Topic 5-L1 - Microbial Genomes Flashcards
All cells store their genetic information as
DNA
information flow & the central dogma of life
- DNA is copied (DNA replication) as the first step in cell division
- Genetic info of DNA is copied to RNA in
transcription o Open reading frames from messenger RNA (mRNA) are converted to proteins via translation - Other RNAs (non-coding RNAs, such as
ribosomal RNA – rRNA) are not converted to
protein, but serve their cellular function as RNAs
DNA is a polymer comprised of strings of
nucleotide monomers
Nucleotides 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.
Nucleotides connected via. All linear
phosphodiester bonds between 5’-phosphate groups and 3’hydroxyl (OH) groups
- DNA has 5’ end & 3’ end
Two complementary DNA strands run
anti-parallel to form a helix via interaction of their nucleobases
– genomic DNA is double stranded
C/T are
pyrimidines (6 membered rings)
A/G are
purines (fused 5/6 membered rings).
A/T base pair, forming a
weaker interaction with 2 hydrogen bonds
C/G base pair, forming a
stronger interaction with 3 hydrogen bonds
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.
Differences between DNA and RNA
- RNA contains a 2’-hydroxyl group (OH) on its sugar (ribose) that is absent in DNA.
- RNA less stable then DNA (2’-OH can attack the sugar phosphate backbone - hydrolysis of the phosphodiester bond.)
- urical
- RNA single stranded
Structure of prokaryotic 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
- makes DNA compact enough to fit in cell
- nucleoid
Nucleoid –
region of cell containing the chromosome (not membrane bound, but synonymous to the concept of the nucleus)
Bacteria and archaea almost always have
one, circular chromosome
Vibrio Cholerae is an example of a bacterium with
two (circular) chromosomes – one is ~3 Mbp (million bp), other ~1Mbp
Streptomyces (those antibiotic producers) have
linear chromosomes!
Eukaryotes have
multiple linear chromosomes
Saccharomyces cerevisiae, has
12 chromosomes that vary in size
Eukaryotes, including microbes, generally have
larger and less compact genomes (fewer genes per kbp of DNA) than prokaryotes
eukaryotic microbes
smaller/more compact genomes than higher eukaryotes.
karyotic microbes have more compact genomes than higher eukaryotes, in part because they have
fewer introns (non- coding gene segments removed during splicing) per gene
Genes are segments of genetic material that encode a functional
protein or RNA product
A typical microbial genome is comprised of:
~85-90% protein-coding genes
~1-2% RNA coding genes (tRNA, rRNA, other functional RNAs)
~10% non-coding DNA (E.g., regulatory sequences, junk DNA)
Genes can run in
either direction (be encoded by either DNA strand) and can overlap
Genes often organized into functionally-related
clusters – function of surrounding genes can offer insight into a gene’s function
Genes of a related function can also be
scattered around chromosome
Not always together
Endosymbionts
(can only live within the cells of another organism)
parasites
(require another organism) can have very small genomes – rely on host for many functions
Mycoplasma (parasite - canlive freely) has a 0.5 Mb genome ~500
genes –
smallest genome capable of independent life?
Free-living bacteria/archaea have
larger genomes. (E.g. E. coli ~4.5 Mb )
Some bacteria with complex life cycles
(lots of regulation, different needs for
different stages) have genomes as
large as ~15 Mb
In prokaryotic genomes, as genome size increases, so does
of genes
Genes that encode specialized functions for adapting to different
environments or operating in different lifestyles
increase in larger genomes.
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.
Genomes of closely-related lineages often exhibit significant
synteny
synteny –
homologous genes arranged in the same order in their genomes
Unique genes of a particular genome are often found in blocks of genes
large blocks = genomic island
small blocks = genomic islet
Genomic island and islets often represent
horizontally acquired genes.
In many cases, the genes have a related function that confers that lineage with unique properties.
Diagram of SalmonellaPathogenicity 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).
Bacteriophages (or phages)
are viruses that infect bacteria (archaea are also infected by similar viruses)
Some bacteriophage, known as temperate phage, can integrate into
bacterial genomes, where they become a part of the genome called a __________. Can be stable or transient.
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.
Prophage content can vary from
strain to strain.
Prophage can carry cargo genes that have
nothing to do with phage biology - can provide the bacterial host with useful new genes.
important bacterial toxins are encoded by
prophage
In this specific map:
- Genes on one strand in blue
- Genes on other strand in red
- Green shows bacteriophage genes (prophage)
- Specialized biosynthetic genes in yellow (a feature of special interest for this particular paper)
- Grey genes are thought to be horizontally-acquired
- Squiggly line is % GC content - Inner rings show tRNA and rRNA genes
In addition to their genomes, many Bacteria and Archaea contain
plasmids
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
