Anticodons and Wobble Base Pairing:

 

 

 

 

 

 

 

 

 

 

Anti codon 3’ <----5’:

3’ XXC       XXA   XXU     XXU    XXG  XXG   XXI   XXI   XXI

IIIIII         IIIIII    IIIIII    IIIIII   IIIIII  IIIII   IIIII    IIIII   IIIII

5’ XXG,     XXU,   XXA,   XXG,   XXC,   XXU, XXU, XXC, XXA

Codon 5’---->3’:

 

Wobble Base pairing Between Anti Codon 5’ Position: Codons’3’ Position:

 

AntiCodon 5’ = 3’ Codon

C = G

A = U

U = A

U = G

G = C

G = U

I  =  U

I  =  C

                         

In addition to wobble base pairing, the third base in the codon (in most of the cases) shows degeneracy.  What is advantage of such degeneracy? - Point mutations are absorbed.

 

 

 

Missense and nonsense mutations are often suppressed by mutations in respective tRNAs; such mutations are called suppressor mutations or intergenic suppressors.

 

 

 

Seleno-Cysteine:

 

 

 

 

 

                        --------A C U---=---5’ sel-cys

                                --U G A----=--3’ mRNA

 

Addition of selenium to the SH group of the R-chain

 

 

Vadim Gladyshev Publications

Selenocyteine (Sec) uses the UGA codon and it is read as sel-cysteine

Fig 1 full size

 

a)       The SECIS element in the 3' untranslated region of the mRNA (stem loop in light blue) recruits SBP2 (red), which in turn recruits EFSec (blue) and tRNASec (yellow). The complex interacts at the ribosome to decode UGA as selenocysteine. (b) Mutation of SBP2 results in preservation of the synthesis of essential selenoproteins but a decrease in the synthesis of nonessential ones. Essential proteins include thioredoxin reductase, plasma glutathione peroxidase and phospholipid hydroperoxide glutathione peroxidase; nonessential proteins include type 2 iodothyronine deiodinase, selenoprotein P and glutathione peroxidase 1. Sec, selenocysteine. Marla J.Berry; http://www.nature.com/

 

 

 Artemy Beniaminov , Akiko Takeuchi , Laurence Wurth , Christine Allmang; http://www-ibmc.u-strasbg.fr/

 

TRNA Sec and a stem-loop structure in the 3'UTR of the mRNA of selenoproteins (the SECIS) play a key role in reprogramming the codon UGA Sec. We have previously proposed structures models tRNA SecSECIS pattern and isolated and functionally characterized the elongation factor of the mammalian EFSEC specialized dictionaries and the SBP2 protein binding to SECIS element. To better understand the principles of interaction SBP2-SECIS RNA and the function of SBP2, which are at the heart of the mechanism of synthesis of selenoproteins, the resolution of the crystal structure of this complex was undertaken in collaboration with the team Philippe Dumas. In addition, we devote great efforts to research and functional characterization of proteins interacting with SBP2.

 

http://www.chemguide.co.uk/

Codon-Reverse Codon Symmetry

A reverse codon of any codon XYZ is defined as ZYX, where X,Y,Z can be any base. The arrows in table represent pairs of “codon - reverse codons”. For instance, the reverse codon of CCU (Pro) is UCC (Ser). There exist 15 different amino acids in the rows 000, 101, 010 and 111 where the codon is reverse to itself, e.g. Lys (AAA), Tyr (UAU).  Considering codons and their reverse codons we report three observations.

http://www.imb-jena.de/

 Codon-Reverse Codon Symmetry:

1. Table  can be divided into four blocks (codon - reverse codon groups) of the same size, for instance the upper left block with Pro (P), Ser (S), Ala(A) and Thr (T). Each block shows the same arrow pattern. All strongly evolutionary conserved groups of amino acids (Thompson et al., 1994) are subsets of exactly one codon - reverse codon group, e.g. the MILV amino acids belong to the upper right block in the table. The other conserved strong groups belonging to one block are STA, NEQK, NHQK, NDEQ, QHRK, MILF, HY. The only exception is FYW.

