DNA and Bacterial Chromosomes

DNA: The Genetic Material

• DNA is the genetic material that determines an organism's characteristics.
• It stores the information required to build and maintain an organism.
• The DNA molecule carries this information through its base sequence.
• DNA sequences are necessary for RNA and protein synthesis.
• DNA sequences are also necessary for chromosome replication and proper segregation.
• DNA is compacted so it fits into the cell.

Bacterial Chromosomes

• Bacterial chromosomes are usually circular molecules.
• Bacterial chromosomes are a few million base pairs (bps) long.
• E. coli chromosomes are approximately 4.6 million bps long.
• Haemophilus influenzae chromosomes are approximately 1.8 million bps long.
• A typical bacterial chromosome contains several thousand genes.
• Protein-encoding genes are the majority of bacterial DNA.
• Intergenic regions are the nontranscribed DNA segments between genes.
• Repetitive sequences play various roles in DNA structure, gene regulation, and recombination.
• The origin of replication is the initiation site for DNA replication.
• Bacterial chromosomes are located in the nucleoid region of the bacterial cell.
• The nucleoid is not membrane-bound.
• To fit within the bacterial cell, the chromosomal DNA is compacted about 1000-fold.

Compaction

• Bacterial chromosomal DNA is compacted within the cell.
• It has a central core with loops (microdomains) emanating from the core.
• Microdomains are typically 10,000 bp long in E. coli.
• An E. coli chromosome has 400-500 microdomains.
• Adjacent microdomains are organized into macrodomains (800-1000 kbp long).
• Nucleoid-associated proteins (NAPs) form micro and macrodomains.
• These proteins either bend DNA or act as bridges between DNA regions.

DNA Supercoiling

• Twisting forces change DNA conformation, creating additional coils.
• Coiling due to twisting forces is called DNA supercoiling.
• Underwinding or overwinding of the DNA double helix results in supercoiling.
• DNA structures that differ in supercoiling are called topoisomers.
• Supercoiling is related to the number of helical turns (twist) and crossings (writhe).
• The relationship is expressed as S = T + W.
• Positive supercoiling results from extra helical twists.
• Negative supercoiling results from subtractive twisting.
• Supercoiling is a manifestation of structural strain.

How Supercoils are Formed

• Cellular events like replication and transcription separate DNA strands.
• This reduced twist creates tension in the DNA.
• Writhe is formed to compensate for the resulting tension in the strand.
• Topoisomerases, like topoisomerase, relieve this stress.
• This reduces the linking number.

Eukaryotic Chromosomes

• Eukaryotic species have one or more sets of linear chromosomes.
• Each set contains multiple different linear chromosomes.
• Chromosomes in eukaryotes are located in the cell nucleus.
• Typical eukaryotic chromosomes are tens to hundreds of millions of base pairs (bp) long.
• Eukaryotic chromosomes contain origins of replication, centromeres, kinetochore proteins, and telomeres.

Organization of Eukaryotic Chromosomes

• Eukaryotic chromosomes contain a long, linear DNA molecule.
• Origins of replication are numerous within each chromosome.
• Centromeres are a constricted region critical for chromosome segregation during mitosis and meiosis.
• Kinetochore proteins attach the centromere to the spindle apparatus.
• Telomeres are at the ends of chromosomes; they prevent translocations and maintain chromosome length.

Eukaryotic Genes

• Genes are located between the centromeric and telomeric regions along the entire chromosome.
• A single chromosome often has hundreds to thousands of genes.
• Genes in less complex eukaryotes (like yeast) are relatively small, mainly encoding polypeptides.
• Genes in complex eukaryotes (like mammals) are longer, with numerous introns.

Sizes of Eukaryotic Genomes and Repetitive Sequences

• Genome sizes vary greatly between species.
• Variations may not be related to complexity but may involve repetitive sequences.
• Repetitive sequences are non-coding and may be found in various chromosomal positions.

Sequence Complexity

• Sequence complexity refers to how often a specific base sequence appears in the genome.
• Unique sequences appear once or a few times.
• Moderately repetitive sequences repeat a few hundred to a few thousand times.
• Highly repetitive sequences occur tens of thousands to millions of times within the genome.
• Examples include transposable elements.

Transposable elements (TEs)

• Transposable elements are DNA segments capable of moving to different locations within the genome.
• The two basic transposition pathways are simple transposition and retrotransposition.
• Simple transposition involves a "cut and paste" mechanism, where the TE is removed from its original site and inserted into a new site.
• Retrotransposition involves transcription of TE to RNA, reverse transcription to DNA and then insertion into a new site.
• Some TEs can move within the genome by transposition mechanism.
• TEs include both autonomous and non-autonomous TEs.
• Autonomous elements contain all necessary information for transposition while non-autonomous need a host element for transposition.

Transposase

• Transposase monomers bind inverted repeats, dimerize (join into pairs) the repeats, and cleave DNA between repeats to remove/excise the TE from the chromosome.
• Transposase carries the TE to a new site and cleaves the target DNA at specific locations.
• The TE is then inserted and ligated to the target DNA.

Reverse Transcriptase

• Retroelements use RNA intermediates during transposition.
• The process requires reverse transcriptase and integrase enzymes.
• Reverse transcriptase creates a DNA copy from an RNA template.
• Integrase catalyzes the insertion of the DNA copy into the target site.

Biological Significance of TEs

• TEs can introduce new functions or even cause the loss of genes or functions.
• The role of TEs in evolution is still under debate.
• Beneficial effects: Transposition introduces changes which can lead to greater biodiversity or potentially new functions.
• Negative effects: They can cause mutations or chromosomal rearrangements.
• Some TEs can be important in regulation of gene expressions and may contribute to evolution.