Test II Molecular Microbiology Terms

SigmaF

Flagellar synthesis sigma factor

SigmaH

Heat shock sigma factor.

SigmaS

Starvation sigma factor

Helix-turn-Helix motif

A two-helix DNA binding motif. Comprised of a 7 amino acid long helix which binds to the minor groove, a 4 amino acid turn-loop, and a 9 amino acid helix which binds to the major groove.

Winged Helix-turn-Helix

Variant of the helix-turn-helix motif but contains more complicated structures with overall longer helix sizes (~10 AA).

Zinc finger motif

A loop-shaped DNA binding motif that contains a central [Zn2+] ion which binds to the DNA.

Leucine zipper motif

Short helical proteins that function as dimers. They have a heptad repeat with Leucine residues every 7th aa.

Alternative Sigma Factors

Alternative sigma factors are used for niche situations requiring unique regulatory control. They are needed for long term survival but are not necessary for bacterial viability. They are used for transcription of heat shock, oxidative stress, iron acquisition, metal resistance, and nutrition genes.

Sensor Kinase

A transmembrane receptor with internal kinase domain. In a two component system, upon receiving a signal the protein activates the internal kinase to phosphorylate the Response Regulator.

Response Regulator

An internal DNA binding protein. When phosphorylated by the Sensor Kinase in a two-component system, the Response Regulator gains its DNA binding ability and modifies gene expression in the cell.

Quorum Sensing

The ability of bacteria to sense their population density. Useful for processes which are only productive when large amounts of bacteria are present, such as biofilm formation or toxin secretion.

Quorum sensing molecule for gram-negative bacteria?

Acyl homoserine lactones (AHL)

Quorum sensing molecule for gram-positive bacteria?

Ogliopeptides

agrA

The Response Regulator in the agr quorum sensing system.

agrC

Sensor Kinase in the agr system.

agrD

The peptide that is cleaved to form AIP, the oligopeptide autoinducer in the agr system.

agrB

The membrane protease that cleaves agrD into AIP.

Hld

Hemolysin-D, the toxin product of the agr quorum sensing system.

What is the glucose effect?

The glucose effect is the tendency of bacteria to only metabolize glucose even when other carbohydrates are present. This is due to the catabolite repression system.

What pattern of growth measures the catabolite repression system?

Diauxic growth

What is the key molecule in catabolite repression?

cAMP

What enzyme produces cAMP, and what enzyme inhibits its function.

Adenylyl cyclase.

Unphosphorylated IIA inhibits adenylyl cyclase.

What is LuxI

LuxI is the enzyme which creates AHL autoinducers.

What is luxR

The promoter which binds to the autoinducer AHL and activates the lux genes in Vibrio fisheri.

What is parC and what does it do?

Protein binding sequence on plasmids which parR binds to in.

What is parR and what does it do?

ParR binds to the parC sites on plasmids and serves as the staring site for parM-ATP polymeration.

What is parM and what does it do?

ParM-ATP binds to a parR-plasmid complex and begins polymerizing. When it binds to another parR-plasmid, it pushes the two away in opposite directions. When it hydrolyzes its ATP cofactor it depolymerizes.

ParS

Plasmid binding side for ParB.

ParA

ParA-ATP grows along the bacterial chromosome in both directions. When a ParB-plasmid complex contacts parA-ATP it hydrolyzes to parA-ADP and depolymerizes, pulling parB to the next parA-ATP. This continues and pulls the plasmid to one pole of the bacteria.

parB

Binds to the parS site on plasmids. Depolymerizes parA-ATP on chromosomal DNA.

What role does the Phd gene play?

Anti-toxin in the Phd-Doc plasmid addiction system. The Phd anti-toxin is less stable.

What roles does the Doc gene play?

The Doc gene is the toxin in the Phd-Doc plasmid addiction system. Produces a resilient toxin which persists even if the bacteria loses its plasmid.

What role does the relaxsome play in F-plasmid conjugation?

The relaxsome nicks the plasmid and begins Rolling Cell replication upon MPF pore formation. After the plasmid is replicated, it guides the ssDNA plasmid to the pore and pulls it through.

What is traJ?

TraJ is the activator for the F-plasmid genes. Inhibited by genes finP and finO (cis-sRNA).

What is virA?

The Sensor Kinase in the Ti plasmid system. Binds phenolic compounds during host damage.

What is virG?

VirG is the response regulator in the Ti plasmid system.

What is virD2?

The relaxase that cleaves the Ti virulence genes at both 25 bp border repeat sequences. It binds to the single stranded DNA and guides it into the host plant cells.

What is ComEA (G+)

The dsDNA receptor/binding protein competence factor in bacillus sub.

What is ComG (G+)

Holds ComEA and acts as a pore through the cell wall.

Nuclease (G+)

Bound to the bottom of ComG and cleaves off one strand of the dsDNA.

What is comEC-comFA (G+)

A transmembrane ssDNA pore (comEC) and an ATPase pump which actively pulls the DNA through (comFA).

What is pilQ (G-)

The outer membrane dsDNA channel.

What is pilE? (G-)

A structural pseudopilus.

What is ComE (G-)?

A DNA binding protein which anchors the dsDNA in the intramembrane space.

Nuclease (G-)

Free-floating nuclease in the intramembrane space. Cleaves one strand and leaves a ssDNA molecule.

What is ComA-PilT (G-)?

A transmembrane pore on the inner membrane (ComA) coupled with a ATPase (PilT) which pulls the ssDNA through,

Quorum sensing of competence in B. subtilis.

ComX is produced by ComG. ComX binds to the sensor kinase ComP which phosphorylates ComA. This leads to activation of competence genes.

Transposons

DNA elements that can transpose from one DNA site to another.

IS Element

A transposon containing only the transposase gene flanked by two inverted repeats.

Composite transposons

A complex transposable element consisting of a genetic element (non transposon genes) flanked by two complete IS elements on both sides.

Noncomposite transposons

Consists of multiple different gene elements, always including transposase and has two repeat sequence caps. Does not contain a IS element.