Regulation of gene expression in bacteria and archea

Question 1

Why should we care about bacteria?

Answer 1

They dominate the living world! Single-cell organisms (bacteria, archea, protozoa etc) are highly evolved creatures and might even be more modern than eukaryotes because of their fast evolution.

Remember, the world looks very different to a bacterium, imagine being one cell large, how big your surroundings are!

Question 2

The microbial world/lifestyle dictates certain special
solutions, give three examples of situations that bacteria need to handle.

Answer 2

• Alone or together: sometimes it’s better to be alone (live planktonically) and do their thing if the conditions are good, but if the conditions are terrible it might be good to team up (in biofilm) to survive, or to take over a host.
• Rapid changes in environment warrants rapid adaptive responses: needs a lot of signaling and fast, like responding to temp change, predators, or nutrients. A signal received a fraction of a second early can mean it can outcompete all other bacteria!
• competition or altruism: bacteria compete for resources but behaves altruistically by setting of apoptosis if infected by a phage to protect surrounding brothers and sisters.
• Differentiation: Is the environment so bad that they won’t survive? Then they can go through sporulation for example, to ensure the survival of “offspring”.

Question 3

What kind of information/signals need to be perceived by a bacterium? Name four.

Answer 3

• Nutrient availability (food, energy)
• Stresses (very common) such as: Heat, cold, salt, acid, drought, oxidative stress, starvation for N, P, C etc., anoxic conditions, iron deficiency, membrane stress etc.
• Who else is around (bacteria)?
• Who else is around? eg plant/animal cells that injured that’s a way in.
• Where am I? (in soil, in host..)
• How many are we? - quorum sensing

Bacteria are masters of dealing with stresses, as almost no environment is optimal and to deal with the stresses, they need changes in gene expression. With the speed of growth of bacteria in optimal conditions, they could overpopulate the earth in a matter of days. Fortunately, there’s always a limiting factor.

Question 4

For bacteria to handle these stresses, gene expression must be adequately controlled. In what three ways can genes be expressed in bacteria?

Answer 4

• Constitutive expression: “housekeeping” genes that are on at all times (not many)
• Most genes are either controlled as single genes or…
• Operon controlled: many genes in a row that are controlled by a “master switch” which enables many genes in a coordinated way. Eg many genes needed to fix a dsDNA break are all enabled in one go to move faster.

Question 5

Gene regulation frequently exerted at several levels. On which three levels can gene expression be controlled?

Answer 5

• Transcriptional control: is transcription started or not? if not: transcriptional control like TFs binding to a repressor. Riboswitches are not on this level, but are post-transcriptional since transcription starts in order for a riboswitch to do it’s thing
• Post-transcriptional: Promote/inhibit transcription after it has started, or stabilizing/destabilizing the RNA being transcribed.
• Post-translational control: Protein degradation/stabilization, sequestration or modification. Basically anything that makes protein not do it’s job or do a better job etc.

Question 6

In what three steps does transcription work in bacteria?

Answer 6

1. RNA polymerase binds to a promoter site on DNA to
   form a closed complex. The RNA polymerase initiates transcription after opening the DNA duplex to form a transcription bubble.
2. During elongation, the transcription bubble moves along DNA and the RNA chain is extended in the 5′ → 3′
   direction by adding nucleotides to the 3′ end of the
   growing chain.
3. Transcription stops and the DNA duplex reforms when RNA polymerase dissociates at a terminator site.

Note: The RNA polymerase itself catalyzes the reactions to open the DNA and add nucleotides.

Question 7

What is an operator?

Answer 7

An operator is the site where transcription factor (TF) bind to to regulate transcription. TFs can bind to the operator to either activate or repress transcription.

Question 8

Why would it be useful to both be able to control gene expression transcriptionally and post-transcriptionally?

Answer 8

Because sometimes “on” or “off” is not enough, you might need to have more or less of a protein/RNA so post-transcriptional regulation fills those gaps. Furthermore, RNAs are fairly “cheap” to make energetically so kinetically there’s no big difference in transcriptional vs post-transcriptional control, but speed differs a lot so it’s good to be able to do both to cater for different needs.

Question 9

The discovery of post-transcriptional control by regulatory RNA came quite late (in the 2000s) why?

Answer 9

There were ideas of RNA being regulatory already in 1961, but they couldn’t isolate it biochemically. Around the same time we were able to isolate regulatory proteins and that took away all the research about regulatory RNAs unfortunately and also post-transcriptional control in prokaryotes.

