severe anoxia and may lead to death. The specific toxicity to the lung can be explained in part by the accumulation of paraquat into the alveolar type I and type II epithelial cells by a process that has been shown to accumulate endogenous diamines and polyamines. When accumulated, paraquat undergoes an NADPH-dependent, one-electron reduction to form its free radical, which then reacts avidly with molecular oxygen to reform the cation and produce superoxide anion, which in turn will dismutate to form H2O2. This may lead to the formation of more reactive (and hence toxic) radicals which have the potential to cause lipid peroxidation and lead to cell death. Biochemical changes provoked by paraquat in the lung suggest that it causes a rapid, pronounced and prolonged oxidation of NADPH that initiates compensatory biochemical processes in the lung. NADPH may be further depleted as it is consumed in an attempt to detoxify H2O2 or lipid hydroperoxides. Thus it is possible that with toxic levels of paraquat in the cell, compensatory biochemical processes are insufficient to maintain levels of NADPH consistent either with cell survival or with the ability to detoxify H2O2 or prevent lipid peroxidation.     

The biophysics of differential growth

The intrinsic control of uniform and differential growth of plant cells can be traced to a small number of physical parameters. These are cell wall rheology, membrane and tissue hydraulic conductivity, and membrane and tissue solute transport. Water and solute effects are manifested as alterations in turgor pressure. Environmental and biochemical processes always channel their effects through one or more of these parameters. Technical developments such as the pressure probe and Instron tensiometer, together with a reappraisal of older techniques, are beginning to allow assessment of the relative roles of these factors. Although the importance of cell wall rheology is becoming increasingly apparent, there is still insufficient information to allow generalized conclusions regarding the role of turgor pressure in differential growth. This review considers attempts to correlate these parameters with observed anatomical growth patterns.     

Thermodynamic analysis of lignocellulosic biofuel production via a biochemical process: guiding technology selection and research focus

The aim of this paper is to present an exergy analysis of bioethanol production process from lignocellulosic feedstock via a biochemical process to asses the overall thermodynamic efficiency and identify the main loss processes. The thermodynamic efficiency of the biochemical process was found to be 35% and the major inefficiencies of this process were identified as: the combustion of lignin for process heat and power production and the simultaneous scarification and co-fermentation process accounting for 67% and 27% of the lost exergy, respectively. These results were also compared with a previous analysis of a thermochemical process for producing biofuel. Despite fundamental differences, the biochemical and thermochemical processes considered here had similar levels of thermodynamic efficiency. Process heat and power production was the major contributor to exergy loss in both of the processes. Unlike the thermochemical process, the overall efficiency of the biochemical process largely depends on how the lignin is utilized.     

Signal transduction networks: topology, response and biochemical processes

Conventionally, biological signal transduction networks are analysed using experimental and theoretical methods to describe specific protein components, interactions, and biochemical processes and to model network behavior under various conditions. While these studies provide crucial information on specific networks, this information is not easily converted to a broader understanding of signal transduction systems. Here, using a specific model of protein interaction we analyse small network topologies to understand their response and general properties. In particular, we catalogue the response for all possible topologies of a given network size to generate a response distribution, analyse the effects of specific biochemical processes on this distribution, and analyse the robustness and diversity of responses with respect to internal fluctuations or mutations in the network. The results show that even three- and four-protein networks are capable of creating diverse and biologically relevant responses, that the distribution of response types changes drastically as a function of biochemical processes at protein level, and that certain topologies strongly pre-dispose a specific response type while others allow for diverse types of responses. This study sheds light on the response types and properties that could be expected from signal transduction networks, provides possible explanations for the role of certain biochemical processes in signal transduction and suggests novel approaches to interfere with signaling pathways at the molecular level. Furthermore it shows that network topology plays a key role on determining response type and properties and that proper representation of network topology is crucial to discover and understand so-called building blocks of large networks.