Evolution of the genomes The concept of ‘genome’ –The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (‘episomes’) –Plasmids –Mitochondrial chromosomes and plasmids –Chloroplast chromosomes and plasmids The contents of genomes change by: –Mutation –Recombination (broad sense)
The first genetic exchange programs The concept of ‘genome’ –The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (‘episomes’) –Plasmids –Mitochondrial chromosomes and plasmids –Chloroplast chromosomes and plasmids Two kinds of exchanges –The whole molecules (Assortments) –Sequence rearrangements (Recombination) Between homologous DNA ‘Homologous recombination’ Between non-homologous DNA –Site-specific recombination, transposition, illegitimate recombination
Recombination or mutation? Fig. 18.12 Frequencies of occurrences Proper controls
Plasmids 質體 Universal presence –Prokaryotic cell Bacterial Archaea –Eukaryotic cell Cytoplasm Mitochondria Chloroplast Most are circular and some are linear –Promoters of genetic exchanges –Carriers of useful genes Drug resistance, metabolite degradation, etc.
Virus infection is specific Host range –‘Lock and key’ fit between virus and receptors on the host’s surface –Some viruses have a broad host ragne, and other infect only a single species Most eukaryotic viruses attack specific tissues.
Three kinds of genetic exchanges between prokaryotes Three kinds –Transformation Mediated by free DNA –Conjugation Mediated by plasmids –Transduction Mediated by phages All involving merozygote (partial diploid) All require even number of crossovers
Transposable elements Insertion sequence Fig. 18.16 Fig. 18.18
Transposable elements Responsible for most spontaneous mutations fin many bacteria –60% in E. coli Natural genetic engineers —Promote deletions, inversion, translocation, replicon fusion B. subtilis does not have transposable elements!
Natural genetic engineers Create mutations –Mostly bad –Rarely good - become conserved Promote genome rearrangements and exchanges –Same or similar TE sequences provide sustrates for homologous recombination –Sometimes transposition itself causes rearrangement
Transposable elements, plasmids, viruses They are all mobile elements They close related in evolution Some transposable elements (Tn916) are also conjugative plasmids Some prophages (N15) are like like plasmids Some phages (Mu) are transposable elements
The newest phase in bacterial genetics The genomic approach
Bacterial Genomics A revolution in the practice of bacteriology Learning the life style without biochemistry Evolution studies becoming practical Contribution to our vision of the whole living world
Metabolism with doing chemistry Primary metabolism –Energy management –Body building Information process –Replication –Transcription –Translation –Repair Pathogenicity Secondary metabolites What is absent is as interesting as what is present
新陳代謝重建 Physiology without biochemistry Metabolic reconstructio n from the genomes
Genome sizes and content Sizes: 0.6 kb - 9.4 Mb, about 1.0 - 1.1 kb/gene The larger the genomes, the more complex the life styles The larger the genomes, the more paralogous genes G+C content: 25 - 75% Topology: Circular vs. linear Single or multiple chromosomes and plasmids
Studies of evolution relationship Conservation of protein families Diversity of gene repertoires and organizations Incongruities abundant in the phylogenetic tree Common and intensive horizontal gene transfers –between bacteria and between bacteria and Archeae –Mosaic nature of genomes ‘Gene evolution does not equal species evolution’ Which set of parameters to rely on for a particular task?
The third domains — Archeae Originally based on rRNA sequences –Carl Woese Bacteria-type morphology and yet different inside –Genetic system (Replication, transcription, translation -Eukaryotic-like –Metabolic system - bacterial-like
Virus infection by membrane fusion Fig. 18.6 Viruses equipped with an outer envelope –Glycoproteins on the envelope bind to specific receptors on the host’s membrane. The envelope fuses with the host’s membrane, transporting the capsid and viral genome inside. –The viral genome duplicates and directs the host’s protein synthesis machinery to synthesize its own proteins. –After the capsid and viral genome self- assemble, they bud from the host cell covered with an envelope derived from the host’s plasma membrane, including viral glycoproteins. These enveloped viruses do not necessarily kill the host cell.
RNA viruses In some with single-stranded RNA (class IV), the genome acts as mRNA and is translated directly. In others (class V), the RNA genome serves as a template for mRNA and for a complementary RNA. –This complementary strand is the template for the synthesis of additional copies of genome RNA. All viruses that require RNA -> RNA synthesis to make mRNA use a viral enzyme that is packaged with the genome inside the capsid.
Viroids Smaller and simpler than viruses Tiny naked circular RNA molecules (several hundred nt) that infect plants –No protein-coding sequence –Can replicate in the host The RNA molecules disrupt plant metabolism and stunt plant growth, perhaps by disturbing the regulatory systems.
Prions Prions are infectious proteins. A prion is a misfolded form of a normal brain protein. It can convert a normal protein into the prion version, creating a chain reaction. –degenerative brain diseases such as scrapie in sheep, “mad cow disease”, and Creutzfeldt-Jacob disease in humans. Fig. 18.10