In order to be able to manipulate microorganisms to produce maximally materials of
economic importance to humans, but at minimal costs, it is important that the physiology
of the organisms be understood as much as is possible. In this section  relevant elements
of the physiology of industrial organisms will be discussed.
A yeast cell will divide and produce carbon dioxide under aerobic conditions if offered a solution
of glucose and ammonium salts. The increase in cell number resulting from the growth
and the bubbling of carbon dioxide are only external evidence of a vast number of chemical reactions going in the cell. The yeast cell on absorbing the glucose has to produce various
proteins which will form enzymes necessary to catalyze the various reactions concerned
with the manufacture of proteins, carbohydrates, lipids, and other components of the cell
as well as vitamins which will form coenzymes. A vast array of enzymes are produced as
the glucose and ammonium initially supplied are converted from one compound into
another or metabolized. The series of chemical reactions involved in converting a chemical (or a
metabolite) in the organism into a final product is known as a metabolic pathway.When the
reactions lead to the formation of a more complex substance, that particular form of
metabolism is known as anabolism and the pathway an anabolic pathway. When the
series of reactions lead to less complex compounds the metabolism is described as

catabolism.The compounds involved in a metabolic pathway are called intermediates and the final product is known as the end-product.
Catabolic reactions have been mostly studied with glucose. Four pathways of glucose
breakdown to pyruvic acid (or glycolysis) are currently recognized. They will be
discussed later. Catabolic reactions often furnish energy in the form of ATP and
other high energy compounds, which are used for biosynthetic reactions. A second
function of catabolic reactions is to provide the carbon skeleton for biosynthesis.
Anabolic reactions lead to the formation of larger molecules some of which are

constituents of the cell. Although anabolism and catabolism are distinct phenomena some pathways have
elements of both kinds Metabolic intermediates which are derived from catabolism and
which are also available for anabolism are known as amphibolic intermediates.

Products of industrial microorganisms may be divided into two broad groups, those
which result from primary metabolism and others which derive from secondary
metabolism. The line between the two is not always clear cut, but the distinction is useful

in discussing industrial products.
Products of Primary Metabolism:
Primary metabolism is the inter-related group of reactions within a microorganism
which are associated with growth and the maintenance of life. Primary metabolism is

essentially the same in all living things and is concerned with the release of energy, and the synthesis of important macromolecules such as proteins, nucleic acids and other cell
constituents. When primary metabolism is stopped the organism dies.
Products of primary metabolism are associated with growth and their maximum
production occurs in the logarithmic phase of growth in a batch culture. Primary
catabolic products include ethanol, lactic acid, and butanol while anabolic products
include amino-acids, enzymes and nucleic acids. Single-cell proteins and yeasts would also be regarded as primary products.

Products of Secondary Metabolism:
In contrast to primary metabolism which is associated with the growth of the cell and the
continued existence of the organism, secondary metabolism, which was first observed in
higher plants, has the following characteristics(i) Secondary metabolism has no apparent
function in the organism. The organism continues to exist if secondary metabolism is
blocked by a suitable biochemical means. On the other hand it would die if primary
metabolism were stopped. (ii) Secondary metabolites are produced in response to a
restriction in nutrients. They are therefore produced after the growth phase, at the end of
the logarithmic phase of growth and in the stationary phase (in a batch culture). They can
be more precisely controlled in a continuous culture. (iii) Secondary metabolism appears
to be restricted to some species of plants and microorganisms (and in a few cases to
animals). The products of secondary metabolism also appear to be characteristic of the
species. Both of these observations could, however, be due to the inadequacy of current
methods of recognizing secondary metabolites. (iv) Secondary metabolites usually have
‘bizarre’ and unusual chemical structures and several closely related metabolites may be
produced by the same organism in wild-type strains. This latter observation indicates the
existence of a variety of alternate and closely-related pathways. (v) The ability to produce
a particular secondary metabolite, especially in industrially important strains is easily
lost. This phenomenon is known as strain degeneration. (vi) Owing to the ease of the loss
of the ability to synthesize secondary metabolites, particularly when treated with acridine dyes, exposure to high temperature or other treatments known to induce plasmid
loss  secondary metabolite production is believed to be controlled by plasmids
(at least in some cases) rather than by the organism’s chromosomes. A confirmation of the
possible role of plasmids in the control of secondary metabolites is shown in the case of

leupeptin, in which the loss of the metabolite following irradiation can be reversed by conjugation with a producing parent. (vii) The factors which trigger secondary metabolism, the inducers, also trigger morphological changes (morphogenesis) in the organism.

