GENOMICS OF EMERGING

MARINE MODEL ORGANISMS AND

APPLICATIONSSubmitted by:

Kumar Kashyap

M. Tech Marine Biotechnology

NCAAH, CUSAT

Ist Semester

Marine Genomics and Proteomics

INTRODUCTION Model Organisms: A non human

species, extensively studied, discovery made in this can be applied in others.

Example: Escherichia coli are the first model organism used in molecular biology.

Cell cycle is almost similar to humans and regulated by homologous proteins.

CHARACTERISTICS OF MODEL ORGANISMS

Easily grown and easy maintainance Easy to provide necessary nutrients for

growth Short generation time

(birth→reproduction→death) Well understood growth and

development Closely resemble to other organisms

MARINE MODEL ORGANISMS Model organisms of marine origin are

called marine model organisms. A few examples include Ectocarpus, a filamentous brown algae, Chondus crispus also known as Irish moss (a red sea weed) etc.

Any non-human species, which is used to understand biological processes, is called a model organism. A marine model organism is model organism of marine origin.

Ostreococcus tauri: Eukaryotic picophytoplanktonSmallest free living eukaryoteUsed to study conserved biological

functions such as the circadian clock and the response to environmental stress

Chondrus crispus:o Irish mosso red sea weedo rocky shores and other hard substratao Northern North Atlantic.

Ectocarpus:filamentous brown algaefound in temperate coastal regions

worldwideused to study a broad range of aspects of

brown algal biologylife cycle regulation, sex determination,

morphogenesisecology and population geneticsresistance to abiotic and biotic stress and

cell wall metabolism

GENOMICS OF EMERGING MARINE MODEL ORGANISMS Ectocarpus, a brown algae with a

complex photosynthetic mechanism An evolutionary tree showing the five major groups

that have evolved into complex multicellularity

From the diagram we can see that though the group brown algae has evolved into complex multicellularity, but its evolution pathway is different from that of the rest of the four groups.

Dominant in rocky coastal systems and have adaptations for that harsh environment.

Developed an extended set of light harvesting and pigment biosynthesis genes

New metabolic pathways such as halide metabolism

To withstand the highly variable tidal environment

The Ectocarpus genome sequence represents an important step towards developing this organism as a model organism.

Genome size – 214 million base pairs 16,256 protein coding genes They are rich in introns (seven per gene

on an average) Also have long 3’ UTR’s upto 845 base

pairs long These genes are often very close to

each others on chromosome

Repeated sequences, including DNA transposons, retrotransposons and helitrons, make upto 22.7%

Also small RNAs are mapped preferentially on these transposons, indicating that they have certain role in silencing these transposons elements

Sequencing also revealed the presence of an integrated copy of large DNA virusFound to be closely related to Ectocarpus Phaeovirus EsV-1 In nature, about 50% of the individuals show symptoms of viral infection One of the strains, strain EC 32, was never observed to produce any virus particles Also expression analysis showed that almost all of the viral genes were silent in this strain

(a). It shows a circular DNA from the Ectocarpus Phaeovirus EsV-1 and its linear form present in the genome of Ectocarpus.

(b). This figure shows the absence of protein expression from the viral DNA sequence that has been incorporated in the Ectocarpus genome. The red line shows no protein expression.

Habitat is shallow water of inter tidal region This area is a hostile environment Cope up with tidal changes in light intensity,

temperature, salinity and wave action, etc It has evolved effective mechanism for survival

in its harsh environment For e.g., a large family of Light Harvesting

Complex (LHC) genes is present in Ectocarpus (present at 53 loci, although some are probably pseudogenes)

Also there are a cluster of 11 genes, with highest similarity to the LI818 family of light stress realted LHCs

Encode for a light independent protochlorophyllide reductase (DPOR), allowing efficient synthesis of chlorophyll under dim light Together the above data clearly indicates that Ectocarpus has a very complex photosynthetic system that enables it to adapt to an environment with highly variable light conditions High level of phenolic compounds present in the brown algae may be responsible for its protection from ultraviolet light The diverse complement of enzymes involved in the metabolism of reactive oxygen species is also likely to represent an important adaptation to osmotic and light stresses.

Codes for 21 putative dehalogenases and two haloalkane dehalogenases

Protect the organism from the halogenated compounds produced by kelps

Cell wall contains some unusual polysaccharides namely – alginates and fucans, which provide resistance from mechanical stress and protection from predators

APPLICATION OF MARINE MODEL ORGANISMS Ecotoxicology detection. Tigriopus

species. Respond to natural or artificial stress. Short life cycle and is easily cultured under laboratory conditions.

Oryzias melastigma, toxicological studies. Effects of chemical pollutants in the marine environment.

Euplotes crassus, used to detect copper and oxytetracycline temperature related toxicity.

REFERENCE http://www.nih.gov/science/models/ http://genome.wellcome.ac.uk/doc_WTD020803.html foothilltech.org/dperez/.../model%20organisms%202b/Lecture.ppt http://mmo.embrc-france.fr/ Raisuddin, S. et al. “The copepod Tigriopus: A promising marine model

organism for ecotoxicology and environmental genomics”. Aquatic toxicology, vol – 83 (2007), pages 161-173.

Chen, X., et al. “Molecular staging of marine medaka: A model organism for marine ecotoxicity study”. Marine pollution bulletin, volume – 63 (2011), issue 5 – 12, pages 309-317.

Goemiro, A., et al. “Effects of elevated temperature on the toxicity of copper and oxytetracycline in the marine model Euplotus crassus: A climate change perspective”. Environmental pollution, volume 194 (2014), pages 262-271.

Matranga, V., et al. “Toxic effects of engineered nanoparticals in the marine environment: model organisms and molecular approaches.” Marine environmental research, May 2012, pages 32-40.

Philipp, E., et al. “Marine bivalves as model organisms for ageing research”.

thomaspradeu.com/wp-content/.../10/Chenevert-_Model-organisms.pdf Cock, J. M., et al. “The Ectocarpus genome and the independent

evolution of multicellularity in brown algae” (2010). Nature, Volume 465, pages 617 – 621