Description of the ratios between metabolite concentrations in a polyenzyme system

It was demonstrated that the relations between substrate and product concentrations for a reaction catalyzed by michaelian enzyme incorporated in a multienzyme system can be graphically represented by a diverging set of straight lines intersecting in one point, the flux velocity being treated as a parameter. A competitive inhibitor shifts the intersection point along the line of equilibrium state. The relations between the concentrations of more than two reagents are represented by a set of equivelocity surfaces. The relations between substrate and product concentrations for a kinetically cooperative reaction conforming to the graphical representation by the second--order curves were analyzed. The stability criterion was obtained for a multienzyme system with the first enzyme allosterically regulated by products of subsequent reactions.     

Purification and characterization of a cellulolytic multienzyme complex produced by Neocallimastix patriciarum J11

Understanding the roles of the components of the multienzyme complex of the anaerobial cellulase system, acting on complex substrates, is crucial to the development of efficient cellulase systems for industrial applications such as converting lignocellulose to sugars for bioethanol production. In this study, we purified the multienzyme complex of Neocallimastix patriciarum J11 from a broth through cellulose affinity purification. The multienzyme complex is composed of at least 12 comprised proteins, based on sodium dodecyl sulfate polyacrylamide gel electrophoresis. Eight of these constituents have demonstrated β-glucanase activity on zymogram analysis. The multienzyme complex contained scaffoldings that respond to the gathering of the cellulolytic components. The levels and subunit ratio of the multienzyme complex from N. patriciarum J11 might have been affected by their utilized carbon sources, whereas the components of the complexes were consistent. The trypsin-digested peptides of six proteins were matched to the sequences of cellulases originating from rumen fungi, based on identification through liquid chromatography/mass spectrometry, revealing that at least three types of cellulase, including one endoglucanase and two exoglucanases, could be found in the multienzyme complex of N. patriciarum J11. The cellulolytic subunits could hydrolyze synergistically on both the internal bonds and the reducing and nonreducing ends of cellulose. Based on our research, our findings are the first to depict the composition of the multienzyme complex produced by N. patriciarum J11, and this complex is composed of scaffoldin and three types of cellulase.     

Stability of multienzyme systems with feedback regulation: a graph theoretical approach

Stability of multienzyme systems with feedback regulation has been analyzed on the basis of the Lienard-Chipart criteria. The rules governing the topological graph construction for multienzyme systems have been developed. A theorem about correspondence of the graph constructed and coefficients of the characteristic polynomial of linearized kinetic equations is proved. The graph-theoretical stability analysis proposed is illustrated by a number of examples of multienzyme systems with feedback regulation.     

The protease problem in Neurospora. Structural modification of the arom multienzyme system during its extraction and isolation.

The “aromatic complex” or “arom aggregate” of Neurospora crassa catalyzes five consecutive reactions in the central pathway leading to the biosynthesis of the aromatic amino acids. Previously, this multienzyme system was shown variously to have a molecular weight of 230,000 to 300,000 and to contain up to four subunits. Recently, a protease and a corresponding specific inhibitor have been isolated from N. crassa and, as described in this report, a new method for isolating the multienzyme system has been developed. We have made the following observations: (a) Detergent (sodium dodecyl sulfate) gel electrophorograms of the “complex” isolated by two different methods are not comparable. In an earlier method, which involved more manipulations and time, the detergent gel banding patterns showed four polypeptides with molecular weights totaling about 300,000. With the new purification procedure, there are two major bands: the first with an apparent molecular weight of about 150,000 and the second with a molecular weight of 50,000. (b) When the freshly purified multienzyme system is incubated at 25 °C, four new bands appear within 30 h and a fifth is visible after 40 h. (c) The formation of these new bands is prevented for up to 40 h by the addition of phenylmethanesulfonylfluoride or a purified preparation of the specific N. crassa protease inhibitor, (d) The multienzyme system appears to remain intact, as shown by standard polyacrylamide gel electrophoresis, even after it has suffered several proteolytic clips. These results demonstrate that the purified complex is contaminated with a small but influential quantity of the inhibitable N. crassa protease and show that this protease is capable of creating an artificial subunit structure in the multienzyme system. Based on these observations, we hypothesize that the arom enzyme system is a five-component multifunctional enzyme.     

