Environmental Engineering Reference
In-Depth Information
Typically, this involves extraction of total genomic DNA from an organism, use of restriction
enzymes to cut the DNA into manageable fragments, and ligation of the fragments into DNA
vectors known as plasmids or cosmids. The collection of fragments is known as a “library,”
and screening of the library by molecular or genetic methods ultimately leads to identification
of the vector bearing the desired gene. Further manipulation, including gene isolation through
subcloning of the genomic fragment, is then possible [1].
Gene cloning is a well-established technology that has nevertheless become far more
efficient with advances in enzyme and DNA purification technologies. The cloning of
industrially-important genes is essential to convenient gene expression because, while
desirable genes may be found in numerous organisms, only a few organisms are sufficiently
durable and productive for industrial bioprocesses. Because genes are expressed through the
action of numerous enzymes that are conserved to some extent among organisms, it is often
possible to express a cloned gene from one organism in another; moreover, it is also often
possible to control the extent of expression very closely, as described below.
2.2 Genomics
The field of genomics-the study of the sequence, structure, and function of an organism's
complete set of genetic information (its genome) [2]-is expanding rapidly due to the
invention of numerous high-efficiency and high-throughput technologies capable of handling
large amounts of DNA as well as sequence data. A key player in this field, and especially
important from the perspective of environmental biotechnology, is the Joint Genome Institute
(JGI) (www.jgi.doe.gov). The JGI was established in 1997 to unite the expertise and
resources in genome mapping, DNA sequencing, and information sciences among the DOE
genome centers at the Lawrence Berkeley National Laboratory, the Lawrence Livermore
National Laboratory, and the Los Alamos National Laboratory. Its mission is to advance
high-throughput, genomescale, computational technologies that facilitate understanding of
relationships among genome structure and function, and it now has the capacity to generate
DNA sequences of two billion nucleotide bases per month. The JGI contributed complete
sequences of Chromosomes 5, 16, and 19 to the Human Genome Project but now, in contrast
to National Institutes of Health (NIH)- funded genome sequencers that continue to
concentrate on human targets and applications, the project has turned its efforts toward the
broader biosphere. Importantly, a primary goal of the JGI is to make high-quality genome
sequence data freely available to the scientific community through its Web site
(http://www.jgi.doe.gov/sequencing/seqplans.html). The sequences of numerous bacteria,
fungi, trees, green algae, protists, crop plants, fish, and amphibians, either presently available
or are planned to be available, will continue to be a tremendous resource for the development
of bioplastics and biofuels as well as other areas of environmental biotechnology.
Another highly important component of the current genomics landscape is GenBank®,
the annotated NIH genetic collection that holds all publicly available DNA sequences in a
searchable database [3]. This set includes virtually all sequences published, because many
journals require submission of sequence information to a database prior to publication and
because GenBank exchanges data daily with other members of the International Nucleotide
Sequence Database Collaboration (the DNA DataBank of Japan and the European Molecular
Biology Laboratory). GenBank is accessible through the National Center for Biotechnology
Information (NCBI) search engine, which integrates data from the DNA and protein sequence
