The Overview of Orthogonal (Aegisafe) Ribosome

Ribosome

Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. Because they are formed from two subunits of non-equal size, they are slightly longer in the axis than in diameter. Prokaryotic ribosomes are around 20 nm (200 Å) in diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30 nm (250–300 Å) in diameter and the ratio of rRNA to protein is close to 1. Bacterial subunits consist of one or two and eukaryotic of one or three very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesize protein rather than directly participating in catalysis (See: Ribozyme).

Ribosomes translate polypeptide chains (e.g., proteins) from the genetic instructions held within messenger RNA, using amino acids delivered by transfer RNA (tRNA). Free ribosomes are suspended in the cytosol (the semi-fluid portion of the cytoplasm); others are bound to the rough endoplasmic reticulum, giving it the appearance of roughness and thus its name, or to the nuclear envelope. Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site (see Function section below) adenosine in a protein shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations. Since their catalytic core is made of RNA, ribosomes are classified as "ribozymes," and it is thought that they might be remnants of the RNA world.

The unit of measurement is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size and accounts for why fragment names do not add up (70S is made of 50S and 30S).Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins. Affinity label for the tRNA binding sites on the E. coli ribosome allowed the identification of A and P site proteins most likely associated with the peptidyl transferase activity; labelled proteins are L27, L14, L15, L16, L2; at least L27 is located at the donor site, as shown by E. Collatz and A.P. Czernilofsky. Additional research has demonstrated that the S1 and S21 proteins, in association with the 3'-end of 16S ribosomal RNA, are involved in the initiation of translation. Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and ~49 proteins. During 1977, Czernilofsky published research that used affinity labeling to identify tRNA-binding sites on rat liver ribosomes. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the peptidyl transferase center.

16s ribosome RNA

16S ribosomal RNA (or 16S rRNA) is a component of the 30S small subunit of prokaryotic ribosomes. It is approximately 1.5kb (or 1500 nucleotides) in length. The genes coding for it are referred to as 16S rDNA and are used in reconstructing phylogenies.

Multiple sequences of 16S rRNA can exist within a single bacterium. It has several functions:

• Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the rebosomal proteins.
• The 3' end contains the anti-Shine-Dalgarno sequence, which binds upstream to the AUG start codon on the mRNA. The 3'-end of 16S RNA binds to the proteins S1 and S21 known to be involved in initiation of protein synthesis; RNA-protein cross-linking by A.P. Czernilofsky et al. (FEBS Lett. Vol 58, pp 281–284, 1975).
• Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S)
• Stabilizes correct codon-anticodon pairing in the A site, via a hydrogen bond formation between the N1 atom of Adenine (see image of Purine chemical structure) residues 1492 and 1493 and the 2'OH group of the mRNA backbone.

For the 16s of them has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. The 3' end contains the anti-Shine-Dalgarno sequence, which binds upstream to the UG start codon on the mRNA. We note that the complementary position and length can have big impact on the translational result of back gene. This feature stimulates our thinking about the blueprint of our project. That is to reform some part of 16s to create our experiment result. WE do some exact test according to the paper, at last we choose this sequence to change to make our project come true.

Orthogonal (Aegisafe) Gibson Free Energy

Orthogonal Ribosome (O-Key)

Gene expression involves two steps, transcription and translation. While a number of genetic tools exist for reprograming transcription in cells, far fewer tools exist for translation. Of the tools available in bacteria, the most popular are riboregulators, both cis- and trans- activating, and Aegisafe O-key (orthogonal ribosome), also known as specialized ribosomes. In terms of reprograming translation, O-key are especially powerful as they enable one to partially decouple translation from the native protein synthesis machinery. In particular, O-key can translate genes with altered Shine-Dalgarno (SD) sequences not recognized by host ribosomes. Because of the fact, O-key can be used to explore translational regulatory mechanisms such as coupling and to probe ribosome structure. Furthermore, O-key can be used to explore gene expression dynamics as they potentially provide a method for tuning translation rates. Finally, O-key may have application in synthetic biology as they introduce new functionality within cells. O-key are duplicated ribosomes with mutations in the 3' end of 16s rRNA that alter their specificity for mRNA. In bacteria, translation initiation is primarily mediated by interactions between the 30s ribosomal subunit during the initiation process. The strength of this interaction is thought to influence translational efficiency as mutations in either the SD or ASD sequence that weaken the interaction reduce the amount of protein made. In the case of O-key, mutations are introduced into the ASD region such that they can based pair with complementary noncanonical SD sequences not recognized by host ribosomes.

