REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA

By Shruti Gupta

GENOME

Entirety of an organism's hereditary information

Includes both the genes and the non-coding sequences of the

DNA/RNA

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

organism

Background

Biologists have organized living things into large groups called kingdoms.

There are six of them:

Archaebacteria

Eubacteria

Protista

Fungi

Plantae

Animalia

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

1. Bacteria

2. Archaea

3. Eukarya

The domain

ARCHAEA

“Ancient” bacteria

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.

Basic Facts 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.

3 Main Types

Methanogens

Euryarchaeota

Crenarchaeota

Nanoarchaeota

Korarchaeota

Thaumoarchaeota.

Thermoacidophiles

Halophiles

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 projects

Published studies involving genomic analyses

Genome analysis of some cultivated archaea

published in NCBI

a. Methanobrevibacter smithii

(Human gut methanogen)

b. Sulfolobus islandicus

(Hyperthermophilic acidophilic

sulfur-metabolizing archeon)

A genomic analysis of the archaeal

system Ignicoccus hospitalis-

Nanoarchaeum 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 chromosome

General features of I. hospitalis genome

Materials & Method

Genome sequencing and functional annotation

DNA isolation

proteinase K digestion method

Sequencing & assembly

Automated gene prediction

Sequence translation

tRNAScanSE tool

tRNA genes were fined

BLASTn

rRNA genes were fined

Comparative genomic analysis

Analysis of the I. hospitalis and N. equitans genomes

IMG system

operons were identified

Phyre tool

Structure fold prediction

blastclust analyses

frequency of paralogs

Phylogenetic analysis

protein sequence was blasted

sequences with significant hits were retrieved

CLUSTALW

and aligned with the query sequence

PAUP tool

Phylogenetic trees were then constructed

Conclusion….. 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.