Mubeen Ghazanfar14071714-003M.Phil zoology3rd semester2014-2016

Topic:

mt DNA

Contents

• Origin of mt• role of mt DNA• Pseudogenes• Structure and composition of mt DNA• Genome rearrangements

Mitochondria

Matrix

Inter membrane space

Inner membraneOuter membrane

mtDNA

Origin of EukaryotesEndosymbiosis to explain the origin of mitochondria and chloroplasts

1.5 billion years ago.

How Mitochondria Resemble Bacteria• Mitochondria resemble bacteria in size and morphology.• They are bounded by a double membrane: the outer

thought to be derived from the engulfing vesicle and the inner from bacterial plasma membrane.

• Some enzymes and inner membrane transport systems resemble prokaryotic plasma membrane systems.

• Mitochondrial division resembles bacterial binary fission• They contain a small circular loop of genetic material

(DNA). Bacterial DNA is also a circular loop.• They produce a small number of proteins using their own

ribosomes which look like bacterial ribosomes.• Their ribosomeal RNA resembles eubacterial rRNA.

How Mitochondria Don’tResemble Bacteria

Mitochondria are not always the size or morphology of bacteria:

• In some Trypanosomes (i.e., Trypanosoma brucei) • Variation in morphology is common in protistansCircular mtDNA replication via D loops is different from

replication of bacterial DNA

How Mitochondria Don’tResemble Bacteria

• mtDNA is much smaller than bacterial chromosomes.• Mitochondrial DNA may be linear, examples include:

Plasmodium, Ochromonas, Tetrahymena, • Mitochondrial genes may have introns which eubacterial

genes typically lack (these introns are different from nuclear introns so they cannot have come from that source)

• The genetic code in many mitochondria is slightly different from bacteria (Gray et al., 2012).

mitochondrial genome arose only once in evolutionFollowing observations support this contention:1) In any particular genome, genes that have an assigned

function are a subset of those found in R. americana mt DNA

2) Mt protein coding clusters retain the gene order of their bacterial homologs, but these clusters retain the gene order of their bacterial homologs,but these clusters exihibit mitochondrian specific deletions that are parsimoniously explained as having occurred in a common ancestor of mitochondrial genomes, subsequent to its divergance from the bacterial ancestor

3) Mitochondria form a monophyletic assemblage to the exclusion of bacterial species in phylogenetic reconstructions using protein sequences as well in small rRNA trees.

Why we select mt DNA not nucleous

Nuclear mtDNA•3.2 Billion bps•2 copies per cell

•Linear

• Inherited from father and mother•Diploid genome

•Recombination

•Unique

•17,000 bps

•Hundred’s copies

•Circular

•Inherited from mother only

•Haploid genome

•No recombination

•Shared by everyone within maternal lineage

Gen BankGenBank® (http://www.ncbi.nlm.nih.gov) • publicly available nucleotide sequences for almost 260

000 formally described species• GenBank is accessible through the NCBI Entrez retrieval

system,DNA and protein sequence databases along with

taxonomy,• genome, • mapping,• protein structure and domain information,

First sequence of mt DNA

• the first wave of mtDNA sequence information• were data on aspects of mitochondrial

chromosomes,• including their conformations • replication strategies • inheritance patterns • transcriptional • translational • mutational and population genetic landscapes

mtDNA• Mitochondrial DNA is generally small in animal cells,

about 16.5 kb• Plant mtDNA is highly variable in size and content with

the large Arabidopsis mtDNA being 200 kb.• The largest known number of mtDNA protein genes is 97

bp in the protozoan R. americana mtDNA of 69,034 bp.

Mitochondria• Mitochondria are organelles found in most

eukaryotic organisms.• The site of Krebs cycle and electron transport energy

producing processes during aerobic respiration• Are inherited only from the mother during sexual

reproduction in mammals and probably all other vertebrates.

• Because of their mode of inheritance genetic material found in mitochondria appears to be useful in determining the maternal lineage of organisms.

(mt) genomes have become a major data sources for comparative genomics

play an important role in: • metabolism• apoptosis• disease• aging• mutations of the mtDNA have been implicated with a wide

range of age-related pathologies, including cancers, neurodegenerative diseases and, in general, processes that regulate cellular and organismal aging.

• insect mt genome as used molecular marker:• for population genetics,• phylogeography,• molecular diagnostics • phylogenetic studies (DNA barcoding)• Forensic entomology

forensic investigations • Example—In Brindisi County (southern Italy) a police

informant identified a cellar in an isolated farmhouse where a murder had occurred and the body had been left.

• It was later learned that the criminal organization responsible for the murder learned of this “betrayal” and removed the body in an effort to discredit the informant.

• Police investigators recovered only a large number of Chrysomya albiceps larvae, and no other biological evidence, from the cellar.

forensic investigations

• Situation 2: Maggots are Not Found Directly on a Corpse, and an Alternative Food Source is Nearby

• Situation 3: Maggots are Found on a Corpse, but May Have Come from Somewhere Else

mitochondrial pseudogenes

• The first record of a mitochondrial pseudogene in Metazoa was for Locusta migratoria

• a total of 82 species of eukaryotes,• 21 species of insects, in Orhtoptera and

Hemiptera.

