gene regulation - signalling. efficiency poor rbs sequestering riboswitches stringent response...
TRANSCRIPT
Efficiency Poor RBS
SequesteringRiboswitches
Stringent Response
Transcription
Replication
Translation
DNA
mRNA
Protein
ProcessingStabilityStatus
StabilityAmount
Adenylation
Coupling
InitiationElongation
TerminationTemporalTandem Promoters
Signals: intra- and extracellular
MethylationSuperhelicity
Rearrangement
Gene Regulation
Two component response- regulator system
Covalent modification of the effector by the modulator
Involves phospho-relay
Three component response-regulator system: Quorum sensing
Modification?
Involved diffusible molecules, the acyl-homoserine lactones
Regulation via Signaling
Sense minute fluctuations in chemical and physical conditions
The process:
Stimulus detection
Signal processing including amplification
Integration of sensory inputs
Production of appropriate output responses
Two components: Sensor and Response Regulator
They have “transmitters” and “receivers”
Input domain
Transmitter
Sensor
Receiver Output domain
Response Regulator
Input
Signal
Output
Signal
Two-Component Signal Transduction
CytoplasmIM
Input domain Transmitter
Sensor
Receiver Output domain
Response Regulator
Input
Signal
Output
Signal
Transmitters and receivers communication involves phosphorylation activities
Transmitters:
Autokinase activity
Attach phosphate from ATP to histidine --> Histidine kinases
High-energy intermediate that transfers the Pi to and Aspartate residue on the “Receiver”
Localization
Transmitter: Cytoplasmic membrane
Receiver: Cytoplasm
+ P
Periplasm
Two-Component Signal Transducer Components
Three reactions:
(I) ATP + His <--> ADP + His ~ P
(II) His ~ P + Asp <--> His + Asp ~ P
(III) Asp ~ P + H2O <--> Asp + Pi
These reactions transduce information - also called the “phospho-relay’
(I) The phosphoryl group in ATP is first transferred to a histidine side-chain
in response to a stimulus
(II) The phosphoryl group is then transferred from the phosphohistidine residue to an aspartate side-chain --> phosphorylation induced conformational change --> eliciting response
stimulate or repress the transcription of specific genes
(III) Finally the phosphoryl group from a phosphoaspartae residue is transferred to water
Always have to function in pairs
Widespread - prokaryotic and eukaryotic
Two-Component Signal Transducer Components
The genes for the two components are linked.
Part of an operon
Sensor Response Regulator
SensorResponse Regulator
Two-Component Signal Transduction System
Localized in the cytoplasm
Stimulate or repress the transcription of specific genes - DNA-binding Domains
Conserved regions
N-terminal Phosphorylation Domain
C-terminal DNA-binding Domain
Example:
OmpR circuitry
Activates transcription of ompF and ompC
Represses transcription of ompF
Histidine kinases Reference Pageshttp://www.uni-kl.de/FB-Biologie/AG-Hakenbeck/TGrebe/HPK/Classification.htm
Receiver
Phosphorylation Domain
Output domain
DNA-binding
Domain
Response Regulators
http://info.bio.cmu.edu/Courses/03441/TermPapers/99TermPapers/TwoCom/osmoregmech.html
The proteins involved are
EnvZ Sensor Kinase
OmpR Response Regulator
Three reactions:
(I) Mg-ATP + EnvZ-His <--> ADP + EnvZ-His ~ P
(II) EnvZ- His ~ P + OmpR-Asp <--> EnvZ-His + OmpR-Asp ~ P
(III) OmpR-Asp ~ P + H2O <--> OmpR-Asp + Pi
The phosphorylated residues:
His 243
Asp 55
Osmoregulation
Cytoplasmic membrane protein with at least two membrane spanning domain
Unconserved regions provide the specificity (80 %)
Highly conserved regions
Sensory Domain ~115 residues
Catalytic Domain ~270 residues
Signal Transduction
Domain
IM
H Box (His-243)
N Box - Kinase domain
G Box - ATP Binding
EnvZ
Histidine phosphorylation is NOT intra-molecular, requires a second monomer
Can also act as phosphatase - dephosphorylate the response regulators
Sensor Kinases or Histidine Protein Kinases
http://www.science.siu.edu/microbiology/micr425/425Notes/03-Osmoreg.html
OmpR bindig Sites: High and Low affinity
Low OP
OmpR-P form binds to the high affinity site --> activate ompF transcription
High OP
Increase in OmpR-P,
• Bind to both high & LOW affinity sites --> inhibit ompF transcription
• Bind to ompC promoter --> activate transcription
• Activate micF expression --> inhibit ompF translation
OmpR Regulation of OmpF and OmpC
Gene Regulation: Regulation of Luminesence in
Marine Bacteria
Light Production Costs Energy and Is Regulated…..