In situ monitoring of 3D in vitro cell aggregation using an optical imaging system

Bioreactor systems that maintain cells and tissues in suspension are increasingly popular for culturing 3D constructs to avoid the loss of in vivo cell function associated with traditional 2D culture methods. There is a need for the online monitoring of such systems to provide better understanding and control of the processes involved and to prevent the disruption of these processes caused by offline sampling and endpoint analysis. We describe a system for the imaging and analysis of cell aggregation, over long periods, within a high aspect rotating vessel (HARV). The system exploits side illumination, using an adjustable beam pattern, to restrict the detected light to that scattered by the cell aggregates, thus eliminating the need for the fluorescent labeling of the cells. The in situ aggregation of mammalian cells (MCF-7 breast carcinoma cells) was monitored over an 8 h period and image sequences showing the growth and motion of the aggregates within the bioreactor were obtained. Detailed size and population data have been derived characterizing the development of the aggregates during this time. We show how the number of resolvable aggregates increases to reach a peak and then declines as these aggregates merge. Once formed, remaining aggregates are found to consolidate to form more tightly packed bodies, typically reducing in cross-sectional area by one third. These results provide the basis for the development of an automated feedback system to control the growth of 3D cell cultures for repeatable, reliable, and quality controlled experimentation.     

Analysing grouping of nucleotides in DNA sequences using lumped processes constructed from Markov chains

The most commonly used models for analysing local dependencies in DNA sequences are (high-order) Markov chains. Incorporating knowledge relative to the possible grouping of the nucleotides enables to define dedicated sub-classes of Markov chains. The problem of formulating lumpability hypotheses for a Markov chain is therefore addressed. In the classical approach to lumpability, this problem can be formulated as the determination of an appropriate state space (smaller than the original state space) such that the lumped chain defined on this state space retains the Markov property. We propose a different perspective on lumpability where the state space is fixed and the partitioning of this state space is represented by a one-to-many probabilistic function within a two-level stochastic process. Three nested classes of lumped processes can be defined in this way as sub-classes of first-order Markov chains. These lumped processes enable parsimonious reparameterizations of Markov chains that help to reveal relevant partitions of the state space. Characterizations of the lumped processes on the original transition probability matrix are derived. Different model selection methods relying either on hypothesis testing or on penalized log-likelihood criteria are presented as well as extensions to lumped processes constructed from high-order Markov chains. The relevance of the proposed approach to lumpability is illustrated by the analysis of DNA sequences. In particular, the use of lumped processes enables to highlight differences between intronic sequences and gene untranslated region sequences.     

Mathematical analysis of multienzyme systems. II. Steady state and transient control.

The control theory of steady states, previously presented for linear enzymatic systems (Heinrich and Rapoport, 1974) is extended to nonlinear systems. On the basis of three theorems a new procedure for the calculation of the control strength and of the control matrix is developed. The theory is applied to the extended model of glycolysis of erythrocytes, which includes also ATP-consuming processes. Also in this model the glycolytic flux is mainly controlled by the hexokinase-phosphofructokinase-system. The control strengths of the pyruvate kinase and of the enzymes of the 2.3 P2G-bypass are negligibly small. The control strength of the ATPase is negative, i.e. an activation of this enzyme leads to a decrease of the flux. For transition states of multienzyme systems definitions are given for the mean time required for the transition of the metabolites and for the "transient control" of enzymes. Enzymes with a pronounced influence on the transition time are called time-limiting enzymes. Enzymes which excert strong control on the time-dependent processes may have little influence under steady state conditions and vice versa. The transition times of ATP have been calculated for transient states of glycolysis.     

The diffuse neuroendocrine system. Studies of this newly discovered controlling system in health and disease

Numerous peptides (neuropeptides) have been recently found to be present in both the nervous and endocrine systems composing what is now known as the diffuse neuroendocrine system. Two immunological methods, radioimmunoassay and immunocytochemistry, have been used here in combination to study their distribution and cellular localization. A number of these neuropeptides have recently been found to be abnormal in disease state, thus providing further information as to their role in normal and pathological conditions.     

