Integration of molecular genetics and proteomics with cell metabolism: how to proceed; how not to proceed!

There now exists a resurgence of interest in the role of intermediary metabolism in medicine; especially in relation to medical disorders. Coupled with this is the contemporary focus on molecular biology, genetics and proteomics and their integration into studies of regulation and alterations in cellular metabolism in health and disease. This is a marriage that has vast potential for elucidation of the factors and conditions that are involved in cellular metabolic and functional changes, which heretofore could not be addressed by the earlier generations of biochemists who established the major pathways of intermediary metabolism. The achievement of this present potential requires the appropriate application and interpretation of genetic and proteomic studies relating to cell metabolism and cell function. This requires knowledge and understanding of the principles, relationships, and methodology, such as biochemistry and enzymology, which are involved in the elucidation of cellular regulatory enzymes and metabolic pathways. Unfortunately, many and possibly most contemporary molecular biologists are not adequately trained and knowledgeable in these areas of cell metabolism. This has resulted in much too common inappropriate application and misinformation from genetic/proteomic studies of cell metabolism and function. This presentation describes important relationships of cellular intermediary metabolism, and provides examples of the appropriate and inappropriate application of genetics and proteomics. It calls for the inclusion of biochemistry, enzymology, cell metabolism and cell physiology in the graduate and postgraduate training of molecular biology and other biomedical researchers.     

Cellular metabolism and disease: what do metabolic outliers teach us?

An understanding of metabolic pathways based solely on biochemistry textbooks would underestimate the pervasive role of metabolism in essentially every aspect of biology. It is evident from recent work that many human diseases involve abnormal metabolic states--often genetically programmed--that perturb normal physiology and lead to severe tissue dysfunction. Understanding these metabolic outliers is now a crucial frontier in disease-oriented research. This Review discusses the broad impact of metabolism in cellular function and how modern concepts of metabolism can inform our understanding of common diseases like cancer and also considers the prospects of developing new metabolic approaches to disease treatment.     

Compartmentation in plant metabolism

Cell fractionation and immunohistochemical studies in the last 40 years have revealed the extensive compartmentation of plant metabolism. In recent years, new protein mass spectrometry and fluorescent-protein tagging technologies have accelerated the flow of information, especially for Arabidopsis thaliana, but the intracellular locations of the majority of proteins in the plant proteome are still not known. Prediction programs that search for targeting information within protein sequences can be applied to whole proteomes, but predictions from different programs often do not agree with each other or, indeed, with experimentally determined results. The compartmentation of most pathways of primary metabolism is generally covered in plant physiology textbooks, so the focus here is mainly on newly discovered metabolic pathways in plants or pathways that have recently been revised. Ultimately, all of the pathways of plant metabolism are interconnected, and a major challenge facing plant biochemists is to understand the regulation and control of metabolic networks. One of the best-characterized networks links sucrose synthesis in the cytosol with photosynthetic CO(2) fixation and starch synthesis in the chloroplasts. One of the key features of this network is how the transport of pathway intermediates and signal metabolites across the chloroplast envelope conveys information between the two compartments, influencing the regulation of several enzymes to co-ordinate fluxes through the different pathways. It is widely accepted that chloroplasts and mitochondria originated from prokaryotic endosymbionts, and that new transporters and regulatory networks evolved to integrate metabolism in these organelles with the rest of the cell. Curiously, the present-day locations of many metabolic pathways within the cell often do not reflect their evolutionary origin, and there is evidence of extensive shuffling of enzymes and whole pathways between compartments during the evolution of plants.     

Cryptosporidium: Genomic and biochemical features

Recent progress in understanding the unique biochemistry of the two closely related human enteric pathogens Cryptosporidium parvum and Cryptosporidium hominis has been stimulated by the elucidation of the complete genome sequences for both pathogens. Much of the work that has occurred since that time has been focused on understanding the metabolic pathways encoded by the genome in hopes of providing increased understanding of the parasite biology, and in the identification of novel targets for pharmacological interventions. However, despite identifying the genes encoding enzymes that participate in many of the major metabolic pathways, only a hand full of proteins have actually been the subjects of detailed scrutiny. Thus, much of the biochemistry of these parasites remains a true mystery.     

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of 'elementary flux modes' provides a mathematical tool to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes. We have used this concept to analyze the interplay between the pentose phosphate pathway (PPP) and glycolysis. The set of elementary modes for this system involves conventional glycolysis, a futile cycle, all the modes of PPP function described in biochemistry textbooks, and additional modes that are a priori equally entitled to pathway status. Applications include maximizing product yield in amino acid and antibiotic synthesis, reconstruction and consistency checks of metabolism from genome data, analysis of enzyme deficiencies, and drug target identification in metabolic networks.     

