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MICROBIAL BIOTECHNOLOGY
PLANTS AS BIOREACTORS
NO. 12
MICROBIAL BIOTECHNOLOGY
Microbes (or microorganisms) are minute living things that individually are too small to
be seen with the naked eye. Microorganisms are a diverse and unique life form. They
include bacteria, fungi (yeasts and molds), protozoa, microalgae, and viruses. This
group of organisms is usually associated only with uncomfortable infections, major
diseases such as AIDS or such common inconveniences as spoiled food. Microbes live in
familiar settings such as soil, water, food, and animal intestines, as well as in more
extreme settings such as rocks, glaciers, hot springs, and deep-sea vents. The wide
variety of microbial habitats reflects an enormous diversity of biochemical and
metabolic traits that have arisen by genetic variation and natural selection in microbial
populations.
Historically, humans have exploited some of this microbial diversity in the production of
fermented foods such as bread, cheese, yoghurt, alcoholic beverages like wine and beer
and condiments like vinegar, fish sauce and soy sauce. Some soil microbes release
nitrogen that plants need for growth by breaking down waste and incorporating
nitrogen gas into the organic compounds thereby recycling and maintaining the critical
composition of the Earth's soil, water and atmosphere. Other microbes challenge the
food supply by causing yield-reducing diseases in food-producing plants and animals. In
our bodies, different microbes help to digest food, synthesize some vitamins, ward off
invasive organisms, and engage in skirmishes and pitched battles with the human
immune system in the give-and-take of the natural disease process. In general,
microorganisms make crucial contributions to the welfare of the world's inhabitants by
helping to maintain the balance of living organisms and chemicals in our environment.
5. Production of products that have high yield and enhanced nutritional value; and
Genetically modified (GM) wine has been marketed in the United States for the past two
years (Cummin, 2005). Presently, only one modification has been acknowledged but
there are a number of modifications reported in wine yeast and bacteria and a number
of modifications reported for grapes. The United States Food and Drug Administration
(FDA) in 2003 designated the yeast, Saccharomyces cereviseae strain ML01 to be a
substance generally recognized as safe (GRAS). The strain included a gene for malolactic
enzyme from the bacterium Oenococcus oeni and a malate permease gene from the
fission yeast Schizosaccharomyces pombe. Wine making consists of alcoholic
fermentation employing the metabolic pathways of yeast and malolactic fermentation to
convert malic acid to lactic acid to reduce the acidity of the wine. Malolactic acid
fermentation is usually achieved using lactic acid bacteria which have a permease for
malic acid. Having the two fermentations in one organism spares the need for the lactic
acid fermentation. The recombinant yeast softened the wine’s mouth feel by decreasing
its acidity. Its use also reduces buttery flavors (diactyl) due to lactic acid secondary
metabolism. The company distributing the GM yeast is Springer Oenologie, Lesaffre
Group, of North America.
In 1990, the United Kingdom became the first country to permit the use of a live,
genetically-modified organism in food. This was a special strain of bakers' yeast
engineered to make the bread dough rise faster. Existing genes were placed under the
control of stronger, constitutive promoters, which help the yeast to break down the
sugar maltose faster than usual. This yeast was and is not used by any food
manufacturers, however.
Molecular diagnostics provide outstanding tools for the detection, identification and
characterization of microbial strains for bio-processing applications and for the
improvement of fermentation processes. Many of the classical food microbiological
methods used in the past were culture-based, with microorganisms grown on agar plates
and detected through biochemical identification. These methods are often tedious, labor
intensive and slow. Genetic based diagnostic and identification systems can greatly
enhance the specificity, sensitivity and speed of microbial testing. Molecular
methodologies, including polymerase chain reaction (PCR) and ribotyping, can be used
for typing microbial strains, for characterizing and monitoring the presence of improved
microbial strains as well as detection of spoilage microflora (microbes causing food to
become unfit for eating), food chain or to identify the causal agents of food borne
illnesses. Monoclonal and polyclonal antibodies can also be used for diagnostics, e.g. in
enzyme-linked immunosorbent assay (ELISA) kits (FAO, 2000, 2004). Microarrays are
also referred to as biochip, DNA chip, DNA microarray or gene arrays and offer
unprecedented opportunities and approaches to diagnostic and detection methods. They
can be used for the detection of pathogens, pesticides and toxins and offer considerable
potential for facilitating process control, the control of fermentation processes and
monitoring the quality and safety of raw materials (FAO, 2000, 2004; BREI, 2006).
