bio 207 lecture 8: molecular regulation

gene regulation occurs at multiple levels including

• alteration of DNA sequence

• control of transcription thru repressors, activators, sigma factors, sRNAs

• control of mRNA stability

• translational control - hiding ribosome binding sites or other mRNA sequences

• post-translational control - cleavage, phosphorylation, methylation

regulation or control at the (?) level is most drastic and least reversible; at the (?) level it is the most rapid and most reversible

DNA sequence; protein

regulatory sequence

• aka operators (in repression)

• usually upstream of a coding gene

• can control initation of transcription at promoters by binding regulatory proteins

regulatory protein activity is affected by

changes to environment in cell or outside the cell

ligands

alter DNA binding affinities of regulatory proteins → affects ability to stimulate or block transcription initiation at gene promoters

repressors

regulatory proteins that down-regulate gene expression at operators

activators

regulatory proteins that up-regulate gene expression at activator sequences

in repression, a ligand is an inducer when

repressors are able to bind to operators in the absence of the ligand

inducer causes repressor to fall off

in repression, a ligand is a corepressor when

the repressor binds to the operator after binding with the ligand

corepressor causes repressor to bind

activators

• bind to regulatory sequences

• typically with the help of their ligand inducer - opposite of binding pattern with repression

• contact RNA polymerase positioned nearby → initiate transcription

sensing the extracellular environment involves

a two-component signal transduction system:

• sensor kinase

• response regulator

sensor kinase

• signal transduction system allowing cell to sense extracellular environment

• protein that spans membrane and senses a particular molecule

• binds to environmental signal

• autophosphorylates and passes phosphates down to response regulators that bind to DNA → repression or activation of gene

response regulator

• signal transduction system allowing cell to sense extracellular environment

• occurs in cytoplasm

• takes phosphate from sensor kinase

• binds to chromosome and alters transcription rate for genes

induction

process involved in catabolic regulation

• molecule to be catabolized is sensed → inducer binds to repressor → repressor dissociates from operator → transcription

derepression

process involved in biosynthetic regulation

• corepressor binds to repressor → repressor able to bind to operator → repression of transcription

catabolite repression

method that allows preferential metabolism; an operon allowing catabolism of one nutrient is repressed by presence of a more favorable nutrient

• creates a biphasic curve from the two carbon sources (diauxic growth)

aporepressor

inactive repressor that binds with a co-repressor

how do aporepressors regulate biosynthetic enzymes and regulation?

bind to end product of biosynthetic pathway (corepressor) → complex binds to operator → represses target gene expression → negative feedback mechanism that stops building when unnecessary

how is tryptophan an example of repression of an anabolic pathway?

• trp operon encodes enzymes involved in tryptophan production

• tryptophan = corepressor

• TrpR = aporepressor

• when trp is on, tryptophan produced in excess →tryptophan binds to TrpR → complex binds to operator → represses transcription of trp structural genes

gene expression can be regulated after transcription in these ways

• regulatory sequences in mRNA can cause premature termination of transcription (ex. attenuation)

• mRNA sequences may prevent their own translation into proteins (ex. riboswitches)

• other regulatory RNAs influence fates of transcribed mRNAs (ex. untranslated RNAs)

attenuation

• bacteria

• translation of leader peptide affects transcription of operon’s downstream structural genes

• prevents unregulated and unnecessary gene expression

• attenuator RNA region contains areas capable of base pairing and forming loops

riboswitches

• can happen during translation or transcription

• untranslated mRNA

• folds into three dimensional structures that bind specific metabolites to sense their abundance in the cell

untranslated small regulatory RNAs (sRNAs)

• transcribed independently from mRNA transcript it controls (contrary to attenuators and riboswitches)

• posttranscriptional regulation

• do not require protein synthesis, diffuse rapidly, act on preexisting messages

in high tryptophan protein levels, attenuation causes

transcription termination

• ribosome translates trp codons until the stop codon

• ribosome will stop over mRNA regions 1 and 2 while RNA polymerase transcribes regions 3 and 4

• 3:4 termination loop forms, the RNA ending site

• loop binds RNA polymerase and the polymerase is picked off before it can transcribe trpE

in low tryptophan protein levels, attenuation causes

transcription to proceed

• ribosome translates leader mRNA

• ribosome stalls at trp codons of the leader sequence, covering region 1

• loop forms between region 2 and 3 - more energetically favorable than 3:4 so forms instead of it

• no termination; RNA polymerase continues to transcribe

what is the leader sequence in attenuation?

• always transcribed and translated but no enzymatic activity

• regulates transcription of the structural trp genes after the operon

• contains code for a leader peptide

how do ribosomes sense availability of tryptophan in the cell before attenuation?

in the operon, there are two consecutive tryptophan codons in the sequence encoding the leader peptide; gauges availability of tryptophan-charged tRNAs for peptide synthesis

why is transcription stopped with formation of a 3:4 stem loop but not a 2:3 stem loop?

3:4 stem loop ends with a poly-u tail that is a transcription termination signal ejecting RNA polymerase

quorum sensing

the process where bacterial cells work together at high density

induction of quorum sensing genes requires accumulation of a molecule called an

autoinducer

in quorum sensing, when cell density increases,

secreted autoinducer molecules reenter the cell and bind to regulatory molecules

(?) sometimes use quorum sensing to time the expression of their virulence genes within the host

pathogens

quorum sensing can be used for interspecies communication so bacteria can tell each other whether

they are in the majority or minority

chemotaxis

ability of organism to sense chemical gradients and modify the direction of motility in response

receptors in the cell membrane sense chemical gradients and are called

methyl-accepting chemotaxis proteins (MCPs)

how does chemical gradient affect movement?

• no attractant: cheA kinase phosphorylated → Che-Y phosphorylated into Che-YP → increase Che-YP reverses flagellar motor into clockwise motion → cell tumbling

• attractant: attractant binds to MCP → MCP conformational change → Che-A kinase inhibited → Che-YP stops forming → CheZ dephosphorylates Che-YP to CheY → counterclockwise turn, straight swimming (no tumbling)

reversible methlyation (sensitizes/desensitizes) MCPs, while reversible demethylation of MCPs (sensitizes/desensitizes) MCPs

desensitizes; sensitizes

provides a primitive form of memory for favorable movements

how does memory and methylation allow a cell to move up a chemical gradient?

• begins with attractant binding to MCP → straight swimming

• MCP can be methylated by CheR, which desensitizes MCP to attractant

• cells will tumble until higher concentration of attractant

• CheA-P can demethylate MCP leading to resensitivation