物理专业生物化学教学的探索与实践

生物化学是一门基础课程,其课程体系严谨,理论知识较难,更新速度很快,新知识、新技术层出不穷。对开设了生物化学课程的物理专业学生来讲,他们化学基础差,有机化学知识的相对缺乏,掌握好该课程还存在一定的难度。从教材的选择、教学内容的优化和更新、课堂研讨的开展、考试形式的优化等方面对物理专业《生物化学》选修课进行了教学改革探讨,将对拓宽学生专业视野、提升学生的综合素质及创新能力、培养跨学科综合性人才起到积极作用。     

Mitochondria as we don't know them

Biochemistry textbooks depict mitochondria as oxygen-dependent organelles, but many mitochondria can produce ATP without using any oxygen. In fact, several other types of mitochondria exist and they occur in highly diverse groups of eukaryotes - protists as well as metazoans - and possess an often overlooked diversity of pathways to deal with the electrons resulting from carbohydrate oxidation. These anaerobically functioning mitochondria produce ATP with the help of proton-pumping electron transport, but they do not need oxygen to do so. Recent advances in understanding of mitochondrial biochemistry provide many surprises and furthermore, give insights into the evolutionary history of ATP-producing organelles.     

The role of PHB metabolism in the symbiosis of rhizobia with legumes

The carbon storage polymer poly-β-hydroxybutyrate (PHB) is a potential biodegradable alternative to plastics, which plays a key role in the cellular metabolism of many bacterial species. Most species of rhizobia synthesize PHB but not all species accumulate it during symbiosis with legumes; the reason for this remains unclear, although it was recently shown that a metabolic mutant of a nonaccumulating species retains the capacity to store PHB in symbiosis. Although the precise roles of PHB metabolism in these bacteria during infection, nodulation, and nitrogen fixation are not determined, the elucidation of these roles will influence our understanding of the metabolic nature of the symbiotic relationship. This review explores the progress that was made in determining the biochemistry and genetics of PHB metabolism. This includes the elucidation of the PHB cycle, variations in PHB metabolism among rhizobial species, and the implications of these variations, while proposing a model for the role of PHB metabolism and storage in symbiosis.     

Metabolic acidosis and the importance of balanced equations

Balancing biochemical equations for both mass and charge in metabolic networks is critical but unfortunately ignored too often. Failure to do so, for example, results in a common misconception about the origin of protons during lactic fermentation. Lactate, rather than lactic acid, is produced by glycolysis, and its production is a mechanism for alleviating intracellular acidosis due to glycolysis. This error is at the core of some recent papers, and is often ambiguous in biochemistry textbooks.     

Scent engineering: toward the goal of controlling how flowers smell

Floral scent has an important role in the reproductive processes of many plants and a considerable economic value in guaranteeing yield and quality of many crops. It also enhances the aesthetic properties of ornamental plants and cut flowers. Many floral scent volatiles fall into the terpenoid or phenylpropanoid/benzenoid classes of compounds. Although the biochemistry of floral scent is still a relatively new field of investigation, in the past decade investigators have begun to identify 'scent genes'. Several of these genes, most of which, but not all, encode enzymes that directly catalyze the formation of volatile terpenoid or phenylpropanoid/benzenoid compounds, have now been used to manipulate, through genetic engineering techniques, the mix of volatiles emitted from the flowers of several plant species. The outcomes of these experiments, which are discussed here, have indicated that the genetic engineering approach to altering floral scents has potential; however, they have also revealed the limitations that result from our inadequate knowledge of the metabolic pathways responsible for scents and their regulation.     

Selenium, the element of the moon, in life on earth

The present status of selenium biochemistry is reviewed with particular emphasis on biomedical problems related to the selenium status of humans and experimental animals. Historical milestones of selenium biochemistry starting from the identification of the first selenoenzymes up to the elucidation of prokaryotic and eukaryotic selenoprotein biosynthesis are compiled. Topical hypotheses on the biological role of selenium in general and of individual selenoproteins in respect to antioxidant defense, redox regulation of metabolic processes, thyroid function, spermatogenesis, oncogenesis, and atherogenesis are critically evaluated.     

Biosynthesis and Catabolism of L-Ascorbic Acid in Plants

L-Ascorbic acid (AsA) is a vital antioxidant compound that plays a critical role in the cellular metabolism of plants and animals. Research on plant AsA metabolism experienced a significant resurgence after 1998 following the identification of AsA-deficient Arabidopsis mutants and the elucidation of a biosynthetic pathway accepted by the overwhelming majority of the plant science community. The identification and cloning of novel biosynthetic genes and the ensuing metabolic engineering of plant AsA content has however revealed a more complex picture. Additional biosynthetic routes have been identified and unexpected biochemical phenotypes were observed upon expression of animal AsA biosynthetic genes. The isolation of novel AsA conjugates from plant tissues and the evidence for long distance transport of AsA in plants have provided additional facets to its functionality. Although some progress has been made regarding the impact of AsA recycling on pool size, we still do not have a clear picture of the biochemistry of AsA degradation. This communication comprehensively reviews new developments in the AsA metabolic system and prompts directions for future research.     

