Phylogenetic Analysis of Metabolic Pathways

The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship of species from phylogenetic trees comparing individual enzymes. In this article we extend conventional phylogenetic analysis of individual enzymes in different organisms to the organisms' metabolic networks. For this purpose we suggest a method that combines sequence information with information about the underlying reaction networks. A distance between pathways is defined as incorporating distances between substrates and distances between corresponding enzymes. The new analysis is applied to electron-transfer and amino acid biosynthesis networks yielding a more comprehensive understanding of similarities and differences between organisms. Received: 14 August 2000 / Accepted: 4 January 2001     

The ENZYME database in 2000

The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/ ).     

The ENZYME data bank in 1995.

The ENZYME data bank is a repository of information relative to the nomenclature of enzymes. The current version (October 1995) contains information relevant to 3594 enzymes. It is available from a variety of file and ftp servers as well as through the ExPASy World Wide Web server (http://expasy.hcuge.ch/).     

Predicting acidic and alkaline enzymes by incorporating the average chemical shift and gene ontology informations into the general form of Chou's PseAAC

Knowledge of the adaptation mechanism of enzymes to extreme pH values and distinguishing them from one another are necessary in the proteomics field, and would help in the drug design of stable enzymes. In this work, we have systematically analyzed the information of 105 acidic and 112 alkaline enzymes, and propose an approach for distinguishing acidic enzymes from alkaline enzymes by combining the amino acid composition, reduced amino acid composition, gene ontology, evolutionary information, and auto covariance of averaged chemical shift (acACS). The overall prediction accuracy is 94.01% by 10-fold cross-validation using the algorithm of support vector machine. This result is better than that obtained by other existing methods. The improvement of the overall prediction accuracy reaches up to 3.3% higher than those of the random forest algorithm and secondary structure amino acid composition. The acACS performance is excellent, indicating that our approach is better than other existing methods in the literature. A user-friendly web-server pred-enzymes for predicting acidic and alkaline enzymes has been established, which is accessible to the public.     

Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information.

The abundance of information provided by completely sequenced genomes defines a starting point for new insights in the multilevel organization of organisms and their evolution. At the lowest level enzymes and other protein complexes are formed by aggregating multiple polypeptides. At a higher level enzymes group conceptually into metabolic pathways as part of a dynamic information-processing system, and substrates are processed by enzymes yielding other substrates. A method based on a combination of sequence information with graph topology of the underlying pathway is presented. With this approach pathways of different organisms are related to each other by phylogenetic analysis, extending conventional phylogenetic analysis of individual enzymes. The new method is applied to pathways related to electron transfer and to the Krebs citric acid cycle. In addition to providing a more comprehensive understanding of similarities and differences between organisms, this method indicates different evolutionary rates between substrates and enzymes.     

厌氧真菌纤维降解酶及其应用潜力的研究进展

反刍动物的瘤胃是已知的纤维降解能力最强的天然发酵罐,其发酵粗纤维的能力很大程度上依赖于其中栖息的各类微生物的功能。厌氧真菌作为瘤胃内的一类低丰度菌群,最先定殖到宿主动物摄入的纤维质饲料上,并通过分泌大量高效的碳水化合物活性酶降解粗纤维。然而,由于缺乏足够的基因组信息和有效的厌氧真菌遗传操作系统,目前国内外对厌氧真菌分泌的纤维降解酶及其降解机制的研究进展有限。本文对厌氧真菌的分类及已发表的基因组信息进行概述,介绍了各类纤维降解酶及纤维小体的组成结构和催化机制特点,并对纤维降解酶在生物质能、饲料处理、纺织造纸及食品加工等方面的应用进行总结。研究厌氧真菌纤维降解酶的作用特性,将有助于完善其在瘤胃环境中有效竞争资源并降解粗纤维的知识体系,也将进一步了解其生物技术应用潜力,为工业生产中应用酶制剂提供新思路。     

Some Common Themes for Enzymes and Verbs

Enzymes are remarkable molecules which make metabolism possible. Their processing powers are considerable for not only are they catalysts they also contribute to information processing, integration, coherence and memory in the cell. This complex of attributes suggests that a complementary perspective to enzyme nature and activity is needed related to what enzymes and verbs have in common. The value of this kind of thinking is that it shifts the focus from objects and mechanisms to processes and information. In order to support this idea a number of features which enzymes and verbs share are discussed including, context-dependence, occurrence, cases, voice, mood and glue/integrative capacities. The paper concludes with some reflections on the utility of a view of enzymes as verbs.     

