Chapter 14: Regulation of Bacterial Cellular Processes

lag

A ______ occurs in diauxic growth after the preferred substrate is exhausted followed by resumption of growth using the second source. Catabolite repression plays a role in this pattern of growth.

two-component signal transduction

A ______-______ ______ _______ system is a regulatory system that uses the transfer of phosphoryl groups to control gene transcription and protein activity.

riboswitch

A _______ is a regulatory segment of a messenger RNA molecule that binds a small molecule (metabolite), resulting in a change in production of the proteins encoded by the mRNA.

sensor kinase, response-regulatory

A two-component signal transduction system has two major components: 1.) A ______ ______ which spans the plasma membrane so that part of it is exposed to the extracellular environment while another is exposed to the cytoplasm. It phosphorylates itself and then transfers the phosphate to the second component when it detects changes in the environment. 2.) A ______-_______ protein which functions as either an activator or repressor of transcription initiation when phosphorylated.

repressible

A(n) ______ gene is a gene that encodes a protein whose level drops in the presence of a small molecule. If the gene product is a biosynthetic enzyme, the small molecule is often an end product of the metabolic pathway in which it functions.

inducible

A(n) ______ gene is a gene whose expression level can be increased by a regulatory molecule.

constitutive

A(n) ______ gene is a housekeeping gene that is expressed at nearly the same level at all times.

upstream, promoter, subunits

Activator proteins attach to activator-binding sites. These are often ______ of the promoter (i.e. farther away from the coding region). Binding of an activator to its regulatory site generally facilitates RNA polymerase binding. This is accomplished in two main ways: 1.) In some cases, binding of the activator alters the structure of the ______, making it a better target for RNA polymerase. 2.) More often, the activator protein interacts with RNA polymerase's ______ to facilitate binding.

THI-element

An example translational regulation is observed for the thiamine biosynthetic operons of numerous bacteria. The leaders of thiamine operons contain a structure called the ______-_______, which can bind thiamine pyrophosphate. Association of thiamine pyrophosphate with the element causes a conformational change in the leader that sequesters the Shine-Dalgarno sequence and blocks translation initiation.

effector, DNA

Bacterial transcriptional regulatory proteins have two binding sites, one for a small ______ molecule and one for ______. Binding of the molecule changes the regulatory protein's ability to attach to the second site.

cAMP

CAP isn't always active (able to bind DNA). Instead, it's regulated by a small molecule called ______.

Active, Inactive

Catabolite Activator Proteins (CAP) also called cyclic AMP receptor protein (CRP) brings about the coordination regulation of catabolite operons. CAP exists in two forms: 1.) The _______ form when 3',5'-cyclic adenosine monophosphate (cAMP) is bound 2.) The ______ form when free of cAMP

antisense

Cis-encoded sRNAs are synthesized from the nontemplate strand (i.e. the sense strand) of the gene that gives rise to their mRNA target. Thus they are complementary to the target mRNA and are called _______ RNAs.

leader

Folding of the mRNA _______ sequence (the riboswitch) determines if transcription will continue or terminate. The folding pattern is altered in response to mRNA binding of an effector molecule.

sporulation

In B. subtilis, ______ is a global regulatory system controlled by phosphorelay, posttranslational modification of proteins, numerous transcription initiation regulatory proteins, and alternate sigma factors.

downstream, binding, movement

In bacteria, repressor proteins attach to a region of DNA called the operator, which usually overlaps or is ______ of the promoter (i.e. closer to the coding region). When bound, the repressor protein either blocks ______ of RNA polymerase to the promoter or prevents its ______.

adenylyl cyclase

Levels of cAMP are controlled by ______ ______ (which converts ATP to cAMP and 2 free phosphate).

AHL synthase, light

LuxR stimulates transcription of genes for ______ ______ (encoded in the luxl gene) and proteins needed for ______ production.

EnvZ, osmolarity, OmpR

Porin proteins are regulated by a two-component signal transduction system. In this system, the sensor kinase protein _______ loops through the cytoplasmic membrane so that both its C- and N-termini are in the cytoplasm. When it senses an increase in ______, it autophosphorylates a histidine residue at its C-terminus. The sensor kinase then passes the phosphoryl group to the response regulator ______, which accepts it on an aspartic acid residue located in its N-terminus. This activates OmpR so that it is able to bind DNA and repress ompF expression and enhance that of ompC.

initiation, palindromes, DNA-binding domains

Proteins are often used to regulate transcription ______, and therefore induction and repression. Many of the transcriptional regulatory proteins are DNA-binding proteins that form dimers and attach to short, inverted sequences of bases in the DNA called ______. Only a small portion of the proteins actually interacts with these inverted sequences, and these are referred to as ______-______ ______.

