Microbial Genome Structure, Organization, and Regulation Flashcards

Vocabulary flashcards focusing on microbial genome structure, supercoiling, plasmids, global regulation networks, catabolite repression, signal transduction pathways, and nitrogen regulation.

Operon

A cluster of genes in bacteria that are functionally related and transcribed together as a single polycistronic mRNA under the control of a shared promoter and operator.

DNA Gyrase

A type of topoisomerase enzyme that introduces negative supercoils into DNA by creating double-strand breaks, passing an unbroken double helix through the break, and resealing the strand.

Negative Supercoiling

The predominant form of DNA supercoiling found in most prokaryotic cells, resulting from DNA under torsion, which aids in compacting the bacterial chromosome into the nucleoid.

Positive Supercoiling

A form of DNA supercoiling found in certain hyperthermophilic Archaea that helps stabilize and maintain double-stranded DNA structure at extremely high temperatures.

Replicon

A genetic unit of DNA or RNA that contains all the necessary elements required to initiate and complete its own replication independently.

Plasmid

A relatively short, usually circular double-stranded extrachromosomal DNA molecule that replicates autonomously and carries non-essential accessory genes.

Plasmid R100

A $94.3\,\text{kbp}$ resistance plasmid encoding resistance to multiple antibiotics and mercury, as well as genes for conjugation transfer ($tra$) and insertion sequences.

Minimal Genome

The estimated baseline set of approximately $250\text{--}300$ essential genes required to support a viable, self-replicating cellular life form.

Sorangium cellulosum Genome

The largest known bacterial genome, composed of a single circular chromosome of $14.8\,\text{Mbp}$ encoding $508$ protein kinases to regulate its complex lifestyle.

Bacterial DNA Methylation

An epigenetic mechanism where a methyltransferase (MTase) transfers a methyl group from S-adenosyl-L-methionine (SAM) to DNA bases, forming 4mC, 5mC, or 6mA to regulate expression and defend against phages.

Quorum Sensing

A mechanism of cell-to-cell communication in bacteria where secreted signaling molecules coordinate population density-dependent gene expression, such as bioluminescence in Vibrio harveyi.

Global Regulation

A regulatory network that simultaneously coordinates the expression of multiple independent operons and regulons across the genome in response to broad environmental changes.

Regulon

A group of individual genes and operons distributed across the genome that are under the control of a single common regulatory protein.

Stimulon

A higher-level collection of multiple regulons that respond synchronously to the same specific environmental stimulus or stress condition.

Diauxic Growth

A biphasic growth pattern produced when bacteria preferentially consume a primary carbon source (e.g., glucose) before undergoing a lag phase to express genes for a secondary carbon source.

Cyclic AMP (cAMP)

An intracellular secondary messenger molecule synthesized from ATP by adenylate cyclase that accumulates when glucose levels are depleted in Escherichia coli.

Catabolite Activator Protein (CAP / CRP)

A DNA-binding transcriptional activator protein that, upon binding cAMP, interacts with promoter CAP sites to recruit RNA polymerase and activate catabolic operons.

Inducer Exclusion

A regulatory mechanism in high-glucose conditions where unphosphorylated enzyme $\text{IIA}^{\text{Glc}}$ directly inhibits non-glucose sugar transporters (e.g., lactose permease LacY), blocking secondary sugar uptake.

Phosphotransferase System (PTS)

A multi-protein cascade that transports sugars into bacterial cells while phosphorylating them, using the phosphoenolpyruvate (PEP) to pyruvate ratio as a metabolic sensor.

Sensor Kinase

A membrane-bound or cytoplasmic receptor protein in a two-component signal transduction system (such as NtrB) that autophosphorylates in response to a specific signal.

Response Regulator

A cytoplasmic protein in a two-component regulatory system (such as NtrC) that receives a phosphate group from a sensor kinase to alter target gene transcription.

GlnD

A bifunctional uridylyltransferase/uridylyl-removing sensor enzyme that measures cellular nitrogen availability via glutamine and $\alpha$-ketoglutarate levels to modify the $P_{\text{II}}$ protein.

PII Protein ($P_{\text{II}}$)

A regulatory signal transduction protein in nitrogen metabolism whose uridylylation state determines whether it stimulates or inhibits the kinase activity of NtrB.

RpoN (\sigma^N)

An alternative sigma factor expressed under low-nitrogen conditions that directs RNA polymerase to specialized promoters containing conserved $-24/-12$ consensus sequences.