Update of microbial genome programs for bacteria and archaea 421
Genetics and Molecular Research 3 (3): 421-431 (2004) www.funpecrp.com.br
Update of microbial genome programs for
bacteria and archaea
Patricia Borges Santos Celestino1,3, Lydston Rodrigues de Carvalho2,
Leandro Martins de Freitas3, Fernanda Alves Dorella3,
Natalia Florêncio Martins4, Luiz Gustavo Carvalho Pacheco3,
Anderson Miyoshi3 and Vasco Azevedo3
1Department of Botany and Microbiology and Department of Zoology,
Ohio Wesleyan University, Delaware, OH, USA
2Departamento de Bacteriologia, Instituto Oswaldo Cruz,
Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
3Departamento de Biologia Geral, Instituto de Ciências Biológicas,
Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
4Laboratório de Bioinformática,
Embrapa Recursos Genéticos e Biotecnologia, Brasilia, DF, Brasil
Corresponding author: V. Azevedo
E-mail: vasco@mono.icb.ufmg.br
Genet. Mol. Res. 3 (3): 421-431 (2004)
Received August 2, 2004
Accepted August 31, 2004
Published September 30, 2004
ABSTRACT. Since the Haemophilus influenzae genome sequence
was completed in 1995, 172 other prokaryotic genomes have been com-
pletely sequenced, while 508 projects are underway. Besides pathogens,
organisms important in several other fields, such as biotechnology and
bioremediation, have also been sequenced. Institutions choose the or-
ganisms they wish to sequence according to the importance that these
species represent to them, the availability of the microbes, and based on
the similarity of a species of interest with others that have been se-
quenced previously. Improvements in sequencing techniques and in as-
sociated methodologies have been achieved; however, scientists need to
continue working on the development of this field. In Brazil, a multicentered,
centrally coordinated and research-focused network was adopted and
successfully used for the sequencing of several important organisms.
We analyzed the current status of microbial genomes, the trends for
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P.B.S. Celestino et al. 422
Genetics and Molecular Research 3 (3): 421-431 (2004) www.funpecrp.com.br
criteria used to choose new sequencing projects, the future of microbial
sequencing, and the Brazilian genome network.
Key words: Microbial genome project, Biotechnology, Bioinformatics,
Genomics, Prokaryotes, Brazil
INTRODUCTION
Prokaryotic microorganisms comprise the largest part of the planet’s total biomass.
This group contains a vast array of species, with enormous genetic, metabolic, physiological and
behavioral diversity; however, less than 1% of them have been cultured. Despite their ubiquity,
little is known about their fundamental properties, about their range of diversity, about how they
interact with the environment, about their evolution, and about the roles they play in global
biogeochemical cycles (Rodrìguez-Valera, 2004). It is believed that progress towards filling
these knowledge gaps will advance significantly when more whole genome sequences become
available.
The bacteria have long been the subject of scientific study due to their ability to cause
disease in humans (Lederberg, 2000). One of the major advances in the health and well-being of
human civilizations was the development of antibiotics. Although the introduction of antibiotics
has had an enormous impact on the ability to treat bacterial infections, bacteria continue to be
the leading cause of death worldwide. Moreover, the effectiveness of antibiotics has been eroded
by the appearance of pathogenic strains that are resistant to nearly all classes of antibiotics,
coupled with the fact that only one new class of antibiotics has been introduced by the pharma-
ceutical industry since the mid-1970s (Binder et al., 1999).
Clearly, the discovery of new therapies against diseases caused by bacterial pathogens
is a critical necessity of the 21st century. Over the past decade, the field of genomics has
revolutionized both basic research, and particularly the pharmaceutical industry. The field of
genetics was also fundamentally affected by bacterial genetic research. Starting in 1928, stud-
ies on transformation of pneumococcus by Griffith established a new critical concept in genet-
ics: that DNA was the genetic material of life. Over the next few decades, other genetic break-
throughs, including determination of the mechanisms of replication, transcription and trans-
lation of the genetic code, and of the structure and expression of genes, were made avail-
able through microbiological research using bacteriophages and the workhorse bacterium
E. coli. In addition, a number of molecular tools were discovered in bacteria, such as DNA
ligases and restriction enzymes. However, it was not until the landmark work of Cohen (1993)
that these enzymes were used together along with plasmid replicons to enable the cloning of
DNA fragments (Lederberg, 2000). This led to the birth of the field of molecular biology, which
had a profound effect on drug discovery and development. Instead of using brute force
protein purification to isolate targets for small molecular compounds or therapeutic pro-
teins, cloning and expression technologies allowed these entities to be supplied in bulk. The age
of molecular biology transformed the pharmaceutical industry, and the newly spawned biotech-
nology industry, on an unprecedented scale, perhaps only matched by the recent breakthroughs
in genomics.
The current availability of bacterial genome information, originated from molecular biol-