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Mitochondrial genomes and their functions in plants
- 2. Mitochondria Well-defined cytoplasmic organelles Provide biological energy Richard Altmann (1890) – bioblasts Carl Benda (1898) – mitochondrion
- 4. • Regulate metabolic activity • Maintains concentration of Calcium ions • Detoxify ammonia • Apoptosis • Aging Function of Mitochondria
- 5. Plant mitochondrial genome Size = ~200kb - 2400kb Extra genes: Open Reading Frames Ribosomal proteins Universal genetic code. Arranged as different size circles, sometimes with plasmids The plant mtDNA contains chloroplast sequences, indicating exchange of genetic information between organelles Coding regions are larger than animals and fungi Smallest mtDNAs -Plasmodium and its relatives (6 kb) Encode proteins for oxidative phosphorylation
- 6. Structure of plant mt Genome
- 7. Size of mitochondrial genome Name Scientific Name Size Liver wort Marchantia polymorpha 186 kb Maize Zea mays 700 kb Watermelon Citrullus lanatus 300 kb Rice Oryza sativa 492 kb Arabidopsis Arabidopsis thaliana ~367 kb Squash Cucurbita pepo 1 Mb Caulobacter Caulobacter crescentus 4.017 Mb Rhizobium Bradyrhizobium japonicum 9.1 Mb Human Homo sapiens 16.5 kb White musterd B. hirta 208kb Muskmelon C melo 2500kb
- 8. Comparison of mitochondrial genomes Size Non-coding DNA Mutation rate High Very Low 14kb - 42kb Recombination Introns Universal genetic code Low Variable 17kb - 180kb / Mostly Very Low Very High 184kb - 2,400kb Animals Fungi Plants
- 9. Nuclear vs. Mitochondrial DNA • Nuclear DNA – found in nucleus of the cell – 2 sets of 23 chromosomes – maternal and paternal – double helix – bounded by a nuclear envelope – DNA packed into chromatin • Mitochondrial DNA – found in mitochondria of the cell – each mitochondria may have several copies of the single mt DNA molecule – maternal only – circular – free of a nuclear envelope – DNA is not packed into chromatin 9
- 10. Replication, Transcription and Translation
- 11. RNA EDITING Trypanosome mitochondrial cox2 transcripts. Genomically encoded C residues are converted post-transcriptionally to U residues. RNA editing can create new initiation codons (ACG to AUG) and new termination codons (CGA to UGA). Ex: nad1 initiation codon created by editing of ACG to AUG in all known angiosperm mitochondrial genomes.
- 12. • common genes for both plant and animal mtDNA for component of oxidative phosphorilation • 9 subunit – respiratory – chine complex –I • 1 sub unit of complex –III(cob) • 3 sub unit of complex – IV(cox1, cox2, cox3) • 2 sub unit of complex –V(atp6, atp8) • rRNA genes • tRAN genes • Ribosomal proteins • Cytochrome c biogenesis (ccm) • Mtt - B- like transporter • Apocytochrome b (cob) • Cytochrome oxidase subunit (cox 1) • large (26S) and Small(18S) ribosomal RNAs Gene content of mt genome
- 13. Gene content of mt DNA
- 19. CODING CONTENT OF PLANT MITOCHONDRIAL GENOMES
- 20. G C CONTENT • The base composition of mtDNA is nearly constant among all sequenced plant mitochondrial genomes • variable intergenic regions do not exhibit lower or higher average GC content than does the rest of the genome • No discrete regions of higher or lower GC content are present in the genomes. Z mays NB 43.9% O sativa 43.9% B vulgaris 43.9% A thaliana 44.8% B napus 45.2% M polymorpha 42.4%
- 21. Protein-coding genes, tRNA genes, rRNA genes Rapeseed 222kb have 54 genes functional genes 34genes for protein coding 3 rRNA genes 17 tRNA genes
- 22. Z mays NB 121 O sativa 113 B vulgaris 93 A thaliana 85 B napus 45 liverwort 32 Open reading frames (ORFS) : reading frame of at least 100 codons with in frame start and stop codons Chimeric genes : •The first chimeric gene-urf13 in the CMS-T mitochondrial genome of maize urf13 is the cause of the sterility •The production of proteins resulting from chimeric genes is directly associated with CMS (maternally inherited trait) Pseudo genes : defective versions of genes that no longer produce a functional product
- 23. • Introns : Saccharomyces cerevisiae. • Classes • Group I : released as a linear molecule with a covalently added G residues • Group II : released as lariat structures • liverwort mitochondrial genome contains both group I and group II introns. • cox1 intron is the only reported group I intron in the mitochondrial genomes of vascular plants Introns
- 24. Chloroplast sequence in plant mitochondrial genome Rice 7.0% Rapeseed 5.9% Maize 4.4%, Sugar beet, 2.1% Arabidopsis 2.1% Liverwort 0%