Heme-containing dioxygenases involved in tryptophan oxidation

Heme iron is often used in biology for activation of oxygen. The mechanisms of oxygen activation by heme-containing monooxygenases (the cytochrome P450s) are well known, and involve formation of a Compound I species, but information on the heme-containing dioxygenase enzymes involved in tryptophan oxidation lags far behind. In this review, we gather together information emerging recently from structural, mechanistic, spectroscopic, and computational approaches on the heme dioxygenase enzymes involved in tryptophan oxidation. We explore the subtleties that differentiate various heme enzymes from each other, and use this to piece together a developing picture for oxygen activation in this particular class of heme-containing dioxygenases.     

Hepatocytes: the powerhouse of biotransformation

Liver is the most important organ involved in biotransformation of xenobiotics. Within the main organisational unit, the hepatocyte, is an assembly of enzymes commonly classified as phase I and phase II enzymes. The phase I enzymes principally cytochrome P450 catalyse both oxidative and reductive reactions of a bewildering number of xenobiotics. Many of the products of phase I enzymes become substrates for the phase II enzymes, which catalyse conjugation reactions making use of endogenous cofactors. As xenobiotic metabolising enzymes are responsible for the toxicity of many chemicals and drugs, testing the role of the biotransformation enzymes and the transporters within the hepatocyte is critical. New methodologies may be able to provide information to allow for better in vitro to in vivo extrapolation of data.     

Polysaccharases for microbial exopolysaccharides

Microbial exopolysaccharides (EPS) are the substrates for a wide range of enzymes most of which are highly specific. The enzymes are either endoglycanases or polysaccharide lyases and their specificity is determined by carbohydrate structure with uronic acids often playing a major role. The presence of various acyl substituents frequently has little effect on the action of many of the polysaccharases but markedly inhibits some of the polysaccharide lyases including alginate and gellan lyases. The commonest sources of such enzymes can be either microorganisms or bacteriophages. These specific polysaccharide-degrading enzymes can yield oligosaccharide fragments, which are amenable to NMR and other analytical techniques. They have thus proved to be extremely useful in providing information about microbial polysaccharide structures and were routinely used in many such studies. Complex systems containing various mixtures of enzymes may also be effective in the absence of single enzymes but may be difficult to obtain with reproducible activities. Such preparations may also cause extensive degradation of the polysaccharide structure and thus prove less useful in providing information. Commercially available enzyme preparations have seldom proved capable of degrading microbial heteropolysaccharides, although some are active against bacterial alginates and homopolysaccharides including bacterial cellulose and curdlan.     

(31)P NMR spectroscopy senses the microenvironment of the 5'-phosphate group of enzyme-bound pyridoxal 5'-phosphate

In this review it is demonstrated that (31)P NMR spectroscopy can be used to elucidate information about the microenvironment around the phosphate group of enzyme-bound pyridoxal 5'-phosphate (PLP). The following information can be obtained for all PLP-dependent enzymes: 1) the protonation state of the 5'-phosphate and its exposure to solvent, and 2) tightness of binding of the 5'-phosphate. In addition, the 5-phosphate can report on the protonation state of the Schiff base lysine in some enzymes. Changes in the 5'-phosphate chemical shift can be used to determine changes in tightness of binding of the phosphate as the reaction pathway is traversed, providing information on the dynamics of the enzyme. (31)P NMR spectroscopy is thus an important probe of structure, dynamics and mechanism in native and site-directed mutations of PLP-dependent enzymes. Examples of all of the above are provided in this review. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.     

Predicting enzyme function from protein sequence

There are two main reasons to try to predict an enzyme's function from its sequence. The first is to identify the components and thus the functional capabilities of an organism, the second is to create enzymes with specific properties. Genomics, expression analysis, proteomics and metabonomics are largely directed towards understanding how information flows from DNA sequence to protein functions within an organism. This review focuses on information flow in the opposite direction: the applicability of what is being learned from natural enzymes to improve methods for catalyst design.     

Enzymes of Tryptophan Biosynthesis in Serratia marcescens

In Serratia marcescens, the tryptophan biosynthetic enzymes were formed coordinately. A number of tryptophan auxotrophs showed single biochemical lesions; several mutants showed pleiotropic effects. Sucrose density gradient centrifugation revealed an unique pattern of migration of the tryptophan biosynthetic enzymes. The repression response of the Serratia enzymes to exogenous tryptophan was fivefold more sensitive than that found in Escherichia coli. When this information is contrasted with the available information on the other Enterobacteriaceae, one is compelled to conclude that S. marcescens enjoys a rather marked evolutionary divergence from the other enteric organisms.     