AHL, LuxR

Quorum sensing in V. fischeri is controlled by the signaling molecule ______. High concentrations of this molecule produced by a high density of cells diffuse back into the cell and bind the transcriptional regulator _______ which activates transcription.

squid

Quorum sensing to control AHL synthase and light production was first discovered in the pouches of bioluminscent _______ in which light-responding bacteria were expelled and refilled daily.

gene expression

Regulation that occurs by controlling the processes of transcription initiation, transcription elongation, and translation is often called regulation of ______ ______.

negative

Riboswitches in Gram-_______ bacteria regulate translation of mRNA.

positive

Riboswitches in Gram-________ bacteria function in transcriptional termination.

Shine-Dalgarno

Riboswitches that function at the translational level contain effector-binding elements at the 5' end of the mRNA. Binding of the effector molecule affects the folding pattern of the mRNA leader, which often results in occlusion of the _______-_______ sequence and other elements of the ribosome-binding site. This inhibits ribosome binding and initiation of translation.

T box, amino acid

The ______ ______ riboswitch system is found in many Gram-positive bacteria and targets genes that encode ______ ______ biosynthetic enzymes. It is regulated by uncharged tRNA; anticodon base-pairs to 5' end of mRNA, preventing formation of transcriptional terminator.

S box, methionine

The ______ ______ riboswitch system, found in low G+C Gram-positive bacteria, targets genes that encode ______ biosynthetic enzymes. S-adenosylmethionine (SAM) causes premature transcription termination.

operator

The ______ is a negative regulatory site bound by the lac repressor protein. It overlaps with the promoter and when the lac repressor is bound, RNA polymerase cannot bind to the promoter and start transcription.

promoter

The ______ is the binding site for RNA polymerase, the enzyme that performs transcription.

posttranslational

The alteration of enzymes and proteins is known as _______ regulation.

negative, repressible

The figure shows ______ control of a(n) ______ gene. In the absence of a corepressor, the repressor is unable to bind DNA and transcription occurs. When the corepressor interacts with the repressor, the repressor is able to attach to DNA and transcription is blocked.

negative, inducible

The figure shows ______ control of a(n) ______ gene. In the absence of an inducer, the repressor protein blocks transcription. The presence of an inducer prevents the repressor from binding DNA and transcription occurs.

positive, repressible, inhibitor

The figure shows ______ control of a(n) ______ gene. The activator protein binds DNA and promotes transcription unless the ______ is present. When it is present, the activator protein undergoes a conformational change that prevents it from binding DNA.

positive, inducible

The figure shows ______ control of a(n) ______ gene. The activator protein is only able to bind DNA and activate transcription when it interacts with the inducer.

C

The following is an example of regulation by _______. A.) Repression B.) Induction C.) Activation If arabinose is present, it binds to AraC. This complex is needed for RNA polymerase to bind to the promoter and transcribe the ara operon.

A

The following is an example of regulation by _______. A.) Repression B.) Induction C.) Activation In the absence of histidine, a repressor is made but it unable to bind DNA and prevent transcription. In the presence of histidine, the amino acid reacts with the repressor and activates it so that it can bind to the operator site on the DNA.

B

The following is an example of regulation by _______. A.) Repression B.) Induction C.) Activation In the absence of lactose, a repressor binds to the operator site and blocks transcription. When an inducer becomes available it reacts with the repressor and inactivates it.

lacZ, lacY, lacA

The lac operon contains three genes which are all transcribed as a single mRNA under the control of one promoter: 1.) ______ - encodes the enzyme β-galactosidase which splits lactose into glucose and galactose 2.) ______ - encodes lactose permease (a membrane protein) which allows the cell to import lactose 3.) ______ - encodes the enzyme transacetylase which attaches a particular chemical group to target molecules

lacI

The lac repressor, ______, acts as a lactose sensor. It normally blocks transcription of the operon, but stop acting as a repressor when lactose is present.

MicF

The ompF mRNA encodes the porin OmpF. Translation of this mRNA is regulated by the trans-encoded sRNA _______, a product of the ______ gene. It is partially complementary to ompF mRNA and, when bound to it, prevents translation (same answer for both blanks).

