Lecture 10: Signal Transduction

Signal transduction is the _____ and _____ to specific cellular conditions

sensing; responding

What 2 things is signal transduction used for?

sensing the environment, energy conservation

signal transduction can be used to sense both the _____ and _____ environment

intracellular; extracellular

the extracellular environment is what happening _____ the cell

outside

sensing the intracellular environment can determine the _____ of metabolites or other factors in the _____

presence; cytosol

how is signal transduction used for energy conservation?

only transcribes genes when they are needed

single transduction allows the cell to perform _____

logical operations

an example of a signal transduction logical operation is only transcribing a certain set of genes _____ lactose is present _____ glucose is absent

IF; AND

what are the 5 mechanisms of gene regulation

ligand-responsive transcription factors, riboswitches, two component signaling, sigma/anti-sigma factors, second messengers

cells can _____ OR _____ transcription in response to a ligand that is senses

active; repress

presence of a ligand waters _____ state of the transcriptional regulator

DNA-binding

repressors typically bind to the _____, while activators bind _____

promoter; next to the promoter

how do activators increase transcription?

recruit RNAP to promoter

ligand-INACTIVATED transcriptional repressors are bound to the promoter in _____ of a ligand, and are released in the _____ of a ligand

absence; presence

in the lac operon _____ is the repressor protein, it represses transcription of the lac operon when _____ is _____

lacI; lactose; absent

once lactose is present in the cell, what does lacI do?

releases from DNA, allowing transcription

ligand-ACTIVATED transcriptional repressors are bound to the promoter in _____ of a ligand, and are released in the _____ of a ligand

presence; absense

what is an example of a ligand-INACTIVATED transcriptional repressor?

lac operon

what is an example of a Ligand-INACTIVATED transcriptional repressor

trp operon

ligand-ACTIVATED transcriptional repressors are often used for _____

feedback inhibition

where there are HIGH levels of tryptophan in the in the cell, the repressor will _____ and repress _____

bind to the DNA; tryptophan synthesis

co-repressors are ligands that must bind to the _____ in order for _____ to occur

repressor; repression

feedback inhibition is when the _____ of an enzyme inhibits its own _____

product; synthesis

what is the repressor called when the ligand is NOT BOUND?

aporepressor

what is the repressor called when the ligand is BOUND?

halorepressor

in the _____ of a ligand, the ligand-responsive transcriptional activators will _____ transcription

presence; promotes

what is the ligand for the lac operon that activates the ACTIVATOR?

cAMP

under what circumstances is cAMP made?

made during glucose starvation

why do repression vs. activation?

speed of response → repression has a long lag time but activation is quick

riboswitches are _____ mechanisms that only use _____

gene regulatory; RNA

riboswitches are very _____ and part of the _____ predating cellular life

ancient; RNA World

riboswitches are RNA that forms _____ structures that binds to ligand and changes _____ in response

secondary; gene expression

what are two common ligands for riboswitches?

metal ions, metabolites

true or false: Riboswitches only regulate translation of the controlled genes?

FALSE; they can impact transcription OR translation

when riboswitches bind to ligands, there is a change in _____ that can either _____ or _____ the RBS

folding; expose; hide

what are the two main components of the two-component system?

sensor kinase and response regulator

sensor kinases are often a _____ protein

membrane

sensor kinases respond to a specific _____ signal and _____ itself in response

environmental; phosphorylates

what residue do sensor kinases phosphorylate in response to environmental signals?

histidine

in two component systems, phosphate on the sensor kinase is transferred to an _____ residue on the _____

aspartic acid; response regulator

in its _____ form, the response regulator binds to a set of gene promoters to _____ or _____ them

phosphorylated; repress; activate

the set of genes controlled is called the _____

regulon

most bacteria have _____ of two component systems

100s

sigma factors are a component of _____ that _____ transcription by binding to gene _____

RNAP; initiates; promoters

alternative sigma facts bind to _____ promoters and recruit RNAP to transcribe _____ sets of genes

unique; different

bacteria have default _____ sigmas that are always used, and _____ sigmas that are more specific

housekeeping; alternative

sigma factors are often held _____ by an _____ which is displayed or destroyed in response to a signal

inactive; anti-sigma factor

sigmas/sigma factors are used to make _____ because they are a huge energy investment

flagellum

what is the sigma factor that controls the flagellum operon?