Question 10

There are two classes of transcriptional control in bacteria, which?

Answer 10

• TF + ligand transcriptional control
• Transcriptional control by two-component systems

Question 11

There are two types of TF + ligand transcriptional control in bacteria, which are these and what do they mean?

Answer 11

• Negative control (can be of either the repressible or inducible type): A mechanism of gene regulation in which a regulator is required to turn the gene off.
  Repressor control. eg. a repressor protein binds to an operator to prevent a gene from being expressed.
• Positive control: a system in which a gene is not expressed unless some action turns it on. Activator control. e.g. a transcription factor is required to bind at the promoter to enable RNA polymerase to initiate transcription.

Question 12

Transcriptional control (TF+ligand) also have two subtypes, beside from positive or negative control, repressible and inducible regulation. What do these types of regulation mean?

Answer 12

• In inducible regulation, the gene is regulated by the
  presence of its substrate. For example the lac operon in which the presence of lactose induce transcription of genes needed for lactose metabolism.
• In repressible regulation, the gene is regulated by the
  product of its enzyme pathway, eg. the Trp operon in which tryptophan (Trp) co-represses the genes involved in Trp synthesis.

Question 13

One classic example of negative (repressible type) transcriptional control (TF+ligand) is the Trp operon. How does this work in detail?

Answer 13

So, negative = something bound –> transcription blocked and repressible = the gene is regulated by it’s product.

When tryptophan (Trp) is abundant in the cell, there’s no need to synthesize it, so Trp is a co-repressor that binds to the TrpR (repressor) and the complex bind to the operator and the transcription is blocked.

When Trp is not present/abundant in the cell, the TrpR is inactivated and can’t bind to the operator which leads to transcription of the gene and subsequent Trp synthesis.

Question 14

A classic example of negative (inducible type) transcriptional control (TF+ligand) is the Lac operon. How does this work in detail?

Answer 14

So, negative = something bound –> transcription blocked and inducible = The gene is regulated by its substrate.

When lactose abundant in the cell, you need to express the genes encoding for enzymes involved in metabolizing it! Lactose is an inducer that binds to LacI (repressor) which disables it from binding to the operon –> transcription allowed.

When Lactose is not present in the cell, there’s no need to express the genes encoding for the enzymes needed in lactose metabolism. So the LacI repressor is bound to the operator to block transcription.

Question 15

Catabolite repression is an example of positive transcriptional control, how does it work?

Answer 15

Catabolite repression is a form of global control regulating many genes, by a secondary messenger binding to deactivating many genes.

One example of catabolite repression is of the lac operon in E. Coli, where cAMP - a metabolite that is lowered when glucose is metabolized - further repress genes involved in the metabolism of less effective energy sources.

When glucose is scarce, the levels of cAMP is high in the cell, and then cAMP binds to CAP and the cAMP-CAP complex binds upstream of the lac promoter, helping RNA polymerase begin transcription. So it induces transcription further by binding –> positive control.

When glucose is present in the cell, cAMP levels are low –> no cAMP-CAP complex and no induction of expression.

Basically: cAMP binding activates transcription.

Question 16

Transcriptional control can also be carried out by two-component systems. How does this work?

Answer 16

You have a sensor that senses an environmental stimuli and respond by in turn activating a response regulator that regulates gene expression.

Example: a histidine kinase (HK) with an input and a catalytic domain, that relays the signal by it’s catalytic domain carrying out a reaction (often phosphorylation of the RR) that leads to the activation of the response regulator that subsequently acts on DNA to regulate gene expression (usually turn genes on but can also be off). Need adaptation (resetting) by dephosphorylation of RR to detect more signaling (necessary to determine “size” of signaling/stimuli)

Note: can be more than two components (maybe to provide the cell with more possibilities of regulation).

Question 17

What is the definition of post-transcriptional control (PTC)?

Answer 17

Any kind of control exerted after initiation of transcription!

Question 18

PTC can be controlled in cis or in trans. What is meant by this? Provide an example of each.

Answer 18

• Control in cis: Acting on the same RNA (less common). Any sequence of RNA that functions exclusively as a RNA sequence, affecting only the RNA to which it is physically linked. Example: riboswitches
• Control in trans: Acting on another RNA (dominant). Any gene product that is free to diffuse to find its target is described as trans-acting. Example: small RNAs (sRNAs), regulatory RNA-binding proteins.

Question 19

PTC is like a second layer of regulatory possibilities. Give two examples of PTC mechanisms in bacteria.