- 25. MultiPipMaker—Graphical comparisons of the sequenced plant mtDNAs
- 26. Mutations in mitochondria Mutation rate in mtDNA is very high (10 times) Large amounts of “reactive oxygen species” (peroxide and superoxide) are present, and they are quite mutagenic. The D loop has an especially high rate of mutation Part of the effects of aging have been attributed to the gradual loss of mitochondria due to accumulated mutations in individual cells
- 27. Mutations in mitochondria A combination of aberrant, rare and normal, high-frequency recombination within mitochondrial genomes and between mitochondrial sub genomes leads to the origin of deletion mutations such as those responsible for the non-chromosomal-stripe (NCS) abnormal growth mutants reversions of cytoplasmic-male-sterile (CMS) plants to fertility
- 28. Cytoplasmic male sterility cytoplasmic male sterility (CMS) in plants is often caused by the expression of chimeric genes. Rearrangement mutations can lead to the loss of CMS- associated sequences from the mtDNA and recovery of male fertility, a process known as cytoplasmic reversion NCS mutants Maternally inherited, abnormal growth mutations (such as maize NCS) usually reflect deletions within functional mitochondrial genes coding for subunits of respiratory complexes or ribosomal proteins. These mutations affect the plant throughout its life cycle and are lethal during some stages, particularly seed development.
- 29. An Arabidopsis Mitochondrial Uncoupling Protein Confers Tolerance to Drought and Salt Stress in Transgenic Tobacco Plants. Kevin Begcy et al., August 30, 2011 Orian S. Shirihai, Boston University, United States of America Plant Materials: Nicotiana tabacum SR1 plants were transformed with an expression cassette comprising a double 35S promoter that controls the AtUCP1 gene from A. thaliana, as described previously. Three independent and homozygous lines of AtUCP1- expressing tobacco plants (AtUCP1-7, AtUCP1-32, and AtUCP1-49) were chosen for this study.
- 30. 30 Figure 1. Seed germination under drought and salt stress. (A) control; equeal 5-80 60 (B)200mM mannitol;10 complet ger 15 did not (C) 300mM mannitol; sign effect more wt (D) 400 mM mannitol;40% (E) 100 mM Nacl ; 80-95 45%-10d (F) 175 mM Nacl 50-7d 11d 60
- 31. 31
- 32. A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice Dangping Luo et al., 2013 Nature America
- 33. Identification and functional analyses of the new mitochondrial gene WA352 for CMS-WA 33
- 34. 34 A model for the mechanism of the CMS-WA system
- 35. Conclusion The mitochondria of plants share functions with mitochondria of other eukaryotes, and thus share many of the same genes. However, the organization, structure, expression and evolutionary dynamics of plant mitochondrial genomes are unusual when compared with those other organisms. Structurally, plant mitochondrial genomes are very diverse relative to their fungal and animal counterparts, both of which tend to be quite uniform in organization and gene content.
- 38. Secondary structure model of plant mitochondrial group II introns
- 39. Repeated sequences in plant mitochondrial genomes • Large repeats are more frequent in larger mitochondrial genomes and vice versa • More than 50% of the 369-kb rice 16 repeats at least 1 kb long. • The 570 kb maize NB mitochondrial genome contains only 8 repeats 1kb or longer, which represent only 17% of the genome.
- 40. Nuclear genes control the mitochondria biogenesis Transcription Pre-mRNA processing Translation of the mRNAs into mitochondrial proteins The assembly of ribosomes and respiratory complexes and are also required for the targeting and degradation of organellar subunits.
- 41. Nuclear genes control the mitochondria biogenesis Transcription Pre-mRNA processing Translation of the mRNAs into mitochondrial proteins The assembly of ribosomes and respiratory complexes and are also required for the targeting and degradation of organellar subunits.
- 42. 42 Alternative oxidase impacts the plant response to biotic stress by influencing the mitochondrial generation of reactive oxygen species MARINA CVETKOVSKA & GREG C. VANLERBERGHE Plant, Cell and Environment (2013) 36, 721–732
- 43. 43 Conductivity (ion leakage) of tobacco leaf (a,b) and bacterial proliferation in tobacco leaf (c,d) at different times post-inoculation with P. syringae pv. maculicola (a,c) or pv. phaseolicola (b,d).
- 44. 44 Laser-scanning confocal microscope images of mitochondrial O2- in tobacco mesophyll cells at different times post-inoculation with P. syringae pv. phaseolicola.