Genomics
In recent years, the genome sequences of many food-related microorganisms have been
completed (e.g. S. cerevisiae, commonly known as baker's or brewer's yeast, was the
first eukaryote to have its genome sequenced - in 1996) and large numbers of microbial
genome sequencing projects are also underway. Functional genomics, a relatively new
area of research, aims to determine patterns of gene expression and interaction in the
genome, based on the knowledge of extensive or complete genomic sequence of an
organism. It can provide an understanding of how microorganisms respond to
environmental influences by expressing specific genes in different situations or
ecologies. For a range of microorganisms, it is now possible to observe the expression of
many genes simultaneously, even those with unknown biological functions, as they are
switched on and off during normal development or while an organism attempts to cope
with pathogens or changing environmental conditions.
Agriculture
Applications of biotechnology to plants or animals have improved their food processing
properties and the production of proteins from genetically modified (GM)
microorganisms to improve plant or animal production and a hormone- increasing milk
production in dairy cows using GM bacteria (Lemaux, 2000; Tietyen et al., 2000).
Scientists are not able to exchange genetic information between bacteria, plants, and
animals (including humans). These new techniques have prompted considerable debate
on the ethical and moral aspects of this branch of science.
Also, Upjohn Company of Kalamazoo, Michigan developed a squash line (called ZW 20)
that contains the coat protein genes of watermelon mosaic virus 2 (WMV2) and zucchini
yellow mosaic virus (ZYMV). The modifications have demonstrated remarkable field
resistance against the two viruses.
To control weeds, chemical herbicides have come to play a significant role in agriculture.
However, there are risks associated with the use of chemical herbicides. In addition to
causing serious environmental problems due to chemical contaminants, chemical
herbicides themselves have undesirable effects on non-target organisms. With the help
of rDNA technology, scientists are hoping to genetically modify plants tolerant to
herbicides. Herbicide tolerance can occur when the phytotoxic compound fails to be
taken up by living tissue or is rendered non-phytotoxic by conjugation, hydrolysis, or
another metabolic event (detoxification).
By using rDNA technology, the genes that code for the protein involved can be
identified, isolated and modified by directed mutagenesis and introduced into plant
cultivar to confer the herbicide-tolerant phenotype. To reduce dependency on chemical
fertilizers, agricultural biotechnologists are conducting considerable research using
genetic manipulation to increase the range of plants that can fix atmospheric nitrogen.
Microbial Biotechnology in Chemical Industries
Chemical industries are involved in the production of specialty chemicals such as amino
acids, enzymes, polysaccharides, vitamins, sweeteners, food additives, flavors,
fragrances, etc. These industries are also interested in converting biomass to produce
specialty chemicals from either plants or biological wastes, such as those generated from
agriculture and food processing. Although advanced techniques of biotechnology have
not yet played a significant role in chemical production, there are areas of chemical
industries, however, where this technology can have substantial impact, such as the
production of amino acids, enzymes and polysaccharides. Manufacturers are
particularly interested in the potential for producing existing and new chemicals at
lower cost with reduced energy requirements and waste disposal problems. Biocatalytic
chemical production has the added advantage of specificity, controllability, low
temperature operation, environmental acceptability and simplicity. For example, much
of the present organic chemical industry is based upon petroleum and most of the
chemical intermediates generated are partial oxidation products. Specific, controlled,
partial oxidation is difficult to achieve by conventional catalysis. By using
microorganisms, this type of reaction can be easily realized.
Amino Acids
Amino acids are the building blocks of proteins in animals, plants and microorganisms.
They can be produced either by isolation from natural materials – from hydrolysis of
plant proteins – or by chemical, microbial or enzymatic synthesis. Whereas chemical
synthesis produces a racemic (optically inactive) product that may require additional
resolution, microbial and enzymatic syntheses give rise to optically pure amino acids.
Commercially, amino acid producing bacteria have been used since the 1950s. With the
help of biotechnology, strains have been subsequently improved genetically by the
generation of auxotroph or regulatory mutants.
Enzymes
Industrial applications of enzymes include the production of cheese, the clarification of
apple juice, the development of more efficient laundry detergents, pulp and paper
production and the treatment of sewage. These processes have been dramatically
enhanced by the use of recombinant DNA techniques to design enzymes of increased
activity, stability and specificity. Enzymes are biological catalysts used to facilitate and
speed up metabolic reactions in living organisms. They are proteins and require a
specific substrate on which to work. Their catalyzing conditions are set within narrow
limits, e.g. optimum temperature, pH conditions and oxygen concentration. Most
enzymes are denatured at temperatures above 42°C. However, certain bacterial enzymes
are tolerant to a broader temperature range. Enzymes are essential in the metabolism of
all living organisms and are widely applied as processing aids in the food and beverage
industry (FAO, 2000, 2004; BREI, 2006).
