Test 3 (Lecture 1) Genomes & Virology: Structure, Diversity, and Sequencing in Microbiology

Genomes & Virology

Overview of Genomes in Microbiology

Microbial genomes vary widely in size and complexity, reflecting the diversity of life forms from viruses to bacteria, archaea, and eukaryotes. Understanding genome structure and sequencing is fundamental to microbiology, as it informs on organismal capabilities, evolutionary relationships, and pathogenic potential.

• Genome: The complete set of genetic material (DNA or RNA) in an organism.

• Genome size: Measured in base pairs (bp), kilobase pairs (kbp), or megabase pairs (Mbp).

• Gene density: Typically, 1 gene per 1000 base pairs in bacteria; each gene codes for a protein of about 300 amino acids.

Comparative Genome Sizes

Genome sizes differ significantly among viruses, bacteria, archaea, and eukaryotes. The following table summarizes these differences:

Organism Type	Genome Size	Example
Plant/Eukaryote	Very large (up to billions of bp)	Human (3.2 Gbp)
Bacteria	Moderate (0.5–10 Mbp)	Escherichia coli (4.6 Mbp)
Archaea	Similar to bacteria	Halobacterium (2.6 Mbp)
Bacteriophage (virus infecting bacteria)	Smallest (3.5 kbp–0.5 Mbp)	Lambda phage
Other Viruses	Up to 2.5 Mbp	Mimivirus

Key Point: Plant and animal genomes are much larger than those of bacteria, archaea, or viruses. Bacteriophages have the smallest genomes.

Genome Sequencing in Microbiology

Genome sequencing allows scientists to determine the complete DNA sequence of an organism, providing insights into its biology and evolution.

• First bacterial genome sequenced: Haemophilus influenzae in 1995 (1.8 million base pairs, ~1700 genes).

• Sequencing methods: Modern techniques allow rapid sequencing and comparison of genomes.

• Applications: Identifying pathogenicity, metabolic capabilities, and evolutionary relationships.

Table: Select Prokaryotic Genomes (from Table 10.1)

This table compares genome sizes and features among various prokaryotes:

Organism	Type	Genome Size (Mbp)	Genes	Comment
Haemophilus influenzae	Bacteria	1.8	~1700	First sequenced bacterial genome
Mycoplasma genitalium	Bacteria	0.58	~470	Obligate pathogen, minimal genome
Pseudomonas aeruginosa	Bacteria	6.3	~5600	Large genome, environmental adaptability
Halobacterium	Archaea	2.6	~2500	Archaeal genome

Additional info: Endosymbionts and obligate pathogens tend to have smaller genomes due to dependence on host functions.

Pan Genome and Core Genome

Definitions and Concepts

The core genome consists of genes shared by all strains of a species, while the pan genome includes all genes found in any strain, encompassing both core and accessory genes.

• Core genome: Essential genes for basic cellular functions.

• Pan genome: Includes core genes plus strain-specific genes, often acquired via horizontal gene transfer.

• Accessory genome: Genes present in some but not all strains, often related to adaptation or pathogenicity.

Example: Different E. coli strains share a core genome but differ in accessory genes that confer specific virulence factors and disease symptoms.

Pathogenicity Islands

Pathogenicity islands are regions of the genome containing clusters of genes that contribute to an organism's ability to cause disease.

• Definition: Genomic regions acquired via horizontal gene transfer, often encoding toxins, secretion systems, or antibiotic resistance.

• Example: Pseudomonas aeruginosa has multiple pathogenicity islands, while Mycoplasma genitalium has none.

Genome Adaptation and Environmental Interaction

Organisms exposed to diverse environments tend to have larger genomes, allowing for greater adaptability.

• Obligate pathogens: Smaller genomes, rely on host for many functions.

• Free-living bacteria: Larger genomes, more self-reliant.

Additional info: About 1300 genes are required for an organism to be considered "free-living"; 250–300 genes are needed to create a minimal cell capable of basic life functions.