Dale_Molecular Genetics of Bacteria 4th ed

Post-replication repair: DNA repair process involving the exchange of DNA between damaged and undamaged strands.

Post-translational modification: modification of the structure of a polypeptide after synthesis, e.g. by phosphorylation, glycosylation, proteolytic cleavage.

Pribnow box: consensus sequence within a promoter, centred at the -10 position with respect to the start of transcription.

Primary structure: the sequence of a nucleic acid or a protein.

Primer: synthesis of a new DNA (but not RNA) strand can only occur by extension of a preexisting partial DNA strand. If a specific oligonucleotide (a primer) is provided, complementary to a defined region of the template strand, all the new DNA strands made will start from that point.

Probe: a DNA or RNA molecule that will hybridize to a specific target sequence. Labelling the probe (using radioactive isotopes or non-radioactive markers) enables it to be used to detect the specific target DNA/RNA.

Prokaryote: a cell that does not have a discrete nucleus bounded by a membrane; in this book referring to bacteria, but also includes the Archaea (cf. eukaryote).

Promoter: region of DNA to which RNA polymerase binds in order to initiate transcription.

Proof-reading: the ability of DNA polymerase to check the accuracy of the newly made sequence.

Prophage: the repressed form of bacteriophage DNA in a lysogen; it may be integrated into the chromosome or exist as a plasmid.

Protein engineering: altering a gene so as to produce defined changes in the properties of the encoded protein, e.g. thermal stability, substrate profile.

Proteome: the complete content of different proteins in a cell (cf. genome, transcriptome).

Protoplast: formed by complete removal of the cell wall using osmotically-stabilized conditions. Used for transformation and for protoplast fusion.

Prototroph: a nutritionally wild-type organism that does not need any additional growth supplement (cf. auxotroph).

Proximal: sequence before a given point, usually referring to the direction of transcription or translation (see distal).

Pulsed-field gel electrophoresis: separation of large DNA molecules by application of an intermittently varying electric field; generic term for a number of ways of achieving this.

Purine: one of the two types of bases in nucleic acids (adenine, guanine; see pyrimidine).

Pyrimidine dimer: covalent linkage between adjacent pyrimidines on a DNA strand caused by UV irradiation. Commonly referred to as thymine dimers but not restricted to thymine.

Pyrimidine: one of the two types of bases in nucleic acids (cytosine and thymine in DNA; cytosine and uracil in RNA; see purine).

Quorum sensing: mechanism whereby bacteria respond to cell density.

Random mutation: mutation occurring irrespective of its benefit to the cell (contrast directed mutation).

Reading frame: a nucleic acid sequence is translated in groups of three bases (codons); there are three possible ways of reading the sequence (in one direction) depending on where it is started. These are the three reading frames.

Real-time PCR: a PCR technique which allows monitoring of the amplification of the product as it happens. Especially useful for quantitative applications of PCR.

Recombinant: product of recombination (q.v.) using either definition, which leads to recombinant bacteria resulting from some form of gene transfer or recombinant plasmids arising from in vitro manipulation

Recombination repair: see post-replication repair.

Recombination: (a) the production of new strains by mating two genetically distinct parents; (b) the generation of new DNA molecules by breaking and re-joining the original molecules; this may occur naturally within the cell (in vivo) or artificially in vitro. There is considerable overlap between these definitions but they are not always synonymous.

Regulon: a set of genes that are coordinately regulated without being contiguous (see operon).

Relaxation: conversion of supercoiled circular DNA to an open circular form.

Relaxed plasmid: (a) open circular structure after nicking one strand of a plasmid; (b) plasmid which replicates to high copy number without being tied to chromosomal replication.

Replacement vector: a cloning vector in which a piece of DNA (the stuffer fragment) can be removed and replaced by the cloned fragment (cf. insertion vector).

Replica plating: using a velvet pad or some equivalent apparatus to transfer a number of colonies to several different media in order to compare their growth requirements or other characteristics.

Replication: synthesis of a copy of a DNA molecule using the original as a template.

Replicon: (a) a DNA molecule (such as a plasmid) that contains an origin of replication and is capable of autonomous replication within a suitable host cell; (b) the replication control region of a plasmid.

