Bacterial Genome

Marina Lowang
UID-20MSZ1109
The word “genome,” coined by German botanist Hans
Winkler in 1920, was derived simply by combining gene and the final
syllable of chromosome. An organism’s genome is defined as the
complete haploid genetic complement of a typical cell.In diploid
organisms, sequence variations exist between the two copies of each
chromosome present in a cell. The genome is the ultimate source of
information.
Bacterial genomes are generally smaller and less variant in size
among species when compared with genomes of eukaryotes.
Bacterial genomes can range in size anywhere from about 130 kbp to
over 14 Mbp. In bacteria, the chromosome is not enclosed by a
membrane but is instead located in the nucleoid. The nucleoid is the
cytoplasmic location of the bacterial genetic material.

Bacteria possess a compact genome architecture distinct from

eukaryotes in two important ways: bacteria show a strong
correlation between genome size and number of functional genes in
a genome, and those genes are structured into operons. The main
reason for the relative density of bacterial genomes compared to
eukaryotic genomes (especially multicellular eukaryotes) is the
presence of noncoding DNA in the form of intergenic regions and
introns. Some notable exceptions include recently formed
pathogenic bacteria. This was initially described in a study by Cole et
al. in which Mycobacterium leprae was discovered to have a
significantly higher percentage of pseudogenes to functional genes
(~40%) than its free-living ancestors.
Furthermore, amongst species of bacteria, there is relatively little
variation in genome size when compared with the genome sizes of
other major groups of life. Genome size is of little relevance when
considering the number of functional genes in eukaryotic species. In
bacteria, however, the strong correlation between the number of
genes and the genome size makes the size of bacterial genomes an
interesting topic for research and discussion.
The general trends of bacterial evolution indicate that bacteria
started as free-living organisms. Evolutionary paths led some
bacteria to become pathogens and symbionts. The lifestyles of
bacteria play an integral role in their respective genome sizes. Free-
living bacteria have the largest genomes out of the three types of
bacteria; however, they have fewer pseudogenes than bacteria that
have recently acquired pathogenicity.
Facultative and recently evolved pathogenic bacteria exhibit a
smaller genome size than free-living bacteria, yet they have more
pseudogenes than any other form of bacteria.
Obligate bacterial symbionts or pathogens have the smallest
genomes and the fewest pseudogenes of the three groups. The
relationship between life-styles of bacteria and genome size raises
questions as to the mechanisms of bacterial genome evolution.
Researchers have developed several theories to explain the patterns
of genome size evolution amongst bacteria.
Genome comparisons and phylogeny
As single-gene comparisons have largely given way to genome
comparisons, phylogeny of bacterial genomes have improved in
accuracy. The Average Nucleotide Identity (ANI) method quantifies
genetic distance between entire genomes by taking advantage of
regions of about 10,000 bp. With enough data from genomes of one
genus, algorithms are executed to categorize species. This has been
done for the Pseudomonas avellanae species in 2013 and for all
sequenced bacteria and archaea since 2020.
To extract information about bacterial genomes, core- and pan-
genome sizes have been assessed for several strains of bacteria. In
2012, the number of core gene families was about 3000. However,
by 2015, with an over tenfold increased in available genomes, the
pan-genome has increased as well. There is roughly a positive
correlation between the number of genomes added and the growth
of the pan-genome. On the other hand, the core genome has remain
static since 2012. Currently, the E. coli pan-genome is composed of
about 90,000 gene families. About one-third of these exist only in a
single genome. Many of these, however, are merely gene fragments
and the result of calling errors. Still, there are probably over 60,000
unique gene families in E. coli.
 The number of universally maintained genes is small and
inadequate for independent cellular growth and replication, so that
small genome species must achieve such feats by means of varying
genes. This is done partly through nonorthologous gene
displacement. That is, the role of one gene is replaced by another
gene that achieves the same function. Redundancy within the
ancestral, larger genome is eliminated. The descendant small
genome content depends on the content of chromosomal deletions
that occur in the early stages of genome reduction.

The very small genome of M. genitalium possesses dispensable

genes. In a study in which single genes of this organism were
inactivated using transposon-mediated mutagenesis, at least 129 of
its 484 ORGs were not required for growth. A much smaller genome
than that of the M. genitalium is therefore feasible.
Doubling time
One theory predicts that bacteria have smaller genomes due to a
selective pressure on genome size to ensure faster replication. The
theory is based upon the logical premise that smaller bacterial
genomes will take less time to replicate. Subsequently, smaller
genomes will be selected preferentially due to enhanced fitness. A
study done by Mira et al. indicated little to no correlation between
genome size and doubling time. The data indicates that selection is
not a suitable explanation for the small sizes of bacterial genomes.
Still, many researchers believe there is some selective pressure on
bacteria to maintain small genome size.
Deletional bias
Selection is but one process involved in evolution. Two other major
processes (mutation and genetic drift) can account for the genome
sizes of various types of bacteria. A study done by Mira et al.
examined the size of insertions and deletions in bacterial
pseudogenes. Results indicated that mutational deletions tend to be
larger than insertions in bacteria in the absence of gene transfer or
gene duplication. Insertions caused by horizontal or lateral gene
transfer and gene duplication tend to involve transfer of large
amounts of genetic material. Assuming a lack of these processes,
genomes will tend to reduce in size in the absence of selective
constraint. Evidence of a deletional bias is present in the respective
genome sizes of free-living bacteria, facultative and recently derived
parasites and obligate parasites and symbionts.

