BS1040 Topic 4 Lecture 1 The bacterial genome

Who coined the term "genome" and when?

Hans Winkler in 1920.

What is the modern definition of a genome?

All DNA within a cell, including chromosome(s), plasmids, and other genetic elements.

What is genomics?

The study of genomes and genome sequences through mapping, sequencing, and characterization.

What is the typical structure of a bacterial chromosome?

Usually a single circular double-stranded DNA molecule; may be linear or multiple in some species.

Give examples of bacteria with unusual chromosome arrangements.

Borrelia burgdorferi - linear; Vibrio cholerae - two circular chromosomes.

Where is the bacterial chromosome located?

In the nucleoid, a non-membrane-bound region of the cytoplasm.

How is the bacterial chromosome compacted?

Into supercoiled domain loops bound by histone-like proteins such as HU.

How large is the E. coli chromosome?

4.639 Mbp (~1.5 mm long), 500-1000× the cell's length.

What is binary fission?

A form of asexual reproduction where one bacterial cell divides into two identical daughter cells.

What happens during binary fission?

The chromosome replicates, the cell elongates, and a septum forms at midcell to divide the cytoplasm.

What is the origin of replication (oriC)?

The DNA site where replication begins, forming two replication forks.

What is the termination point (terC)?

The site where replication forks meet and DNA synthesis ends.

What does bidirectional replication mean?

DNA replication proceeds in two opposite directions from oriC until the forks meet at terC.

What is the function of the FtsZ protein?

Forms a Z-ring at the midcell to initiate septum formation and cell division.

How is chromosome replication coordinated with cell division?

Replication completion triggers FtsZ assembly, ensuring chromosomes are separated before division.

How does growth rate influence DNA replication frequency?

Faster-growing cells can start new rounds of replication before the previous one finishes.

Can E. coli divide faster than it replicates its genome?

Yes - replication takes 40 minutes, but E. coli can divide every 20 minutes by overlapping replication rounds.

What are extrachromosomal genetic elements?

DNA molecules outside the main chromosome, such as plasmids, bacteriophages, and transposons.

What are plasmids?

Small circular DNA molecules that replicate independently of the chromosome and often carry adaptive genes.

Are plasmids essential for bacterial survival?

No, but they provide selective advantages under specific conditions.

What is the size range of plasmids?

Thousands to hundreds of thousands of base pairs.

What is the origin of replication in plasmids?

The oriV site.

How is plasmid replication regulated?

By control systems linked to initiation frequency at oriV; determines copy number per cell.

What are incompatibility groups?

Plasmids with similar replication mechanisms that cannot coexist in the same cell.

Give examples of plasmid copy numbers.

F plasmid - 1 copy; R6 - 5-6 copies; ColE1 - ~15 copies.

What are conjugative plasmids?

Plasmids capable of transferring themselves between cells via conjugation (e.g., F and P plasmids).

What are resistance plasmids (R plasmids)?

Plasmids that carry genes for antibiotic or metal resistance.

What are Ti plasmids?

Tumour-inducing plasmids in Agrobacterium used in plant genetic engineering.

What is a bacteriophage?

A virus that infects bacteria ("bacteria eater").

How were bacteriophages discovered?

By Twort and d'Herelle in the 1920s.

How are phages detected?

By plaques—clear zones on a bacterial lawn where cells have lysed.

What is a prophage?

A phage genome inserted into the bacterial chromosome, not undergoing the lytic cycle.

What are insertion sequences (IS)?

Short DNA segments that can move (transpose) within the genome using transposase.

What are transposons?

Mobile genetic elements that can carry additional "cargo" genes, often including antibiotic resistance genes.

What is transposition?

The process by which transposons move between chromosomal, plasmid, or phage DNA.

Why is transposition important?

It spreads antibiotic resistance and promotes genetic diversity but can be mutagenic.

What is horizontal gene transfer (HGT)?

The exchange of genetic material between bacteria, either within or across species.

What is the benefit of HGT?

Allows rapid acquisition of new traits, promoting adaptation and evolution.

What are the three main mechanisms of HGT?

Conjugation, transformation, and transduction.

What is conjugation?

Transfer of DNA (usually plasmid) directly between bacterial cells via a pilus.

What is transformation?

Uptake of naked DNA from the environment by competent cells.

What is transduction?

Transfer of bacterial DNA by a bacteriophage.

Why is studying genomes important?

Genomes reveal an organism's metabolism, phylogeny, virulence, gene expression, and ecological roles.

What was the first sequenced gene?

The bacteriophage MS2 coat protein gene in 1972.

What was the first sequenced genome?

The RNA genome of bacteriophage MS2 (3569 nts) in 1976.

What was the first sequenced DNA genome?

Bacteriophage ΦX174 (5368 nts) in 1977.

What was the first bacterial genome sequenced?

Haemophilus influenzae (1.83 Mbp) in 1995.

What was the first eukaryotic genome sequenced?

Saccharomyces cerevisiae (12.5 Mbp) in 1996.

When was the human genome reported?

In 2003, with ~3.3 billion nucleotides.

Which organism has the largest known genome?

The Japanese flower Paris japonica - 149 billion nucleotides.

What is the relationship between genome size and bacterial capabilities?

Larger genomes correlate with more metabolic pathways, regulation, and structural complexity.

What is the smallest known free-living bacterial genome?

Mycoplasma genitalium - 580,074 nucleotides and 483 genes.

What is the smallest known endosymbiont genome?

Candidatus Tremblaya princeps - 138 kb with 167 genes.

What is a minimal gene set?

The smallest collection of genes required for a cell to grow and replicate.

What causes genetic variation in bacteria?

Mutations, recombination, and acquisition of new DNA via genetic elements.

What is the mutation rate in bacteria?

~10⁻⁵ per base pair per replication (reduced to 10⁻¹⁰ with repair mechanisms).

What is a pangenome?

The entire set of genes found across all strains of a species.

What is the core genome?

Genes shared by all strains of a species.

What is the non-core (accessory) genome?

Genes found only in some strains, often acquired via horizontal gene transfer.

What is an open pangenome?

A species with extensive horizontal gene transfer, resulting in many variable genes.

What is a closed pangenome?

A species with limited horizontal gene transfer, resulting in fewer variable genes.