ABCE1 Case Study

The small ribosomal subunit, amongst other things, is initiates the engagement of the mRNA and is responsible decoding the genetic information during translation [4].

The association of FMRP with ribosomes is mRNA dependent via large ribonucleoprotein (RNP) particles. RNP particles contain other proteins including FXR1P, FXR2P, YB-1, CYFIP1, CYF1P2, NUFIP1 and nucleolin.

The siRNA directs RISC to the target mRNA. RISC uses the siRNA guide strand to bind to a certain target site of mRNA. The siRNA and the mRNA have complementary sequence which is determined by base pairing. The target mRNA is then cut and split when bound to Argonaut and is then degraded. The siRNA completely eliminates the mRNA as it is degraded. The mRNA is needed to for the translation process so without the mRNA the protein would not be produced.

RNA stands for ‘ribonucleic acid’ and it is present in all living cells. RNA’s main job is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins. RNA is similar in structure and properties to DNA. RNA, however, has only a single strand of bases. Also, rather than having the base thymine, RNA has the base uracil. Anyways, the guide RNA is composed of a miniscule pre-designed RNA sequence. This sequence is roughly 20 bases long and is located within a longer RNA framework. The scaffold part of the RNA binds to DNA and the pre-designed sequence. It ‘guides’ Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.

During the process of transcription, an enzyme called RNA polymerase binds to DNA at a gene's promoter, then begins unwinding the DNA and making a complementary strand of RNA from the exposed DNA template. Depending on the gene being transcribed, the result can be a molecule of mRNA (messenger RNA), tRNA (transfer RNA), or rRNA (ribosomal RNA). Each type of RNA performs a specific function later in translation. Ribosomal RNA (rRNA) along with ribosomal proteins make up ribosomes, the "workbenches" on which polypeptides (proteins) are synthesized. It turns out that it is actually rRNA, and not a protein, in the large subunit of the ribosome that performs the peptidyl transferase function of linking amino acids together via peptide bonds. In eukaryotes, the genes coding for rRNAs are located in the nucleolus of the nucleus. A ribosome has 3 binding sites: an A (aminoacyl) site, a P (peptidyl) site, and an E (exit) site. The message carrying the information needed to make a particular polypeptide exists in the mRNA molecule. It binds with a ribosome and the ribosome starts reading it one codon - 3 consecutive mRNA bases - at a

It is triggered by Dicer, an enzyme that assists in the activation of the RNA induced silencing complex, an important component for RNAi in fungi, plants, and animals, according to the article, “Pathway Central: RNAi Pathway”. The process is first activated by dsRNA molecules and requires a specific set of gene products. The dsRNA is then cut into smaller pieces by the Dicer enzyme in an ATP-dependent reaction. The dsRNA in fungi, animals, and plants are exogenous, meaning that the RNA is directly sent to the cytoplasm and cut into shorter lengths by Dicer. As of yet, endogenously expressed dsRNA molecules have not been discovered in mammals, where the RNA would first be shaped into the stem- loop structure in the nucleus, then sent to the cytoplasm to be further modified by Dicer. In RISC, the enzyme Dicer also supplies the initial RNA material to activate the complex as well as the first RNA substrate molecule. RISC with a bound siRNA targets complementary mRNA molecules and degrades them, resulting in lower levels of protein translation and the eventual inhibition of the

transfer RNA or tRNA, has a complementary triplet of nucleotides to the mRNA codon attached

The core of the structure of the C-domain in whole DT is formed by eight β-strands forming two sheets of three and five strands, respectively. These two sheets are surrounded by six short α-helices6. The active site of the C domain is located in a cleft formed by three beta strands named CB2, CB3, CB7, a helix, CH3, and a loop, CL2. The loop CL2 including amino acids 32-54 which covers active site, becomes disordered from residues 39 to 46 upon binding of NAD7. This suggests a potential role for this loop in the recognition of the ADP-ribose acceptor substrate, EF-2. The ADP-ribosylation reaction has been proposed to proceed by a direct displacement reaction, with the pi-imidazole nitrogen of diphthamide being activated by Glu148 for nucleophilic attack on the N-glycosidic bond of NAD8. The loop of 14 amino acid residues linking the C domain to the T domain must be cleaved in order to activate DT9. More work is still needed to fully understand the mechanism of translocation of DT. The precise molecular and dynamic description of the contacts between the T and the C-domains, the cell membrane and maybe other cell components remain to be

Post-transcriptional gene regulation by sRNAs may occurs in various patterns of base-pairing with a target RNA resulting in different outcomes or by directly binding to proteins to modulate their function.12-14 Two classes of sRNAs are identified: trans-encoded RNAs which are transcribed from intergenic regions of the genome, and cis-encoded RNAs which are encoded on the strand complementary to coding sequences or the 5′ or 3′ untranslated region (5′ UTR, 3′ UTR) of transcripts.15-17 The family of trans-encoded sRNAs usually requires the chaperone Hfq to stabilize the often imperfect base-pairing interaction with target mRNA.18 In contrast, cis-encoded sRNAs possess a region of perfect complementarity to their target mRNA and Hfq is not needed for target binding. It shows that sRNAs are involved in many important physiological processes including anaerobic growth, nutrient availability, iron homeostasis and the response to oxidative, envelope and osmotic

Once dsRNA is injected it binds to Dicer, an endonuclease protein that cuts RNA into short segments of 21 nucleotides long that are siRNA or micro RNAs. The short dsRNA binds to an argonaute protein and a guide strand is selected. The RNA, argonaute protein, and other proteins are called the RNA Induced Silencing Complex (RISC). Micro RNA’s help guide RISC to messenger RNA’s. The seed, part of the micro RNA, pairs with a target messenger RNA. Targeting by a micro RNA can lead to messenger RNA to be degraded or translation from being inhibited. Antisense RNA alone is not sufficient to evoke an RNAi response because the RNA needs to go through many steps with the help of other proteins to be able to have the ability to achieve RNAi.

In the N-terminal region, the heavy chain forms a motor domain that is globular in structure. The motor domain has an α-helix that extends from the C-terminus, which becomes part of the light chain binding domain. At this binding domain, the essential and regulatory light chains wrap around the α-helix to thicken and support its structure. The motor domains can be divided into three domains: the actin-binding site, the nucleotide binding site (P-loop NTPase domain core as an ATP catalytic site), and the converter domain. A converter domain is present at the junction between the ATP catalytic site of the motor domain and the light chain binding domain. The converter domain and the light chain binding domain compose the “lever arm”, which has a significant role in producing the mechanical force needed to generate movement during muscle

The hexameric p97 protein belongs to the type II AAA ATPase protein family and is conserved

In the event that the retargeting of CLAMP and roX2 alone and along with additional factors proves insufficient for MSL recruitment there is a possibility that there may be undiscovered interacting RNA partners required for the targeting of

Approximately, one third of all proteins in the cell interact with the ER making it a breeding ground for new proteins and an indispensable site for quality control. Endoplasmic-reticulum-associated degradation (ERAD) is the leading form of ER quality control in eukaryotes and consists of three distinct steps:

Ribosomal ribonucleic acid, or rRNA, is the principle component of the ribosome and is crucial in the development of proteins for living cells. Approximately 80-85% of a cell’s total RNA is made up of rRNA. The low molecular weight transfer RNA (tRNA), which aids in bringing amino acids to the site of ribosomal translation, comprises only 15-20%. The remaining 1-5% is made up by messenger RNA (mRNA), which is essentially the encoding blueprint for the synthesis of a given protein.