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Summary Glycolysis is a fundamental metabolic pathway for glucose catabolism across biology, and glycolytic enzymes are among the most abundant proteins in cells. Their expression at such levels provides a particular challenge. Here we demonstrate that the glycolytic mRNAs are localized to granules in yeast and human cells. Detailed live cell and smFISH studies in yeast show that the mRNAs are actively translated in granules, and this translation appears critical for the localization. Furthermore, this arrangement is likely to facilitate the higher level organization and control of the glycolytic pathway. Indeed, the degree of fermentation required by cells is intrinsically connected to the extent of mRNA localization to granules. On this basis, we term these granules, core fermentation (CoFe) granules; they appear to represent translation factories, allowing high-level coordinated enzyme synthesis for a critical metabolic pathway., Graphical abstract, Highlights • Glycolytic mRNAs colocalize and are translated in RNA granules • The glycolytic mRNA granules are important when cells are fermenting • Glycolytic protein translation is likely coordinated in these translation factories • Therefore, “CoFe granules” are core fermentation factories for glycolytic proteins, Molecular biology; cell biology

Bioactive peptides are the small protein fragments, which have many positive benefits to mankind. Bioactive peptides are organic compounds formed of amino acids covalently attached by peptide bonds. However, some of them may exist freely in nature but most bioactive peptides are encrypted into the parent protein structure, which can be extracted or produced through processes like enzyme synthesis, chemical synthesis or microbial synthesis. Selection of production method depends upon the source from used for extraction of bioactive peptides. There is a wide range of sources for bioactive peptides production ranging from food products to marine and animal resources. These food resources are known to produce most efficient and health beneficial bioactive peptides. Bioactive peptides can be categorized on the basis of functional capabilities. Bioactive peptides contribute significantly toward human health by affecting the cardiovascular, digestive, immune, nervous and endocrine systems. Bioactive peptides can be produced only in a limited quantity using natural resources, which are not sufficient to meet growing need of bioactive peptides. To tackle this mismatch synthetic bioactive peptides are produced using biotechnological tools and processes. Synthetic bioactive peptides not only meet the required demand but they are also much more efficient than the conventional bioactive peptides. In this context, the present chapter will highlight about bioactive peptides, their sources, production techniques, major uses and biotechnological applications.

Microorganisms are the main sources of the most demanded commercial enzymes. They are produced in large scale with the employment of different strains, which can be parental strains or molecularly modified. The capacity of a strain to synthesize higher concentrations of the protein of interest depends not only on the selected microorganism but on the condition of cultivation and media composition. Currently, agro-industrial by-products are viewed as potential economical feedstocks for microroganism cultivation for enzyme production serving dual purposes: to solve environmental problems and to add value to these substrates. Some aspects of enzyme synthesis are described in this chapter, including the main factors that affect the productivity. Some aspects of the enzyme’s process development, mainly hydrolases, such as cellulases, xylanases, phytases, mannanases, amylases, lipases, and others, from batch to industrial scale are reported. General downstream operations for the separation, recovery, and purification of these enzymes are also presented. Finally, the most important hydrolases produced and commercialized are also listed.

A simple, non-aseptic, low-cost single process had been developed for the treatment of starch processing wastewater (SPW) with the production of fungal protein and glucoamylase enzyme. The selected fungus Rhizopus oligosporus DAR 2710 has the ability to covert more than 95% starch materials in SPW to produce 4.5–5.2 g of dry fungal biomass from a litre of SPW in 14 h cultivation at 35°C and initial pH 4.0. The fungal biomass contained 46% protein and was safe for human and animal consumption. The process using an air lift bioreactor was successfully carried out in a batch system without sterilization and/or preliminary hydrolysis of SPW. In addition to the production of fungal protein and glucoamylase, the removal of 95% COD and total suspended solids would lead to a potential benefit to the environment.

Publisher Summary This chapter focuses on bioprocessing, which is defined as processing that involves cells or biological molecules as products, as raw materials, or as integral components of the process itself. The central problems of bioprocess engineering derive from lack of knowledge concerning the intrinsic behavior of cells and proteins. High-leverage opportunities for chemical engineering contributions to bioprocessing involve systematic manipulation of these intrinsic characteristics, often employing genetic methods. Present process use of biological activities is limited by their inability to conduct the desired step; by rates that are too small; by requirements for low substrate, product, or antigen concentrations; by rapid loss of activity; by excessive costs; or by some combination of these factors. There has been an explosive growth in research, development, and recently in sales of new products based on biological processes. This new industrial activity is a direct consequence of the emergence—in the late 1970s—of two new genetic technologies-recombinant DNA and cell fusion that have made possible the construction of new types of cells with new characteristics. To date, biochemical engineers have concentrated heavily on modeling and analysis of the enzyme synthesis process and have almost completely ignored the enzyme decomposition processes that are important in many types of cells. Long-term genetic drift is important in recently conceived processes for manufacturing valuable proteins using mammalian cells. Although only anecdotal observations are available at present, it is clear that the important engineering properties of these cells can change significantly over numerous generations.

