Mother of GreenMother of Green

Phylogenomics of the Phylogenomics of the P. falciparumP. falciparum ApicoplastApicoplast

Indiana Center for Insect GenomicsIndiana Center for Insect GenomicsAn International Center of ExcellenceAn International Center of Excellence

University of Notre DameUniversity of Notre DamePurdue UniversityPurdue UniversityIndiana UniversityIndiana University

Mother of GreenMother of Green

• Malaria causes Malaria causes 1.5 - 2.7 million deaths every year1.5 - 2.7 million deaths every year

• 3,000 children under age five die of malaria every 3,000 children under age five die of malaria every

dayday

•Plasmodium falciparum Plasmodium falciparum causes human malariacauses human malaria

• Drug resistance a world-wide problemDrug resistance a world-wide problem

• Targeted drug design through phylogenomicsTargeted drug design through phylogenomics

• Malaria causes Malaria causes 1.5 - 2.7 million deaths every year1.5 - 2.7 million deaths every year

• 3,000 children under age five die of malaria every 3,000 children under age five die of malaria every

dayday

•Plasmodium falciparum Plasmodium falciparum causes human malariacauses human malaria

• Drug resistance a world-wide problemDrug resistance a world-wide problem

• Targeted drug design through phylogenomicsTargeted drug design through phylogenomics

P. falciparumP. falciparum

Mother of GreenMother of Green

• P. falciparumP. falciparum has three genomes has three genomesNuclear, mitochondrial, plastidNuclear, mitochondrial, plastid

• Animals and insects have only twoAnimals and insects have only two• Target the third genomeTarget the third genome• No harm to animalsNo harm to animals• New antimalarial drugNew antimalarial drug• High risk, high tech, high payoffHigh risk, high tech, high payoff

J. Romero-SeversonJ. Romero-SeversonDepartment of Biological SciencesDepartment of Biological SciencesGreg MadeyGreg MadeyDepartment of Computer ScienceDepartment of Computer Science

J. Romero-SeversonJ. Romero-SeversonDepartment of Biological SciencesDepartment of Biological SciencesGreg MadeyGreg MadeyDepartment of Computer ScienceDepartment of Computer Science

Mother of GreenMother of Green

•Plastids are the third genome•Intracellular organelles •Terrestrial plants, algae, apicomplexans•Functions in plants and algae

PhotosynthesisOxidation of water Reduction of NADPSynthesis of ATPFatty acid biosynthesisAromatic amino acid biosynthesis

•Functions in apicomplexans ?

•Plastids are the third genome•Intracellular organelles •Terrestrial plants, algae, apicomplexans•Functions in plants and algae

PhotosynthesisOxidation of water Reduction of NADPSynthesis of ATPFatty acid biosynthesisAromatic amino acid biosynthesis

•Functions in apicomplexans ?

Chloroplast in plant cell

Plastid in Toxoplasma sp.

Apicoplast in P. falciparum

plastid

Mother of GreenMother of Green

•The apicoplast appears to code for <30

proteins.

• Repair, replication and transcription

proteins

•Why is the apicoplast essential?

• Find the ancestors of the apicoplast• Identify genes in the ancestors• Determine gene function • Look for these genes in the P. falciparum nucleus• Then study regulatory mechanisms in candidate genes

Mother of GreenPhylogenomicsMother of GreenPhylogenomics

Phylogenomics of plastids

• Very old lineage (> 2.5 billion years)• Cyanobacterial ancestor• Three main plastid lineages

GlaucophytesGroup of freshwater algaeChloroplast resembles intact cyanobacteria

ChlorophytesGreen plant lineageChloroplast genome reducedMany chloroplast genes now in nuclear genome

RhodophytesRed algal lineage

Chloroplast genome bigger than in green plantsOomycetesApicomplexans

Phylogenomics of plastids

• One cyanobacterial ancestor ?• Many?• Lineages are not linear

One plastid origin

Multiple plastid origins

The process of endosymbiosis.

Horizontal Gene Transfer (arrows) from the plastid to the nucleus.

The nucleomorph is a remnant of the original endosymbiont nucleus.

Primitive eukaryote

Endosymbiont plastid

Secondary endosymbionts

Second eukaryote

Secondary nonphotosynthetic endosymbiont

Cyanobacteria

Nucleus

Nucleus

Nucleomorph

Plastid disappears

Secondary endosymbiont

Tertiary endosymbionts

Third eukaryote

Tertiary nonphotosynthetic endosymbiont

Plastid disappears

Tertiary endosymbiosis. Horizontal Gene Transfer

P. falciparum

The information gathering problem

• Rapid accumulation of raw sequence information~100 sequenced chloroplast genomes~55 sequenced cyanobacterial genomesRate of accumulation is increasingInformation accumulates faster than analyses finishInformation in forms not readily accessible

• SolutionSemi-automated web-services “Smart” web-services

The computational problem

•Phylogenetic trees NP-hardPoisoned by information conflict

•Phylogenies based on individual genesMaximum likelihood models exist Processes are parallelizableAccess to compute farms inadequateRAW number-crunching powerGreedy

• Similar genealogies may be mergedConvergence not possible for allMakes computational problem more daunting

The synthesis of ATP

Candidate genes for deep phylogeny

Light-dependent ATP synthesis (photophosphorylation)

Hypothesis:Evolution of ATP synthase severely constrained

Candidate for ascertainment of deep phylogeny

1st: Individual subunit genealogy

2nd: Merge the data, reanalyze

ATP synthaseThe wheel that powers life

Phylogenomics of the P. falciparum Apicoplast

• Extract data from public and private databasesWeb services

• Choose a metric for sequence comparisonMegablast and others

• Choose a method to infer genealogy Maximum Likelihood (ML)

• Develop a strategy to use ML that is feasiblefastDNAml and others

• Create a computational infrastructureCompute farmsDedicated chunks of compute farms

• Deal with management issues• Solve band width problems• Convince someone to fund this!

Indiana Center for Insect GenomicsIndiana Center for Insect Genomics

MissionMissionCreate genomics tools for high impact arthropods lacking such toolsCreate genomics tools for high impact arthropods lacking such tools

Develop integrated bioinformatics programs for arthropod genomicsDevelop integrated bioinformatics programs for arthropod genomics

Develop specific projects with potential practical applicationDevelop specific projects with potential practical application

Foster high risk ideas with mini-grantsFoster high risk ideas with mini-grants

Jeanne Romero-Severson, DirectorFrank Collins, Co-PI at University of Notre DamePeter Cherbas, Co-PI at Indiana UniversityJeff Stuart, Co-PI at Purdue University

Jeanne Romero-Severson, DirectorFrank Collins, Co-PI at University of Notre DamePeter Cherbas, Co-PI at Indiana UniversityJeff Stuart, Co-PI at Purdue University