REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
By Shruti Gupta
Entirety of an organism's hereditary information
Includes both the genes and the non-coding sequences of the
The genome is vast in terms of its informational content. Composed
of chemical symbols designated by a four-letter alphabet of A's, T's,
C's, and G's, the human genome is some 3.2 billion letters in length
Availability of genome sequences provides opportunity to explore
genetic variability both between organisms and within the individual
organized living things
into large groups called
There are six of them:
Some recent findings…
In 1996, scientists decided to split Monera into two groups of bacteria:
Archaebacteria and Eubacteria
Because these two groups of bacteria were different in many ways
scientists created a new level of classification called a DOMAIN.
Now we have 3 domains
Some of the first archaebacteria were
discovered in Yellowstone National
Park’s hot springs and geysers.
Numerous in the oceans, and the
archaea in plankton may be one of the
most abundant groups of organisms
on the planet.
Recognized as a major part of Earth's life
and may play roles in both the carbon cycle and the nitrogen cycle.
They live in extreme environments (like hot springs or salty
lakes) and normal environments (like soil and ocean water).
All are unicellular (each individual is only one cell).
No peptidoglycan in their cell wall.
Some have a flagella that aids in their locomotion.
Why to study ARCHAEA?
As one of the most ancient lineages of living organisms, the archaea
set a boundary for evolutionary diversity and have the potential to
offer key insights into the early evolution of life, including the origin
of the eukaryotes.
Many archaea are also extremophiles that flourish at high
temperature, low or high pH, or high salt and delineate another
boundary for life, the biochemical and geochemical boundary, which
sets the physical limits of the biosphere.
Finally, some archaea are fundamental components of the
biogeochemical cycles on earth or dominate special ecosystems that
are of great interest (such as the methanogens).
Archaea with sequenced genome or ongoing
Genome analysis of some cultivated archaea
published in NCBI
a. Methanobrevibacter smithii
(Human gut methanogen)
b. Sulfolobus islandicus
A genomic analysis of the archaeal
system Ignicoccus hospitalisNanoarchaeum equitans
The crenarchaeaote Ignicoccus hospitalis is a specific
host for Nanoarchaeum equitans.
Both the organisms represent hyperthermophilic
lineages and inhabit types of ecosystems that are often
considered to be ancient.
The genome of I. hospitalis consists of a single circular
Genome sequencing and functional annotation
proteinase K digestion method
Sequencing & assembly
Automated gene prediction
tRNA genes were fined
rRNA genes were fined
Comparative genomic analysis
Analysis of the I. hospitalis and N. equitans genomes
operons were identified
Structure fold prediction
frequency of paralogs
protein sequence was blasted
sequences with significant hits were retrieved
and aligned with the query sequence
Phylogenetic trees were then constructed
Pioneering groundwork in the archaeal research field has been the isolation
and cultivation of hyperthermophilic organisms and other extremophiles.
This has not only led to the discovery of novel metabolisms and special
adaptations of archaea, but also to a more fundamental understanding of the
features that unify the organisms of this third domain of life.
It will be as exciting and important to isolate species of those archaeal
groups that have so far solely been studied by molecular techniques. In
particular, some of the organisms that are commonly found in moderate,
aerobic environments should eventually be brought into culture, perhaps
assisted by predictions made in metagenomic studies.
Although the study of model organisms remains crucial, it has become
clear over the past years of archaeal research that cultivation independent
techniques, including population genomics, will be indispensable if we want
to fully understand the diversity and ecological impact of archaea.