BIO 121 Chapter 18: Gene Regulation in Bacteria

Gene Regulation

- ability of cells to control their level of gene expression—which genes will be expressed, to what level, and at what time
- most genes are regulated to ensure that proteins are produced at the correct time and amount
- saves energy by producing only what is needed

Constitutive genes

- never regulated
- have essentially constant levels of expression
- very small proportion of genes
- “housekeeping genes”; necessary for everyday function (daily “housekeeping”)
- ex: genes coding fro DNA polymerase, gyrase, etc

Gene regulation purpose (bacteria)

- respond to the environment quickly

Gene regulation purpose (eukaryotes)

- eukaryotes are unable to quickly respond to the environment because of the complexity of eukaryotic genomes and processes; instead, gene regulation is used for cell differentiation and organism development
- key to multicellularity—every cell has the exact same genome, yet can be morphologically and functionally different because of the selective regulation and expression of certain genes

Developmental gene regulation in mammals

- fetal human stage characterized by continued refinement in body and a large increase in size
- gene regulation determines which globin polypeptides are made to become functional hemoglobin (different globins have different affinities for oxygen)
- fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin, which helps the fetus to harvest oxygen from maternal blood

Transcription (gene regulation)

- regulate which mRNA is made and how much
- most energy- and resource-efficient point of regulation
- most common form of gene expression regulation in both bacteria and eukaryotes

Translation (gene regulation)

- regulate translation rate (increase or decrease)
- least common point of regulation in bacteria, but about as common in eukaryotes

Post-translational modifications (gene regulation)

- phosphorylation, dephosphorylation, methylation, etc
- quickest point of regulation

Regulatory transcription factors

- DNA binding proteins; bind to the DNA in the vicinity of a promoter and affect the transcription of one or more nearby genes
- recognize and bind a distinct sequence

Repressors

- negative control
- inhibit transcription
- binding site is the operator sequence of DNA, which is usually downstream of the promoter
- act as a roadblock to RNA polymerase

Activators

- positive control
- increase rate of transcription
- bind upstream of RNA polymerase and literally push the enzyme forward

Operon

- a cluster/group of genes under transcriptional control of one promoter
- transcribed into a single mRNA (polycistronic mRNA) which encodes more than one protein
- all genes in an operon must be transcribed if one is; clustered genes will make proteins that are all responsible for one structure/pathway, so if you need one of them, you’ll probably need all of them anyways
- Eukaryotes do not have operons

Structural genes

- any gene part of the operon controlled by a common promoter

Operator

- regulatory region controlling the operon

Identifying regulated genes (Jacob and Monod)

- isolated and analyzed E.coli lac- mutants which could not metabolize lactose
- grow mutagenic e.coli on glucose medium —> transfer colonies using the replica plating method (velvet block) to lactose medium —> note which colonies failed to grow on the lactose medium, indicating they have a mutation blocking expression of the lac operon

LacZ- mutants

- could not cleave lactose because they lack functional beta-galactosidase
- cells cannot cleave lactose even in the presence of the inducer (lactose)

LacY- mutants

- do not accumulate lactose in their cells because they lack galactoside permease

lacI- mutants

- produce beta-galactosidase and galatoside permease even when lactose is absent
- cells can cleave lactose even if lactose is absent as an inducer
- constitutive mutant

lac operon

- lacI—lacI promoter—lac operon promoter—operator—lacZ—lacY—lacY
- produces one mRNA, which is translated three separate times to make LacZ, LacY, and LacA (does not make one long polypeptide that is then cleaved)

lacZ

- codes for beta-galactosidase, an enzyme which cleaves the beta-1,4-glycosidic linkage between lactose to form glucose and galactose

lacY

- codes for galactoside permease, which helps transport lactose using a proton gradient (secondary active transport)

lacA

- codes for transacetylase, which we don’t really know the function of

lacI

- codes for LacI inhibitor/repressor, which prevents transcription of lacZ, lacY, and lacA when lactose is absent

1st level of control in the lac operon

- LacI repressor binds the operator and shuts off transcription by default
- in the presence of lactose, lactose (the inducer) and LacI complex, inducing a conformational change that inactivates LacI and activates transcription (negative inducible)

2nd level of control in the lac operon

- controlled by an activator protein called CAP (catabolic activator protein), which complexes with cyclic AMP to make an active form of CAP
- active CAP binds upstream of RNA pol, creating a bend in the DNA that increases the efficiency of RNA pol binding
- when glucose levels are high, adenylate cyclase (creates cAMP) is inhibited, decreasing cAMP levels so there is no CAP activation
- when glucose levels are low, tons of cAMP is produced, so there is more active CAP to activate the operon

trp operon

- repressor complexed with trp is active and blocks transcription
- negative repressible operon

Inducible operon

- default mode is switched off and the inducer turns on transcription
- often operons for catabolism
- genes are turned off unless the appropriate substance is available

Repressible operon

- default is on and the repressor turns transcription off
- operons for anabolism are often repressible
- when enough of the product is present, genes are turned off to prevent overproduction

Global gene regulation

- coordinated regulation of many genes/operons
- needed for the responses that require the expression of dozens or even hundreds of genes

Regulon

- a set of separate genes or operons that contain the same regulatory sequences and are controlled by a single type of regulatory protein
- can be under negative or positive control
- allow bacteria to quickly respond to environmental changes, which is the primary purpose of bacterial gene regulation
- ex: bacterial virulence genes