- 45. 45 Laser-scanning confocal microscope images of mitochondrial O2- in tobacco mesophyll cells at different times post-inoculation with P. syringae pv. maculicola.
- 46. 46 MnSOD (a), CuZnSOD (b) and FeSOD (c) activity in tobacco leaf at different times post-inoculation with P. syringae pv. maculicola.
- 47. 47 H2O2 level in tobacco leaf at different times post-inoculation with P. syringae pv. maculicola (a) or pv. phaseolicola (b).
- 48. 48 Laser-scanning confocal microscope images of cellular NO in tobacco mesophyll cells at different times post-inoculation with P. syringae pv. maculicola Laser-scanning confocal microscope images of cellular ONOO- in tobacco mesophyll cells at different times post- inoculation with P. syringae pv. maculicola.
- 49. 49 Regulation of WA352 expression
- 50. 50 WA352 interacts with the nuclear-encoded mitochondrial protein COX11
- 51. 51
- 52. 52
- 53. 53
- 54. 54
- 55. 55
Editor's Notes
- Mt genomes of seed plants are unusually large and vary in size at least in an order of magnitude. Much of these variations occur within a single family [10]. Seed plant mitochondrial genomes Are for their very low mutation rate, frequent uptake of foreign DNA by intracellular and horizontal gene transfer, and dynamic structure. The evolving land plants have gained new mechanisms to facilitate more frequent gene exchanges between mt and cp genomes as well as between mt and nuclear genomes, which make mt genomes increase their sizes.
- The ribosomes of mitochondria are different from those of chloroplasts and the cytoplasm, using a slightly different genetic code (a sequence of three bases that codes for a particular amino acid). Mitochondrial genomes code for all of the ribosomal RNAs found in mitochondria and for most of the tRNAs. Mitochondria make only a small number of proteins that are needed for electron transport and ATP production. The other proteins needed in mitochondria are coded by nuclear DNA, translated in the cytoplasm of the cell, then transported into the mitochondria. Plant mitochondria do not encode a full set of tRNAs, and some are imported from the cytoplasm.
- One strand is called H strand Guanine rich 28 genes and the other is called L strand with 9 genes.
- Gene organization of the rapeseed mitochondrial genome. Genes homologous to known protein-coding genes are indicated by red boxes. The blue boxes represent rRNA genes. Pink boxes represent unidenti®ed ORFs longer than 150 amino acids. tRNA genes are represented by yellow boxes. Pseudo genes including plastid gene segments are shown in pale green. orf222, a cms-related gene (20), is shown by a green box. Arrowheads indicate the direction of reading frames. Dark green boxes located inside the circle represent 2 kb repeat regions. *From Heazlewood et al. (32); **From Sabar et al. (18).
- Indeed, analyses of cDNAs in Arabidopsis mitochondria suggest that few, if any of these ORFs are expressed as stable mRNAs (Giege and Brennicke, 2001). Skovgaard et al., (2001) examined 34 bacterial genomes and concluded that 30-90% of the annotated ORFs, particularly those that were not present in other species, do not actually encode proteins. It is not unreasonable to expect that most of the ORFs in the endosymbiotic mitochondrial genomes, particularly those not conserved across taxa, are not expressed.
- I to IV identify large regions of homology between NA and NB.
- Neither only wa352 nor only cox11 causes male sterility interaction of both this will causes male sterilty
- . (A) The secondary structure of group II introns is characterized by six double-helical domains (I-VI), arising from a central hub. Each subdomain of DI and DII, DIII, DIV, DV, and DVI are outlined within the structure. All plant mitochondrial intron structures in angiosperms are classified as standard group IIA RNAs (Bonen, 2008). The conserved bulged-A residue in DVI, the exon-intron binding sites (i.e., EBS1/IBS1 and EBS2/IBS2), and tertiary interactions between different intron regions (indicated by roman letters) are shown in the model structure. The ORF encoding the MatR protein in nad1 intron 4 is encoded in intron domain IV. (B) Splicing pathway of the autocatalytic group II introns occurs by a two-step trans-esterification pathway. In the first step of the branching pathway, the 2'-OH group of the branch point adenosine nucleophilically attacks the phosphate at the 5'-splice site. The 5'-exon is released and the attacking adenosine adopts a 2',5'-branched structure that gives the intron a lariat form. Yet, in addition to this classical “branch-point” splicing reaction, some mitochondrial introns which lacks a DVI bulged A are excised as linear molecules which are generated by a “hydrolytic-pathway” of splicing (Li-Pook-Than and Bonen, 2006).
- From above experiments we concluded that arabidnsis uncoupling protein containing transgenic plant are resistance againest abiotic stesses