Prokaryotic Genomes I

prokaryotes in tree of life

bacteria, archaea

what are eukaryotes most closely related to?

Lokiarchaeota, a new group of archaea

what do some archaea have that are similar to those of eukaryotes?

genuine histone proteins

prokaryotic chromosomes are not “naked”, although

the ratio of DNA to protein (mass/mass) is higher than in eukaryotes

prokaryote chromosome structures

circular (E coli)

linear (Streptomyces)

circular and linear (Argobacterium)

megaplasmids

linear prokaryotic chromosomes

can have inverted terminal DNA repeats or special proteins dedicated to maintaining the chromosome ends

megaplasmids

100kb or larger, blurs the distinction between chromosome and extra-chromosomal element

plasmids

>1mb

not considered chromosomes as they are not essential

phase separation in E coli

between cytoplasm with numerous soluble proteins and the nucleoid consisting of a congested network of branched supercoils and relatively few proteins

nucleoid-associated proteins (NAPs)

create negative plectonemic supercoils in bacteria

replication and E coli

process assumed to occur in border region of nucleoid, replisomes synthesize replichores

transcription and E coli

assumed to occur in border region of nucleoid, DNA-binding proteins open up the unconstrained supercoils compacted in the nucleoid centre allowing them to be transcribed by RNAP

prokaryotes and gene density

highly uniform, have a linear relationship between genome length and number of protein-coding genes (in contrast to euks)

gene density

number of genes per unit of DNA length (e.g. x genes per kilobase)

map of bacterial chromosome

diagrams with concentric circles are useful to represent different aspects of the genome such as nucleotide composition, placement, and orientation of genes and other elements such as stop codons, mobile genetic elements, etc

homologous recombination

generates novelty by recombining existing alleles within a population/species

prokaryotes have traditionally been considered clonal, but now clear that many bacteria and archaea recombine their genes the way sexual organisms do and have multiple ways of doing it

rate of recombination in proks

drops exponentially as sequences diverge

bacterial species sometimes defined as having >95% sequence identity

clonal model

novelty comes from mutations arising within asexual populations

insertion sequence (IS) elements

small DNA segments that are capable of transposition, or movement in the genome, and mediating recombination (within and between genomes)

~0.7 - 2.5 kb in length

contain 1-2 ORFs that encode one or more transposases

often found on plasmids, where they can mediate recombination with chromosomal DNA

transposases

proteins that facilitate mobility of IS element via a variety of mechanisms and at different stages of the cell cycle

non-replicative and replicative

non-replicative transposase

IS element is excised from donor site and inserted into a new site

replicative transposases

IS element excised and inserted into multiple sites at the time of DNA replication

what is needed for IS displacement?

inverted repeats (IR), left and right, with signals for recognition by the transposase and for the DNA cleavages

what is it meant by IS elements being highly promiscuous?

they spread within and between a wide variety of different types of organisms, even between archaea and bacterial genomes

genomic islands

large (5-100+ kb) regions of a genome that exhibit a patchy distribution (found in some strains of a given species but not others) and show evidence of having been acquired by lateral gene transfer (LGT)

also known as pathogenicity and resistance islands

often contain functionally related genes

genomic islands are often enriched in

mobile genetic elements

mobility genes such as transposases and integrases

IS elements

tRNA genes (phase integration sites)

repetitive sequences

virulence factors

virulence factors (VFs)

allow a pathogenic organism to replicate and disseminate by subverting or eluding the defense systems of the host

include adhesins, invasions, endotoxins, hemolysins, proteases, etc

majority of them found within genomic islands