Reporter gene: a gene which codes for a readily detected product (such as b-galactosidase); study of a regulatory region of DNA is facilitated by fusion with the reporter gene.

Repression: (a) reduction in transcription of a gene usually due to the action of a repressor protein; (b) also applied to the natural repression of conjugal transfer that occurs with many plasmids and to the establishment of lysogeny with temperate bacteriophages.

Resolution: production of two smaller plasmids from a cointegrate.

Restriction: reduction in the apparent titre of a phage (or transforming ability of DNA) when certain strains are used as a host. These strains produce restriction endonucleases which degrade foreign DNA when it enters the cell (see also modification).

Restriction fragment length polymorphism: variation between strains in the size of specific restriction fragments; used for strain typing and for locating particular genes.

Restriction mapping: determination of the position of restriction endonuclease recognition site on a DNA molecule.

Reverse genetics: starting with specific alterations to the DNA in vitro and then examining the phenotype; contrasts with classical genetics which relies on selecting mutants on the basis of their phenotype and then studying the nature of the mutation. (This term is also used in other ways and is hence avoided in this book).

Reversion: a mutation that reverses the effect of the original mutation.

Ribosomal frameshifting: a change in reading frame used by the ribosome resulting in a fusion protein or re-initiation from an adjacent start codon.

Ribosome binding site: the region on an mRNA molecule to which ribosomes initially attach.

Rifampicin: an antibiotic which interferes with RNA polymerase.

Rolling circle replication: (a) production of a multiple length linear molecule of DNA; (b) replication of some plasmids and phages via single-stranded intermediates or during conjugation.

RT-PCR: reverse transcript PCR. Technique for producing an amplified DNA product from an mRNA template.

Scaffolding: proteins used to assist in the assembly of a bacteriophage particle and removed during maturation.

SDS-PAGE: polyacrylamide gel electrophoresis in which proteins are separated according to molecular weight in the presence of sodium dodecyl sulphate.

Secondary structure: the spatial arrangement of amino acids in a protein or of bases in nucleic acid.

Segregation: in eukaryotic genetics, this refers to the distribution of genes among the progeny following meiosis. By extension, when bacteria contain two versions of a gene (e.g. following mutational alteration of one strand of DNA), two types of colonies will result. Similarly, a plasmid-containing strain may produce plasmid-free segregants

Selectable marker: a gene that causes a phenotype (usually antibiotic resistance) which can be readily selected.

Sequence polymorphism: variation in the sequence of a gene usually between otherwise closely related organisms such as members of the same species.

Shine–Dalgarno sequence: see ribosome binding site.

Shotgun cloning: insertion of random fragments of DNA into a vector.

Shuttle vector: a cloning vector that can replicate in two different species, one of which is usually E. coli. Facilitates cloning genes in E. coli initially and subsequently transferring them to an alternative host without needing to re-clone them.

Sigma (s) factor: polypeptide that associates with RNA polymerase core enzyme to determine promoter specificity.

Signal peptide: amino acid sequence at the amino terminus of a secreted protein; involved in conducting the protein through the membrane.

Signal transduction: extracellular conditions alter the conformation of a transmembrane protein which in turn alters the regulation of metabolic pathways within the cell.

Signature tagged mutagenesis: a system for identifying virulence genes using mutagenesis with a transposon carrying a variety of unique tags.

Silent mutation: a change in the DNA structure that has no effect on the phenotype of the cell.

Site-directed mutagenesis: a technique for specifically altering (in vitro) the sequence of DNA at a defined point.

Site-specific recombination: recombination between two DNA molecules at a specific sequence; does not require extensive homology (see also illegitimate recombination and homologous recombination).

Slipped strand mispairing: replication error changing the number of copies of short repeated units of DNA.

SOS response: a number of genes involved with DNA repair and related functions are induced by the presence of unrepaired DNA.

Southern blot: the transfer of DNA fragments from agarose or acrylamide gels onto a membrane.

Specialized transduction: transfer of DNA by a bacteriophage that has incorporated a piece of chromosomal DNA.