Chemiluminescence from an Enzyme
Lets Light Up Some Terms:
Fluorescence
Phosphorescence
Luminescence
Energy Source? Excited States?
Excited State Life Times?
Bioluminescence
Energy Change During a Chemical Reaction –
(regardless of the energy source: chemical or light)
Substrate(s) Product(s) + Energy
or
Substrate(s) + Energy Product(s)
Thermodynamics
In honor of Lucifer !
In Greek Mythology Lucifer is the Bearer of Light
In Christian Mythology….
Luciferase = Enzyme Catalyzing Bioluminescent Reaction
Luciferin = small molecule whose excited state produces light
Bioluminescent Enzymes Luciferases
FMNH2 + O2 + Fatty Aldehyde FMN + Fatty Acid + H2O + hv
(Light)
Fatty-CHO Fatty-COOH
Reduced (energy rich) oxidized (energy poor)
FMNH2 FMN
both oxidized by O2
Luciferase is a Mixed Function Oxidase
Bacterial Luciferase Reaction
E = hν
Energy = Planck’s Constant x vibrational frequency of light
The smaller the Wavelength (λ), the larger the v.
Planck-Einstein Equation
Proton Motive Force
1. ATP
2. Rotate Flagella
3. Active Transport
4. Reversed electron transport
It costs energy to produce light !
Bacterial BioluminescenceA Shunt from Electron Transport
Nealson, Platt and Hastings, 1970. Their Photobacterium fischeri MAV was reclassified Beneckea harveyi and now Vibrio harveyi MAV.
Is Luciferases Constitutive or Inducible?
is called AUTOINDUCTION
bacterial growth results in production of “autoinducer”…. a small diffusible molecule that when it accumulates in the medium to sufficient concentration induces the synthesis of luciferase.
Nealson, Platt and Hastings, 1970
Also called Quorum Sensing (since 90’s) … the molecules are called AutoInducers. AI-1, AI-2, etc.
Phenomenon of Luciferase Induction
The number of members of a group or an organization required to be present to transact business legally, usually a majority. - Webster
Quorum
Quorum Sensing - 1995
Widespread phenomena but have to go through the drill:
“Every novel idea in science passes through three stages:
1. First people say it isn’t true, 2.Then they say it’s true but not important, and3. Finally they say it’s true and important, but not new”
Peter Greenberg
What was unique?
Covalent Modification is not NEW – but new for bacteria
Diffusible chemicals to mediate regulation is NEW for bacteria
The Inevitable Science Drill
0.01
0.1
1
10
A 6
60 n
m
1
10
100
1000
LUC
IFE
RA
SE
AC
TIV
ITY
(qp
s X
107 )
0 2 4 6 8 10
TIME (hours)
Population density-dependent OR Growth-phase-dependent
Cell-Density Dependent Expression
Luminescent bacteria in marine environment
Why do they produce light??
The genes that regulate luminescence are lux genes
Intracellular communication
Quorum sensing
60s:The first report on cell-density dependent phenomenon in the marine bacterium Vibrio fisheri and V. harveyi
by Nealson, Hastings, Eberhard, Makemson.
70s: V. fisheri lives in specific light organs (Euprymma ecolopsis) as pure culture (107/ml). Bioluminescence phenomenon - at stationary phase called autoinduction
70’s-80s: The details of the regulation and mechanisms of luminescence were worked out. The genes involved in autoinduction, luxR and luxI, were cloned. Other effectors: Arginine, glucose (c-AMP), iron, oxygen, salt.
90s: The term quorum sensing was coined. Discovery of LuxR-LuxI systems in many gram negative bacteria.Homology of LasR in Pseudomonas aeruginosa to LuxR.Discovery of anti-quorum sensing molecules - Furanone
History
A network of cellular transduction mechanisms.
Integrate signals from the bacterial environment to control gene expression,
and thereby the bacterial phenotype.
Relies on the accumulation of small diffusible, extracellular signaling molecules to modulate the transcription of target operons.
Autoinducers/Communication Molecules/Bacterial Pheromones.
Interaction between autoinducers and a positive transcriptional activator.