Answer 19

• Attenuation: two conformations of leader RNA “on/off” switch for continued transcription. cis
• structural mimicry: competition of enzyme binding sites, feedback loop. trans?
• Riboswitches: small ligands regulating an “on/off” switch by switching between two conformations. cis

Question 20

Explain how attenuation works in detail with an example.

Answer 20

In the Trp operon, attenuation works as a second layer of regulation and utilizes the fact that transcription and translation are coupled in bacteria. The site for attenuation is in the leader, a 5’-ORF upstream of the genes containing two UGG codons (tryptophan) and four interacting elements followed by a tandem uracil sequence. In the leader, two secondary RNA conformations are possible and mutually exclusive. One terminator conformation (interaction between elements 1-2 and 3-4) and one anti-terminator conformation (interaction between element 2-3).

If the Trp concentration is low, this results in the ribosome being stalled at the UGGUGG-sequence which physically hinders the interaction between elements 1-2 and the anti-terminator forms, allowing translation. If the Trp conc is high in the cell, the ribosome quickly transverses the tandem UGG sequence and the terminator forms (mainly the element 3-4 interaction - which is a G-C rich hairpin structure), which causes transcription to terminate.

The transcription termination happens by the stable G-C hairpin destabilizing the RNA-DNA hybrid in the RNA pol stalled in the UUUUU region, causing it to fall off and terminate transcription. So the placement of the ribosome matters, and secondary mRNA structures physically hinders transcription to be continued.

Note: same principle applies to histidine/leucine operons but with histidine/leucine codons in the beginning instead.

Question 21

Bacteria also use post-transcriptional control
of aminoacyl tRNA synthetases (aaRS), what are aaRS and why control them?

Answer 21

Aminoacyl tRNA synthetases (aaRS) are the enzymes that add the respective amino acids to tRNAs.

It’s good to have a feedback control for aaRS gene expression as there’s no need to express it if there is little substrate around.

The general principle is:
- when the majority of tRNA are uncharged (without amino acid), more aaRS are needed –> derepress gene expression of aaRS (allow translation).
- when the majority of tRNAs are charged, less aaRS are needed –> repress gene expression of aaRS (degrade mRNA)

Question 22

How does PTC of aaRS work in detail in both gram positive and gram - bacteria?

Answer 22

The mechanism for aaRS feedback control varies, in many gram+ bacteria it works like attenuation while in many gram- bacteria it works by structural mimicry.

• Structural mimicry type (G-) example: ThrRS bind to thr-tRNA (uncharged) to add the Thr to the tRNA usually. If there is no/low uncharged thr-tRNA the ThrRS will instead bind to the leader of its own mRNA which structurally mimics uncharged thr-tRNA. When bound to the leader, this physically hinders the ribosome from further translating the ThrRS-mRNA and it degrades. So basically, it enzyme is busy: bound to tRNA and if not busy: bound to its own mRNA. So the competition between binding sites for the Thr-RS provides a feedback loop that regulated Thr-RS output!
• Attenuation type (G+) example: In the leader of aaRS mRNA, there are two mutually exclusive conformations possible: a terminator that hides Shine-Dalgarno (SD) seq, and antiterminator structure which allows readthrough to RS gene, SD open. When charged tRNA is abundant, it interacts weakly and short with the leader and the terminator forms –> transcription is repressed. When uncharged tRNA binds to the leader, the binding is strong and stable and the anti-termination structure forms which allows read through of the gene. This works for all amino acid RS and their respective genes.

Question 23

What is a “riboswitch”?

Answer 23

A riboswitch is an RNA domain that contains a sequence that can change in secondary structure in response to binding if a ligand, to control it’s activity. (Always occurs in cis)

Basically, it’s ligand-mediated transcription attenuation (in G+/-) but can also be transcription blocking (G-).

Question 24

Explain the terms “aptamer platform”, “expression platform” and “effector” in relation to a riboswitch.

Answer 24

• The ligand binding sequence is called the “aptamer” platform and has extremely high affinity to the ligand.
• The part of the mRNA that changes conformation is called the “expression” platform.
• The ligand is often called an “effector” and are usually low molecular weight ligands like vitamins or guanine for example.

Question 25

Explain how a riboswitch work with an example.

Answer 25

The G-riboswitch: A riboswitch located in the 5’UTR of the genes for purine (G, C) synthesis.

• When the guanine conc is high in the cell, it binds to the aptamer of the riboswitch (located in a junction between two stem loops), which stabilizes the structure (very stable) and the terminator structure forms downstream, leading to repressed gene expression.

