BIO 504 - Prokaryotic Genome V - Riboswitches

riboswitches

mechanisms used to regulate transcription of the 5’ end of an ACTUAL GENE via an

• aptamer domain which binds to a ligand

• expression platform whose conformation changes when ligand binds to aptamer domains, and thus creating a terminator OR anti-terminator and regulating expression of the open reading frames

during

ligand binding to riboswitches happens ___ transcription

lysC

riboswitch which regulates the expression of its ligand, lysine.

• regulates the translation of its biosynthetic genes and transporters

translation

riboswitches can regulate transcription but also ___ as the change in conformation of the expression platform can prevent the 30S recognition of the ribosome binding site (RBS)

sequestering stem

when the expression platform conformation changes, it forms a hairpin on which the RBS is isolated and unrecognizable, thus preventing translation. The hairpin duplex is called a ____ in that case.

after

for riboswitches, ligands binding ___ transcription can alter conformation of expression platform which exposes RNaseE recognition sites and marks mRNA for degradation

RNaseE

ss specific endonuclease which recognizes A/U rich sequences

nucleolytic repression mechanism

blocks translation AND degrades the message itself when ligand concentration is high enough

non-nucleolytic repression mechanism

blocks translation via RBS sequestering stem when ligand concentration is high enough, but the message itself is NOT degraded

find, 5’ end

ncRNA are coded from somewhere else in the genome and have to __ the message they regulate, making them slower. Due to that speed issue, they regulate very little on the transcription level.

On the other hand, riboswitches are part of the ___ of the message they regulate, making them faster.

downstream

riboswitches have to be ___ of a promoter as they are part of the 5’ untranslated part of the gene they regulate

responsive, 5’ untranslated region

Riboswitches have to be __ to something (domain binding to ligand) & expression platform to effectuate some kind of change & has to be in _

faster, earlier

The ADVANTAGE of regulating translation instead of transcription is that translation is ___than transcription, thus regulating it would give you the results desired ___.

slow

Transcription is a relatively __ process as forming the complex and recruiting the RNA poly to the gene in question takes some time.

positive regulation

An ACTIVATOR is bound to and recognized by an operator sequence which FACILITATES transcription, wither when free of or bound to its ligand.

• ligand causes dissociation from DNA or binding to DNA

negative regulation

A REPRESSOR binds to and is recognized by its operator sequence and INHIBITS transcription, either when free of or bound to its ligand

• ligand causes either dissociation from DNA or binding to DNA

operator

DNA sequence that binds to a regulatory protein, whether repressor or activator.

inducible

catabolic genes are usually ___ operons, meaning that when ligand is absent, the operon is repressed, and when ligand is present the operon is activated/induced.

• example: lac operon for lactose in prokaryotes

repressible

biosynthetic genes are usually ___ operons in prokaryotes, meaning that the operons are ON BY DEFAULT, and are repressed/deactivated when the ligand is present in high enough concentration.

• basically, a FEEDBACK LOOP

• example: trp operon

lacZ

• first gene of lac operon

• codes for beta-galactosidase

• break down lactose

lac Y

• 2nd gene of lac operon

• codes for lactose permease

• facilitates entry of lactose into cells

lac A

• 3rd gene in lac operon

• code for beta-galactosidase transacetylase

• unknown function

lac I

Tetramer (dimer of dimers) which binds to 2 operator sites, and binding to DNA induces DNA looping.

• gene found in the promoter of the lac operon

• codes for lac repressor protein

• blocks RNA poly from functioning

• binds lactose and thus lose affinity for its operator by falling off DNA, making operon active when lactose is present

structural analogs

cannot be acted upon by enzyme and thus can still be measured unlike the native ligand

• IPTG is the ___ of lactose

absence, presence

lac I binds to its operator in the __ of lactose but dissociates in the _ of lactose

cAMP

__ levels are LOW when glucose levels are high in a cell, and vice versa _ levels are HIGH when glucose levels are low in the cells

• ligand for regulator protein CAP

• necessary for lac operon activation (needs to co-happen with lactose presence to make lac I dissociate)

catabolite activator protein (CAP)

__ only binds to its binding site in the presence of cAMP, gene for it also found in lac operon promoter.

blocked

transcription of lac operon is __

• high glucose

• no lactose

low

transcription of lac operon is __

• high glucose

• high lactose

high

transcription of lac operon is __

• low glucose

• high lactose

apo structure

structure of a regulatory protein in the ABSENCE of ligand

stabilizes, extends, turns

Binding of cAMP to CAP ____ and ___the central alpha helix, and ___ the F helices 60 degrees, allowing them to bind to DNA