lec 18:Bacterial Genomes and Replication: Structure, Organization, and Regulation

Bacterial Genomes and DNA Structure

DNA: The Genetic Material

DNA (deoxyribonucleic acid) is the primary molecule responsible for storing genetic information in nearly all living organisms. Its structure and function are fundamental to understanding microbial genetics.

• Structure: DNA is a double helix composed of two strands. Each strand contains four types of nitrogenous bases: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). The sugar-phosphate backbone forms the sides of the helix, while base pairs (A–T and C–G) form the rungs.

• Function: DNA encodes the instructions for building and maintaining an organism, and transmits this information across generations.

• Components: Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base.

• Information Encoding: The sequence of bases stores genetic information, analogous to how letters form words.

Location of DNA

• Eukaryotes: DNA is mainly in the nucleus, with some in mitochondria.

• Prokaryotes: DNA is found in the nucleoid region, not enclosed by a membrane.

DNA vs. RNA

While DNA serves as the stable, long-term storage of genetic information, RNA (ribonucleic acid) is involved in gene expression and protein synthesis. Messenger RNA (mRNA) carries instructions from DNA to the ribosome.

• DNA: Double-stranded, contains thymine.

• RNA: Single-stranded, contains uracil instead of thymine.

Genome Organization

Definition and Function

The genome is the complete set of genetic material in an organism, containing all instructions for life. It controls cell structure, metabolism, growth, reproduction, and environmental response.

Genes

A gene is a DNA sequence encoding a functional product, usually a protein.

Genome Organization in Prokaryotes

Basic Characteristics

Prokaryotic genomes are typically compact and efficient, with most DNA coding for proteins.

• Usually one circular chromosome located in the nucleoid region.

• Very little non-coding DNA.

• Genes often organized into operons.

Operons

An operon is a cluster of genes controlled by a single promoter, allowing coordinated expression of related proteins.

• Operons are mainly found in prokaryotes and some viruses.

• Enable rapid response to environmental changes.

Key Components of an Operon

• Promoter: DNA sequence where RNA polymerase binds to start transcription.

• Operator: Regulatory site where proteins bind to turn operon on/off.

• Structural Genes: Encode proteins/enzymes for a metabolic pathway.

• Regulatory Gene: Produces regulatory protein (repressor/activator).

Lac Operon Example

The lac operon in E. coli is an inducible operon activated by lactose. It produces enzymes for lactose metabolism only when lactose is present.

• β-galactosidase (lacZ): Breaks lactose into glucose and galactose.

• Permease (lacY): Transports lactose into the cell.

• Transacetylase (lacA): Assists lactose metabolism.

Plasmids and Secondary Chromosomes

Plasmids

Plasmids are small, circular DNA molecules separate from the main chromosome. They carry accessory genes that provide advantages, such as antibiotic resistance or virulence factors.

• Non-essential for cell survival.

• Can be transferred between bacteria via horizontal gene transfer.

Secondary Chromosomes

Some bacteria possess a second large DNA molecule, called a secondary chromosome, which contains essential housekeeping genes and is required for survival.

• Replication is coordinated with the main chromosome.

• Example: Vibrio cholerae has two chromosomes.

Chromosomization

Over evolutionary time, plasmids can acquire essential genes and become secondary chromosomes, a process known as chromosomization.

Genome Organization in Eukaryotes and Archaea

Eukaryotic Chromosome Structure

Eukaryotic genomes are organized into multiple linear chromosomes located in the nucleus. DNA wraps around histone proteins to form nucleosomes, which further compact into chromatin and chromosomes.

• Humans have 23 pairs of chromosomes.

• DNA packaging allows meters of DNA to fit inside the nucleus.

Histones and Nucleosomes

DNA wraps around histone octamers (H2A, H2B, H3, H4) to form nucleosomes, the basic unit of chromatin structure.

Coding vs Non-Coding DNA

Eukaryotic genomes contain large amounts of non-coding DNA, including introns, regulatory regions, and repetitive sequences. Only about 1–2% of human DNA codes for proteins.

• Coding DNA: Sequences that produce proteins.

• Non-coding DNA: Includes introns, regulatory regions, and repetitive DNA.

Introns and RNA Splicing

Introns are non-coding sequences within genes, transcribed into RNA but removed during RNA processing. Splicing joins exons to form mature mRNA.

• Spliceosome: A complex of snRNAs and proteins that removes introns.

• Self-Splicing Introns: Group I and II introns can self-remove, acting as ribozymes.

Functional Roles of Introns

• Enable alternative splicing, allowing one gene to produce multiple proteins.

• Contain regulatory elements for gene expression.

• Act as a buffer for mutations, protecting coding regions.

• May contain small genes for non-coding RNAs (e.g., miRNAs).

MicroRNAs (miRNAs) and Gene Regulation

MicroRNAs (miRNAs)

MicroRNAs are small non-coding RNAs (19–25 nucleotides) that regulate gene expression post-transcriptionally. They act as molecular switches to control protein production.

Mechanism of miRNA Action

• Target Recognition: miRNA binds to complementary sequences on mRNA via the seed region (nucleotides 2–8).

• RISC Complex Formation: miRNA associates with the RNA-induced silencing complex (RISC) to locate target mRNA.

• Gene Silencing: The miRNA-RISC complex represses translation or degrades mRNA, preventing protein synthesis.

Chromosome Structure in Archaea and Eukaryotes

Archaeal Chromosomes

• Usually one circular chromosome.

• DNA packaged with histone-like proteins.

• Structure is intermediate between bacteria and eukaryotes.

Eukaryotic Chromosomes

• Multiple linear chromosomes located in the nucleus.

• Chromosomes have telomeres, protective ends.

DNA Packaging: Histones

Both Archaea and Eukaryotes use histone proteins to package DNA into nucleosome-like structures, though eukaryotic nucleosomes are more complex.

Replication Origins and Molecular Machinery

• Archaea often have multiple origins of replication, similar to eukaryotes.

• Proteins involved in DNA replication, repair, and transcription in Archaea are more similar to eukaryotic proteins than bacterial ones.