Protein Engineering
Using modern techniques of biotechnology, scientists are attempting to improve the
yield of an enzyme by transferring the encoding gene to a microorganism capable of
producing the enzyme in larger amounts. Because they are large and fragile molecules,
enzymes tend to change their nature when exposed to heat, solvents and other extreme
conditions that characterize most industrial processes. To remedy these problems, the
current research seeks to modify the genetic information coding for an enzyme in order
to introduce new chemical properties into the molecule, such as new chemical bonds
that stabilize its structure. Enzymes, of (hyper) thermophilic, psychrophilic and/or
extremophilic origin as well as those engineered and/or evolved to exhibit function even
in a very unusual environment as currently being explored for understanding of the
structure and function relationship for proteins and also for its biotechnological
potential.
In the past, enzymes were isolated primarily from plant and animal sources, and thus a
relatively limited number of enzymes were available to the food processor at a high cost.
Today, bacteria and fungi are exploited and used for the commercial production of a
diversity of enzymes. Several strains of microorganisms have been selected or
genetically modified to increase the efficiency with which they produce enzymes. In
most cases, the modified genes are of microbial origin, although they may also come
from different kingdoms. For example, the DNA coding for chymosin, an enzyme found
in the stomach of calves, that causes milk to curdle during the production of cheese, has
been successfully cloned into yeasts (Kluyveromyces lactis), bacteria (E. coli) and molds
(Aspergillus niger var. awamori). Chymosin produced by these recombinant
microorganisms is currently commercially produced and is widely used in cheese
manufacture (FAO, 2000, 2004).
Directed evolution is one of the main methods currently used for protein engineering.
This technique involves creating large numbers of new enzyme variants by random
genetic mutation and subsequently screening them to identify the improved variants.
This process is carried out repeatedly, thus mimicking natural evolution processes
(Arnold, 1996; Tietyen et al., 2000; IFIC, 2000; Biotech, 2000; ADA, 2000; Arnold et
al., 2001).
Polysaccharide
Polysaccharide has important application in the food, cosmetics, chemical, medical and
oil industries. Polysaccharides are produced by yeast, fungi and bacteria. They are also
naturally available as cellulose, lignin and chitin. Polysaccharides are used as lubricants,
viscosifiers, flocculating and gelling agents in food processing, and for stabilizing liquid
suspensions. At present, significant research is being conducted to apply modern
techniques of biotechnology to the production of microbial polysaccharide. Using
advanced biotechnology, current research is also directed toward the conversion of
biomass feedstocks to fermentable substrates, such as cellulose to glucose. While this
generally requires relatively expensive microbial enzymes (cellulose) possessing
desirable characteristics such as thermostability and high activity, manufacturers are
also able to combine the desirable characteristics of several less optimal cellulose
enzyme producers using recombinant DNA technology. Many laboratories are involved
in detection, identification, isolation and gene transfer for strain improvement.
Vaccines
Interferons are a family of proteins that have two important biological effects –
inhibition of cellular proliferation (potentially with anti-cancer action) and modulation
of the immune system. Prior to using rDNA technology, interferon was obtained from
human white blood cells. With the help of rDNA technology, “a human leucocyte
interferon (gene 514) base pair long ago was synthesized, incorporated into a plasmid,
and subsequently cloned into E. coli.” It is interesting to note that while natural
interferon is a glycosylated protein, the interferon produced by rDNA technology is not.
DNA Probes
Using “restriction enzymes” scientists are able to cut DNA into fragments and devise
DNA probes, and thereby identify defects and mutations that can cause diseases. DNA
probes have been used in the diagnosis of the bacteria that cause periodontal (gum)
disease, and a variety of genetic diseases such as Duchenne muscular dystrophy, cystic
fibrosis and Huntington's disease.
Gene Therapy
Both natural and chemically enhanced microbial products can be used to control
human, animal and plant diseases. Using traditional genetics or recombinant DNA
techniques, the microorganism can be modified to improve the yield or action of
antibiotics and other antimicrobial agents. New research directions are aimed at
discovering microbial metabolites with pharmacological activities useful in the
treatment of hypertension, obesity, coronary heart disease, cancer and inflammation.
Vaccines are essential to protect humans and animals from microbial diseases.
Recombinant DNA technology has allowed the production of novel vaccines that offer
protection without the risk of infection (e.g. hepatitis B vaccine). Other examples
include the use of microbial cells to produce human or animal biologicals such as
insulin, growth hormone and antibodies. The industrial microbiologist/biotechnologist
may screen new microbial sources (e.g., marine microorganisms) for their ability to
produce new pharmaceuticals.
Microbial Biotechnology in the Industries
Energy
Biotechnology can play an important role in the production of fuels from organic matter
via biomass conversion. The most prominent fuel presently, petroleum, is a
nonrenewable source that poses environmental risks in its extraction and use.