REBASE--restriction enzymes and methylases

REBASE contains comprehensive information about restriction enzymes, DNA methylases and related proteins such as nicking enzymes, specificity subunits and control proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal data and sequence data. Homing endonucleases are also included. Most recently, extensive information about the methylation sensitivity of restriction enzymes has been added and a new feature contains complete analyses of the putative restriction systems in the sequenced bacterial and archaeal genomes. The data is distributed via email, ftp (ftp.neb.com) and the Web (http://rebase. neb.com).     

Metabolic capacity of nasal tissue: interspecies comparisons of xenobiotic-metabolizing enzymes

High levels of xenobiotic-metabolizing enzymes occur in the nasal mucosa of all species studied. In certain species, including rats and rabbits, unique enzymes are present in the nasal mucosa. The function of these enzymes is not well understood, but it is thought that they play a role in protecting the lungs from toxicity of inhalants. The observation that several nasal xenobiotic-metabolizing enzymes accept odorants as substrates may indicate that these enzymes also play a role in the olfactory process. Xenobiotic-metabolizing enzymes were found in the nasal cavity around 15 years ago. Since that time, much has been learned about the nature of the enzymes and the substrates they accept. In the present review, this information is summarized with special attention to species differences in xenobiotic-metabolizing enzymes of the nasal cavity. Such differences may be important in interpreting the results of toxicity assays in animals because rodents are apparently more susceptible to nasal toxicity after exposure to inhalants than are humans.     

Molecular physiology of glutamine and glutamate biosynthesis in developing seedlings of conifers

Nitrogen is a limiting factor in tree growth and development. The incorporation of ammonium ions in carbon skeletons is catalyzed by the sequential action of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT). Most studies on nitrogen‐assimilating enzymes have been reported for annual crop plants. Knowledge of these enzymes in woody plants is much more limited, particularly at the molecular level. Here, we review current available information on glutamine/glutamate biosynthesis and chloroplast development in conifers.     

Folds and activities of peptidoglycan amidases

Bacterial peptidoglycan amidases are a large and diverse group of enzymes. During the last few years, genomic sequence information has accumulated to an extent such that lists of proven or predicted peptidoglycan amidases can now be expected to be fairly complete. Moreover, representative crystal structures for most groups of phylogenetically related peptidoglycan amidases have been solved. Here, sequence and structural information is combined with published biochemical findings to demonstrate that (a) peptidoglycan amidases have evolved for almost every bond that occurs in peptidoglycan, (b) there are enzymes that share the fold, yet cleave different bonds and (c) there are enzymes that have entirely different folds and must have evolved independently, and yet cleave the same peptide bond. It is shown that despite these complications, some rules can be deduced from the available biochemical and structural information that can be useful to predict the specificity of hypothetical peptidoglycan hydrolases, for which only sequence information is available.     

A possible origin of RNA catalysis in multienzyme complexes

Numerous attempts have recently been made to ascribe a preeminent role to RNA enzymes in primitive life systems. A model is proposed in which coenzyme-dependent RNA enzymes were initially organized in multienzyme complexes featuring (1) the continuous attachment of substrates to CoA-like carriers, as in fatty acid synthesis; and (2) the ordering of RNA enzymes via mRNA-like instructional strands. In this format, RNA enzymes would not have been required to recognized and specifically bind soluble substrates. The enzymes in this case may have required far less complexity than contemporary protein enzymes and thus less genetic information for their synthesis. An analogy is made between the proposed scheme and the protein translation mechanism, for which it may have been an evolutionary precursor.     

The enzymes responsible for the metabolism of prostaglandins in bovine placenta

The following review presents some data on the enzymes of synthesis and catabolism of prostaglandins in bovine placenta. The available literature confirms the anabolic and catabolic ability of bovine placenta to metabolise prostaglandins, but there is little direct information about the pathways involved. The aim of the review is to describe what is known about the physico-chemical properties and activity of enzymes involved in prostaglandin metabolism in bovine placenta.     

食线虫真菌侵染性胞外酶和生防应用

食线虫真菌作为重要的植物寄生线虫的生物防治资源,深入了解它们的侵染方式、毒力因子是了解食线虫真菌侵染的分子机理和开发高效、稳定的生物杀线虫制剂的关键。目前的研究表明,食线虫真菌能分泌具有降解线虫体壁或线虫卵壳的胞外酶,它们在食线虫真菌侵染线虫的过程中起着非常重要的作用。对这些侵染性胞外水解酶的深入研究将促进人们对食线虫真菌的侵染过程和侵染机制的了解以及高效生防制剂的开发。综述了近年来食线虫真菌侵染性胞外酶的研究概况,对食线虫真菌胞外丝氨酸蛋白酶进行同源性分析,对以后食线虫真菌侵染性胞外酶的研究和高效生防制剂开发进行了评述。