Ch2 prokaryotic gene regulation

• Lessons from prokaryotic gene regulation include transcription initiation regulation, co- and posttranscriptional regulation, attenuation, antitermination, riboswitches, and other RNA switches such as RNA thermosensor, T-box RNA switch, and sRNA switch.
• Transcription initiation regulation in prokaryotic gene regulation involves the regulation of promoter strength and the regulation of promoter specificity.
• Co- and posttranscriptional regulation in prokaryotic gene regulation involves the regulation of mRNA stability and the regulation of translation.
• Attenuation in prokaryotic gene regulation is the process where the leader peptide sequence of an operon is shortened, resulting in the termination of transcription.
• CII high: lysogeny (Int needed) involves Rnase III.
• Translation initiation inhibition (Ribosome) is a mechanism of gene regulation.
• Activation and repression are signaling mechanisms in gene regulation.
• Lessons from prokaryotes include co- and posttranscriptional gene regulation.
• Ribosomes, metabolites, ions, temperature, sRNA, proteins are all factors in gene regulation.
• Transcription termination (RNAP) is a mechanism of gene regulation.
• mRNA destabilization (RNase) is a mechanism of gene regulation.
• Retroregulation occurs at 5’, 5’, 5’39.
• Antitermination in prokaryotic gene regulation is the process where the transcription termination signal is inactivated, allowing for the completion of transcription.
• Riboswitches in prokaryotic gene regulation are RNA switches that regulate gene expression through ligand-induced changes in mRNA structure.
• Other RNA switches in prokaryotic gene regulation include RNA thermosensor, T-box RNA switch, and sRNA switch.
• Translational (de)repression in prokaryotic gene regulation is the process where the translation of a gene is inhibited or activated.
• Translational coupling in prokaryotic gene regulation is the process where the translation of a gene is coupled to the regulation of its own transcription.
• In the absence of integrase, lysis occurs.
• Rnase III and Rnase II are involved in delayed early and late decay, respectively.
• Hfq is involved in 32 sRNA switches, including 100 sRNAs found in E. coli.
• The effects of intergenic distance on re-initiation are: the shorter, the faster re-initiation; if negative, faster dissociation.
• Integration involves the integration of a transcription unit into an existing gene.
• Retroregulation is the regulation of mRNA stability by altered 3’ end.
• Secondary structures attenuate de novo initiation and are unfolded by elongating ribosome, facilitating re-initiation.
• Ribosomal proteins are translational repressors of their own synthesis.
• Tian et al. (2015) found that in E. coli, 50% of intergenic distances are ≤10 nt and 36% of ORFs overlap.
• Ribosomes may initiate de novo (free 30S) or re-initiate (upstream 30S remains bound to mRNA).
• Regulation by in trans-encoded small RNAs binding to mRNA 5’ UTR includes DsrA, RprA, and ArkZ, which control the E. coli rpoS gene for stress sigma factor sS (= s38) by transcription antitermination and translational derepression.
• A 30 sRNA switch is protein-dependent and translational derepression is protein-dependent.
• Retroregulation in prokaryotic gene regulation is the process where the translation of a gene is inhibited or activated in response to the regulation of its own transcription.
• The regulation of the trp operon involves repression and attenuation.
• Riboswitch diversity and distribution is estimated to be greater than 2% of all genes, with many being widely conserved in bacteria, others being rare.
• Many riboswitches remain to be discovered.
• RNA thermosensor is another type of RNA switch that regulates gene expression.
• The Amino acid biosynthesis riboswitch regulates the expression of the aminoacyl-tRNA synthetase gene.
• The E. coli rpoH gene for heat shock sigma factor s32 and the prfA gene from L. monocytogenes are examples of genes regulated by riboswitches.
• The ligands for known riboswitches can be grouped by ligand type.
• Aptamers are used as expression platforms in riboswitches.
• The mechanism of action of the Vitamin B12 riboswitch involves premature transcription termination.
• The TPP riboswitch is widely occurring in bacteria, fungi and plants.