RNA EditingProtein SplicingCodon Bias

RNA EditingAny process, other than splicing, that

results in a change in the sequence of a RNA transcript such that it differs from the sequence of the DNA template

Discovered in trypanosome mitochondria

Also common in plant mitochondria

Also occurs in a few chloroplast genes of higher plants, and at least a few nuclear genes in mammals

As a consequence of RNA editing, functionally distinct proteins can be produced from a single gene.

One gene- many proteins

Editing and modification are done post-transcriptional.

Base modification (A – I, C – U, or U – C, etc) Insertion/Deletion

Mechanism:Guide RNA dependent Editing

gRNAs are small and complementary to portions of the edited mRNA

Base-pairing of gRNA with unedited RNA gives mismatched regions, which are recognized by the editing machinery

Machinery includes an Endonuclease, a Terminal UridylylTransferase (TUTase), and a RNA ligase

Editing is directional, from 3’ to 5’

C – U RNA editingHuman Apolioprotein (ApoB100) essential for

removal of LDL in Liver ; Tissue specific cytidyl deamination (C6666-U) introduces in-frame stop codon giving truncated ApoB48 by ApoB mRNA editing enzyme catalytic polypeptide 1 (ApoBEC1) in intestine.

A – I RNA editingOnly adenosines within the context of

RNA molecules are targeted by ADARs.

ADARs (Adenosine deaminases acting on RNAs) catalyze A to I only on dsRNA structures.

A-to-I RNA editing by ADARs proceeds via a hydrolytic deamination mechanism without the requirement for RNA backbone breaks.

RNA editing in tRNA

Protein Splicing

Protein splicing is a form of posttranslational processing that consists of the excision of an intervening polypeptide sequence, the intein, from a protein, accompanied by the concomitant joining of the flanking polypeptide sequences, the exteins, by a peptide bond.

Inteins are internal protein elements that self-excise from their host protein and catalyze ligation of theflanking sequences (exteins) with a peptide bond.

Intein excision is a posttranslational process thatdoes not require auxiliary enzymes or cofactors.

Appl Microbiol Biotechnol (2010) 87:479–489

Intein structure

Appl Microbiol Biotechnol (2010) 87:479–489

Mechanism: a 4 step process

Appl Microbiol Biotechnol (2010) 87:479–489

Appl Microbiol Biotechnol (2010) 87:479–489

Begins with an N−O shift if the first intein residue is Ser, or N−S acyl shift, if the first intein residue is Cys. This forms a (thio)ester bond at the N-extein/intein junction.

The (thio)ester bond is attacked by the OH- or SH-group of the first residue in the C-extein (Cys, Ser, or Thr). This leads to a transesterification, which transfers the N-extein to the side-chain of the first residue of the C-extein.

The cyclization of the conserved Asn residue at the C-terminus of the intein releases the intein and links the exteins by a (thio)ester bond.

rearrangement of the (thio)ester bond to a peptide bond by a spontaneous S-N or O-N acyl shift.

Codon Bias

Codon bias is the probability that a given codon will be used to code for an amino acid over a different codon which codes for the same amino acid.

This influence the protein folding, function, translation speed and accuracy.

Possible Explanations For Codon Bias: Selection Theory

◦ According to the selectionist explanation, codon bias contributes to the efficiency and/or the accuracy of protein expression and is thus generated and maintained by selection.

Mutational Theory◦ The mutational or neutral explanation, by contrast,

posits that codon bias exists because of nonrandomness inthe mutational patterns. Some codons are moremutable and thus would have lower equilibriumfrequencies. Mutational biases are known to differ between organisms, possibly leading to differences in the patterns of codon bias across organisms.

Relation to gene expressionGenes that are always expressed at a

high rate should have a different codon bias than those genes that are always expressed at a low rate.

Genes whose expression varies from low expression to high expression as a given environmental condition changes may have a codon bias similar to the highly expressed genes.

Escherichiacoli

SaccharomycescerevisaeAmino Acid Codon

High Low High LowUUA 1% 20% 8% 25%

UUG 1% 15% 89% 25%

CUU 2% 12% 0% 12%CUC 3% 11% 0% 9%

CUA 1% 5% 3% 15%

Leucine

CUG 92% 37% 0% 14%

GUU 60% 27% 52% 28%

GUC 2% 25% 48% 19%

GUA 28% 16% 0% 30%

Valine

GUG 10% 32% 0% 23%AUU 16% 46% 42% 43%

AUC 84% 37% 58% 22%

Isoleucine

AUA 0% 17% 0% 35%UUU 17% 67% 10% 69%Phenylalanine

UUC 83% 33% 90% 31%

Reference Elleuche, S., & P??ggeler, S. (2010). Inteins, valuable

genetic elements in molecular biology and biotechnology. Applied Microbiology and Biotechnology, 87(2), 479–489. http://doi.org/10.1007/s00253-010-2628-x

Maas, S., & Rich, A. (2000). Changing genetic information through RNA editing. BioEssays, 22(9), 790–802. http://doi.org/10.1002/1521-1878(200009)22:9<790::AID-BIES4>3.0.CO;2-0

Hershberg, R., & Petrov, D. A. (2008). Selection on codon bias. TL  - 42. Annual Review of Genetics, 42 VN  - r, 287–299. http://doi.org/10.1146/annurev.genet.42.110807.091442