Microbial Genome Replication and Gene Expression Lecture Notes PDF

Microbial genome replication and gene expression Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology  Molecular Biology and Genetic Elements I. DNA and Genetic Information Flow II. Genetic Elements:...

Microbial genome replication and gene expression Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology  Molecular Biology and Genetic Elements I. DNA and Genetic Information Flow II. Genetic Elements: Chromosomes and Plasmids III. Copying the Genetic Blueprint: DNA Replication IV. RNA Synthesis: Transcription in Bacteria  I. DNA and Genetic Information Flow Functional unit of genetic information is the gene. Genes are part of genetic elements: large molecules and/or chromosomes. Nucleic acids: contain genetic information via nucleotides (monomers of nucleic acids) DNA (genetic blueprint) and RNA (transcription product) are polynucleotides. Informational macromolecules include nucleic acids and proteins. Figure 4.1 Table 4.1  II. Genetic Elements: Chromosomes and Plasmids Genome size and shape Size is expressed in base pairs. 1000 base pairs = 1 kilobase pair = 1 kbp one million base pairs = 1 megabase pair = 1Mbp E. coli genome = 4.64 Mbp and encoding around 4000 genes Linear DNA length is several hundred times longer than cell, so supercoiling compacts DNA to accommodate genome. (Figure 4.4) Histone-like basic Figure 4.4  Topoisomerases insert and remove supercoils. DNA gyrase introduces supercoils into DNA via double-strand breaks (Figure 4.5b) Figure 4.5 Supercoil and topoisomerase video https://www.youtube.com/watch?v=5hwaDamU-jo  Chromosomes and Plasmids Chromosome: main genetic element in prokaryotes Most Bacteria and Archaea have single circular chromosome carrying all/most genes. Plasmids: double-stranded DNA that replicate separately from chromosome usually circular generally beneficial for the cell (e.g., antibiotic resistance) NOT extracellular, unlike viruses Transposable elements segments of DNA that can move from one site to another site on the same or a different DNA molecule inserted into other DNA molecules (e.g., chromosomes, plasmids, viral genomes)  Some features of the Escherichia coli K-12 chromosome about five Mbp in size GC content (% of G and C in the genome) is 50.8 %. Almost 4300 possible protein-encoding genes make up 88 percent of the genome. compact relative to eukaryotes Many genes encoding enzymes of a single biochemical pathway are clustered into operons, transcribed to form single mRNA - efficiently and conveniently regulated as a unit. Many genes for biochemical pathways are not clustered. Thus, operons appear to be exceptions instead of the rule.  Plasmids found in many Bacteria and Archaea genetic information encoded on Gnomic DNA plasmids not essential for cell function under all conditions may confer a selective growth advantage under certain conditions range in size from one kbp to more than one Mbp; typically less than five percent of the size of the chromosome (Figure 4.9) Some cells contain multiple plasmids Plasmids abundance (copy number) variable (one or a few to 100+ copies) – making more efficient than the single copy genome in terms of expressing proteins  Example: R plasmids resistance plasmids; confer resistance to antibiotics or other growth inhibitors (Figure 4.10) widespread and well- studied group of plasmids Several antibiotic resistance genes can be on one R plasmid (e.g., R100).