The evolution of reproductive systems and sex-determining mechanisms within rumex (polygonaceae) inferred from nuclear and chloroplastidial sequence data

The genus Rumex includes hermaphroditic, polygamous, gynodioecious, monoecious, and dioecious species, with the dioecious species being represented by different sex-determining mechanisms and sex-chromosome systems. Therefore, this genus represents an exceptional case study to test several hypotheses concerning the evolution of both mating systems and the genetic control of sex determination in plants. Here, we compare nuclear intergenic transcribed spacers and chloroplast intergenic sequences of 31 species of Rumex. Our phylogenetic analysis supports a systematic classification of the genus, which differs from that currently accepted. In contrast to the current view, this new phylogeny suggests a common origin for all Eurasian and American dioecious species of Rumex, with gynodioecy as an intermediate state on the way to dioecy. Our results support the contention that sex determination based on the balance between the number of X chromosomes and the number of autosomes (X/A balance) has evolved secondarily from male-determining Y mechanisms and that multiple sex-chromosome systems, XX/XY1Y2, were derived twice from an XX/XY system. The resulting phylogeny is consistent with a classification of Rumex species according to their basic chromosome number, implying that the evolution of Rumex species might have followed a process of chromosomal reduction from x = 10 toward x = 7 through intermediate stages (x = 9 and x = 8).     

Purification of the fengycin synthetase multienzyme system from Bacillus subtilis b213

The purification of the multienzyme system producing the lipodecapeptide fengycin in Bacillus subtilis b213 was investigated. By gel filtration of a cell free extract of this organism three enzyme fractions were obtained from which five multifunctional components of fengycin synthetase were separated by high resolution anion-exchange FPLC procedures. These proteins were characterized by their thioester formation activities with ¹⁴C-labeled substrate amino acids and by N-terminal sequencing. Correlation of these data with the DNA sequences of the pps (fen) operons in three B. subtilis strains provided detailed knowledge on the structural and functional organization of fengycin synthetase.     

Analysis of point process signals applied to motor unit firing patterns: I. Superposition of independent spike trains

The aim of the present study was to examine whether statistical methods common for the analysis of point process signals could be applied to the electromyogram, in order to extract information concerning the physiological mechanisms involved. This was carried out on the assumption that the electromyogram can be treated as the superposition result of a number of point process signals, each representing the firing pattern of one motor unit. No correlated activity between the different spike trains was assumed at this stage. A digital model for the superposition of event sequences was constructed, assigning to the individual sequences a Gaussian interval distribution. The effects of varying the number of spike trains participating in the superposition process, and changing the mean rates of firing were explored. The statistical methods used in the analysis were serial correlation, event autocorrelation, and power spectrum studies. It has been found that serial correlograms of the superimposed processes may be helpful in detecting the number of spike trains involved in the superposition, whereas power spectrum studies are useful in determining the mean rates of firing of the individual sequences.     

Studies on the association of cytochrome P-450 and NADPH-cytochrome c reductase during catalysis in a reconstituted hydroxylating system.

The interaction between cytochrome P-450 and NADPH-cytochrome c reductase during catalysis has been investigated with a reconstituted monooxygenase system composed of the two purified enzyme components and synthetic phospholipid. Steady state kinetic data are consistent with a scheme in which the formation of a binary complex between the two proteins precedes catalysis. The formation of this binary complex is described by a simple mass action equation. In agreement with this equation, the observed Vmax for benzphetamine N-demethylation was found to be directly proportional to the calculated concentration of the cytochrome P-450 . reductase complex. Furthermore, with appropriate reductase/cytochrome P-450 mole ratios, the Vmax could be shown to be linearly dependent on either the reductase or the cytochrome P-450 concentration alone. In contrast, the Km parameter is independent of the complex concentration, indicating that no change in the rate-limiting step has occurred. Thus a distinction should be made between a rate-limiting enzyme component and the rate-limiting step in this multienzyme system.     

