Week 12 - Regulation of mRNA Stability Flashcards
Transcript number
regulated by the gene producing the transcripts
- transcripts have 1/2 life where they’re degraded
- when transcription turned off = exponential decay, first order kinetics
steady state
balance between number of transcripts added and degraded
2 methods of bacterial regulation of mRNA stability
- Global regulation
- Gene specific regulation
Global regulation
environmental changes alter the growth rate of bacteria
rapidly growing bacteria = conditions are good such that transcripts are created but degraded at a rapid rate
- transcriptome-wide rapid decay
slowly growing bacteria = transcripts are more stable under low conditions, decay occurs slower
- transcriptome-wide slow decay
Degradosome
composed of:
- RNA helicases (unwind secondary RNA structure of mRNA)
- RNase scaffold
- Intrinsically disorder protein (assemble like protein droplet such that protein liquid holds protein together)
- 3’ to 5’ exonuclease
Rapidly growing bacteria have ___ degradosomes and stressed bacteria have ____ degradosomes
active, inactive
RNase cleavage site
recognizes specific sequence to start degradation process
- when hidden in stem-loop = less accessible and slow RNA degradation
Lysine Ribsoswitch
- absence of lysine
ON state
- 5’ end folded into structure and RBS is exposed such that mRNA is translated
Lysine Ribsoswitch
- presence of lysine
OFF state
- 5’ ends fold differently and another stem loop forms where RBS is hidden from ribosome
Lysine Ribsoswitch - mRNA stability levels of regulation
- Inhibition of ribosome from binding
- Destabilization of mRNA due to riboswvitch
sRNA
- can bind to mRNA and cover RNase cleavage site = SLOWER DEGRADATION
when sRNA covers RBS site there is _____ degradation of mRNA
faster
- blocks access to ribosome so it cannot bind
PolyA tails in bacteria _____ degradation because ______
increase
- some bacteria have stem loop near 3’ end which occludes access of RNases
- Poly A polyermases (ex: PAP1) add to polyA tail allowing RNA to recognize 3’ end and start degrading transcripts
- uses 3’ to 5’ exonuclease to degrade
Eukaryotic regulation of mRNA stability is most commonly identified at the _______
maternal-zygotic-transition
Protein Z within the complex __ initiation of translation
inhibits
Protein X (ex; Smaug, bicoid)
recruits factors (AGO and enzymes) important for degrading mRNA = miRNA recruitment
N^6 - methyl adenosine
degrades maternal RNA and destabilizes mRNA
- places tags on mRNA, proteins recognize tags and bring in ribonuclease that degrade mRNA
8-Oxo-7,8-dihydroguanosine
destabilizes mRNA by degraded mRNA that have tags
N6,2’-O-Dimethyladenosine
stabilizes mRNA
5’Methylcytidine
stabilizes mRNA
RNA editing - C to U
APOBEC1 - editing enzyme
CAA -> UAA (stop codon)
- edited in intestine = intestine differentiation
- united seq = hepatic/liver differentiation
RNA editing - A to I
CAG -> CIG
- edited = Ca2+ impermeable
- united seq = Ca2+ permeable
Non-coding editing –> RNA STABILITY
- stabilizes RNA
- secondary structures and alternative accessibility
Intron editing –> pre-mRNA SPLICING
- modifies splice sites resulting in varying protein isoforms
Exon editing –> mRNA TRANSLATION
- protein recoding through aa changes
3’ UTR/miRNA editing –> miRNA regulation
- regulates gene expression through miRNA biogenesis and target recognition
RNA localization
RNA is eukaryotic cells are not only localized to cellular compartments
- within these compartments RNA is localized further which is important for gene expression
