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Chapter 6

Biological Sciences 55-237 Chapter 6: Microbiology Topic 6 part 1


Department
Biological Sciences
Course Code
BIOL 2070
Professor
tanyanoel
Chapter
6

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Microbiology Topic 6: Genetics, Genomics, and Studying the Microbiome
Organization of DNA, genomics, and microbiome studies
Genetics: the study of heredity and variation of inherited characteristics
Bacterial and archaeal cells contain chromosome(s) in nucleoid
Bacteria do not have histones; they have different DNA-binding proteins
Archaea have histones, though they are a little different from those in eukaryotes
Eukaryotic cells contain chromosome(s) in membrane-bound nucleus and the DNA
is wound around histone proteins
There are some differences in structure and organization of genetic material across
the three domains
All organisms have at least one chromosome, which includes the hereditary
information encoded in DNA sequences
Bacteria and archaea do not have a nucleus
o They usually have circular chromosomes
Eukaryotic linear chromosomes are found in the nucleus of the cell
In addition to DNA, when looking at chromosomes, there are some associated
proteins, and these also differ depending on which organism we are looking at
DNA organization- Bacteria
Most bacteria have single, circular, dsDNA chromosome
Extra-chromosomal DNA plasmids present in some cells
Plasmids are considered non-essential and they replicate independently of the host
chromosome
In bacteria, the chromosome contains most of the organisms genes
A number of bacteria have additional DNA in the form of plasmids
Plasmids are circular and contain genes that are considered to not be essential to
the bacterium, but may be advantageous under some circumstances
They also replicate independently of the chromosome
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Nucleoid proteins or nucleoid-associated proteins (NAPs) involved in spatial
organization of bacterial DNA
In all types of cells, DNA is organized to make it more compact
In bacteria, there are nucleoid associated proteins that are present with the DNA
There are ways that bacteria have to supercoil the DNA, which allows large lengths
of DNA to be able to fit into a tiny cell
DNA Organization- Eukaryotes
Eukaryotes have linear dsDNA chromosomes within a nucleus (plasmids are
uncommon)
Histone proteins help pack DNA into highly coiled/compact structures
Eukaryotic DNA is also condensed, primarily organized around histone proteins
o Positively charged proteins associated with negatively charged DNA
Histones act as spools tht the DNA is wrapped around
Nucleosomes are formed
Each nucleosome has DNA around the 8 proteins (octamer) that acts as a spool
Chains of nucleosomes are further organized and wrapped into a solenoid spiral
o This also allows the DNA to become more compact
DNA organization- Archaea
Cells contain nucleoid (no nucleus); plasmids may be present
Chromosomal DNA packaged with archaeal histone proteins
Bacteria do not have histones but most archaea do
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Although archaea do not have a nucleus, their DNA is associated with archaeal
histones, which are very similar to eukaryotic histones
Archaeal histones form tetramers rather than octamers
Genetic Elements
Genetic elements include
o Genome
o Chromosome
o Plasmid
o Mobile DNA/elements (e.g., transposons)
o Organelle genome
An organism’s genome is the complete set of DNA sequences (including genes and
non-coding regions)
The core genome is present in all members of a species; the pan genome is the core
plus DNA present in one or more, but not all strains
We normally think of genetic information as being chromosomes, but there are
several things that are considered to be genetic elements
The genome is the largest of these as it includes all of the DNA in an organism
Chromosomes are major, essential genetic elements
Plasmids and mobile DNA are present in some organisms, including many types of
bacteria
Eukaryotes that have things like mitochondria and chloroplasts also have organelle
genomes as these organelles carry their own DNA
When we look at bacteria, because the species are so broad and there are genetic
differences between strains, we sometimes discuss the pan genome and the core
genome
The core genome are the genes and DNA sequences that are shared by all members
of a species
o Alleles may differ but the gene is present in all of them
Some bacterial strains may have genes that are not found in other strains of the
same species
The pan genome includes the core genome and includes any additional genes
present in some, but not all strains of the particular species
Many different strains of Salmonella have been sequences
o A core genome shared by all strains has been identified (contains 2811
genes)
o Individual strains contain unique genes that are not necessarily present in
other types of Salmonella)
Genomics
Genomics- the study of genome(s)
o Sequencing, assembling, analyzing all the DNA of an organism to determine
structure/function
Genomics involves molecular biology and computational/bioinformatics
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