Splicing: removal of introns from RNA and joining together of the exons.

Start codon: position at which protein synthesis starts; usually AUG or GUG, but occasionally other codons are used.

Stem–loop structure: a nucleic acid strand containing two complementary sequences can fold so that these sequences are paired (stem) with the region between them forming a loop of unpaired bases.

Stop codon: a codon with no corresponding tRNA which signals the end of a region to be translated.

Streptomycin: an antibiotic of the aminoglycoside group.

Stringency: conditions affecting the hybridization of single-stranded DNA molecules. Higher stringency (higher temperature and/or lower salt concentration) demands more accurate pairing between the two molecules.

Stringent response: amino acid starvation leads to a reduction in synthesis of ribosomal and transfer RNAs.

Structural genes: genes coding for enzymes (or sometimes other proteins) to distinguish them from regulatory genes.

Stuffer fragment: piece of DNA that is removed from a replacement vector and replaced by the cloned DNA fragment.

Supercoiling: coiling of a double-stranded DNA helix around itself.

Superinfection immunity: resistance of a lysogen to infection by the same (or related) bacteriophage.

Suppression: the occurrence of a second mutation which negates the effect of the first without actually reversing it.

Synonymous codons: two or more codons that code for the same amino acid.

Tag: a short sequence of amino acids added (by gene cloning) to one end (usually the N-terminus) of a protein to facilitate purification and/or antibody recognition.

Tandem repeat: occurrence of the same sequence two or more times directly following one another.

Tautomerism: representation of a chemical as an equilibrium between two alternative structures.

Temperate: a bacteriophage that is capable of establishing a lysogenic relationship with a susceptible host cell.

Template: the use of a nucleic acid strand to carry the information required for the synthesis of a new (complementary) strand.

Terminal redundancy: sequence of bases at one end of a linear molecule is repeated at the other end (as in T4).

Termination: (a) synthesis of a mRNA molecule will stop when it reaches a terminator site;

(b) protein synthesis stops (usually) when it reaches a stop (termination) codon.

Terminator: site at which transcription stops.

Tertiary structure: folding of secondary structure components of a protein.

Tetracycline: antibiotic that affects protein synthesis.

Theta replication: replication of bacteriophage as a circular molecule (see rolling circle replication).

Thymine dimer: see pyrimidine dimer.

Ti plasmids: tumour-inducing plasmids of Agrobacterium tumefaciens. Used for introducing DNA into plant cells.

Trans-acting: a control region that influences other DNA regions whether or not they are on the same molecule, e.g. by means of a diffusible repressor protein (cf. cis-acting).

Transconjugant: a recipient cell that has received DNA by means of conjugation.

Transcription: synthesis of RNA using a DNA template.

Transcriptome: the complete mRNA content of a cell (cf. genome, proteome).

Transduction: bacteriophage-mediated transfer of genes from one bacterium to another.

Transfection: introduction of bacteriophage DNA into competent bacteria.

Transformation: introduction of extraneous DNA into competent bacteria. Also used to mean the conversion of an animal cell into an immortalized tumour-like cell.

Translation: synthesis of proteins/polypeptides by ribosomes acting on a mRNA template.

Translocation: movement of a ribosome along a mRNA molecule.

Transposon mutagenesis: disruption of a gene by insertion of a transposon.

Transposon: a DNA element carrying recognizable genes (e.g. antibiotic resistance) that is capable of inserting itself into the chromosome or a plasmid independently of the normal host cell recombination machinery.

Twist: a measure of the turning of the DNA double helix (see also linking number and writhe).

Two-component regulation: a sensor in the cell envelope detects environmental changes and responds by phosphorylating a cytoplasmic protein (the response regulator); this activates or inhibits its regulatory function.

Two-dimensional gel electrophoresis: separation of a complex mixture of proteins by a combination of isoelectric focusing and SDS-PAGE.

Upstream activator sequence: a sequence upstream from the promoter which is required for efficient promoter activity.

Vector: a replicon (plasmid or phage) into which extraneous DNA fragments can be inserted, forming a recombinant molecule that can be replicated in the host cell.