Glutaminyl-tRNA synthetase as a component of the high-molecular weight complex of human aminoacyl-tRNA synthetases. An immunological study

The human glutaminyl-tRNA synthetase is three times larger than the corresponding bacterial and twice as large as the yeast enzyme. It is possible that the additional sequences of the human glutaminyl-tRNA synthetase are required for the formation of the multienzyme complex which is known to include several of aminoacyl-tRNA synthetases in mammalian cells. To address this point we prepared antibodies against three regions of the human glutaminyl-tRNA synthetase, namely against its enzymatically important core region, and against two sections in its large C-terminal extension. In intact multienzyme complexes the core region was accessible to specific antibody binding. However, the C-terminal sections became available to specific antibody binding only when certain components of the multienzyme complex were either absent or degraded. These findings allow first conclusions as to the relative position of some components in the mammalian aminoacyl-tRNA synthetase complex.     

Fatty acid synthetase activity in Mycobacterium smegmatis. Characterization of the acyl carrier protein-dependent elongating system.

Mycobacterium smegmatis extracts contain two fatty acyl synthetase systems (Brindley, D.N., Matsumura, S. and Bloch, K. (1966) Nature 224, 666-669). One is the extensively studied multienzyme complex, (molecular weight 1.39 - 10(6)) which produces shorter C16 and C18) and longer (C24 and higher) fatty acids in a bimodal pattern. The second synthetase is acyl carrier-protein (ACP) dependent and elongates the CoA derivatives of C12 and longer chains. In contrast to the type I synthetase which also extends long fatty acyl chains, the ACP-dependent system produces homologous fatty acids up to 30 carbon atoms long in approximately equal proportions. Other properties which distinguish the ACP-dependent system from the multienzyme complex include the resistance to high concentrations of palmitoyl-CoA and to low ionic strength and the lack of stimulation by mycobacterial polysaccharides. The possibility that the two fatty acid synthetases are complimentary in their function is discussed.     

Enzymic studies on adrenocortical deoxycorticosterone 11beta-hydroxylase system.

Radiometric methods for the assay of deoxycorticosterone 11beta-hydroxylase and for the determination of NADP on a microscale were developed. The determination of NADP was based on the quantitative conversion of 6-phospho[1-14C]gluconate to 14CO2 by the action of 6-phosphogluconate dehydrogenase. Using these methods NADPH oxidase activity of the adrenodoxin reductase-adrenodoxin system as well as kinetic properties of deoxycorticosterone 11beta-hydroxylase (cytochrome P-450) were investigated. The NADPH oxidase activity observed in the presence of adrenodoxin reductase, adrenodoxin, and O2, but in the absence of cytochrome P-450 and deoxycorticosterone, were functions of O2 and adrenodoxin concentrations and represented the autooxidation of reduced adrenodoxin which resulted in the production of H2O2. Due to the rapid autooxidizability of reduced adrenodoxin, only a small fraction of electrons conveyed from NADPH to adrenodoxin by way of adrenodoxin reductase was utilized for the deoxycorticosterone 11beta-hydroxylase reaction under the conditions employed.     

Bimolecular systems: I. Linear systems of complexes

A vast number of biologically important processes are based upon bimolecular systems. In these systems intermediate complexes are formed. Bimolecular systems in which no complex-complex interactions occur are called linear systems of complexes. A definition and some characteristic properties of these systems are given here. There may exist a contradiction of Onsager's principle of detailed balancing in these systems; however, no principal differences are found between the steady state behavior of an open system and that of a closed system. It is shown that the steady state behavior of a linear system of complexes of arbitrary complexity has some similarities with the steady state behavior of a simple bimolecular system, e.g., Michaelis-Menten enzymatic reaction. Multiplicity of action of the substances participating in biomolecular processes may produce some qualitative differences in the steady state behavior of the system.     

