Wohlleben

Helps a cell sense internal changes & alter its gene expression to match

Two forms: repressor & activator

Bind to regulatory sequences in the DNA & prevent transcription of target genes (some must first bind a small ligand)

Bind to regulatory sequences in the DNA & stimulate transcription of target genes (most must first bind a small ligand)

LacI binds as a tetramer to the operator region lacO & laxOi: it represses the lac operon by preventing open complex formation of RNA polymerase

Beta-galactosidase (lacZ) when at low levels cleaves & rearranges lactose to make the inducer allolactose: allocaltose binds to lacI reducing its affinity to the operator & thus allowing iduction of the operon

Maximum expression of the lay operon requires the presence of cAMP & cAMP receptor protein (CRP): the cAMP-CRP complex binds to the promoter & interacts with RNA pol to increase the rate of the rate of transcription

• glucose transport by the phophotransferase system is used to measure the metabolic state of the cell: the adenylate cyclase (AC) is activated by the phosphorylated II A protein

• Glucose transport by the PTS causes catabolite repression by inhibiting the LacY permease activity: inducer exclusion

• If lactose cannot enter the cell the lacZYA operon cannot be induced

• in catabolite repression an operon enabling the catabolism of the nutrient is repressen by the presence of a more favorable nutrient (commonly glucose)

• The biphasic curve of a culture growing on two carbon sources is called diauxic growth

Genes for transport system of Zn2+ are transcribed Zn2+ is taken up

Zn2+ binds to zinc regulator (repressor) which then can bind to the operator & prevent transcription -> no Tn2+ transport can occur

• Its genes convert arabinose into xylose-P, an intermediate in biosynthetic pathways

• The major regulator AraC can repress or activate gene expression on wether the substare is availabke

• AraC form a dimer that can assume one of two confomations on wether arabinose is avaiable

• When arabinose is absent the AraC shape is rigid & elongated, it represses he expression of the genes that breakdown arabinose

• When arabinose is present the AraC shape is more compact, it stimulates the binding of RNA pol which transcribes the genes

-> AraC is activator & repressor

Repressing anabolic pathways is fundamentally different from repressing catabolic sytems

• sometimes genes encoding biosynthesis enzymes are regulated by repressors called inactive aporepressor

-> these bind the end product of the pathway which is called corepressor

• the complex can now bind the operator sequence upstream of the target gene or operon: blocks RNA pol & so transcription is off

-> if sufficient amounts of biosynthetic product (e.g. an amino acid) are synthesized further production has to be prevented

• The trp operon is a biosynthetic operon encoding enzymes that are involved in tryptophan production

• When internal tryptophan levels exceed cellular needs the excess tryptophan (the corepressor) will bind to an inactive aporepressor TrpR

• The holorepressor then binds to an operator DNA sequence upstream of the trp operon: represses expression of the structural genes by blocking RNA polymerase, repression lower expression about 11-fold

• attenuation is a regulatory mechanism in which translation of a leader peptide affects transcription of a downstream structural gene

• The attentuator region of trp operon has two trp codons & is capavle of forming stem-loop structures

• High trp levels: trp can be incorporated, ribosome can move along -> stem loop causing RNA pol to stop

• Low trp levels: trp can not be incorporated, ribosome stalls -> antiattenuater loop is formed & RNA pol can move along

• Second level of regulation “fine tuning” of the transcription in response to trp availability

• Sensing the external environment

• Sensor kinase in the cell membrane: binds to environmental signal & activates itself via phosphorylation

• Response regulator: takes phophate from sensor & binds to chromosome & alters transcription rate for several genes

• the process where bacterial cells work togehter at high density

• Induction of a quorum sensing gene system requires the accumulation of secreted small molecule called an autoinducer (N-acyl-L-homoserine lacton)

• At a certain extracellular concentration the secreted autoinducer reenters the cell (stochastical, in most cases by diffusion)

• It binds to a regulatory molecule: the regulator-autoinducer complex then activates transcription of the target genes

• E.g. Alivibrio fischeri bioluminescence

Second messenger interfering with transcription

• When energy sourced dwindle, ribosome synthesis slows

• Idling ribosomes (RelA) synthesize the signal molecule ppGpp which then decreases the affinity of RNA pol for promotors of rRNA genes & other genes

-> lower transcription of genes required for rapid growth as well as fewer ribosomes

• in many cases bacteria need to coordinately activate genes, operons & regulons of seemingly disparate function that are needed for survival: one way to do this is to first regulate the synthesis or activity of the sigma factor that directs the expression of all those genes

• To regulate sets of related genes the call can use alternative sigma factors

• These can be controlles by altered transcription, translation, proteolysis & anti-sigma factors

• secondary structires at the 5’ end of mRNA obscure access to ribosome binding sites

• Heat melts the secondary structure & increases translation of the alternate sigma factor

• Moreover heat draws chaperones away from the alternate sigma factor which can now accumulate

small RNA

• usually 100-200nt in length

• They affect the expresion of other genes

• Do not require protein synthesis: energetically inexpensive

• Diffuse rapidly

• Typically act on preexisting messages

• E.g. RNA III of Staphylococcus aureus

• the sense DNA form many protein encoding genes are transcribes to make so called cis-antisense RNAs (asRNAs)

• Antisense RNAs can also be encoded by genes located somewhere else in the chromosome: trans antisense DNA

• Typicalle 700-3000 nt long and affect only their specific target gene

• asRNA can have different effects on theit traget gene: when bound to their sense mRNA counter parts as RNAs can stop transcription, prevent mRNA translation or trigger mRNA degradation

• Transcription of genes from oppposite sites can lead to block transcription of the sense RNA by clashing polymerases

• E.g. antisense mccA of Clostridium acetobutylicum

Phase variations by shifty pathogens

• some microbes use gene regulation to periodically change their appearance in a process called phase variations: this “shape shifting” provides immune avoidance

• E.g. phase variations of flagellar proteins in Salmonella enterica: occurs by gene inversion, an invertible promotor switch regulates two genes encoding different flaggelin types depending on its orientation

• Glutamine synthetase (glnA) uses nitrogen to convert glutamate into glutamine:

Glutamate + ATP + NH4+ -> Glutamine + ADP + Pi

• when glutamne is in excess the cell has plenty of nitrogen & it is nitrogen starved when glutamate is in excess

• The NtrB-NtrC two component signal transduction pathway regulates nitrogen assimilation by altering transcription of the glnA gene in many gram- bacteria

• The glutamins synthetase activity is additionally regulated on posttranslational level