Publisher Summary The chapter surveys the occurrence of apomixis in micro-organisms, outlines the basic molecular information on apomixis derived from yeast, and assesses its relevance to apomixis-related cellular phenomena. Some useful features of Sacch.cerevisiae as an experimental organism for research on apomixis are summarized. It is conceivable that mutations responsible for apomixis in Sacch.cerevisiae are pleiotropic by derepressing enzyme synthesis for carbohydrate catabolism under conditions of glucose catabolite repression, thereby improving fermentation performance through enhancement of rates of carbohydrate assimilation and hence of ethanol production. Its possible introduction into higher organisms of economic importance may aid development of techniques to improve control of their reproduction. The tendency towards apomictic in place of sexual reproduction occurs almost universally throughout the biotic world, and that the lower eukaryotic micro-organisms are no exception in this regard

Following axonal injury, there is a 45% reduction in the amount of DBH in the neurons of the locus coeruleus (LC). To determine if this is due to reduced enzyme synthesis, 3H-leucine was infused into the IVth ventricle of control and lesioned rats. The relative rate of DBH synthesis (3H-DBH/3H-total protein) was reduced 40% in the LC of lesioned rats as compared to controls, indicating a selective reduction in DBH synthesis. During axonal regeneration, there may be a selective reordering of protein synthesis favoring synthesis of proteins for axonal regeneration rather than neurotransmission.

Publisher Summary This chapter discusses the methods used for the analysis of enzyme synthesis and degradation in animal tissues. It is well established that the amount of an enzyme present in animal tissues results from opposing processes of continual synthesis and degradation and that either process can be altered by hormonal, nutritional, developmental, or genetic factors. There are a number of methods to assess the contributions of altered synthesis and/or degradation to changes in enzyme (protein) level, including immunologic methods, uses of tracer techniques, and analysis of time courses of changes in enzyme levels. Each method embodies certain assumptions, as well as limitations, and unambiguous conclusions generally can be made only when independent estimates of the rates of synthesis and degradation are made and when more than one method is employed. Tracer techniques are used most commonly for estimating degradation rates. Although such techniques may seem direct, they are full of pitfalls that can result in ambiguous results. Isotope methods can be divided into two general techniques: (1) single isotope administration and (2) continuous isotope administration. The use of reutilizable isotopes in pulse-decay experiments, although commonly employed, has severe limitation(s) in interpretation. They do not, by themselves, provide measures of true half-lives of enzymes. They can, under suitable conditions, provide information on whether two or more proteins in a similar tissue have different rates of turnover.

Publisher Summary The comparative survey of induction mechanisms used by different bacterial genera to govern the synthesis of enzymes for a single pathway can give insight into some of the factors that contributed to the selection of particular compounds as inducers and to the evolution of patterns of inductive control. This chapter presents different types of inductive control and discusses the regulation of inducer levels. Inductive control evolves through the modification of preexisting genetic material. The chapter discusses β-ketoadipate pathway, which is a multistep route for the dissimilation of aromatic compounds. It highlights the regulation of β-ketoadipate pathway in two bacterial species, Acinetobacter calcoaceticus and Pseudomonas putida . This provides a background for tracing the development of concepts about four evolutionary factors that influence the evolution of induction mechanisms: (1) the economy of enzyme synthesis, (2) unification of inductive control, (3) the preexisting genetic material from which genes evolved, and 4) the role of nutritional opportunities in the natural environment in the selection of organisms with specific patterns of induction.

It is perhaps self-evident that the metabolism of micro-organisms, and indeed of all living organisms, is under strict in vivo control. Micro-organisms show a remarkable reproducibility in structure and composition, a reproducibility that is maintained even when they are grown in media of widely different chemical composition. Moreover, rapidly growing micro-organisms usually accumulate, either intracellularly or in the environment, only very small quantities of compounds that could be used in synthesis of new cell material, which indicates that there is extremely little wastage during cell metabolism. There are many other examples that could be quoted to show the remarkable degree of control and economy that operates in the metabolism of micro-organisms.

This chapter provides an overview of the molecular mechanism of phytochrome action, the processes through which phytochrome regulates development, and function of phytochrome in plants growing in the natural environment. The great plurality and diversity of phytochrome-controlled biochemical changes pose major difficulties for the construction of a unified hypothesis of the phytochrome control of development. As yet, there is no direct evidence for the regulation of mRNA synthesis by phytochrome. Therefore, it is no longer possible to hold to the view that phytochrome controls development by regulating gene expression at one locus only. There are basically two general hypotheses to account for the manifold and rapid effects of phytochrome on cell metabolism and development. The first proposes that one or more second messengers act as intermediaries between the single primary action of phytochrome at the membrane, and its ultimate effects on enzyme synthesis and activity. The alternative view is that more than one primary reaction of phytochrome is possible, depending perhaps on its location within the cell.