Week 3 - Organisation and Division of
The Bacterial Chromosome
Tuesday, 14 March 2023 16:40
LO1: Describe the basic principles of organisation & division of the bacterial
chromosome
LO2: Appreciate the range of microbial genome sizes & the correlation to
microbial lifestyle
A) Introduction to the bacterial chromosome (how big, how many genes?)
- 1995: First complete bacterial genome sequence
- New Routine
- Many thousands of bacterial genomes have been sequenced
Land et
al.
(2015)
Funct
Integr
Genomi
cs. 15:
141–16
1.
First genomes in 1995:
- Haemophilus influenza (1.8 MB)
- Mycoplasma genitalium (0.5 MB)
- Notice these genome sizes are relatively small, they were the first
microorganisms sequenced
- As can be seen in the graph, the number of genomes sequenced is exponentially
increasing each year
- Important to understand that the detailed information that we have on
genomes is actually relatively NEW
- Before full genome sequencing, we knew lac operon structures and some
genetic structures, but NOT how genes are arranged along the genome,
how big a genome is (is it the same size for any microorganism…), what's
the minimum # of genes needed for an organism to live etc…
- NOW genome sequencing is a routine technique because it has become
, genomes is actually relatively NEW
- Before full genome sequencing, we knew lac operon structures and some
genetic structures, but NOT how genes are arranged along the genome,
how big a genome is (is it the same size for any microorganism…), what's
the minimum # of genes needed for an organism to live etc…
- NOW genome sequencing is a routine technique because it has become
cheaper, and in terms of technique its less laborious to do
- Early years, the genomes were from organisms that could be grown easily in the
lab, meaning lots of genomes could be prepared, extracted and have a lot of
material to work with to get information out of it
- BUT it didn’t tell us much about the different range of bacteria/
microbes that are out in the environment
- EVEN TODAY WE STILL CANT GROW A CULTURE OF EVERY MICROBE
THAT’S OUT THERE IN THE ENVIRONMENT
§ Please please pleaseeee note that yes we cannot grow a
culture of it but we can sequence its genome from a small
wild sample because we don’t need to grow a culture to do
that, it would be redundant
○ Means there's not good representation of the microbes out in the
wild if we only relied on the early techniques of genome
sequencing
○ SO what I'm getting is that the early techniques of genome
sequencing (the ones seen below) needed to be cultured before
sequenced, but because we can't culture every single bacteria there
is, we had a limitation on the representation of wild bacteria and
microbes found in the wild
- Now techniques have been refined so we can use only small amounts of
genomic material that we can get from environmental samples
- BASICALLY BEFORE IT WAS A NUMBERS PROBLEM THAT WE NEEDED LOADS
OF SAMPLE BUT NOW ITS NOT NECESSARY
BEFORE
- Need larger sample by growing a pure strain culture grown in a lab, the large
sample means the technique used to sequence the genome didn't have to be so
elaborate and good
- But, means that certain microbes of certain species taken from an
environmental samples couldn't be grown so we wouldn't get so much genomic
material SO a more sensitive method is needed
NOW
- We developed complicated, sensitive techniques in the past 20 years allowing us
to deal with even teensy amounts of genomic material
- Means we can now sequence environmental samples
- MEANS we now have a much better representation of the microbial fauna out
there in the wild
, to deal with even teensy amounts of genomic material
- Means we can now sequence environmental samples
- MEANS we now have a much better representation of the microbial fauna out
there in the wild
“Traditional” methods now supplemented by:
- Environmental genome sequencing
- Sequence DNA from environmental sample, without isolating & culturing
strains first
- RNA sequencing
- Deep sequencing of RNA to reveal the frequency of different RNA
molecules
- Means we now can: sequence the DNA and know which genes are there, how
many genes are there AND how many of the genes are expressed at any one
point in time
- Done via RNA sequencing because we can sequence both the DNA AND
the RNA to know which of the genes is expressed at a certain condition at
a certain time
Things we got out of all the genome sequencing
1. Some Representative Prokaryotic Genomes
- From all the sequencing done over the past 20 years, we have found…