When the guanine conc is low in the cell, the part where the aptamer is located is destabilized, leading to the formation of the antiterminator conformation, which allows further transcription.

Question 26

Give two examples of translational control in bacteria.

Answer 26

• RNA thermometer
• Antisense RNAs aka sRNAs: cis or trans
• Riboswitches

Question 27

How does “RNA thermometers” commonly used by pathogens or to regulate heat-shock proteins work?

Answer 27

RNA thermometers are based on destabilizing structures that blocks translation in response to higher temperatures to enable translation. Basically, the structure is in it’s “off” state with the SD sequence bound in structures that hinders the ribosome to bind. When the temperature rises, the secondary structures unfold to expose the SD sequence which enables translation.

The temperature specificity is acquired by different G-C content (as G-C bonds are stronger than A-U/T) or interruptions to base baring or helical structure.

Used in pathogens to know when to turn on virulence genes and heat shock proteins to only be translated when needed.

Question 28

Antisense RNA is another mechanism of PTR in bacteria. What are antisense RNAs and what two types are there?

Answer 28

Antisense RNAs are sRNAs that base pairs with mRNA to activate or inhibit target mRNA. (present in all bacteria/archaea)

Can be:
- Cis encoded: encoded by the same gene as the mRNA it acts on, but on opposite strand. Not perfect pairing but is very quick and has only one target.

• Trans encoded = called sRNAs: encoded on another gene than the mRNA it acts on. Not fully compatible base pairing bc it’s not evolving on the same chromosome, but enough to be able to regulate. Often have many different targets!

Note: one sRNA can have many different mRNA targets, and some mRNAs can be targeted by several sRNAs.

Question 29

sRNAs can regulate translation in several different ways, give three examples of modes of action for sRNAs.

Answer 29

• Inhibition of translation by binding to the ribosome binding site (RBS) and blocking it. Which can also lead to degradation of the mRNA.
• Activation of translation by binding to a sequence that blocks the RBS and by that enable translation by opening up the RBS.
• Inhibition of ribosome standby: binding to the stand-by site and thereby hindering translation.
• Enabling degradation: By binding to a coding region and recruiting endonuclease activity (by binding to Hfq).

Question 30

Hfq is a key player in sRNA-mediated control, why?

Answer 30

Hfq is a protein that brings RNAs together by being a very strong RNA binder.

• it enhances sRNA-target binding
• increase the stability of sRNA
• acts as a chaperone to help RNA do it’s thing.

Question 31

Regulation of protein sequestration is a common way to perform protein regulation in bacteria. Give two examples of mechanisms for protein sequestration.

Answer 31

• protein dimer regulator: Having a regulatory RNA (CrsB) that binds proteins (like CsrA) that usually represses different targets, to enable translation of the usually repressed mRNA. A way to perform derepression on multiple targets regulated by the same protein.
• sRNA: 6S RNA which is a structural mimic of a promoter recognized by RNA polymerase. Functions as a storage site for the RNA polymerase in not-so-favorable conditions to enable quick increase of gene expression when the conditions are better! When the conditions are better, the RNA polymerase starts to transcribe, and this cause a secondary structure to form which makes the RNA polymerase to fall off and able to diffuse away to start transcribing.

Question 32

sRNAs (Trans-encoded antisense RNAs) can repress multiple targets, explain how this can be useful with an example.

Answer 32

As the sRNAs are trans encoded, they don’t have perfect complementarity with one target, but instead can act on multiple targets as limited complementarity is sufficient. (Similar to microRNAs in eukaryotes.)

An example of when this is useful is membrane stress, where a signal about one misfolded outer membrane protein (eg bc of heat) can increase the expression of sRNAs that can inhibit translation of many different outer membrane proteins as they’ll get destroyed anyway! Better to use the energy to translate things that helps in the situation. If you would regulate this on transcriptional level, all the existing mRNAs would still be translated and the cell would be “sick” for a long time. So it’s a very quick solution (less than a minute!).

Question 33

Describe the similarities and differences between sRNAs in bacteria and microRNAs in eukaryotes.

Answer 33

Similarities:
- Both act by antisense, using limited, non-contiguous complementarity
- Both are trans-encoded
- Both are rarely constitutively expressed, under transcriptional control
- both act on multiple target mRNAs (families, functionally related)
- By affecting TF mRNAs, they can have extended downstream effects.

Differences:
- sRNAs are “true” regulators – though they may need helpers while miRNAs are adaptors that target effector proteins to mRNAs.
- sRNAs do up- and down-regulation, miRNAs do not (?)