Biotechnology, by using available and abundant sources of biomass, could generate a
renewable and less environmentally hazardous source of energy called bio-energy. Bio-
energy, in the form of methane gas, may also be produced by bacteria consuming sewage
sludge in anaerobic conditions. Modern techniques of biotechnology can also be used to
enhance oil recovery. It is believed that conventional oil-extracting technologies are
capable of extracting only 50% of the world's oil supply, while the remaining 50% is
trapped in rock or is too thick to pump.
Mining
The environmental and health hazards associated with traditional mining technologies
have led many mining industries in the past few years to turn to a more efficient and
environmentally risk-free method for extracting minerals from ores that use micro-
organisms to leach metals from mine dumps. Microbial mining has improved recovery
rates and reduced costs. The iron-oxidizing bacterium Thiobacillus ferooxidans has
been used for bacterium-catalyzed leaching.
In 1989, bioremediation with naturally occurring microbes was used to aid in the
cleanup of a massive oil spill in Alaska. The Exxon Valdez oil tanker spilled
approximately 11 million gallons of crude oil that contaminated over 1,000 miles of
shoreline (Princeton, 1990). To encourage the oil-degrading bacteria, nitrogen and
phosphorous were sprayed over the beaches for an extended period of time. Several
months later, Exxon and the EPA had treated 70 million miles of coastline (Princeton,
1990). In a study by the National Marine Fisheries Service, not only did they find oil
from the spill still present on some of the beaches, but also that it was enough to still be
harmful to the native wildlife (Rosen, 2003). These data disprove the presumed
successful outcome of the bioremediation efforts of the Exxon Valdez spill.
Through genetic engineering, scientists believe they can increase the effectiveness of
bioremediation. With biotechnology, bioremediation has great potential. Microbes can
be modified to be able to survive and degrade toxins and pollutants that would normally
be fatal or impossible to break down.
As encountered above, there are many bacteria that can break down different wastes.
However, much of the problem remains in the bacteria not being able to survive in the
environment where the waste is located. Aquatic bacteria may not be able to live in soil,
soil dwelling bacteria may not be able to live in the water, warmer climate bacteria may
not be able to flourish enough in cold environments to break down waste. All these are
obstacles that may be eluded by genetic engineering.
GM bioremediation is still in the experimental stage, and has not yet been approved for
use in the environment. This is for fear of the negative aspects listed above coming true.
Once more studies have been done, and we have a better understanding of how these
organisms will behave in the environment, bioremediation may prove be our best
alternative. Future possibilities are endless; problems concerning radioactive waste
disposal may be obsolete, land that has been rendered unviable could be restored, and
lakes, streams, and rivers could be completely decontaminated. There is a lot of
potential for a safer, healthier, cleaner environment through GM bioremediation.
PLANTS AS BIOREACTORS
Industrially important enzymes are not only produced by microorganisms. There are
plant proteins that are being considered for industrial applications. Higher plants,
however, are usually not regarded as prolific producers of many commercially important
proteins because many industrially important proteins synthesized in plants are also
found in other biological sources and other sources becomes choice for both technical
and economic reasons. Plant growth is seasonal in nature and hence a constant source
of material is not always possible. Higher plants also tend to accumulate waste
substances in structures called vacuoles. Upon cell disruption of these wastes, which
include a number powerful precipitating and denaturing agents, often irreversibly
inactivate many plant proteins
Examples of Plant Proteins for Industry
Monellin and thaumatin – two plant proteins recognized as the sweetest-known
naturally occurring substances
-amylases (like barley) play important role in starch processing industry
Papain – proteolytic enzyme (also known as the vegetable pepsin from papaya
used as meat tenderizer, used for batting of animal skin for the leather industry,
digestive aid, and debriding agent (for cleaning of wounds)
Ficin – commercially available protease (used in food processing industry)
Chymosin
Calf tobacco 0.5% of soluble proteins
Cyclodextrin
Bacteria potato 0.01% of soluble tuber
Glycosyltransferase
tobacco
Phytase Fungi 14.4% soluble leaf protein
tobacco
Xylanase Bacteria 4.1 % of soluble leaf protein
Table 7-2. Plants as bioreactors. Advantages and disadvantages of
plants used as bioreactors in industry.
Advantages Disadvantages
Use of antisense gene which inhibits the expression of normal gene that leads to the
accumulation of a desired intermediate rather than another product.
Sweetness for example in protein monellin, a fruit of an African plant that is 100,000
times sweeter than sucrose and therefore could be a candidate sugar substitute but
which readily loses its sweetness upon heating or when exposed to acid and there are
studies on manipulation of these genes and its expression to address the limiting
characteristics.