Structure and composition of mitochondrial genomes of insects

• is a double-stranded circular genomes, range from 14, 503 bp to 19, 571 bp in size.

• Coding region: contain 37 genes: • two for rRNAs, • 13 for proteins • 22for tRNAs.

Structure and composition of mitochondrial genomes of insects

• 13 protein-coding subunits: • (COI-III, CytB, ND1-6, ND4L, ATP6 and ATP8) • 2 ribosomal RNA (rrnS and rrnL) • 22 transfer RNA (trnI, trnQ, trnM, trnW, trnC,

trnY, trnL1, trnK, trnD, trnG, trnA, trnR, trnN, trnS1, trnE, trnF, trnH, trnT, trnP, trnS2, trnL2, trnV) genes necessary to translate the protein-coding genes

Structure and composition of mitochondrial genomes of insects

• Non coding region: control mt DNA• mt genomes of insects contain one large AT-

rich non-coding control elements,• involved in the initiation, regulation of mt

transcription and replication, and are therefore referred to as the AT-rich

Structure and composition of mitochondrial genomes of insects

• Largest mt genome: Drosophila melanogaster, (19, 517 bp) 14 coding genes compared to 13 in most

insects• Smallest mt genome: Rhopalomyia pomum, (14, 503 bp)• 4.6 kb (Diptera: Drosophila melanogaster

• initiation codons (ATA or ATG), encoding the amino acid methionine, are usually used in most PCGs

• translation initiation signal for the COI • In Drosophila melanogaster and D. yakuba a TCG

triplet opens the COI• gene reading frame, a tetranucleotide ATAA, • termination codon: TAA or TAG

Genome rearrangements

can be characterized in several aspects: (1) the types of genes rearranged, tRNAs only (termed

minor rearrangements) protein-coding and rRNA genes (major

rearrangements)(2) whether genes are translocated along the same

strand or inverte between coding strands(3) the localization of the rearrangement

Genome rearrangements

• different mechanistic models of how genome arrangements occur

• duplication-random loss model• mtDNA duplication and nonrandom gene loss.

mitochondrial gene rearrangements83 species belonging to11 orders,

• Drosophila yakuba

• three spp Hemiptera• one spp Lepidoptera • one spp Psocoptera• one spp Coleoptera

• much common in tRNA genes and very rare in protein-coding genes and rRNA genes

• protein-coding genes

• Thysanoptera and Phthiraptera

• protein-coding genes and rRNA genes

hemipteroid orders (Hemiptera, Thysanoptera, Psocoptera, and Phthiraptera) and Hymenoptera have increased rates of gene rearrangements in the mt genomes.

mitochondrial gene rearrangements

Thysanoptera: rearrangements of 24 genes has two very similar non-coding regions, with 18 genes rearranged between them.

phthirapteran spp: Almost all 37 genes are transposed from their ancestral position in the two sequenced phthirapteran species.

So lice are an ideal group in which to study rearrangements due to the heightened rearrangement rate. It is found that 11 of the 13 protein-coding

mitochondrial gene rearrangements

• Rearrangements appear much more common in insects and variability in gene order can be found within groups at many taxonomic levels.

• With few exceptions, gene arrangements are relatively stable within major groups, but variable between them,

• and comparisons of these gene arrangements have great potential for resolving some of the deepest branches of insect phylogeny.

Homoplasmy and heteroplasmy

CONCLUSION

References • Margulis, L. 1981. Symbiosis in Cell Evolution: Life and its Environment on the Early Earth. W. H. Freeman and Co.

San Francisco.• https://girlmeetsbiochemistry.wordpress.com/2013/04/06/endosymbiotic-theory/• Vickermann K. 1971. “Morphological and physiological considerations of extracellular blood protozoa.” In Ecology and

Physiology of Parasites. A. M. Fallis, ed. University of Toronto Press reprinted in Roberts, L. S. and J. Janovy 1996. Gerald D. Schmidt and Larry S. Roberts’ Foundations of Parasitology 5th edition. Wm. C. Brown Publishers. Dubuque.

• Lloyd, D. 1974. The Mitochondria of Microorganisms. Academic Press, London.• Gray et al., 2012. origin and evolution of mt dna. Genome biology, vol. 2 no. 6• http://www.ncbi.nlm.nih.gov/pubmed/23193287• Smith.2015.The past, present and future of mitochondrial genomics: have we sequence enough mtDNA, Oxford

University Press. doi: 10.1093/bfgp/elv027• Total number of sequences (5319) as of 5 February 2015.sss• Li Hu et al., 2009. progress in the researches on insect mitochondrial genome and analysis of gene order, science

foundation in china; Vol.17, No.2,• Anderson et al., 2000. Mitochondrial DNA sequence variation and phylogeography of oceanic insects (Hemiptera:

Gerridae: Halobates spp.), marine biology., 136: 421-430• Wells et al., 2000. Human and Insect Mitochondrial DNA Analysis from Maggots. Journal Of Forensic Sciences: pp no.

685-687• Leite et al.,2012. Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue, Biota

Neotrop., vol. 12, no. 3

• Li Hu et al., 2009. progress in the researches on insect mitochondrial genome and analysis of gene order, science foundation in china; Vol.17, No.2,

• HIRANO et al., 1997. Apparent mtDNA heteroplasmy in Alzheimer’s disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 14894–14899

Thank You