Chapter 14 Microbio

Constitutive gene expression

• continuous expression of a gene at a relatively constant level for basic cellular functions

Regulated gene expression

• gene expression that changes in response to environmental conditions, nutrients, or cellular signals

What’s the difference between constitutive and regulated gene expression?

• constitutive genes support housekeeping functions and are expressed at a relatively constant level

• regulated genes are produced only in response to environmental or cellular signals

At what points can bacteria regulate the flow of genetic information?

• transcription initiation and elongation

• translation

• post-translational control (protein activity)

Why is regulation of transcription initiation usually considered energy-saving?

• blocking transcription initiation prevents production of unnecessary RNA which conserves energy and raw materials

Inducible gene

• a gene that’s usually off or low that is turned ON when a specific inducer or substrate is present

Repressible gene

• a gene that is usually on that is turned OFF when its end product or a corepressor is abundant

Positive control

• an activator increases transcription by helping RNA polymerase bind or initiate efficiently

Negative control

• a repressor blocks transcription by binding an operator near the promoter

Operator

• DNA site where a regulatory protein such as a repressor binds to influence transcription

Activator binding site

• DNA site upstream of a promoter where an activator binds to help RNA polymerase initiate transcription

Helix-turn-Helix motif

• common DNA binding motif in bacterial regulatory proteins

• the recognition helix binds the major groove

Basal transcription

• low, leaky background transcription that occurs even when an operon is mostly off

Operon

• cluster of genes transcribed together from one promoter into a single polycistronic mRNA

Lac operon

• a set of inducible genes in E. coli that enables the metabolism of lactose when glucose is absent

Trp operon

• a set of genes in bacteria (notably E. coli) that encodes enzymes for tryptophan biosynthesis

How is the lac operon controlled when lactose is absent and when lactose is present?

• when lactose is absent, LacI binds the operator and inhibits transcription

• when lactose is present, lactose is converted to allolactose: which binds LacI and prevents it from binding to operator, permitting transcription

Why is the lac operon not fully induced when lactose is present but glucose is abundant?

• strong transcription also requires CAP-cAMP

• high glucose lowers cAMP so CAP is not activated

• RNA polymerase binds less efficiently

• lac expression remains low even if lactose is present

How does the trp operon show repressible control?

• the trp operon is usually on to make tryptophan biosynthetic enzymes

• but when tryptophan is abundant it binds to the trp repressor as a corepressor allowing the repressor to bind DNA and shut off transcription

What happens to trp operon transcription when tryptophan is abundant?

• ribosome does not stall the leader peptide

• a terminator hairpin forms

• transcription terminates prematurely

Why is the area operon a useful teaching example

• one regulatory protein can both repress and activate

• it shows dual control because AraC represses transcription in the absence of arabinose but promotes transcription in its presence

Allolactose

• inducer derived from lactose that binds LacI and relieves repression of lac operon

Corepressor

• small effector molecule that activates a repressor protein (as tryptophan does for the trip repressor)

Attenuation

• premature transcription termination in a leader region

• often controlled by coupled transcription and translation

• occurs during transcription elongation

Why does attenuation work especially well in bacteria?

• transcription and translation are coupled

• ribosome movement on the leader mRNA can influence RNA folding while the transcript is still being made

Antiterminator

• RNA secondary structure that allows RNA polymerase to continue transcription

Riboswitch

• regulatory RNA element that binds a ligand directly and changes RNA structure to control transcription or translation

How do riboswitches differ from many protein-mediated regulatory systems?

• riboswitches are regulatory RNAs that directly bind ligands and change RNA structure

• protein mediated systems depend on a separate regulatory protein to sense the signal and act on DNA or RNA

What is the key difference between a transcriptional riboswitch and a translational riboswitch?

• transcriptional riboswitch changes RNA folding to terminate or continue transcription

• translational riboswitch changes RNA folding to hide or expose the ribosome binding site after the mRNA has been produced

T-box Riboswitch

• RNA regulator that sense charged vs uncharged tRNA and links amino acid availably to gene expression

RNA thermometer

• temperature-sensitive RNA structure that hides or exposes the ribosome-binding site

How do RNA thermometers regulate gene expression?

• form secondary structures that block the ribosome binding site at one temperature and melt/rearrange at another temperature

sRNA

• small regulatory RNA that base pairs with mRNA to alter translation or mRNA stability

How can sRNA repress translation?

