In silico analyses of genomes and proteomes of extremophiles in quest of novel survival strategies
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
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| Title |
In silico analyses of genomes and
proteomes of extremophiles in quest
of novel survival strategies
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| Creator |
Paul, Sandip
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| Subject |
Structural Biology & Bioinformatics
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| Description |
Life! It exists everywhere on our planet - from the poles to the equator, from
submarine hydrothermal vents to frozen glaciers at the mountain tops, from dry
valleys to wet marshlands, from acid springs to alkaline pools. Over the last 3.7
billion years or so, living organisms have adapted themselves to almost every
environment imaginable – thanks to the process of evolution. The ability to adapt to
varying environments, even the extreme or adverse ones, is a hallmark of life – it’s
only because of this ability that the spectacular diversity gracing the present-day
living world could have arisen!
It is worth mentioning at this point that the word adaption has different meanings in
everyday language and in evolutionary biology. In common language, adapting often
means changing an individual’s behavior or characteristics to suit the circumstances.
But in evolutionary biology, the term adaption has a precise and different meaning. In
evolution, to adapt means to experience natural selection that improves the function
of a trait in a specific environment and/or life-style. The process of evolutionary
adaptation is the one experienced by whole populations over many generations, not
the changes occurring in an individual organism over the course of its lifetime - a
process often referred to as the phenotypic plasticity. While the phenotypic plasticity
in individuals are not, in general, associated with any heritable changes at its gene or
protein level, the process of adaptive evolution often imprint its signatures at the
genome and/or proteome levels of the organisms. And, the primary objective of the
present dissertation was to identify such imprints or macromolecular basis of adaptive
evolution of microorganisms thriving at certain extreme/specialized environments,
namely high temperature, high salinity or varying light intensities. Emphasis has also
been given to a case of obligatory parasitism/symbiosis in the archaeal domain.
Through the current study, an attempt has, therefore, been made to shed light on the
process of microbial evolution occurring at widely varying scales and directions. The
studies on halophiles and hyperthermophiles presented respectively in chapters 3 and
4 have demonstrated the process of convergent macro-evolution taken place on a scale
that transcends the boundaries of a single species, a single phylum, or even a single
domain. In both cases, extensive comparative analyses of various macromolecular
traits of extremophiles and non-extremophiles from archaeal as well as bacterial
domain have been carried out in order to remove any phylogenetic influence. Also
Concluding Remarks
~ 145 ~
comparison have made among organisms with similar genomic G+C-content to
minimize the variations arising from mutational bias of the species under study. The
chapter 5 focuses on the reverse situation, i.e., the process of divergent microevolution
that resulted in remarkable genotypic and phenotypic diversities in different
strains/ecotypes of the same species, namely the cyanobacterium Prochlorococcus
marinus – each specialized to dwell in different conditions of light, temperature and
nutrient abundances. Interestingly enough, mutation, selection & genetic drift, the
principal driving forces of evolution, have manifested themselves at both macro &
micro levels through an assortment of different mechanisms- into an array of diverse
niche-specific trends.
It is worth mentioning at this point that mutation is a random process, but selection is
not. Novel genetic traits emerge within a population because of random and
spontaneous mutations - but selection acts on those traits in highly non-random way.
Two entirely different populations of halophilic microbes of widely varying taxonomy
and geographical locations at different points of time independently might select for
higher usage of Asp or lower usage of Cys, probably because such selections would
help them enhancing the protein flexibility in high salt concentration, while their
hyperthermophilic relatives would prefer to have higher usage of Lys and Tyr, as
these would help them to stabilize their proteins at higher temperatures by enhancing
the cation-pi interactions. Thus, two taxonomically, spatially and temporally distant
populations may gradually acquire similar genomic and/or proteomic traits, if they
intend to thrive at similar ecological niches, while two populations of same species,
when acclimatize to differential environmental conditions like distinct light optima,
may exhibit adaptive radiations through selection of conspicuous traits - starting at the
genomic level. Therefore, various types of extremophiles may evolve under the
influence of mutation, selection & genetic drift - it is only through appropriate
variations in selection criteria that novel molecular strategies emerge, facilitating their
survival in diverse ecological niches. And, here lies the unity amongst the diversity of
the living world.
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| Date |
2009
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| Type |
Thesis
NonPeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/389/1/Thesis_Sandip_Paul.pdf
Paul, Sandip (2009) In silico analyses of genomes and proteomes of extremophiles in quest of novel survival strategies. PhD thesis, Jadavpur University. |
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| Relation |
http://www.eprints.iicb.res.in/389/
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