Products, requirements and efficiency of biosynthesis: a quantitative approach

The question of how many grams of an organism can grow heterotrophically from only 1·0 g of glucose and adequate minerals has been put forward many times. Only a few attempts have been made to answer this question theoretically and these attempts were rather rough. In this paper, it is demonstrated that the yield of a growth process may be accurately computed by considering the relevant biochemistry of conversion reactions and the cytological implications of biosynthesis and growth. Oxygen consumption and carbon dioxide production by these processes are also computed. The weight of the biomass synthesized from 1·0 g of substrate and the quantities of gases exchanged are independent of temperature.These results are obtained by adding the individual equations describing the formation of each compound synthesized by the organism from the substrate supplied. The sum represents an equation which accounts for all substrate molecules required for biosynthesis of the carbon skeletons of an end-product, whose chemical composition is given. It is then calculated how much energy is required for the non-synthetic processes which form a part of biosynthesis, such as intra- and intercellular transport of molecules and maintenance of RNA and enzymes. The additional amount of substrate required to provide this energy by combustion is easily calculated. Adding this substrate to the amount used for skeleton synthesis gives an overall equation which quantifies the substrate and oxygen demand as well as carbon dioxide evolution during biosynthesis of 1·0 g biomass. For example, it requires 1·34 g of glucose with adequate ammonia and minerals to synthesize 1·0 g maize plant biomass in darkness; during this process 0·14 g oxygen are consumed and 0·24 g carbon dioxide are produced. It has been described elsewhere that similar results were obtained experimentally with growing plants.Such results depend considerably upon the chemical composition of the biomass being synthesized and upon the state (oxidized or reduced) of the nitrogen source. Other parameters, such as the number of ATP molecules required for protein synthesis, the possibility for utilization of alternative pathways for synthesis or energy production, the presence or absence of compartmentation of synthetic processes and variations in the P/O ratio between two and three, under many conditions affect results of the computation less than 10%.Since maintenance of cellular structures is not considered, the approach concerns the gross yield of biosynthesis. It predicts therefore the dry matter yield of heterotrophic cells from a given quantity of substrate at high relative growth rates.     

The biological interactions ofRhizobium to its host legume

Conclusion The intensive study of the symbiosis ofRhizobium and its legume host-plant has emphasised how delicate is the equilibrium upon which a satisfactory association depends. The effectiveness of the bacterial strain for a particular host plant, the genetic stability of this strain and its ability to compete with other strains in the soil may all influence the growth of the crop. The plant begins to exert its influence on the bacteria by root secretions before they infect the roots and both the degree of infection and the activity of the nodules that are formed, will be influenced by genes in the plant as well as by environmental conditions that affect its physiology. It is the separation of these complex factors, that is at once the main difficulty and the chief fascination in the study of this symbiosis.     

Metabolism of carbon monoxide

Carbon monoxide is the most abundant atmospheric pollutant released by our technological society. The gas is also a natural by-product of different mammalian, plant and bacterial cell systems. This review describes a few of these cellular CO-evolving activities as part of a natural biological cycle, which ultimately depends upon certain bacteria to oxidize CO to carbon dioxide. Most microbes oxidize CO adventitiously, or accidentally, but one cell can use the gas as its sole energy substrate for growth. The ability of this microorganism to form efficiently both H₂ and CO₂ from CO released by industrial coal gasification procedures is suggested.     

Hydrotropism: root growth responses to water

The survival of terrestrial plants depends upon the capacity of roots to obtain water and nutrients from the soil. Directed growth of roots in relation to a gradient in moisture is called hydrotropism and begins in the root cap with the sensing of the moisture gradient. Even though the lack of sufficient water is the single-most important factor affecting world agriculture, there are surprisingly few studies on hydrotropism. Recent genetic analysis of hydrotropism in Arabidopsis has provided new insights about the mechanisms that the root cap uses to perceive and respond simultaneously to moisture and gravity signals. This knowledge might enable us to understand how the root cap processes environmental signals that are capable of regulating whole plant growth.     