Physiology of aliphatic hydrocarbon-degrading microorganisms

This paper reviews aspects of the physiology and biochemistry of the microbial biodegradation of alkanes larger than methane, alkenes and alkynes with particular emphasis upon recent developments. Subject areas discussed include: substrate uptake; metabolic pathways for alkenes and straight and branched-chain alkanes; the genetics and regulation of pathways; co-oxidation of aliphatic hydrocarbons; the potential for anaerobic aliphatic hydrocarbon degradation; the potential deployment of aliphatic hydrocarbon-degrading microorganisms in biotechnology.     

Are current textbooks good enough for physiology education? For example, the ECL cells are missing

Current textbooks are believed to provide an updated knowledge. Medical students usually read the textbooks but not the literature that contain the original research articles and reviews. Here, we examined the gap between the current textbooks and literature with the enterochromaffin-like (ECL) cells as an example. A total of 70 textbooks that were published for medical education during the last 10 yr was examined. The literature has been searched mainly from the Internet. We found that most textbooks (59 of 70) fail to mention the ECL cells. Due to the lack of information on the ECL cells, the mechanisms behind gastric acid secretion are described variously from book to book. However, up to the year 2000, 574 research articles and reviews have been published on the various aspects of the ECL cells. The role of the ECL cells in the regulation of the acid secretion has been well demonstrated for more than 20 years. The fact that the textbooks are out of date cannot be explained by the time required to write and publish them. Therefore, we question whether or not the current textbooks are good enough for physiology education and suggest both teachers and students read not only the textbooks, but also utilize the other sources such as the Internet to find and fill the gaps between the textbooks and literature. This is one of the approaches of problem-based learning.     

Contribution of R. V. Chagovets, member of the Ukrainian SSR Academy of Sciences, to the development of biochemistry

The paper is concerned with the main stages of scientific activity of R.V. Chagovets (1904-1982). Member Academy of Sciences of the Ukrainian SSR in the field of biochemistry of muscles, metabolism and biochemical functions of vitamins and their derivatives. The creative heredity of the scientist served as a theoretical ground of the present-day vitaminology, base for development of the nutrition theory, practical recommendations and suggestions in public health and husbandry opened the pathways for experimental solution of the problems concerning vitamin and coenzyme metabolism regulation, elucidation of molecular mechanisms of vitamin and coenzyme functioning in the cell.     

Obesity and psychotic disorders: uncovering common mechanisms through metabolomics

Primary obesity and psychotic disorders are similar with respect to the associated changes in energy balance and co-morbidities, including metabolic syndrome. Such similarities do not necessarily demonstrate causal links, but instead suggest that specific causes of and metabolic disturbances associated with obesity play a pathogenic role in the development of co-morbid disorders, potentially even before obesity develops. Metabolomics – the systematic study of metabolites, which are small molecules generated by the process of metabolism – has been important in elucidating the pathways underlying obesity-associated co-morbidities. This review covers how recent metabolomic studies have advanced biomarker discovery and the elucidation of mechanisms underlying obesity and its co-morbidities, with a specific focus on metabolic syndrome and psychotic disorders. The importance of identifying metabolic markers of disease-associated intermediate phenotypes – traits modulated but not encoded by the DNA sequence – is emphasized. Such markers would be applicable as diagnostic tools in a personalized healthcare setting and might also open up novel therapeutic avenues.     

Valine is a precursor of propionyl-CoA.

For some time the metabolism of valine has been misrepresented by several biochemistry textbooks. This article demonstrates that propionyl-CoA occurs as an intermediate in the valine metabolic pathway before the formation of methylmalonyl CoA.     

Biochemistry,Coming Along with Melodies: Instructional Design and Teaching Tips for Introduction of Biochemistry Course

The first class of a higher education course, in most cases, is an introduction that covers the learning goals, course overview, syllabus, and evaluation mode. The effectiveness of an introduction lecture is vital for students to develop an interest in the course. Biochemistry is the foundation of a vast array of scientific disciplines; therefore, it is a core course required for medical schools and life science majors. However, many students are often intimidated by the complex, intertwined metabolic pathways composed of a great variety of structurally diverse biomolecules. Well begun is half done: a good introduction is essential for the success of a course and this is particularly true for teaching of biochemistry. As an educator with over twenty years of teaching experience in biochemistry to students of biology, medicine, pharmacy, and nursing at Peking University, I have successfully enriched the introduction class with delightful biochemistry songs, multiple sources of educational materials, and biochemistry-related knowledge in medical humanities. These strategies and tips have proven effective, and I hope it can be enlightening and helpful to the teaching of biochemistry.