Microbio 310 1st Edition Lecture 15 Outline of Last Lecture I. 11.7 Hosts for Cloning VectorsII. 11.8 Shuttle Vectors and Expression VectorsIII. 11.9 Bacteriophage Lambda as a Cloning VectorIV. 11.10 Vectors for Genomic Cloning and SequencingV. 12. 1 Introductions to GenomicsVI. 12.2 Sequencing and Annotating GenomesVII. 12.3 Bioinformatic Analyses and Gene DistributionOutline of Current Lecture I. 12.4 The Genomes of Eukaryotic OrganellesII. 12.6 MetagenomicsIII. 12.7 Microarrays and the TranscriptomeIV. 12.10 Gene Families, Duplications, and DeletionsV. 12.11 Horizontal Gene Transfer and Genome StabilityVI. 12.12 Transposons and Insertion SequencesVII. 12.13 Evolution of Virulence: Pathogenicity IslandsCurrent Lecture12.4 The Genomes of Eukaryotic Organelles• Mitochondria and chloroplasts contain a small genomeThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.– Also contain the necessary machinery for protein synthesis• Including ribosomes, tRNAs, and all other components necessary for translationformation of functional proteins• Known Chloroplast Genomes– Circular dsDNA molecules– Typically 120–160 kbp– Contain two inverted repeats of 6–76 kbp– Many genes encode proteins for photosynthesis and autotrophy– Introns common; primarily of self-splicing type (evidence that RNA has its own enzymatic activity)• Known Mitochondrial Genomes– Diverse structures; some linear– Typically smaller than chloroplast genomes– Primarily encode proteins for oxidative phosphorylation– Use simplified genetic codes rather than “universal” code– Some contain small plasmids– Mammalian mitochondria encode 13 proteins (tRNA’s)• Many genes in the nucleus encode proteins required for organelle function– Examples: translational machinery, energy generation– Did the DNA from the symbiont (mitochondria/chloroplast) migrate to the DNA genome or did it originate there?12.6 Metagenomics• Metagenome(ics)• PCR 16S rRNA phylogeny– The total gene content of the organisms present in an environment; analyzes pooled DNA or RNA from an environmental sample containing organisms that have not been isolated and identified• Several environments have been surveyed by large-scale metagenome projects (sequence/isolate DNA from the ocean to see what’s living there)– Examples: acid mine runoff waters, deep-sea sediments, fertile soils– About 50–60% of the DNA in the oceans is extracellular DNA found in deep-sea sediments. This is deposited when dead organisms from the upper layers of the ocean sink to the bottom and disintegrate. 12.7 Microarrays and the Transcriptome• Transcriptome– The entire complement (all) of RNA produced under a given set of conditions• Hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression• Microarrays – Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern (often called gene chips)• DNA segments on arrays are hybridized with fluorescently labeled mRNA from cells grown under specific conditions and analyzed to determine patterns of gene expression– Genes that are expressed fluoresce• Arrays are large and dense enough that the transcription pattern of an entire genome can be analyzed• What can be learned from microarray experiments?– Global gene expression– Expression of specific groups of genes under different conditions (ex: aerobic vs. anaerobic)– Expression of genes with unknown function; can yield clues to possible roles– Comparison of gene content in closely related organisms– Identification of specific organisms– Genomics Proteomics, Interactomics, Metabolomics12.10 Gene Families, Duplications, and Deletions• Homologous: related in sequence to an extent that implies common genetic ancestry• Gene families: groups of gene homologs; different members that all do same function• Paralogs: genes within an organism whose similarity to one or more genes in the same organism is the result of gene duplication• Orthologs: genes found in one organism that are similar to those in another organism but differ because of speciation• Gene duplications thought to be mechanism for evolution of most new genes• Deletions can eliminate genes no longer needed• Gene analysis in the three domains of life suggests that many genes present in all organisms have common evolutionary roots12.11 Horizontal Gene Transfer and Genome Stability• Horizontal gene transfer– The transfer of genetic information between organisms, as opposed to vertical inheritance from parental organism(s) to daughter organisms• May be extensive in nature• May cross phylogenetic domain boundaries• Detecting (evidence for) Horizontal Gene Flow– Presence of genes that encode proteins typically found only in distantly related species– Presence of a section of DNA with GC content or codon bias that differs significantly from the remainder of the genome12.12 Transposons and Insertion Sequences• Transposons may transfer DNA between different organisms• Transposons may also mediate large-scale chromosomal changes within a single organism– Presence of multiple insertion sequences (IS)– Recombination among identical IS can result in chromosomal rearrangements• Examples: deletions, inversions, or translocations• Integrons– Genetic elements that collect and express genes carried on mobile segments of DNA (cassettes)• Of those known, most carry genes for antibiotic resistance• Superintegrons– Integrons found on bacterial chromosomes that collect hundreds of gene cassettes12.13 Evolution of Virulence: Pathogenicity Islands• Chromosomal islands– Region of bacterial chromosome of foreign origin that contains clustered genes for some extra property such as virulence or symbiosis (bigger than transposons)• Pathogenicity islands: chromosomal islands containing genes for virulence• Chromosomal islands believed to have a “foreign” origin based on several observations– Extra regions often flanked by inverted repeats– The base composition and codon usage in chromosomal islands often differs from the rest of the genome– Often found in some strains of a species but not others• Chromosomal islands contribute specialized functions not essential to growth/survival– Virulence– Biodegradation of