DNA and Bacterial Chromosomes

DNA: The Genetic Material

• DNA is the genetic material, storing information for producing an organism
• DNA's instructions are carried out through its base sequence
• DNA is necessary for synthesizing RNA and cellular proteins
• DNA also replicates chromosomes, ensuring proper chromosome segregation and compaction within the cell (fitting the cell).

Bacterial Chromosomes

• Typically circular and a few million base pairs long
• Examples, E. coli ~4.6 million base pairs, Haemophilus influenzae ~1.8 million base pairs
• Contain thousands of genes, mostly protein-encoding
• Intergenic regions are non-transcribed DNA segments between genes
• Repetitive sequences play roles in DNA folding, gene regulation and genetic recombination.

Chromosomes and Genomes

• Chromosomes are structures containing genetic material; a genome is all genetic material in an organism
• Bacterial genomes are typically a single circular chromosome
• Eukaryotic genomes include a nuclear genome (complete set of nuclear chromosomes) and potential additional mitochondrial and chloroplast genomes (in plants).

Bacterial Chromosome Structure

• Located in the nucleoid region of the cell
• Not surrounded by a membrane
• DNA is in direct contact with the cytoplasm

Bacterial Chromosome Compaction

• DNA must be compacted ~1000-fold to fit within the bacterial cell
• The chromosome has a central core with loops called microdomains emanating from the core.
• Microdomains are typically ~10,000 bp in length.
• Adjacent microdomains are typically organized into macrodomains, which are 800-1000 kbp long
• Nucleoid-associated proteins (NAPs) form the micro and macro domains.
• NAPs act as bridges, compressing DNA and helping to organize it into distinct regions.

DNA Supercoiling

• Twisting forces on DNA result in supercoiling, where DNA coils around each other
• Supercoiling can either be positive (overwinding) or negative (undertwisting), differing in supercoiling levels
• DNA structures differing in supercoiling are topoisomers of one another
• Supercoiling is a structural strain related to DNA conformation (coiling patterns)
• Supercoiling relieves tension from helical stress, which occurs during processes like DNA replication and transcription when DNA separates.
• Negative supercoiling is common in bacteria, contributing to chromosome compaction and enhancing processes like DNA replication and transcription.
• DNA gyrase (topoisomerase II) and topoisomerase I control supercoiling in bacteria; topoisomerase I relaxes negative supercoils, while DNA gyrase creates negative supercoils using energy from ATP
• Supercoiling is targeted by certain drugs for curing bacterial diseases.

Eukaryotic Chromosomes

• Consist of one or more sets of chromosomes
• Each set contains several different linear chromosomes.
• Chromosomes are tens or hundreds of millions of base pairs long
• Contain origins of replication, centromeres (segregation during mitosis and meiosis), kinetochore proteins, and telomeres (prevent translocation and maintain chromosome length).

Eukaryotic Genes

• Located between telomeric regions
• Single chromosome has hundreds to thousands of genes
• Less complex eukaryotes (like yeast) have relatively short genes concentrated on primarily coding polypeptides.
• More complex eukaryotes like mammals have longer genes, with many introns (non-coding intervening sequences).

Sizes of Eukaryotic Genomes

• Genome size varies considerably amongst species (sometimes due to more genes)
• Size variation in closely related species is often due to repetitive DNA sequences (not extra genes).
• Repetitive sequences may not have coding functions for proteins.

Sequence Complexity

• Complexity refers to the number of times a particular base sequence appears in a genome.
• Classifications of repetitive sequences include: unique/non-repetitive, moderately repetitive, and highly repetitive.

Unique and Repetitive Sequences

• Unique/(non-repetitive) sequences: Found once or a few times, including protein-coding genes and other non-coding DNA
• Moderately repetitive sequences: Found a few hundred to thousands of times, including rRNA genes and transposable elements (TEs).
• Highly repetitive sequences: Found tens of thousands to millions of times, often found in centromeric regions, and with functions not fully understood.
• TEs are segments of DNA that can move, sometimes increasing the number of copies in several different locations within a genome.

Transposition Pathways

• Two transposition pathways exist: simple and retrotransposition.
• Simple transposition: Mechanism: A cut-and-paste mechanism where the transposable element (TE) is removed from its original location and inserted into a new location.
• Retrotransposition: Mechanism: A TE is transcribed into RNA, then reverse transcriptase creates a DNA copy that is inserted into a new location.
• These TEs are called transposons or retroelements.

Transposons

• Simple transposons consist of flanking direct repeats, inverted repeats, and a transposase gene
• Example: antibiotic resistance gene is found in a transposon.
• Retrotransposons (e.g., LTRs and non-LTRs) are based on RNA intermediates using reverse transcription
• Autonomous elements include all necessary information for transposition, whereas non-autonomous elements lack necessary information and rely on autonomous elements.

Transposase

• Enzyme responsible for cutting and rejoining DNA during transposition
• Binds to inverted repeats (IRs), causing DNA cleavage between IRs and direct repeats (DRs).
• Excises TE from the chromosome and inserts it into another location

Transposable Elements Influence on Mutation and Evolution

• Researchers have discovered that transposable elements are present in most species' genomes.
• They can rapidly enter and proliferate within a genome
• Transposable sequences can affect chromosome structure, gene expression, and other processes.

Biological Significance of Transposable Elements

• Selfish DNA hypothesis: TEs exist due to their capability to proliferate within a host organism without substantially harming it (like parasitic behavior)
• TEs can offer adaptive advantages, such as carrying antibiotic resistance genes, causing exon shuffling in genes to enhance functionality by adding exons
• TEs can be harmful, e.g causing hybrid dysgenesis and disruptions of chromosomal structure (and gene activity)

Negative Effects of Transposable Elements

• Transposition can disrupt chromosomal structure and gene expression
• Transposition can be stimulated by radiation, mutagens, or hormones and cause chromosomal issues such as abnormalities and sterility.