2. We studied all known tRNA genes of 104 different organisms (Sprinzl et al., 1999). It is known that the STOP codons do not have any tRNA. We found that there are also no tRNA genes containing anticodons reverse to the STOP anticodons (ACT, ATC and ATT in Table 3). This is true for archaea (16), bacteria (81) and most eukaryotes (7). The only exception is H. sapiens, possessing one tRNAAsn gene with the anticodon ATT, but humans also have three different possible suppressor tRNA genes (Lowe and Eddy, 1997).

3. There are some codon - reverse codon pairs where there only exist tRNAs for one codon, but no tRNA for the reverse codon, e.g. all 104 studied organisms have at least one tRNA for Tyr with anticodon GTA (some organisms, for instance H.sapiens, have different tRNAs with the same anticodon, altogether there are 189 different tRNAs with the anticodon GTA in the 104 species), but no organism has a tRNA for His with anticodon ATG. Table 3 lists different codon - reverse codon pairs. It is interesting to note that in the whole superkingdom bacteria the number of tRNA genes for the reverse part of table 3 is always zero, the few exceptions are only in eukaryotes and archaea. Another unique property of all bacteria is that there is no tRNA with anticodons for the self reverse codons UUU (Phe), UCU (Ser), UGU (Cys) and UAU (Tyr). Generally, table 3 shows that anticodons with an A at the third position are strongly preferred, whereas A** anticodons are significantly suppressed, http://www.imb-jena.de/

Codon-Anticodon-Wobble hypothesis’

http://www.codefun.com/

Wobble between the last alphabet of Codon (mRNA) and the first alphabet of the anticodon (tRNA)

Themedicalbiochemistrypage.org; Translation of Proteins; http://themedicalbiochemistrypage.org/

 

Extended anti-codon: frame shift reading frame:

 

This was proposed by S.H Kim (1973).  In this model the efficiency of anticodon in the recognition of codon is determined by the relationship between anticodon loop and the proximal anticodon stem sequence.

 

 

Cardinal Nucleotides

 

 

A

U

G

C

VII

-------

--------

Py/pu

---------

VI

GC / GC

---------

PY / PU

GC / CG

V

PU / PY

----

--------

----

IV

GC

GC / CG

---

CG

III

AU /UA

AU / CG

---

CG

II

A

A

A / U

A / C

I

Me2I6A

I6A

M2A/ G

Am2A/ m6A

 

 

 

 

 

 

 

 

Extended reading frame:

 

Figure 4.

Figure : Model for the observed +2 frameshift. (A) The normal process of translation in NECB1 lacZ(+GA)begins with the peptidyl-tRNA Formula(U* is the modified uridine at the wobble position, which could be either mnm5-s2-U or mnm5-U) bound to the mRNA in the P-site of the ribosome. The empty A-site is normally filled with a tRNA Formulaand the translational complex can proceed to the next step of elongation by transferring the peptide and translocating the accepted tRNA in the P-site. (B) In mnmE mutants, and probably in gidA mutants, the uridine at the wobble position of the tRNAGlu is hypomodified (U‘: s2-U or some other hypomodified form of the mnm5-s2-U). This hypomodified nucleotide is less efficient at pairing with a guanine in the wobble position. The presence of a rare AGA codon at the A-site results in a pause during the translation process. Therefore, the conjunction of a less efficient pairing between the tRNA and the mRNA at the P-site and the presence of a rare codon at the A-site renders the ribosome prone to shifting. This translation complex moves to (or possibly scans for) the next GAG cognate codon of the tRNA in the P-site, which is easy on this repetitive sequence and then resumes translation, but in a different frame (Damien Brégeon1,4, Vincent Colot2,3, Miroslav Radman1, and François Taddei1

+Author Affiliations).