Microbial Genomes PDF

Topic 3 Genomes, genetics and genomics 3-1: Microbial Genomes Lecture Overview: • An overview of structure/function of DNA and the genomes of microbes. The organization, structure and sizes of microbial genomes. • Textbook: Sections 6.1, 6.2, 10.1-10.3, 13.10 Reminder: information flow & the cen...

Topic 3 Genomes, genetics and genomics 3-1: Microbial Genomes Lecture Overview: • An overview of structure/function of DNA and the genomes of microbes. The organization, structure and sizes of microbial genomes. • Textbook: Sections 6.1, 6.2, 10.1-10.3, 13.10 Reminder: information flow & the central dogma of life o All cells store their genetic information as DNA o DNA is copied (DNA replication) as the first step in cell division o Genetic info of DNA is copied to RNA in transcription o Open reading frames from messenger RNA (mRNA) are converted to proteins via translation o Other RNAs (non-coding RNAs, such as ribosomal RNA – rRNA) are not converted to protein, but serve their cellular function as RNAs Textbook - Fig 6.1 Reminder: structure of DNA o DNA is a polymer comprised of strings of nucleotide monomers o Nucleotides are comprised of 4 different nucleobases (or nitrogenous bases) attached to a deoxyribose (5 carbon sugar) which carries a phosphate at the 5’ carbon. Nucleosides lack a phosphate group. o Nucleotides are connected via phosphodiester bonds between 5’-phosphate groups and 3’hydroxyl (OH) groups. All linear DNA has 5’ end & 3’ end o Sugar-phosphate backbone, with bases sticking out o Two complementary DNA strands run anti-parallel to form a helix via interaction of their nucleobases – genomic DNA is double stranded Textbook - Fig 6.1 DNA base pairs o The 4 bases used in the DNA are adenine (A), cytosine (C), guanine (G) and thymine (T). o C/T are pyrimidines (6 membered rings) and A/G are purines (fused 5/6 membered rings). o A/T base pair has a weaker interaction with 2 hydrogen bonds o C/G base pair has a stronger interaction with 3 hydrogen bonds o Base pairing is the key to DNA’s function: it enables identical copies to be made and genetic information to be converted to RNA/protein. Textbook - Fig 6.1 Differences between DNA and RNA o RNA contains a 2’-hydroxyl group (OH) on its sugar (ribose) that is absent in DNA. o This makes RNA less chemically stable than DNA – 2’-OH can attack the sugar phosphate backbone - hydrolysis of the phosphodiester bond. o Thymine (T) replaced by uracil (U) – similar, but lacks a methyl group o RNA usually singlestranded…but adopts significant structure – still uses base pairing Textbook - Fig 6.1 Structure of prokaryotic chromosomes o Chromosomes usually circular, but within cell not a simple “relaxed circle” there is extensive supercoiling & additional structuring layered on top. Many proteins involved in structuring the chromosome o Required to make DNA compact enough to fit in cell! o Nucleoid – region of cell containing the chromosome (not membrane bound, but similar to the concept of the nucleus) Organization of prokaryotic genomes o Bacteria and archaea almost always have one, circular chromosome o Vibrio cholerae is an example of a bacterium with two (circular) chromosomes – one is ~3 Mbp (million bp), other ~1Mbp o Streptomyces (antibiotic producers) have linear chromosomes! Streptomyces coelicolor’s linear chromosome Okada et al., PLOS ONE, 2014 V. cholerae’s two chromosomes Okada et al., PLOS ONE, 2014 Organization of eukaryotic genomes o Eukaryotes have multiple linear chromosomes o Model yeast species Saccharomyces cerevisiae, for example, has 16 chromosomes that vary in size o Eukaryotes, including microbes, generally have larger and less compact genomes (fewer genes per kb of DNA) than prokaryotes - eukaryotic microbes smaller/more compact genomes than higher eukaryotes. Eukaryotic microbes have more compact genomes than higher eukaryotes, in part because they have fewer introns (noncoding gene segments removed during splicing) per gene Textbook - Fig 10.13 Prokaryotes: Genes and genomes o Genes are segments of genetic material that encode a functional protein or RNA product A typical prokaryotic genome is comprised of: ~85-90% protein-coding genes ~1-2% RNA genes – noncoding RNA (tRNA, rRNA, other functional RNAs) ~10% non-coding DNA (E.g., regulatory sequences, junk DNA) o Genes can run in either direction (be encoded by either DNA strand) and can overlap o Genes often organized into functionally-related clusters – function of surrounding genes can offer insight into a gene’s function o Genes of a related function can also be scattered around chromosome Genome sizes o Endosymbionts (can only live within the cells of another organism) and parasites (require another organism) can have very small genomes – rely on host for many functions o Mycoplasma (parasite - can live freely…sort of) has a 0.5 Mb genome ~500 genes – smallest genome capable of independent life? o Free-living bacteria/archaea have larger genomes. E.g. E. coli ~4.5 Mb o Some bacteria with complex life cycles (lots of regulation, different needs for different stages) have genomes as large as ~15 Mb Textbook - Fig 10.2 Genome size & composition o In prokaryotic genomes, as genome size increases, so does # of genes o Some functions (e.g. translation, DNA replication) essentially constant in all genomes o Genes that encode specialized functions for adapting to different environments or operating in different lifestyles increase in larger genomes. Textbook - Fig 10.7 Textbook - Fig 10.10 Core and pan genomes When comparing a number of different genomes (e.g. – all members of a given species): Core genome – Genes present in all members. Usually conserved genes important for biology of that lineage Pan genome – All genes present in any member. Includes rare genes that encode highly specialized functions. Textbook - Fig 13.22 Core and pan genomes: example o There are many different lineages of Salmonella that have different ecologies & virulence properties o They all share a lot of common genes, important the basic Salmonella lifestyle (core genome) o Different lineages also encode many unique genes that give them their unique properties o E.g. the Typhi serovar is human adapted and encodes unique genes to help it infect & persist within humans Pan genome of Salmonella includes all genes encoded by all serovars Textbook - Fig 13.21 Genomic islands/islets o Genomes of closely-related lineages often exhibit significant synteny – homologous genes arranged in the same order in their genomes o Unique genes of a particular genome are often found in blocks of genes (large blocks = genomic island, small blocks = genomic islet) o Often represent horizontally acquired genes. In many cases, the genes have a related function that confers that lineage with unique properties. Diagram of Salmonella Pathogenicity Island-1 (SPI-1): Encodes many genes required for a type III secretion system, which enables Salmonella to enter host cells. Also encodes iron acquisition genes (iron is hard to acquire inside cells). This is a large cluster of genes found in all Salmonella, but absent from close relatives who cannot actively invade host cells. Prophages o Bacteriophages (or phages) are viruses that infect bacteria (archaea are also infected by similar viruses) o Some bacteriophage, known as temperate phage, can integrate into bacterial genomes, where they become a part of the genome called a prophage. Can be stable or transient. o Prophage content can vary from strain to strain. o Prophages can carry cargo genes that have nothing to do with phage biology - can provide the bacterial host with useful new genes. o Many important bacterial toxins are encoded by prophages Textbook Fig 5.18 Plasmids o In addition to their genomes, many Bacteria and Archaea contain plasmids o Plasmids are typically circular DNA molecules are replicated in the cytoplasm – encode “non-essential” accessory genes – genes important under certain conditions such as antibiotic resistance genes o Vary in size from ~1 kbp to 1Mbp, but typically less than 5% size of genome o Can vary in copy number (how many per cell) from 1 to >100. o Contain genes to ensure their replication using host DNA replication machinery Textbook - Fig 6.9