Development of a multienzyme reactor for dopamine synthesis: I. enzymology and kinetics

The enzymology and kinetics of tyrosine phenol lyase (TPL) from Erwinia herbicola, and tyrosine decarboxylase (TDC) from Streptococcus faecalis have been investigated for potential use in a coimmobilized multienzyme biocatalytic system for the production of dopamine. In this multienzyme biotransformation using whole cells optimized for each of the respective enzymes, TPL catalyzes the production of 3,4-dihydroxyphenyl-L-alanine (L-dopa) from catechol, pyruvate, and ammonium, and this is subsequently decarboxylated by TDC to produce dopamine. Performing the reactions simultaneously, thereby removing L-dopa, is one option for overcoming the TPL equilibrium constraints. The enzymes have different optimal pH values, so the reaction kinetics at a compromise pH of 7.1, where both enzymes could be operated simultaneously, were investigated. For the concentration range investigated, TPL followed pseudo-first-order kinetics with respect to catechol, pyruvate, and ammonium. TDC exhibited significant product inhibition as well as inhibition by combinations of catechol and pyruvate.     

Felix Hoppe-Seyler Lecture 2000. The ubiquitin system and the N-end rule pathway

Eukaryotes contain a highly conserved multienzyme system which covalently links a small protein, ubiquitin, to a variety of intracellular proteins that bear degradation signals recognized by this system. The resulting ubiquitin-protein conjugates are degraded by the 26S proteasome, an ATP-dependent protease. Pathways that involve ubiquitin play major roles in a huge variety of processes, including cell differentiation, cell cycle, and responses to stress. In this article we briefly review the design of the ubiquitin system, and describe two recent advances, the finding that ubiquitin ligases interact with specific components of the 26S proteasome, and the demonstration that peptides accelerate their uptake into cells by activating the N-end rule pathway, one of several proteolytic pathways of the ubiquitin system.     

Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing

We investigated changes in the root-associated fungal communities associated with the ectomycorrhizal herb Bistorta vivipara along a primary succession gradient using 454 amplicon sequencing. Our main objective was to assess the degree of variation in fungal richness and community composition as vegetation cover increases along the chronosequence. Sixty root systems of B. vivipara were sampled in vegetation zones delimited by dated moraines in front of a retreating glacier in Norway. We extracted DNA from rinsed root systems, amplified the ITS1 region using fungal-specific primers and analysed the amplicons using 454 sequencing. Between 437 and 5063 sequences were obtained from each root system. Clustering analyses using a 98.5% sequence similarity cut-off yielded a total of 470 operational taxonomic units (OTUs), excluding singletons. Between eight and 41 fungal OTUs were detected within each root system. Already in the first stage of succession, a high fungal diversity was present in the B. vivipara root systems. Total number of OTUs increased significantly along the gradient towards climax vegetation, but the average number of OTUs per root system stayed unchanged. There was a high patchiness in distribution of fungal OTUs across root systems, indicating that stochastic processes to a large extent structure the fungal communities. However, time since deglaciation had impact on the fungal community structure, as a systematic shift in the community composition was observed along the chronosequence. Ectomycorrhizal basidiomycetes were the dominant fungi in the roots of B. vivipara, when it comes to both number of OTUs and number of sequences.     

Genetic diversity of the submerged macrophyte Hydrilla verticillata (L. f.) Royle in a river system in Japan

The genetic diversity of Hydrilla verticillata was studied in the Kako River system, Hyogo Prefecture, southwestern Japan, including some of its tributaries. Sex expression (monoecy or dioecy), ploidy level (diploid or triploid), and isoenzyme phenotypes were investigated for plant samples collected from 51 sites along the water course. Monoecious plants occurred at 10 sites and dioecious plants at 47 sites. Among dioecious plants, diploid and triploid plants occurred at 1 and 46 sites, respectively. Seven multienzyme phenotypes (MEPs) were recognized by electrophoretic analysis among dioecious triploid plants. The distribution pattern of nine biotypes based on sex expression, ploidy level, and MEPs suggested the possibility of ecological differentiation among different biotypes. The implications of genetic diversity demonstrated in this study were discussed in relation to the conservation strategy of biodiversity in a river system. Received: April 12, 1999 / Accepted: July 7, 1999