Question 34

Name three advantages of using sRNAs for post-transcriptional control.

Answer 34

Possible reasons:
- Stabilize off-states, counteract transcriptional noise (curli, toxins): Transcription happens in bursts, and a repressor of one thing can fall off, which can lead to unwanted effects in that cell (bad in for example biofilm formation). sRNAs help catch this error by regulating the product, no big deal!

• Coordinated removal of unwanted proteins (membrane stress)
• Rapid exit from repressed state by co-degradation (RyhB, others)
• Plasmid copy control requires suitable kinetics (R1, ColE1, others)
• Connecting regulatory pathways (similar to ceRNAs)
• Inversion of TF effect; repressor can indirectly activate (e.g. Fur - RyhB)
• Cheaper energetically

Question 35

Archaea is more closely related to eukaryotes than bacteria, but share many similarities with both. What is similar/different from eukaryotes/bacteria?

Answer 35

Bacteria - Archaea - Eukaryotes
* Size: Small - Small - Big
* Chromosomes: Small, circular - Small, circular - Big, circular or linear
* Operons: Yes - Yes - No
* Introns: No - No - Yes
* Nucleus: No - No - Yes
* Cytoskeleton (aktin): No - Yes - Yes
* True peptidoglycan: Yes - No - No
* Metabolism: Varied - Varied - Oxygen based
(Krebb’s cycle, oxidative phosphorylation)

Question 36

Name three features that are unique to Archaeal cells.

Answer 36

• Ether linked membrane lipids: one head and one tail covalently bound in opposite directions (compared to one head two tails interacting by hydrostatic forces in eukaryotes)
• Thrive in harsh environments including extremes in temperature, pH, and salinity (many, some don’t).
• No fatty acids in the membrane, instead branched isoprene chains.
• Unique stereoisomer of glycerol produced in a different way (L-glycerol in archaea, D-glycerol in eukaryotes and bacteria)
• Targeted by archaea specific viruses (very abundant, more archaeal viruses than bacterial/eukaryotic together!)

Question 37

Why should we care about archaea?

Answer 37

• Cell biology: Not bacteria, not eukaryotes… a third way of doing things, like one archaea with square cells! Sometimes similar to eukaryotes, but simpler so they can be used as models to understand our cells.

– Relatively easy to work with and easy to decontaminate because of extremophile lifestyle.

• Hyperthermophiles = good for protein biochemistry and provide high temperature enzymes that can be used in research, like the Pfu enzyme in PCR comes from the archaeon Pyrococcus furiosus.

– Methanogenic bioreactors! The only organism that naturally produce biogenic methane.

• Evolutionary biology: Archaea are key to TWO mayor evolutionary events: The bacteria/archaea split and the archaea/eukarya split.

Question 38

What was so special with the discovery of the Asgard-archaea?

Answer 38

The asgard archaea are the most closely related to eukaryotes and their discovery changed the way of clustering organisms –> eukaryotes as branch of archaea instead of it’s own branch, meaning a two branch tree of life instead of three as previously thought.

Question 39

The regulation of transcription is very similar in archaea and bacteria, but there are some key differences. What are the key differences and what consequences do they entail?

Answer 39

• Archaea have the same genome organisation as bacteria, with genes arranged in operons, circular chromosomes and plasmids and origin of replication (ori) that RNA polymerase bind to, but a key difference is that archaea often have several ori compared to only one in bacteria. As the genes closest to the ori has the highest expression, having multiple ori sites gives more opportunities for high expression/transcription. Note: some archaea only have one ori like bacteria.
• Archaea have histones (Euryarchaeota, not crenarchaeota), like eukaryotes but unlike bacteria. This give archaea the ability to repress large chunks of the genome, which bacteria don’t have. The histones are homologous to those in euk, but are smaller and lacks N and C terminal tails (which are the sites being regulated in euk) but are instead regulated by chromatin binding proteins.

Note: all archaea have small DNA binding proteins that are functional homologues of bacterial DNA binding proteins. Crenarchaeota which don’t have histones, only rely on these bacterial homologues to regulate transcription.

Question 40

The most well-studied archaeal chromatin binding protein is Alba, which have different functions in Euryarchaeota vs crenarchaeota. How does Alba work and what differences in mode of action to we see in these different families?

Answer 40

Alba is present in almost all archaea and is a small DNA binding protein. When Alba is acetylated = reduced DNA binding affinity and when deacetylated = increased DNA binding affinity.