Inducers of Secondary Metabolites:
Autoinducers include the gamma -butyrolactones (butanolides) of the actinomycetes, the N-acylhomoserine lactones (HSLs) of Gram negative bacteria, the oligopeptides of Gram positive bacteria, and B-factor [3’-(1-butylphosphoryl)adenosine] of rifamycin
production in Amycolatopsis mediterrane. They function in development, sporulation,
light emission, virulence, production of antibiotics, pigments and cyanide, plasmid driven conjugation and competence for genetic transformation. Of great importance in
actinomycete fermentations is the inducing effect of endogenous -butyrolactones, e.g. Afactor (2-S-isocapryloyl-3R-hydroxymethyl- -butyrolactone). A-factor induces both
morphological and chemical differentiation in Streptomyces griseus and Streptomyces
bikiniensis, bringing on formation of aerial mycelia, conidia, streptomycin synthases and
streptomycin. Conidia can actually form on agar without A-factor but aerial mycelia
cannot. The spores form on branches morphologically similar to aerial hyphae but they
do not emerge from the colony surface. In S. griseus, A-factor is produced just prior to
streptomycin production and disappears before streptomycin is at its maximum level. It
induces at least 10 proteins at the transcriptional level. One of these is streptomycin 6-phosphotransferase, an enzyme which functions both in streptomycin biosynthesis and
in resistance. In an A-factor deficient mutant, there is a failure of transcription of the
entire streptomycin gene cluster. Many other actinomycetes produce A-factor, or related
gamma-butyrolactones, which differ in the length of the side-chain. In those strains which
produce antibiotics other than streptomycin, the gamma -butyrolactones induce formation of the
particular antibiotics that are produced, as well as morphological differentiation.
Secondary metabolic products of microorganism are of immense importance to
humans. Microbial secondary metabolites include antibiotics, pigments, toxins, effectors
of ecological competition and symbiosis, pheromones, enzyme inhibitors,
immunomodulating agents, receptor antagonists and agonists, pesticides, antitumor
agents and growth promoters of animals and plants, including gibberellic acid, antitumor agents, alkaloids such as ergometrine, a wide variety of other drugs, toxins and
useful materials such as the plant growth substance, gibberellic acid . They
have a major effect on the health, nutrition, and economics of our society. They often have
unusual structures and their formation is regulated by nutrients, growth rate, feedback
control, enzyme inactivation, and enzyme induction. Regulation is influenced by unique
low molecular mass compounds, transfer RNA, sigma factors, and gene products formed
during post-exponential development. The synthases of secondary metabolism are often
coded for by clustered genes on chromosomal DNA and infrequently on plasmid DNA.
Unlike primary metabolism, the pathways of secondary metabolism are still not
understood to a great degree. Secondary metabolism is brought on by exhausion of a
nutrient, biosynthesis or addition of an inducer, and/or by a growth rate decrease. These
events generate signals which effect a cascade of regulatory events resulting in chemical
differentiation (secondary metabolism) and morphological differentiation
(morphogenesis). The signal is often a low molecular weight inducer which acts by

negative control, i.e. by binding to and inactivating a regulatory protein (repressor protein/receptor protein) which normally prevents secondary metabolism and
morphogenesis during rapid growth and nutrient sufficiency.
Thousands of secondary metabolites of widely different chemical groups and
physiological effects on humans have been found. Nevertheless a disproportionately
high interest is usually paid to antibiotics, although this appears to be changing. It would
appear that the vast potential utility of microbial secondary metabolites is yet to be
realized and that many may not even have been discovered. Part of this ‘lopsided’
interest may be due to the method of screening, which has largely sought antibiotics.  


Bull, A.T., Ward, A.C., Goodfellow, M. 2000. Search and Discovery Strategies for Biotechnology:

The Paradigm Shift Microbiology and Molecular Biology Reviews 64, 573 –606.
Demain, A.L. 1998. Induction of microbial secondary Metabolism International Microbiology 1,

Herrmann, K.H., Weaver, L.M. 1999. The Shikimate Pathway. Annual Review of Plant

Physiology and Plant Molecular Biology. 50, 473–503.
Meurer, G., Hutchinson, C.R. 1999. Genes for the Synthesis of Microbial Secondary Metabolites.
In: Manual of Industrial Microbiology and Biotechnology. A.L. Demain and J.E. Davies, (eds).
ASM Press. 2nd Ed.Washington, DC,USA pp.740-758.

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