Translational Coupling and Plasmid Regulation in Bacteria

Polycistronic mRNA

mRNA encoding multiple proteins in one transcript.

Translational Initiation Region (TIR)

Site where translation begins for coding sequences.

Rho factor

Protein that terminates transcription in prokaryotes.

Nonsense mutation

Mutation creating a premature stop codon.

Frameshift mutation

Insertion or deletion altering the reading frame.

Allelic replacement (KO)

Technique to replace a gene with a knockout.

Protein Knockdown (PKD)

Method to reduce protein levels for functional studies.

Streptomycin resistance

Mutations enabling survival in streptomycin presence.

Luria-Delbruck experiment

Test for random mutations in bacteria.

Intergenic suppressor

Suppressor mutation occurring between different genes.

Intragenic suppressor

Suppressor mutation occurring within the same gene.

Galactose utilization pathway

Pathway for metabolizing galactose in E. coli.

Nonsense suppressor tRNA

tRNA that allows translation past a stop codon.

Replica plating

Technique for transferring bacterial colonies to plates.

Negative selection

Method to identify mutants by selective pressure.

Mutant enrichment

Increasing mutant frequency for easier identification.

5-bromouracil (5-BU)

Antibiotic that targets growing bacterial cells.

Opal codon

UGA stop codon in genetic code.

Ochre codon

UAA stop codon in genetic code.

Amber codon

UAG stop codon in genetic code.

Slippage of DNA

DNA replication error causing frameshift mutations.

Toxic intermediates

Harmful metabolites accumulating during galactose metabolism.

Transposon mutagenesis

Method for inducing mutations via transposons.

Null mutation

Loss-of-function mutation resulting in no gene product.

Sequencing

Technique to determine transposon location in DNA.

Antibiotic resistance cassette

Gene conferring resistance to specific antibiotics.

Single crossover

Recombination event introducing a vector into DNA.

AmpR

Gene providing resistance to ampicillin.

Kan cassette

Gene providing resistance to kanamycin.

sacB

Gene used for counterselection on sucrose.

Complementation test

Method to determine if mutations are allelic.

Allelic mutations

Mutations occurring in the same gene.

hisA1 and hisB1

Mutations in different genes for histidine synthesis.

hisA2

Mutation in the same gene as hisA1.

Nonsense mutation

Mutation resulting in a premature stop codon.

Supercoiling

Twisting of DNA affecting its compactness.

CCC plasmid

Covalently closed circular plasmid structure.

Restriction enzyme

Enzyme that cuts DNA at specific sites.

Alkaline lysis method

Technique to purify plasmid DNA using NaOH.

Potassium acetate

Used to neutralize pH in plasmid purification.

Phenol-chloroform extraction

Method to purify plasmids from contaminants.

TE buffer

Buffer used for storing plasmids.

Plasmid curing

Loss of plasmid from bacterial cells.

Incompatibility

Inability of two plasmids to coexist stably.

Inc group

Group of plasmids unable to coexist in cells.

Copy number control

Mechanism regulating the number of plasmid copies.

Par system

System ensuring proper plasmid segregation during division.

ColE1-derived plasmids

Plasmids derived from ColE1 with specific replication control.

RNA I

Inhibits RNA II processing, regulating plasmid replication.

RNA II

Forms primer for plasmid DNA replication.

pRNAI

Promoter for transcription of RNA I.

pRNAII

Promoter for transcription of RNA II.

Rop protein

Enhances pairing of RNA I and RNA II.

Replication origin

Site where plasmid DNA replication initiates.

RNA endonuclease

Enzyme that cleaves RNA, releasing hydroxyl group.

RNase H

Cleaves RNA in RNA-DNA hybrids.

DNA polymerase I

Catalyzes DNA synthesis during replication.

Antisense RNA

RNA complementary to another RNA, inhibits function.

Double-stranded RNA

Formed by base pairing of complementary RNAs.

Inc group

Plasmid classification based on replication control.

repA mRNA

Transcribed from prepA, regulates plasmid copy number.

CopB protein

Represses transcription from prepA at high copy number.

CopA RNA

Antisense RNA that inhibits repA translation.

Leader peptide

Peptide linked to repA translation regulation.

Rep protein

Initiates plasmid replication by strand separation.

oriV region

Origin of replication for plasmid DNA.

Translational coupling

Process where translation of one mRNA affects another.

Pseudoknot formation

Structural RNA interaction that inhibits translation.

S-D sequence

Shine-Dalgarno sequence essential for ribosome binding.

Structure III

RNA structure that sequesters repZ S-D sequence.