FilA

what is the anti-sigma factor that controls the flagellum operon?

FlgM

FilA is _____ when it is bound to FlgM

inactive

The first step of the flagellum assembly is the assembly of the _____ and _____

hook; basal body

once the hook and basal body are assembled _____ delivers _____ to the secretion channel

FliA; FlgM

how does the Flagella Sigma (FilA) activated?

FlgM is secreted after the hook/body is made

once FliA (flagellum sigma) is bound to the DNA ,the genes encoding for the __(3)__ are transcribed

flagellin subunits, motor, chemotaxis machinery

what is the point of having the sigma factor for flagellum production?

prevent transcription of the genes until the basal body/hook is made (saves resources and energy)

_____ sigma factors respond to changes occurring OUTSIDE the cell

extracytoplasmic function

Extracytoplasmic function sigma factors are typically held _____ at the _____ by an anti-sigma factor

inactive; membrane

sigma E in E. coli is activated in response to _____

outer membrane stress

what is the anti-sigma for Sigma E in E. coli?

RseA

Rse A is cut by a protease which is activated by by the presence of _____ or _____ in the _____

LPS; outer membrane proteins; periplasm

outer membrane proteins that don’t make it to the outer membrane get stuck in the _____

periplasm

what types of genes does Sigma E activate for transcription in E. coli?

components to fix stress point in membrane

Sigma factors/anti-sigma factors can sense _____ forces and _____ in the cell wall

mechanical; physical defects

_____ in the cell wall allow the sigma factor to _____ and cleave the _____, this activates genes that contribute to _____

lesions; enter; anti-sigma; cell wall synthesis

second messengers are small molecules made in response to a _____, which then activate or represses _____ or _____

signal; gene expression; protein activity

what are 2 examples of secondary messengers?

ppGpp, cyclic di-/tri-nucelotides

ppGpp is an _____ that is synthesized by most bacteria in response to _____

alarmone; uncharged tRNA

what are uncharged tRNA?

tRNAs lacking amino acid

uncharged tRNAs are present during _____

carbon starvation

ppGpp binds to _____ and shuts down _____

RNAP; transcription

in some bacteria, ppGpp can also affect _____ and other _____ processes

translation; energetically intensive

what is the main goal of ppGpp?

induce dormancy during carbon starvation

cyclic di-GMP is a _____ composed of _____ guanosine nucleotides linked by _____ phosphodiester linkages

second messenger; 2; 2

what enzymes synthesizes cyclic di-GMPs?

DiGuanylate cyclases (DGCs)

what enzymes degrades cyclic di-GMPs?

PhosphoDiesterases (PDEs)

Cyclic di-GMPs regulate genes by binding to _____-responsive _____

ligand; transcriptional regulators

cyclic di-GMP increase near _____ phase

stationary

cyclic di-GMP causes a decrease in _____ and promotes _____

motility; biofilm formation

bacteria that CANNOT produce gi-GMPs will not be able to _____

form biofilms

cyclic di-nucleotides synthesis is shown to increase in response to _____

bacteriophage infection

what do the cyclic Di/Tri-nucleotides bind to in response to phage infection?

toxins that kill the infected cells (prevent further spread)

what is an example of a di-nucleotide produced in response to phage infection?

cyclic UMP-AMP

cyclic di/tri-nucleotides are made by enzymes called _____ in response to _____

CD-NTases; phage infection

cyclic di-tri-nucleotides activate proteins that cause _____ of the infected cell (what is this called?)

death; abortive infection

in abortive infection, the infected cell _____ but the greater population _____

dies; survives

True or False: upon phage infection, cyclic Di-/Tri-nucleotides will induce transcription of a protein that causes cells death

FALSE: it binds activates a protein that is already made!

cyclic nucleotides don’t do transcriptional regulation, why?

phage infection requires a quick response, much faster to modify a protein already made!

enzymes similar to CD-NTase, like _____, provide antiviral immunity in eukaryotes, including humans

cGAS