Free-living bacteria tend to have large population-sizes and are

subject to more opportunity for gene transfer. As such, selection can
effectively operate on free-living bacteria to remove deleterious
sequences resulting in a relatively small number of pseudogenes.
Continually, further selective pressure is evident as free-living
bacteria must produce all gene-products independent of a host.
Given that there is sufficient opportunity for gene transfer to occur
and there are selective pressures against even slightly deleterious
deletions, it is intuitive that free-living bacteria should have the
largest bacterial genomes of all bacteria types.
Recently-formed parasites undergo severe bottlenecks and can
rely on host environments to provide gene products. As such, in
recently-formed and facultative parasites, there is an accumulation
of pseudogenes and transposable elements due to a lack of selective
pressure against deletions. The population bottlenecks reduce gene
transfer and as such, deletional bias ensures the reduction of
genome size in parasitic bacteria.
Obligatory parasites and symbionts have the smallest genome
sizes due to prolonged effects of deletional bias. Parasites which
have evolved to occupy specific niches are not exposed to much
selective pressure. As such, genetic drift dominates the evolution of
niche-specific bacteria. Extended exposure to deletional bias ensures
the removal of most superfluous sequences. Symbionts occur in
drastically lower numbers and undergo the most severe bottlenecks
of any bacterial type. There is almost no opportunity for gene
transfer for endosymbiotic bacteria, and thus genome compaction
can be extreme. One of the smallest bacterial genomes ever to be
sequenced is that of the endosymbiont Carsonella rudii. At 160 kbp,
the genome of Carsonella is one of the most streamlined examples of
a genome examined to date.

Genomic reduction
Molecular phylogenetics has revealed that every clade of bacteria
with genome sizes under 2 Mb was derived from ancestors with
much larger genomes, thus refuting the hypothesis that bacteria
evolved by the successive doubling of small-genomed
ancestors.Recent studies performed by Nilsson et al. examined the
rates of bacterial genome reduction of obligate bacteria. Bacteria
were cultured introducing frequent bottlenecks and growing cells in
serial passage to reduce gene transfer so as to mimic conditions of
endosymbiotic bacteria. The data predicted that bacteria exhibiting a
one-day generation time lose as many as 1,000 kbp in as few as
50,000 years (a relatively short evolutionary time period).
Furthermore, after deleting genes essential to the methyl-directed
DNA mismatch repair (MMR) system, it was shown that bacterial
genome size reduction increased in rate by as much as 50
times.These results indicate that genome size reduction can occur
relatively rapidly, and loss of certain genes can speed up the process
of bacterial genome compaction.
This is not to suggest that all bacterial genomes are reducing in
size and complexity. While many types of bacteria have reduced in
genome size from an ancestral state, there are still a huge number of
bacteria that maintained or increased genome size over ancestral
states. Free-living bacteria experience huge population sizes, fast
generation times and a relatively high potential for gene transfer.
While deletional bias tends to remove unnecessary sequences,
selection can operate significantly amongst free-living bacteria
resulting in evolution of new genes and processes.
Horizontal gene transfer
Unlike eukaryotes, which evolve mainly through the modification of
existing genetic information, bacteria have acquired a large
percentage of their genetic diversity by the horizontal transfer of
genes. This creates quite dynamic genomes, in which DNA can be
introduced into and removed from the chromosome.
Bacteria have more variation in their metabolic properties,
cellular structures, and lifestyles than can be accounted for by point
mutations alone.
Horizontal gene transfer is often detected via DNA sequence
information. DNA segments obtained by this mechanism often reveal
a narrow phylogenetic distribution between related species.
Furthermore, these regions sometimes display an unexpected level
of similarity to genes from taxa that are assumed to be quite
divergent.
Although gene comparisons and phylogenetic studies are helpful in
investigating horizontal gene transfer, the DNA sequences of genes
are even more revelatory of their origin and ancestry within a
genome. Bacterial species differ widely in overall GC content,
although the genes in any one species' genome are roughly identical
with respect to base composition, patterns of codon usage, and
frequencies of di- and trinucleotides. As a result, sequences that are
newly acquired through lateral transfer can be identified via their
characteristics, which remains that of the donor. For example, many
of the S. enterica genes that are not present in E. coli have base
compositions that differ from the overall 52% GC content of the
entire chromosome. Within this species, some lineages have more
than a megabase of DNA that is not present in other lineages. The
base compositions of these lineage-specific sequences imply that at
least half of these sequences were captured through lateral transfer.
Furthermore, the regions adjacent to horizontally obtained genes
often have remnants of translocatable elements, transfer origins of
plasmids, or known attachment sites of phage integrases.
In some species, a large proportion of laterally transferred genes
originate from plasmid-, phage-, or transposon-related sequences.
Although sequence-based methods reveal the prevalence of
horizontal gene transfer in bacteria, the results tend to be
underestimates of the magnitude of this mechanism, since
sequences obtained from donors whose sequence characteristics are
similar to those of the recipient will avoid detection.
Comparisons of completely sequenced genomes confirm that
bacterial chromosomes are amalgams of ancestral and laterally
acquired sequences. The hyperthermophilic Eubacteria Aquifex
aeolicus and Thermotoga maritima each has many genes that are
similar in protein sequence to homologues in thermophilic Archaea.
24% of Thermotoga's 1,877 ORFs and 16% of Aquifex's 1,512 ORFs
show high matches to an Archaeal protein, while mesophiles such as
E. coli and B. subtilis have far lesser proportions of genes that are
most like Archaeal homologues.
Mechanisms of lateral transfer
The genesis of new abilities due to horizontal gene transfer has three
requirements. First, there must exist a possible route for the donor
DNA to be accepted by the recipient cell. Additionally, the obtained
sequence must be integrated with the rest of the genome. Finally,
these integrated genes must benefit the recipient bacterial organism.
The first two steps can be achieved via three mechanisms:
 Transformation,
 Transduction and
 Conjugation
Transformation involves the uptake of named DNA from the
environment. Through transformation, DNA can be transmitted
between distantly related organisms. Some bacterial species, such as
Haemophilus influenzae and Neisseria gonorrhoeae, are
continuously competent to accept DNA. Other species, such as
Bacillus subtilis and Streptococcus pneumoniae, become competent
when they enter a particular phase in their lifecycle.