Three-component system
Cell-to-cell Communication
Quorum Sensing Molecules
Signaling molecules
(Acyl homoserine lactone/ AHL)
and many others
Synthetase
(LuxI homologue)Quorum-sensing Signal Generators - “I”
Regulator
(LuxR homologue)
Signal Receptors - “R”
Three Component System
luxI C D A B E GluxR(not drawn to scale)
Subunits of luciferase
Fatty acid reductasecomplex
Lux system - Vibrio fischeri
Genes involved in the luminescence
Found in diverse microorganisms
Affects various physiologic functions
Genes are linked but NOT co-transcribed
Divergently or independently transcribed
LuxI and LuxR Family
Synthetase for autoinducers forms amide bond between acyl-acyl carrier protein and S-adenosyl methionine
N-acyl-homoserine lactones (AHLs)
Differ in the structure of their N-acyl side chains (sat/unsat)Vary between 4 to 14 carbons
O
N
H
homoserinelactone
Species Specificity
O
Examples:N-butanoyl-L homoserine lactone (BHL) N-hexanoyl-L-homoserine lactone (HHL) N-octanoyl-L-homoserine lactone (OHL)
LuxI Family
Transcriptional regulators
lux Box Centered around -40
R N S T G Y A X G A T N X T R C A S R TG G G T G T A G G A T G G T G C A G G TA A C C A A A A C A
T T T T C C C C - -
N C250 aaAI - binding
(79-127)DNA- binding
(160-250)HTH
Regulator Domain Activator Domain
Multimerization(120-60)
TranscriptionalActivation(230-50)
LuxR Family
Vibrio anguillarum(Milton et al 1997)
vanI/vanR N-(3-oxodecanoyl)-L-homoserine lactone (ODHL)
ainS/ainRVibrio fischeri(Kuo et al 1994;Gilson et al 1995)
N-octanoyl-L-homoserine lactone (AI-2; OHL)
luxI/luxR N-3-oxohexanoyl-L-homoserine lactone (AI-1; OHHL)N-hexanoyl-L-homoserine lactone (HHL)
Vibrio fischeriPhotobacterium fischeri(Engebrecht & Silverman , 1984;Kuo et al 1994)
rhiI/rhiRRhizobium leguminosarum(Cubo et al 1992; Gray et al 1996;Schripsema et al 1996)
N-(3R-hydroxy-7-cis-tetradecanoyl)-L-homoserine lactone(HTHL; Small bacteriocin )
solI/solRRalstonia solanacearum(Flavier et al 1997)
N-hexanoyl-L-homoserine lactone (HHL) &N-octanoyl-homoserine lactone (OHL)
carl/carRErwinia carotovora(McGowan et al 1995)
N-(3-oxohexanoyl)-L-homoserine lactone (OHHL)
Erwinia stewartii(Beck von Bodman &Farrand 1995)
esaI/esaR N-(3-oxohexanoyl)-L-homoserine lactone (OHHL)
Enterobacter agglomerans(Swift et al 1993)
eagl/eagR N-(3-oxohexanoyl)-L-homoserine lactone (OHHL)
traI/traRAgrobacterium tumefaciensTi plasmid(Zhang et al 1993;Hwang et al 1994)
N-(beta oxo-octan-1-oyl)-L-homoserine lactone ( BOHL) & N-(hexan-1-oyl)-L-homoserine lactone (HHL);Diffusible signal molecule, conjugation factor (CF)
BACTERIUM GENES AUTOINDUCER MOLECULES
Quorum sensing systems - a sample
Bioluminescence Conjugal transferVibrio anguillarum, V. fischeri, V. harveyi Agrobacterium tumefaciens Ti plasmid
Plant-microbe interactions Swarming motilityRhizobium leguminosarum Serratia liquefaciensR. meliloti - rhizosphere-specific genes
Cell divisionVirulence determinants Escherichia coli Pseudomonas aeruginosa - elastase, pyocyanin etcRalstonia solanacearum - a phytopathogen Extracellular lipase synthesisAeromonas hydrophila - serine proteases Streptomyces lividans 66Vibrio cholerae - HA/proteaseBordetella pertussis - pertussis toxin Pigment productionErwinia carotovora - a phytopathogen Chromobacterium violaceum - violaceinStaphylococcus aureus
Antibiotic production Polysaccharide productionErwinia carotovora - carbapenem, -lactam antibiotic Klebsiella pneumoniaeRhodobacter sphaeroides Escherichia coli - colanic acid Pseudomonas aureofaciens- 3 phenazine antibioticsErwinia stewartii - Stewart's wilt of sweet corn Genetic competence Gram +ve lactic acid bacteria - antimicrobial peptide Streptococcus pneumoniaePseudomonas solanacearum - plant pathogen Bacillus subtilis
AHL molecules and their functions
• A cell-density dependent phenomenon.• A global mode of gene regulation, including virulence gene expression.• Alters bacterial behavior/phenotypes.• Involves intra-, inter-species and inter-kingdom communication.
Bacteria act as a community
Quorum Sensing
Classical Paradigm Current Perspectives
Bacteria exist as individuals. Bacteria can act in groups.
Consistent phenotypes. Cell-density dependent phenotypes.
One species, one disease. (Koch postulate)
Multiple species, one disease. (Cross-talk)
Non-interaction between host and pathogens
Close intimacy between host and pathogens.
Courtesy: KKF
Changes in Perspectives
rhlIrhlR
RhlIRhlR
+
TesterP.
aeruginosa
PassiveDiffusion
O
OH
NH
O
+
MonitorE. coli
PluxI-gfpluxR
LuxR
gfpluxR
GFPLuxR
GFP-based detection