prokaryotic genomes and organelles

estimated total number of species of bacteria

10⁷-10¹², most widely diverse group of organism

origin of mitochondria

free-living bacteria

biological tools originating from bacteria

• restriction enzymes

• CRISPR

prokaryotic cell organization

• most bacteria contain a cell wall that surrounds a cellular membrane

• Gramm negative bacteria contain outer membrane that surrounds the cell wall

• typically no membrane-bound organelles

• chromosomes are in contact with the cytoplasm, which allows translation to occur on an RNA before transcription has finished

bacterial chromosomes

• most contain singular circular chromosome

• each contain a single origin of replication, each half is replicated by one replisome

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

• range in length from few hundred kbp to > 14 Mbp

organization of genes in bacterial chromosome

• DNA is gene-rich with little intergenic regions

• contain no introns

• grouped into operons that share a common promoter and transcribed together forming polycistronic mRNA

polycistronic mRNA

mRNA containing multiple genes

bacterial DNA compaction and organization

• use DNA binding proteins to cover DNA

• do not have histones, so DNA is not wrapped around nucleosomes

• require special DNA topoisomerase gyrase to introduce torsion (negative supercoiling) to compact DNA

• SMC proteins generate loops

bacterial chromosome organization

• chromosome and proteins organize into a structure called nucleoid

• different parts of the chromosome occupy specific parts of the nucleoid, with the origin of DNA replication being at the cell center or cell poles

mitochondria and chloroplasts

• organellar DNAs

• important in respiration and photosynthesis, respectively

• originally free organisms that were endocytosed and became endosymbionts

• resemble prokaryotes in their genomes

  • circular

  • genes typically lack introns

  • gene products resemble prokaryotic RNAs and proteins

human mitochondrial DNA (mtDNA)

• 16.5 kbp

• 37 genes

• many genes encode components needed for respiration and translation

• no introns

• gene products stay within mitochondria

chloroplast genome (cpDNA)

• 100-200 genes

• 100-200 kb

endosymbiosis hypothesis

• proposed by Lynn Margulis in 1967

• suggested that mitochondria and chloroplasts originated from free living bacteria

• explains how eukaryotes acquired their organelles

bacteria from the Rickettsia genus

• thought to be closest relatives to the ancestor of mitochondria

• intracellular parasites, cause Typhus fever

Lokiarchea

• thought to be closest relatives of the recipient cell that generated the first eukaryotes

• found near Loki’s Castle hydrothermal vent site in the Arctic ocean

• identified from metagenomic data

• cannot be cultured

examples of bacterial endosymbionts in insects

• mainly insects that eat from plant saps, help them produce nutrients lacking in diet

• also cockroaches, clams, blood-feeding flies, etc.

obligate endosymbiont bacteria

undergo a reduction of their genome

mitochondrion and chloroplast proteins

• most are coded in the nucleus

• there has been gene movement from the organelles to the nucleus over evolution

• mitochondria have their own ribosomes with sequence similarity to bacteria

• all proteins coded in the mitochondria stay in the organelle

inheritance of mitochondria

• cytoplasmic

• mitochondria are distributed evenly among daughter cells

differences in standard and mitochondrial genetic code

• UGA encodes stop in standard code but Trp in mitochondria

• AGA, AGG encode Arg in standard code but stop in mitochondria

mutations in mtDNA

• may be related to aging in mammals

• mice with a mitochondrial DNA polymerase defective for proofreading exhibit premature aging