Vascularization is a general requirement for growth of plant and animal tumours

Solid-tumour growth in animals as in humans depends on angiogenesis. Tumours that fail to induce the formation of new blood vessels do not enlarge beyond a few millimetres in diameter. Plant tumours induced by Agrobacterium tumefaciens can reach diameters of more than 100 mm, thus raising the question of how they are sufficiently supplied with nutrients and water. Until recently, these rapidly growing tumours were considered unorganized or partly organized masses. However, in analogy to animal and human tumours, growth of leaf and stem tumours depends on neovascularization. Plant tumour cells induce the formation of a sophisticated vascular network consisting of water-conducting vessels and assimilate-transporting sieve elements. Similar to animal and human tumours that overexpress angiogenic growth factors, plant tumours overexpress the T-DNA-encoded vascularization-promoting growth factors auxin and cytokinin upon AGROBACTERIUM: infection. High auxin levels induce ethylene emission from the tumours, which has a strong impact on tumour and host stem, as well as on root structure and function. Ethylene apparently stimulates abscisic acid synthesis in the leaves above the tumour, which reduces transpiration and thus protects the host plant from rapid wilting. Hence, for the elucidation of phytohormone-dependent vascular development in plants, such tumours are regarded as an excellent model system. The comparison of analogous requirement of neovascularization for tumour growth in plants, as in animals and humans, is discussed in terms of interdisciplinary strategies of possible prevention and therapy.     

An anisotropic-viscoplastic model of plant cell morphogenesis by tip growth

Plant cell morphogenesis depends critically on two processes: the deposition of new wall material at the cell surface and the mechanical deformation of this material by the stresses resulting from the cell's turgor pressure. We developed a model of plant cell morphogenesis that is a first attempt at integrating these two processes. The model is based on the theories of thin shells and anisotropic viscoplasticity. It includes three sets of equations that give the connection between wall stresses, wall strains and cell geometry. We present an algorithm to solve these equations numerically. Application of this simulation approach to the morphogenesis of tip-growing cells illustrates how the viscoplastic properties of the cell wall affect the shape of the cell at steady state. The same simulation approach was also used to reproduce morphogenetic transients such as the initiation of tip growth and other non-steady changes in cell shape. Finally, we show that the mechanical anisotropy built into the model is required to account for observed patterns of wall expansion in plant cells.     

When microbes and consumers determine the limiting nutrient of autotrophs: a theoretical analysis

Ecological stoichiometry postulates that differential nutrient recycling of elements such as nitrogen and phosphorus by consumers can shift the element that limits plant growth. However, this hypothesis has so far considered the effect of consumers, mostly herbivores, out of their food-web context. Microbial decomposers are important components of food webs, and might prove as important as consumers in changing the availability of elements for plants. In this theoretical study, we investigate how decomposers determine the nutrient that limits plants, both by feeding on nutrients and organic carbon released by plants and consumers, and by being fed upon by omnivorous consumers. We show that decomposers can greatly alter the relative availability of nutrients for plants. The type of limiting nutrient promoted by decomposers depends on their own elemental composition and, when applicable, on their ingestion by consumers. Our results highlight the limitations of previous stoichiometric theories of plant nutrient limitation control, which often ignored trophic levels other than plants and herbivores. They also suggest that detrital chains play an important role in determining plant nutrient limitation in many ecosystems.     

Shoot: Root Allocation with Respect to C, N and P: an Investigation and Comparison of Resistance and Teleonomic Models

Two shoot: root allocation models are described: the transport-resistanceapproach, and a teleonomic (goal-seeking) method based on maximizingspecific growth rate when the system is growing exponentially.These are applied to two growth modes: exponential growth, andthe steady state where all variables are constant with no netgrowth. The dynamic behaviour after shoot defoliation is investigated:the damping/overshoot effects observed are highly dependenton the presence or absence of product inhibition of the inputprocess (e.g. plant substrate N may inhibit the uptake of mineralN by the plant). The teleonomic model is far more damped thanthe resistance model and may therefore be misleading if usedto interpret transient experiments. Ontogenetic effects on allocationare simulated by varying the scaling (with plant size) of thetransport resistances; this may give increasing allocation tothe shoot or the root with the passage of time. The two modelsresemble each other very closely as far as equilibrium responsesare concerned - this applies to exponential growth and to thesteady state. Increasing the nitrogen input may lead to loweror higher whole-plant carbohydrate levels. The response to increasingnitrogen input depends on the other inputs; for instance itcan be much curtailed by low phosphorus inputs. The responseto phosphorus input can be similarly limited.Copyright 1995,1999 Academic Press Partitioning, plant growth, simulation     

A Shoot:Root Partitioning Model

A model for partitioning newly-synthesized structural dry matterbetween shoot and root is developed. It is based on a postulatedpartitioning function, which depends upon the relative levelsof carbon and nitrogen substrates, with parameters determiningthe control point and also the degree of control. The modelis used to investigate the relationships between plant specificgrowth rate, shoot:root ratio, and the specific activities ofshoot and root (which depend upon environment), during steady-stateexponential growth; the transient behaviour of the model isalso explored and oscillations in these quantities are obtained. Shoot:root ratio, specific growth rate, mathematical model, partition of assimilates     

Why Worry about How Many Species and Their Loss?