- Not every microorganism has the same number of genes and not the
same size of their genome
- Mycoplasma genitalium is a microbe that associates with the human host so it
required a lot of material from the human host
- Bacteria are microbes, but not all microbes are bacteria because
microbes are defined as microorganisms causing disease or fermentation
meaning that viruses, bacteria, archaea, fungi and protists are a part of
that group
○ FYI a protist is a protozoan or algae
- Escherichia coli's 4.6MB is very standard size
- Anabaena cylindrica is a cyanobacteria
, meaning that viruses, bacteria, archaea, fungi and protists are a part of
that group
○ FYI a protist is a protozoan or algae
- Escherichia coli's 4.6MB is very standard size
- Anabaena cylindrica is a cyanobacteria
- As you go down, the life style and metabolism of the bacteria gets increasingly
more elaborate
- E.g. M. genitalium has little mega bases (MB) and genes because it uses
material from its human host, compared to S. coelicolor which lives in a
very stressful environment (it's a soil bacterium) so has an unique
necessity to defend itself and have a certain type of metabolism which
requires many more genes to deal with said environment
2. Correlation Between Number of ORFs and Genome Size
- The larger the chromosome, the more genes, the more open reading frames
(ORFs) it contains
- They're roughly proportional, hence the positive correlation in the graph
above
- ORF delineates the boundaries of a gene (the span of DNA sequence between
a start codon and a stop codon)
- ORF are essentially a proxy for a gene
- They're a portion of a DNA molecule that when translated into amino
acids contain no stop codons
- Different to what is seen in eukaryotes where there are many non-coding
regions, in prokaryotes essentially every nucleotide in the chromosome counts
- I must be missing something because I swear this is obvious? If you have more
mega bases obviously you're going to have more genes??? It's like if you keep
adding charms on a bracelet CLEARLY YOU'LL HAVE A LONGER BRACELET
Q1: What is the relationship between genome size, number of genes (ORFs) and
complexity of the bacterial organism?
- As the genome size increases so does the number of open reading frames (ORF)
The Bacterial Chromosome
Tuesday, 14 March 2023 16:40
LO1: Describe the basic principles of organisation & division of the bacterial
chromosome
LO2: Appreciate the range of microbial genome sizes & the correlation to
microbial lifestyle
A) Introduction to the bacterial chromosome (how big, how many genes?)
- 1995: First complete bacterial genome sequence
- New Routine
- Many thousands of bacterial genomes have been sequenced
Land et
al.
(2015)
Funct
Integr
Genomi
cs. 15:
141–16
1.
First genomes in 1995:
- Haemophilus influenza (1.8 MB)
- Mycoplasma genitalium (0.5 MB)
- Notice these genome sizes are relatively small, they were the first
microorganisms sequenced
- As can be seen in the graph, the number of genomes sequenced is exponentially
increasing each year
- Important to understand that the detailed information that we have on
genomes is actually relatively NEW
- Before full genome sequencing, we knew lac operon structures and some
genetic structures, but NOT how genes are arranged along the genome,
how big a genome is (is it the same size for any microorganism…), what's
the minimum # of genes needed for an organism to live etc…
- NOW genome sequencing is a routine technique because it has become
, genomes is actually relatively NEW
- Before full genome sequencing, we knew lac operon structures and some
genetic structures, but NOT how genes are arranged along the genome,
how big a genome is (is it the same size for any microorganism…), what's
the minimum # of genes needed for an organism to live etc…
- NOW genome sequencing is a routine technique because it has become
cheaper, and in terms of technique its less laborious to do
- Early years, the genomes were from organisms that could be grown easily in the
lab, meaning lots of genomes could be prepared, extracted and have a lot of
material to work with to get information out of it
- BUT it didn’t tell us much about the different range of bacteria/
microbes that are out in the environment
- EVEN TODAY WE STILL CANT GROW A CULTURE OF EVERY MICROBE
THAT’S OUT THERE IN THE ENVIRONMENT
§ Please please pleaseeee note that yes we cannot grow a
culture of it but we can sequence its genome from a small
wild sample because we don’t need to grow a culture to do
