Prokaryotic Genomes and Organelles

L12

some bits of wisdom abt bacteria (5 points)

• they are everywhere and do everything

  • snottite eats rocks and spits acid

  • permafrost

  • in clouds

• we only know v little abt them

  • only 10^4 cultured

  • 10^5 sequences

  • (vs tot estimation of spp being 10^7-10^12)

• v huge impact on our lives good and bad

• we are partly bacteria

  • in our body we have abt 10 more bacteria than humans cells or same number

  • mitochondria used to be free living bacteria

• some of most amazing bio tools from bacteria

  • i.e. CRISPR

what is the most diverse grp of organism

bacteria

(also archaea but less)

what is the prokaryotic cell organization

• cell wall surrounding the cellular membrane 

  • gramm negative bacteria contian outer membrane that surrounds cell wall

• typically no membrane bound organelles in the cell

  • chromosomes are in the cytoplasm

    • allows translation to occur on RNA before transcription even finished

bacterial chromosomes

• most contain single circular chromosome

  • abt 10% of the known spp contain more than one

• each chromosome contains a single origin of replication

  • each half of chromosome is replicated by replisome

• length of known ones ranges few hundred kbp to mroe than 14Mbp

• highly transcribed genes are oriented in same direction as the replication fork progression

  • to avoid conflicts

how are genes organized in the bacterial chromosome?

• DNA is gene rich 

  • very little intergenic regions

    • unlike eukaryotes that have a lot of non coding DNA

• no introns

• genes are grouped with operons

  • share common promoter

  • are transcribed together to form polycistronic mRNA

How is bacterial DNA compacted and organized?

• use DNA binding proteins to cover DNA (like eukaryotes)

  • BUT do not have histones

    • so DNA not wrapped around nucleosome

• Gyrase required to introduce torsion (negative supercoiling) to compact DNA

• SMC proteins generate loops to organize DNA

gyrase

a special type of DNA topoisomerase that introduces torsion (negative supercoiling) to compact bacterial DNA

how are chromosomes organized in bacteria (originally surprising because we didn’t think they were organized)

• nucleoid structure of chromosome and protein

  • difft parts of the chromsome occupy specific parts of the nucleoid in the cell

    • origin of DNA replication is at the cell center or at the cell poles

      • this is analogous to eukaryotic higher order organization

Organellar DNAs

• genetic material found in organelles outside of the cell nucleus

• found in mitochondria and chloroplasts

Mitochondria and Chloroplasts

• Mitochondria important for respiraion

• Chloroplasts imp for photosynthesis

• originally free organisms that were endocytosed and became endosymbionts

how do mitochondria and chloroplasts ressemble prokaryotes in terms of their genomes?

• circular

• genes typically lack introns

• gene products resemble prokaryotic RNAs and proteins

where in the mitochondria do we find DNA molecules

in the mitochondrial matrix

how many organelles do cells usually have? what can we say about each organelle’s genome?

• there are usually many mitochondria (and chloroplasts) per cell

• each organelle may have multiple genomes

Human Mitochondrial DNA (mtDNA)

• 16,569bp

• 37 genes only in mtDNA (other organisms can have more or less)

  • many encode components needed for respiration and translation

    • have their own ribosomes for translation

    • have many genes coding for tRNA molecules

• no introns

• gene products stay within mitochondria

Chloroplast genome (cpDNA)

• DNA molecules also inside organelle

• 100-200 genes

• 100-200kb

Lynn Margulis

• evo theorist and biologist and author

• using info at the time proposed that mitochondria and chloroplasts originiated from free living bacteria

• was motivated to explain how eukaryotes acquired their organelles (contrast w bacteria and archea that do not have membrane bound organelles)

• her paper was rejected 12+ times

What is the endosymbiotic theory of the origin of chloroplasts and mitochondria

• ancestral cell endocytosis of bacterium

  • capable of oxidative phosphorilation

  (or)

  • capable of photosynthesis

what is evidence of endosymbiotic theory for mitochondria we have now?

• bacteria from the Rickettsia genus

  • relatives to the ancestor of mitochondria 

  • These are intracellular parasites 

    • cause typhus fever

what are thought to be the closest relatives to the recipient cell that generated the first eukaryotes 

• Lokiarchea 

  • found near the Loki’s Castle hydrothermal vent site in the Acrtic Ocean

  • identified from metagenomic sequence data

  • (as most prokaryotes) cannot be cultured

Other examples of bacterial endosymbionts

• many insects

  • esp those that eat from plant saps => the bacterial endosymbiont help them produce the nutrients lacking in their diet

• other organisms with bacterial endosymbionts include:

  • cockroaches

  • clams

  • blood feeding flies

  • etc

obligate endosymbiont

• can no longer survive wirthout a host cell

• undergoes a reduction in their genome

  • genes that are not necessary for bacterial function are lost 

  • reductive evolution

how do sea slugs (dinoflagellates) use endosymbiosis?

they eat algae and corals and keep the chloroplasts so that they can photosynthesize

where are most of the proteins in mitochondria and chloroplasts cloded

• in the nucleus

  • there has been gene mvmnt to nucleus over evolution

what can we say about mitcochondrial ribosomes?

• Mitochondria have their own ribosomes

  • they have sequence similarity to those in bacteria

• all proteins coded in the mitochondria stay in this organelle

how are mitochondria inherited?

• cytoplasmic inheritance

  • different from that of DNA in the nucleus

• Mitochondria are distributed evenly among daughter cells

  • this is random

  • if once cell has no mitochondria or non functional one then won’t survive in most scenarios

Why do mitochondria not have the same constraints as the genetic code?

• alternation of genetic code

  • i.e. stop codon used for an AA

What are mutations in mtDNA related to in mammals?

• aging

  • Mice with a mitochondrial DNA polymerase defective

    for proofreading exhibit premature agin