Microbial Genomes

Flashcards on Microbial Genomes

Genome

The complete set of genetic material within an organism, defining a species.

DNA

The fundamental heritable unit of genomes.

B-form DNA

Right-handed, double-stranded DNA favored in cellular life.

Transient DNA Structures

Structures formed transiently like Holiday intermediates, heteroduplexes, cruciform, catenanes, hairpins, 3, 4 and 5 stranded DNAs.

dsDNA

Double-stranded DNA with a poly (ADP-deoxyribose) backbone and planar heterocyclic bases.

Major and minor grooves

Molecules* interact with bases at these grooves

Microbial Genomes

They consist of chromosomes, endogenous viral elements (EVEs).

Endogenous Viral Elements (EVEs)

DNA integrated into chromosomes and vertically transmitted

Extrachromosomal ccDNA

Genetic material not considered part of the genome because they are extrachromosomal including plasmids, mitochondrial and chloroplast chromosomes.

Plasmids

Extrachromosomal circular DNA found in all microbial domains

Nucleoid

Region within a prokaryotic cell containing DNA, RNA, proteins, and low molecular weight molecules; not membrane-bound.

Nucleoid Associated Proteins (NAPs)

Proteins associated with the nucleoid in bacteria that are critical to DNA packaging, replication, stability, recombination, gene expression, and regulation.

Topoisomerases (Topos)

Enzymes used by all microbes to package DNA into chromosomes and extrachromosomal elements by altering DNA topology through supercoiling

Class I Topoisomerases

Class of prokaryotic topoisomerases that relax supercoiling.

Class II Topoisomerases

Class of prokaryotic topoisomerases that introduce supercoiling.

Gyrase (GyrAB)

Prototypic class II topoisomerase in E. coli; its A subunit binds and cuts DNA, while its B subunit is an ATPase energizing GyrA.

Quinolone Antibiotics

Antibiotics that target the A subunit of gyrase (GyrA), blocking DNA replication in bacterial pathogens.

Semiconservative Replication

Mechanism of DNA replication where newly replicated dsDNA contains a parental template strand and a de novo strand.

ccDNA Replication

Discrete phases includes initiation, elongation and termination

Origin of Replication (oriC, oriV, OH/OL, ori)

Locus where initiation in ccDNA occurs.

oriC Locus

Site within oriC that contains binding sites for initiation proteins; DnaA binds here in bacteria for strand separation. DnaA binds to oriC at 9-mer sites causing strand separation at the AT-rich 13-mer site

Replisome

Complex consisting of the helicase complex, the DNA polymerase complex, and primase; assembles at each replication fork.

Elongation

Synthesis of de novo DNA from parental template strands in a 5’ to 3’ orientation at both forks.

Pol III (aka DnaE)

Synthesizes DNA on the leading strand continuously and discontinuously on the lagging strand in bacteria

Okazaki Fragments

Fragments formed during discontinuous synthesis on the lagging strand.

Termination Sites (ter sites)

Sites where replication terminates in most ccDNAs; consist of 20-30 bp tandem repeats that act as helicase traps.

Replication Termination Proteins

Proteins(Rtp and Tus) that bind to ter sites and stop the progression of helicase (DnaB) in bacteria