• base pairs near the Shine Dalgarno sequence

• an sRNA can base pairs with target mRNA and occule the ribosome binding site

• alter structure so ribosome cannot bind

• promote degradation of transcript

Antisense RNA

• RNA complementary to a specific mRNA

• usually highly target specific and transcribed from the opposite strand

How does antisense RNA usually differ from many trans-acting sRNAs?

• antisense RNA is usually highly specific for one corresponding mRNA because it is transcribed from the opposite strand of the same genetic region

• many sRNAs can regulate multiple targets through shorter complementary interactions, often with HFQ assistance

Hfq

• RNA chaperone that stabilizes and promotes interactions between many bacterial sRNAs and targets mRNAs

Two component system

• signal transduction system with a sensor histidine kinase and a response regulator

How does a basic two-component signal transduction system work?

• a sensor histidine kinase detects an environmental signal and autophosphorylation

• then transfers the phosphate to a response regulator that changes gene expression or cellular behavior

How is phosphorelay different from a simple two component?

• a phosphorelay extends the pathway with additional receiver or phosphotransfer proteins

• allows more complex integration and timing the simple kinase to response regulator architecture of a two component system

Phosphorelay

• expanded phosphotransfer cascade with additional intermediate steps beyond a simple two component system

Sigma factor

• RNA polymerase specificity factors that directs the enzyme to a distinct promoter class

Why are alternative sigma factors powerful global regulators?

• because switching sigma factors redirects RNA polymerase to a different promoter class

• allowing rapid coordination transcription of an entire regulon involved in a particular physiological state

Regulon

• group of genes or operons controlled by the same global regulatory protein or system

• one regular, many targets

Catabolite repression

• global regulation that favors use of preferred carbon sources such as glucose over alternative substrates

How to CAP and cAMP help create catabolite repression and diauxic?

• when glucose is low: cAMP rises and binds CAP, allowing CAP to activate transcription of operons for alternative carbon sources such as lac

• when glucose is high: cAMP is low and CAP is inactive, cells preferentially use glucose first and contributing to diauxic growth

Diauxic growth

• biphasic growth in which cells use one carbon source first, pause, then switch to another

Alarmones

• stress response nucleotides such as ppGpp and pppGpp that reprioritized transcription during nutrient limitation

c-di-GMP

• cyclic dinucleotide second messenger often associated with BIOFILM formation and reduced motility

MCP

• methyl accepting chemotaxis protein

• membrane chemoreceptor that initiates chemotaxis signaling

Autoinducer

• small diffusible molecule used in quorum sensing to estimate population density

Sporulation

• developmental pathway leading to formation of a resistant endospore under severe stress

Why is sporulation a good example of integrated regulation?

• bacillus subtitles sporulation is controlled by a phosphorelay, post-translational regulation, transcription factors, and alternative sigma factors, all coordinated to drive a developmental program under starvation

Restriction-modification system

• innate antiviral defense that cuts foreign DNA while host DNA is protected by modification

CRISPER-Cas

• adaptive antiviral defense in which spacer acquisition creates sequence specific immune memory

How do restriction-modification and CRISPR-Cas differ as antiviral defense?

• restriction modification is an innate defense that cuts unmodified foreign DNA while protecting host DNA through modification

• CRISPR-Cas is an adaptive defense that stores spacer sequences from prior invaders and uses guide RNAs to target matching nucleic acids during later infections

Catabolite repression

• cells preferentially use glucose or another preferred carbon source

• low glucose raises cAMP and activates CAP

• promotes expression of alternative catabolic operons

Diauxic growth

• 2 carbon sources can produce biphasic growth as cells use the preferred source first and switch later

Stringent response

• amino acid starvation and related stresses increase alarmones that reduce ribosome synthesis and reprioritize survival functions

• global shift triggered by amino acid starvation where alarmones such as ppGpp and pppGpp reduce growth-related transcription especially rRNA synthesis, and redirect resources toward survival and stress adaption

c-di-GMP signaling

• high c-di-GMP commonly promotes sessile

• biofilm-associated behavior and suppresses motility

Quorum sensing

• cells release and detect autoinducers to coordinate gene expression as population density changes

• plays a big role in biofilms

How do MCPs, CheA and CheY work together in chemotaxis?

• MCP chemoreceptors detect chemicals and modulate CheA autophosphorylation

• CheA transfers phosphate to CheY and phosphorylated CheY interacts with the flagellar motor to alter rotation and bias movement toward running and tumbling

What happens when E coli moves up an attractant gradient?

• attractant binding decreases CheA signaling

• lowers CheY phosphorylation

• reduces clockwise tumbling behavior

• increases smooth running toward the attractant source