Transformation in N. gonorrhoeae and H. influenzae is effective only

if particular recognition sequences are found in the recipient
genomes (5'-GCCGTCTGAA-3' and 5'-AAGTGCGGT-3'. respectively).
Although the existence of certain uptake sequences improve
transformation capability between related species, many of the
inherently competent bacterial species, such as B. subtilis and S.
pneumoniae, do not display sequence preference.
New genes may be introduced into bacteria by a
bacteriophage that has replicated within a donor through
generalized transduction or specialized transduction. The amount of
DNA that can be transmitted in one event is constrained by the size
of the phage capsid (although the upper limit is about 100 kilobases).
While phages are numerous in the environment, the range of
microorganisms that can be transduced depends on receptor
recognition by the bacteriophage. Transduction does not require
both donor and recipient cells to be present simultaneously in time
nor space. Phage-encoded proteins both mediate the transfer of
DNA into the recipient cytoplasm and assist integration of DNA into
the chromosome.
Conjugation involves physical contact between donor and recipient
cells and is able to mediate transfers of genes between domains,
such as between bacteria and yeast. DNA is transmitted from donor
to recipient either by self-transmissible or mobilizable plasmid.
Conjugation may mediate the transfer of chromosomal sequences by
plasmids that integrate into the chromosome.
Despite the multitude of mechanisms mediating gene transfer
among bacteria, the process's success is not guaranteed unless the
received sequence is stably maintained in the recipient. DNA
integration can be sustained through one of many processes. One is
persistence as an episome, another is homologous recombination,
and still another is illegitimate incorporation through lucky double-
strand break repair.
Traits introduced through lateral gene transfer
Antimicrobial resistance genes grant an organism the ability to grow
its ecological niche, since it can now survive in the presence of
previously lethal compounds. As the benefit to a bacterium earned
from receiving such genes are time- and space-independent, those
sequences that are highly mobile are selected for. Plasmids are quite
mobilizable between taxa and are the most frequent way by which
bacteria acquire antibiotic resistance genes.
Adoption of a pathogenic lifestyle often yields a fundamental
shift in an organism's ecological niche. The erratic phylogenetic
distribution of pathogenic organisms implies that bacterial virulence
is a consequence of the presence, or obtainment of, genes that are
missing in avirulent forms. Evidence of this includes the discovery of
large 'virulence' plasmids in pathogenic Shigella and Yersinia, as well
as the ability to bestow pathogenic properties onto E. coli via
experimental exposure to genes from other species.
References:
https://en.wikipedia.org/wiki/Bacterial_genome
https://micro.cornell.edu/research/epulopiscium/bacterial-genomes
https://www.ncbi.nlm.nih.gov/genome/microbes/
https://www.sciencedirect.com/topics/biochemistry-genetics-and-
molecular-biology/bacterial-genome