We are astonishingly ignorant about how many species are alive on earth today, and even more ignorant about how many we can lose yet still maintain ecosystem services that humanity ultimately depends upon. Mora et al.'s paper is important in offering an imaginative new approach to assessing total species numbers, both on land and in the sea.     

A new approach to titrating active enzyme centers upon the use of surface-active micellar substances in organic solvents

Micellar solutions of surfactant in organic solvents with rubber additions are proposed for determination of active enzyme concentration. A kinetic theory of enzymatic reactions in reversed micellar systems is developed, suggesting the intermicellar transport of the substrate to be the limiting step in viscous medium. Under these conditions, it is shown that fraction of the product formed after quick transformation of the substrate located in the enzyme-containing micelles depends upon active enzyme concentration and aggregation number of surfactant molecules. The proposed approach is used for the active-site titration of trypsin and cellobiase and for the determination of the aggregation number of Aerosol OT (AOT) molecules in the ternary system AOT/water/cyclohexane.     

cDNA of the Yeast Retrotransposon Ty5 Preferentially Recombines with Substrates in Silent Chromatin

The yeast retrotransposon Ty5 preferentially integrates into regions of silent chromatin. Ty5 cDNA also recombines with homologous sequences, generating tandem elements or elements that have exchanged markers between cDNA and substrate. In this study, we demonstrate that Ty5 integration depends upon the conserved DD(35)E domain of integrase and cis-acting sequences at the end of the long terminal repeat (LTR) implicated in integrase binding. cDNA recombination requires Rad52p, which is responsible for homologous recombination. Interestingly, Ty5 cDNA recombines at least three times more frequently with substrates in silent chromatin than with a control substrate at an internal chromosomal locus. This preference depends upon the Ty5 targeting domain that is responsible for integration specificity, suggesting that localization of cDNA to silent chromatin results in the enhanced recombination. Recombination with a telomeric substrate occasionally generates highly reiterated Ty5 arrays, and mechanisms for tandem element formation were explored by using a plasmid-based recombination assay. Point mutations were introduced into plasmid targets, and recombination products were characterized to determine recombination initiation sites. Despite our previous observation of the importance of the LTR in forming tandem elements, recombination cannot simply be explained by crossover events between the LTRs of substrate and cDNA. We propose an alternative model based on single-strand annealing, where single-stranded cDNA initiates tandem element formation and the LTR is required for strand displacement to form a looped intermediate. Retrotransposons are increasingly found associated with chromosome ends, and amplification of Ty5 by both integration and recombination exemplifies how retroelements can contribute to telomere dynamics.     

Towards new enzymes for biofuels: lessons from chitinase research

Enzymatic conversion of structural polysaccharides in plant biomass is a key issue in the development of second generation ('lignocellulosic') bioethanol. The efficiency of this process depends in part on the ability of enzymes to disrupt crystalline polysaccharides, thus gaining access to single polymer chains. Recently, new insights into how enzymes accomplish this have been obtained from studies on enzymatic conversion of chitin. First, chitinolytic microorganisms were shown to produce non-hydrolytic accessory proteins that increase enzyme efficiency. Second, it was shown that a processive mechanism, which is generally considered favorable because it improves substrate accessibility, might in fact slow down enzymes. These findings suggest new focal points for the development of enzyme technology for depolymerizing recalcitrant polysaccharide biomass. Improving substrate accessibility should be a key issue because this might reduce the need for using processive enzymes, which are intrinsically slow and abundantly present in current commercial enzyme preparations for biomass conversion. Furthermore, carefully selected substrate-disrupting accessory proteins or domains might provide novel tools to improve substrate accessibility and thus contribute to more efficient enzymatic processes.     

Differential Expression of Oncogenicity and Nopaline Synthesis in Intact Leaves Derived from Crown Gall Teratomas of Tobacco

The results reported in the present study demonstrate that oncogenicity and nopaline synthesis are differentially expressed under conditions in which the neoplastic state is persistently suppressed in crown gall teratoma tissues of tobacco. While an active and continued synthesis of nopaline occurs in cells present in intact teratoma-derived leaves, the reexpression of oncogenicity depends on the development of new cell divisions. It is suggested that these new cell divisions are required either (a) to reestablish positive feedback control mechanisms upon which the development of a capacity for autonomous growth of these plant tumour tissues appears to depend, or (b) to establish the pattern of metabolism concerned with cell growth and division which is then maintained in the plant tumour cells by positive feedback control mechanisms.     