Gibson Free Energy

ΔG_tot=ΔG_mRNA:rRNA+ΔG_start+ΔG_spacing-ΔG_standby-ΔG_mRNA

ΔG_mRNA:rRNA is the energy released when the last nine nucleotides(nt) of the E. coli 16S rRNA (3′-AUUCCUCCA-5′) hybridizes and co-folds to the mRNA sub-sequence (ΔG_mRNA:rRNA<0). Intramolecular folding within the mRNA is allowed. All possible hybridizations between the mRNA and 16S rRNA are considered to find the highest affinity 16S rRNA binding site. The binding site minimizes the sum of the hybridization free energy ΔG_mRNA:rRNA and the penalty for nonoptimal spacing, ΔG_spacing. Thus, the algorithm can identify the 16S rRNA binding site regardless of its similarity to the consensus Shine-Dalgarno sequence.

• ΔG_start is the energy released when the start codon hybridizes to the initiating tRNA anticodon loop (3'-UAC-5').
• ΔG_spacing is the free energy penalty caused by a nonoptimal physical distance between the 16S rRNA binding site and the start codon (ΔG_spacing>0). When this distance is increased or decreased from an optimum of 5 nt (or ~17A), the 30S complex becomes distorted, resulting in a decreased translation initiation rate.
• Δ_GmRNA is the work required to unfold the mRNA sub-sequence when it folds to its most stable secondary structure, called the minimum free energy structure (ΔG_mRNA<0).
• ΔG_standby is the work required to unfold any secondary structures sequestering the standby site (ΔG_standby<0) after the 30S complex assembly. We define the standby site as the four nucleotides upstream of the 16S rRNA binding site, which is its location in a previously studied mRNA.

To calculate ΔG_mRNA:rRNA, ΔG_start, ΔG_mRNA and ΔG_standby, we use the NUPACK suite of algorithms with the Mfold 3.0 RNA energy parameters. These free energy calculations do not have any additional fitting or training parameters and explicitly depend on the mRNA sequence. In addition, the free energy terms are not orthogonal; changing a single nucleotide can potentially affect multiple energy terms. The relationship between the spacing and the ΔG_spacing was empirically determined by measuring the protein expression level driven by synthetic RBSs of varying spacing and fitting a quantitative model to this data.

Orthogonality Verification Experiment

Since orthogonal RBS is safe, why don’t we change all the original 16s into orthogonal 16s? The answer is no. that is because if we change all the base 16s, the other housekeeping genes will stop expressing. This will produce orthogonal toxicity, leading to bacterial death. So we are bound to face competition between base and orthogonal 16s. Then we design the following experiment to research this problem. We designed three operon to verify the orthogonality of our system. First, our first experiment is based on an assumption that the fluorescent light intensity can represent the amount of the expression of fluorescent protein. The relevant literature indicates that the with a fluorescent light intensity representative of the amount of the expression of fluorescent protein, the relevant literature indicates that the assumption can be right if the experimental precision is not sensitive.

We constructed two sets of plasmid co-transformed into E. coli to achieve the purpose. One set is induced by the promoter then transcripts the O-key's vector, which is equivalent to the key. The other set is O-RBS/RFP+RBS/GFP, it is constructed to compare the orthogonality of between the O-RBS and N-RBS by GFP and RFP.

From this figure, we can see that there are four competition relationship in the orthogonal cell system, the ideal state is the 1th and 2th path exists while the 3th and 4th path weaken. That means our system has good orthogonality. We did multiple sets of pre-experiments of different O-16s then decided to use this set.

Modeling

Future