Biology Reference
In-Depth Information
The discovery that greatly infl uenced the fi eld of microbiology is the cultivation-independent
approach for the study of microbial diversity with the help of identifi able environmental DNA
sequences. In other words, it is the application of genomic sciences to understand the structure
and function of ecosystems. This subject is known as 'metagenomics' and studies in this direction
have yielded 1.2 million new genes. With this, a change in focus has taken place from an organism-
based study to the environment-based approach (Bertin et al ., 2008; Frias-Lopez et al ., 2008; Ward et
al ., 2008; Biers et al ., 2009). A correlation of genomic features found at a distinct sampling site with
physical, chemical and biotic information led to the identifi cation of organism-specifi c adaptations.
Of all the ecosystems, understanding the structure and function of marine ecosystems attracted the
attention of scientists. The importance given to this fi eld can be gauged by the number of projects
that focus their attention on microorganisms of medical and biotechnological interest. Nearly 130
marine isolates are being sequenced (Moore Foundation; http://www.moore.org). The sequencing
of whole genome of H . infl uenzae was followed by the sequencing of two other bacterial genomes, i.e.
Mycoplasma genitalium and Methanococcus jannaschii sequenced by TIGR (The Institute for Genomic
Research, Rockville, Maryland, USA which is now a part of J. Craig Venter Institute, JCVI). Kaneko
et al . (1996) for the fi rst time sequenced the genome of Synechocystis sp. strain PCC 6803 at Kazusa
DNA Research Institute, Japan. This constitutes the fi rst fully sequenced genome of a cyanobacterium
as well as an autotroph. This was followed by the completion of genome sequence of Escherichia coli
K-12 (Blattner et al ., 1997). Due to the availability of complete genome sequence of Synechocystis sp.
strain PCC 6803 along with complete set of genes provided a platform to the cyanobacteriologists
for furthering research in this direction. A collective effort by Satoshi Tabata (Kazusa), Nori Murata
(Okazaki) and Minoru Kanehisa (Kyoto) resulted into a cyanobacterial DNA chip consortium for the
analysis of gene expression profi les by using Synechocystis DNA microarrays. The consortium with 25
members facilitated collaborative research between molecular biologists and bioinformaticians. The
genome entries made by the sequencing teams at the primary repositories like GenBank (produced at
NCBI; http://www.ncbi.nlm.nih.gov.Genbank/), European Molecular Biology Laboratory (EMBL;
http://www.embl.de/) and DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp/) have
to be updated by the sequencing teams themselves. Due to lack of proper maintenance at these
sites and as the databases such as Swiss-Prot (http://www.ebi.ac.uk.swissprot/; initially founded
at Swiss Institute of Bioinformatics but later European Bioinformatics Institute and Georgetown
University became collaborating partners with UniProt/Swiss-Prot manually annotated and
UniProtKB/TrEMBL automatically annotated protein databases) and KEGG (Kyoto Encyclopedia
of Genes and Genomes, Japan; http://www.genome.jp/kegg/) are unable to keep pace with the
rapidly increasing data on annotated sequences, the bioinformatics centre of Kyoto University (the
home of KEGG) developed a community database system known as CYORF. The collaboration of
scientists at Kazusa, biologists at the DNA chip consortium and Bioinformaticians at Kyoto University
resulted in CYORF database release 1.0. Nakamura et al . (2000) created an online genome database
for Synechocystis sp. strain PCC 6803 termed as CyanoBase that provides annotations for each of the
3168 protein-coding genes deduced from the entire nucleotide sequence of the genome. It can be
accessed at http://www.kazusa.or.jp:8080/cyano. They have also developed another site known
as CyanoMutants as a repository database for the storage and distribution of information about
Synechocystis sp. strain PCC 6803 and its mutants.
Complete genome sequences give us the opportunity to seek answers to unresolved questions
provided powerful comparative methods of analysis are employed. The E . coli K-12 genome is
4,639,221 bp long and possesses 4,288 predicted genes. The genome of Synechocystis sp. strain PCC
6803 constitutes the second largest set after E . coli with 3,168 proteins encoded. Many cyanobacterial
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