• Euryarchaeota: low abundance, sequence specific and main function in transcription regulation. When Alba binds to DNA it creates loops in DNA which organizes it in a sort of nucleosome.
• Crenarchaeota: high abundance of Alba, not sequence specific and main function in chromatine remodelling. In high concentrations, alba dimerizes in cis which form stiff inaccessible regions and in low concentrations, it dimerizes in trans to form loops which has high accessibility.

Question 41

Transcription in archaea also share characteristics with both bacteria and eukaryotes. What are the main features of transcription shared with bacteria vs eukaryotes?

Answer 41

Similarities with eukaryotes:
- The promoter in both E and A is a TATA-box which is recognized by Tbp (TATA binding protein) and uses TFIIB as transcription initiator factor. They also have homologous RNA polymerase (but lack a C-terminal domain, which entails different TFs and regulation).

Similarities with bacteria:
- The other transcription factors (repressors and activators) are of bacterial-type in archaea and the mRNA is uncapped, with no splicing like in bacteria.

Question 42

The transcription cycle in archaea is very much a mix of bac. & euk. Summarize the archaeal transcription cycle in short.

Answer 42

TATA binding protein (TBP) binds to TATA, transcription factor binding protein (TFB) binds to TBP –> bending of the DNA which enables RNAP to bind –> RNAP binds and starts to move –> during initiation it spits out a few small “abortive” RNAs –> After moving along the promoter, there’s a switch in TFs and spt4/5 is recruited which enables elongation –> elongation –> termination and RNAP falls off.

Question 43

How is transcription initiation regulated in archaea?

Answer 43

One way is by chromatin binding proteins (CBP) that compete with the transcription apparatus. Modifications of CBPs can therefore be used to repress/enable transcription. When there’s a lot of CBP –> decrease of transcription rate.

Remember: The core transcription machinery
is like a ”Simplified” version of eukaryotes while transcription regulation is analogous (sometimes homologous) to bacterial system.

Question 44

In archaea there are competing TFs in the transcription cycle, which and how are they affecting the steps in the cycle?

Answer 44

Spt4/Spt5 and TFE.

• TFE Competes with Spt4/5 for RNAP
  binding and stabilizes the open RNAP to facilitate initiation. Prevails over Spt4/5 in the initiation complex.
• Spt4/5 increase the stability of the elongation complex but inhibits initiation when bound to free RNAP. Prevails over TFE in the elongation complex.

Question 45

Describe the characteristics of TFs in archaea and name a common and widespread one.

Answer 45

• Bacterial like
• small
• Few: only a few families of TFs that have many different functions.

Lrp (Leucine-responsive regulatory protein):
- can be an activator/repressor (regulating protein)
- Inhibits recruitment of RNAP by binding TBP-TFB.

Question 46

Archaea have coupled transcription-translation as bacteria, due to no nucleus and no maturation of mRNA transcripts. What consequence does having coupled transcription-translation have?

Answer 46

That the elongation rate of transcription is affected by the elongation rate of translation!

Question 47

What post-transcriptional regulation mechanisms are used by archaea?

Answer 47

Small RNAs, mostly antisense to coding RNA but can also be from UTR. Common in all studied archaea but have mostly unknown regulating roles because of being to understudied.

Can target the mRNA for:
- degradation (although most mRNA transcripts have very short half lives)
- increase/decrease stability
- inhibit transcription (binds DNA)
- inhibit/stimulate translation.

The role of sRNAs is to regulate which proteins are translated: good for extremophile lifestyle and to quickly handle viral infections.

Question 48

mRNA levels are a bad predictor of protein
levels in archaea, why?

Answer 48

Because archaeal mRNA have a half life of about 3-10 min (with some exceptions) while proteins can stick around for a long time.

Question 49

Archaea has a mix between bacterial and eukaryotic characteristics, AND has the highest degree of variation in their domain compared to others, very diverse group! But there is a lot we don’t know yet. Name two things that are unique to the archaeal domain.

Answer 49

Archaea has:

Mix of features: replication machinery similar to eukaryotes while translation machinery partly similar to bacteria: 16S, not 18S rRNA in ribosomes (but distinct from bacterial)
- DNA methylation like euk but not all.
- Post-translational protein modification: Ubiqutinaton, glycosylation, lipid modification, phosphorylation.
- At least two different types of cell division machinery: Bacterial in euryarchaea, Unique in crenarchaea – but with eukaryotic homologes. All the while either of these is more closely related to euk.
- Maaaany different viruses that target them!