5

The trp operon includes ______ genes that encode enzymes needed for tryptophan biosynthesis

absence

The trp operon is an example of negative transcriptional control of repressible genes by the trp repressor. Thus, the operon only functions in the (absence / presence) of trypophan.

corepressor

The trp repressor does not always bind DNA. Instead, it binds and blocks transcription only when tryptophan is present. When tryptophan is around, it attaches to the repressor molecules and changes their shape so they become active. A small molecule, like tryptophan, which switches a repressor into its active state is called a ______.

complementary base pair

Through ______ ______ _______ interactions a small RNA provides specificity for a particular function. For example, the sRNA RhyB in E. coli represses translation of mRNAs encoding iron-containing proteins when iron availability is low.

False (Some sRNAs actually promote translation upon binding to the mRNA.)

True or False: Binding of an sRNA to an mRNA target interferes with either ribosome binding or the ability of the ribosome to move down the mRNA.

False (It is a continuum. Inhibition of transcription does not mean that genes are "turned off" but rather that mRNA synthesis is decreased significantly.)

True or False: Gene expression is an all-or-nothing phenomenon.

False (Riboswitches allows binding of an effector molecule directly to the mRNA)

True or False: Only proteins can bind directly to mRNA.

3 (HAI-1, AI-2, and CAI-1)

Unlike V. fischeri, V. harveyi responds to ______ autoinducer molecules to maximize the expression of bioluminescence. Again, Lux R is not made when there is a low cell density and no autoinducers are present. However, any combination of inducers cause LuxR to be made and bioluminescence occurs.

FMN, RFN-element

Use the figure to fill in the blanks describing the rib operon found in B. subtilis. The production of riboflavin biosynthetic enzymes is repressed by _______, which is derived from riboflavin. When transcription of the rib operon begins, sequences in the leader of the mRNA fold into a structure called the ______-______. This element binds the repressor metabolite and in doing so alters the folding of the leader, creating a terminator that stops transcription. Transcription is stopped with the aid of rho protein, the RNA helicase that functions in factor-mediated transcription termination

Lactose absent, glucose absent

What conditions does the figure indicate about the presence of lactose and glucose?

Lactose absent, glucose present

What conditions does the figure indicate about the presence of lactose and glucose?

Lactose present, glucose absent

What conditions does the figure indicate about the presence of lactose and glucose?

Lactose present, glucose present

What conditions does the figure indicate about the presence of lactose and glucose?

sigma factors

When cells sense a starvation signal, a cascade of events is initiated that results in the production of alternative ______ ______ that are differentially expressed in the developing endospore and mother cell.

allolactose, inducer

When lactose is available, some molecules will be converted to ______ inside the cell. This molecule binds to the lac repressor and makes it change shape so it can no longer bind DNA, thereby acting as a(n) _______ (a small molecule that triggers expression of a gene or operon).

repressor

When there is little tryptophan in the cell, the trp _______ is inactive because no tryptophan is available to bind to and activate it. This allows the trp operon to be transcribed by RNA polymerase.

Catabolite repression

______ ______ is the regulation of transcription by both repressors and activators. This is an important global control system that allows microorganisms to adapt quickly to a preferred carbon and energy source.

CAP

______ acts as a glucose sensor. It activates transcription of the operon but only when glucose levels are low.

Diauxic

______ growth is a biphasic growth pattern that results when a particular carbon source is preferred over another when both are available in the environment. An example is glucose, which is more easily metabolized than lactose.

Negative, repressor

______ transcriptional control occurs when the binding of the protein to DNA inhibits initiation of transcription. Regulatory proteins that act in this fashion are called ______ proteins

Positive, activator

______ transcriptional control occurs when the binding of the protein to DNA promotes transcription initiation. These proteins are called ______ proteins.

Beta-galactosidase, substrate

______-_______ is an example of an inducible enzyme that functions in a catabolic pathway, forming galactose and glucose as a product of lactose hydrolysis. Inducible enzymes are only present when their ______, or inducer-effector molecule, is available.

Trans

______-encoded sRNAs are synthesized from genes located at sites distinct from the genes encoding their target mRNAs. Despite this, they have some regions of complementarity to their targets.

sRNAs

_______ , or noncoding RNAs, are regulatory RNA molecules that do not function as messenger, ribosomal, or transfer RNAs.

Quorum sensing

_______ _______ is a form of cell-to-cell communication mediated by small signaling molecules such as N-acyl-homoserine lactone (AHL).

Attenuation

_______ is a mechanism of control in some bacterial operons which results in premature termination of transcription and is based on the fact that, in bacteria, transcription and translation proceed simultaneously.

glucose

cAMP is a "hunger signal" made by E. coli when ______ levels are low. This is because adenylyl cyclase is only active in such conditions.