Virulent: (a) able to cause disease; (b) a bacteriophage that does not establish lysogeny and hence results in lysis of the bacterial host.

Western blot: transfer of proteins from an acrylamide gel onto a nitrocellulose filter, usually for detection by means of antibodies.

Wobble: the ability of tRNA anticodons to pair with more than one synonymous codon.

Writhe: a measure of the degree of DNA supercoiling (see also linking number and twist).

X-gal: 5-bromo-4-chloro-3-indolyl-b-d-galactoside. Chromogenic substrate for b-galactosidase

Z DNA: alternative left-handed form of DNA helix.

Zygotic induction: conjugative transfer of DNA from a lysogen to a non-lysogen leads to a sudden drop in the number of recombinants when the prophage is transferred due to induction of the phage.

glutamate dehydrogenase: produces glutamate from a-ketoglutarate and ammonia; important in ammonia assimilation.

green fluorescent protein (GFP): intrinsically fluorescent protein used as a reporter.

gyrase: a specific type of topoisomerase; introduces negative supercoils into DNA.

helicase: unwinds DNA, e.g. in conjugal plasmid transfer.

Hin: site-specific recombinase, responsible for inversion of the control element in Salmonella phase variation.

H-NS: histone-like nucleoid structuring protein, a DNA-binding protein which influences local topology of DNA (and hence gene expression).

HU: DNA-binding protein, influences local topology of DNA (and hence gene expression).

Int: integrase, needed for integration of l DNA into the chromosome by site-specific recombination. Related proteins catalyse integration of other elements, such as conjugative transposons (see also Xis).

integration host factor (IHF): a host protein required for efficient integration of l DNA into the chromosome.

kinase: phosphorylating enzyme.

LacI: repressor of the lac operon.

ligase: Seals single-stranded gaps (nicks) in double-stranded DNA. Also used for the formation of recombinant DNA molecules in gene cloning.

LexA: regulator of the SOS response.

luciferase: catalyses a light-emitting reaction; used as a reporter.

LuxI: acyl homoserine lactone synthase, responsible for synthesis of a messenger used in quorum sensing.

LuxR: transcriptional regulator, responding to level of homoserine lactone.

OxyR: global regulatory protein, responding to oxidative stress.

photolyase: responsible for light-activated removal of UV-induced pyrimidine dimers.

pilin: structural subunit of pili.

polynucleotide kinase: transfers a phosphate group from ATP to the 50 -OH end of DNA or RNA.

primase: a special RNA polymerase, which makes a short primer required for DNA synthesis.

RecA: key protein in homologous recombination and in DNA repair.

RecBCD: multifunctional enzyme involved in homologous recombination.

replicase: RNA-directed RNA polymerase, used in replication of some RNA viruses.

resolvase: catalyses site-specific recombination to resolve the cointegrate intermediate in transposition into two separate molecules.

restriction endonuclease: recognizes DNA at a specific site and degrades it by internal cleavage. Most commonly used are the type II restriction enzymes which cut within the recognition site.

reverse transcriptase: RNA-directed DNA polymerase; synthesizes DNA (complementary DNA) using mRNA template.

ribonuclease (RNase): degrades RNA molecules.

RNA polymerase: synthesizes RNA using a DNA template.

RNaseH: a specific RNase which cuts RNA–DNA hybrids; involved in replication of ColE1like plasmids.

Ruv: several proteins involved with events at the Holliday junction during homologous recombination.

sigma (s) factor: dissociable component of RNA polymerase, responsible for promoter specificity.

SSB: single-strand DNA binding protein; stabilizes single-stranded DNA, e.g. during replication.

topoisomerase: a class of enzymes that alters the conformation of DNA, e.g. by changing the degree of winding or supercoiling.

transposase: catalyses the initial steps in transposition.

TRAP: trp RNA-binding attenuator protein; responsible for attenuation of the trp operon in

Bacillus.

TrpR: repressor of the trp operon.

XerC,D: resolution of plasmid dimers by recombination at cer sites.

Xis (pronounced ‘excise’): interacts with Int (integrase) to promote excision of l prophage from the chromosome. Related proteins have similar functions with other elements such as conjugative transposons.