that, it would be redundant
○ Means there's not good representation of the microbes out in the
wild if we only relied on the early techniques of genome
sequencing
○ SO what I'm getting is that the early techniques of genome
sequencing (the ones seen below) needed to be cultured before
sequenced, but because we can't culture every single bacteria there
is, we had a limitation on the representation of wild bacteria and
microbes found in the wild
- Now techniques have been refined so we can use only small amounts of
genomic material that we can get from environmental samples
- BASICALLY BEFORE IT WAS A NUMBERS PROBLEM THAT WE NEEDED LOADS
OF SAMPLE BUT NOW ITS NOT NECESSARY
BEFORE
- Need larger sample by growing a pure strain culture grown in a lab, the large
sample means the technique used to sequence the genome didn't have to be so
elaborate and good
- But, means that certain microbes of certain species taken from an
environmental samples couldn't be grown so we wouldn't get so much genomic
material SO a more sensitive method is needed
NOW
- We developed complicated, sensitive techniques in the past 20 years allowing us
to deal with even teensy amounts of genomic material
- Means we can now sequence environmental samples
- MEANS we now have a much better representation of the microbial fauna out
there in the wild
, to deal with even teensy amounts of genomic material
- Means we can now sequence environmental samples
- MEANS we now have a much better representation of the microbial fauna out
there in the wild
“Traditional” methods now supplemented by:
- Environmental genome sequencing
- Sequence DNA from environmental sample, without isolating & culturing
strains first
- RNA sequencing
- Deep sequencing of RNA to reveal the frequency of different RNA
molecules
- Means we now can: sequence the DNA and know which genes are there, how
many genes are there AND how many of the genes are expressed at any one
point in time
- Done via RNA sequencing because we can sequence both the DNA AND
the RNA to know which of the genes is expressed at a certain condition at
a certain time
Things we got out of all the genome sequencing
1. Some Representative Prokaryotic Genomes
- From all the sequencing done over the past 20 years, we have found…
- Not every microorganism has the same number of genes and not the
same size of their genome
- Mycoplasma genitalium is a microbe that associates with the human host so it
required a lot of material from the human host
- Bacteria are microbes, but not all microbes are bacteria because
microbes are defined as microorganisms causing disease or fermentation
meaning that viruses, bacteria, archaea, fungi and protists are a part of
that group
○ FYI a protist is a protozoan or algae
- Escherichia coli's 4.6MB is very standard size
- Anabaena cylindrica is a cyanobacteria
, meaning that viruses, bacteria, archaea, fungi and protists are a part of
that group
○ FYI a protist is a protozoan or algae
- Escherichia coli's 4.6MB is very standard size
- Anabaena cylindrica is a cyanobacteria
- As you go down, the life style and metabolism of the bacteria gets increasingly
more elaborate
- E.g. M. genitalium has little mega bases (MB) and genes because it uses
material from its human host, compared to S. coelicolor which lives in a
very stressful environment (it's a soil bacterium) so has an unique
necessity to defend itself and have a certain type of metabolism which
requires many more genes to deal with said environment
2. Correlation Between Number of ORFs and Genome Size
- The larger the chromosome, the more genes, the more open reading frames
(ORFs) it contains
- They're roughly proportional, hence the positive correlation in the graph
above
- ORF delineates the boundaries of a gene (the span of DNA sequence between
a start codon and a stop codon)
- ORF are essentially a proxy for a gene
- They're a portion of a DNA molecule that when translated into amino
acids contain no stop codons
- Different to what is seen in eukaryotes where there are many non-coding
regions, in prokaryotes essentially every nucleotide in the chromosome counts
- I must be missing something because I swear this is obvious? If you have more
mega bases obviously you're going to have more genes??? It's like if you keep
adding charms on a bracelet CLEARLY YOU'LL HAVE A LONGER BRACELET
Q1: What is the relationship between genome size, number of genes (ORFs) and
complexity of the bacterial organism?
- As the genome size increases so does the number of open reading frames (ORF)