Management of nursery practices for efficient ectomycorrhizal fungi application in the production of Quercus ilex

The application of ectomycorrhizal (ECM) fungi on forest nursery production is regarded as part of good management practice. However, before employing large scale inoculations in a nursery the interaction between ECM symbionts, growth substrate and fertilisation input should be studied to select the most suitable nursery practices for promoting plant growth and ECM colonisation. In this study, seedlings of Quercus ilex were inoculated with Paxillus involutus, Hebeloma mesophaeum or Cenococcum geophilum and grown in three different substrates commonly used in forest nurseries: peat-based compost, forest soil or composted pine bark. The effect of various fertilisation regimes was also studied. The choice of substrate had a significant effect on plant growth and ECM colonisation. The most appropriate combination of substrate and ECM fungus for Q. ilex growth and nutrition was peat and H. mesophaeum. Plants grown on a peat-based compost and inoculated with H. mesophaeum had a significantly greater biomass and leaf phosphorus concentration without fertilisation. Composted pine bark was found not to be suitable for growth or for mycorrhization. If the appropriate growth substrate is selected, it is possible to replace the use of chemical fertilisers by inoculation with selected ECM fungi. This results in a significant increase in plant development, and thus ECM fungi can be recommended as a more environmental friendly biotechnological approach to plant management in the nursery.     

Analysis of interspecific competition in perennial plants using Life Table Response Experiments

The impact of interspecific competition is usually measured by its effect upon plant growth, neglecting impacts upon other stages of the life cycle such as fecundity which have a direct influence upon individual fitness and the asymptotic population growth rate of a population (λ). We used parameterized matrix models for three perennial plant species grown with and without interspecific competition to illustrate how the methodology of Life Table Response Experiments (LTRE) can be used to link any change in population dynamics to changes in any part of the life cycle. Plants were herbaceous grassland species grown for two years in a field experiment at Rothamsted Experimental Station, England. Interspecific competition reduced λ by over 90% in all species. Survival and growth were slightly affected by competition whereas plant fecundity was greatly reduced. Nearly all of the observed difference in λ between the competition treatments was explained by the fecundity terms, and more precisely by a large difference in the number of seeds, and a high sensitivity of λ to the germination rate. Whereas most competition studies focus on the measurement of change in individual fitness, our study illustrates how informative it is to take account not only of the effect of competition upon vital rates but also of how different vital rates affect population growth rate.     

Herbivore-Mediated Competition between Defended and Undefended Plant Species: A Model to Investigate Consequences of Climate Change

Abstract: Optimal levels of anti-herbivore defence are determined not only by grazing pressure on the target plant, but also by the efficiency of the defence and by competitive interactions with neighbours. In the high Arctic on Svalbard, grazing by reindeer is a process that can be modelled without plant-to-herbivore feedback, as reindeer population sizes are not correlated with plant growth. However, growing conditions are extreme: a short season and low temperatures inhibit optimal growth. Therefore, it is possible to model anti-herbivore defence in competition in this system, assess how its optimum depends on grazing intensity and defence efficiency, and, finally, how global climate change will effect plant-plant interactions. This model, based on a Lotka-Volterra type competition and temperature-dependent growth, indicates that competition is of considerable importance even in extreme environments. Herbivory mediates displacement of the defended plant by releasing it from competition. This process is more pronounced under high grazing pressure than under low pressure. In other words, competition potentially magnifies the effect of herbivory. Elevated temperatures and a longer growing season have no qualitative impact on these processes, as the dominant defended plant profits most.     

SOME THOUGHTS ON NUTRIENT LIMITATION IN ALGAE1

An empirical relation relating specific growth, rate in steady state systems to nutrient status with respect to more than one nutrient simultaneously is proposed, based on 3 experimentally verifiable postulates: (1) that uptake depends on the external substrate concentration; (2) that growth depends on the interval substrate concentration; and (3) in a steady state system specific rate of uptake (in the absence of significant, excretion) is necessarily the product of the specific growth rate and internal substrate concentration. The implications of this model are discussed in particular in respect to the concept of luxury consumption and Liebig's law of minimum. Some aspects of uptake in transient situations are also discussed.