Alternative Start Codons in Eukaryotes
Start codons play a vital role in translation by recuiting ribosomal subunits that will scan the mRNA in the 5' to 3' direction and initiate translation at the first AUG it encounters. Until recently, it was common belief that eukaryotic mRNAs contianed a single start codon that then encoded a single protein. However recent studies suggest that this model can no longer be assumed valid in all cases. In most cases translation of eukaryotic mRNAs follow a linear scanning mechanism where the 40s ribosomal subunits bind to the 5' cap and moves along until reaching the first AUG start codon 1. If the context is optimal, the ribosome recognizes the AUG and continues downstream until reaching a stop codon. However, recent studies found that if the context is suboptimal, the ribosome does not recognize the AUG as the starting point and continues till the next AUG appears in-frame. This type of 'leaky scanning' allows for downstream in-frame AUG codons(dAUG) to act as initiation ponits sometimes resulting in different N-terminal protein variants 2. Additionaly, alternative start sites can alter the location of open reading frames (ORFs) via dAUG, leading to N-end truncated protein isoforms 3. While many annotated AUG start sites do not account for the presence of dAUGs due to suboptimal contexts, linear and leaky mRNA scanning mechanisms have been shown to have a significant impact on translation initiation.
Lignin, a complex compound involved in the secondary cell walls of some plants and algae, is the second most abundant organic compound on Earth. It primarily serves a structural role by strengthening the cell wall through covalently crosslinked polysaccharides 4. Additionally, Lignin plays a vital role in water absorption. The hydrophobic character of lignin along with the hydrophillic polysaccharides creates a gradient that allows for water transport through the plants vascular system 5. While Lignin contains several other important properties such as degradation by fungi and bacterial enzymes (animal's cannot digest lignin), its primary development helped in the movement of plant and algae species from water to land.
From a chemical point of view, lignin is a polymeric compound composed of phenylpropanoid units derived from three monolignols: p-coumaryl, coniferyl, and sinapyl alcohols. The formation of lignin is therefore thought of as bond formation resulting from oxidative (usually radical mediated) coupling between a monolignol and the growing polymer. Formation of lignin occurs within the cell wall matrix. It occupies gaps between wall polysaccharides like xylans and cellulose, adding to the strength of the cell walls. This formation helps to facilitate water transport as well as add protection by impeding the degradation of wall polysaccharides. This defensive mechanism helps to protect against pathogens, insects and herbivores 6.
Currently there are two proposed methods for lignin formation. The first (displayed below as Figure 3 from Hatfield and Vermerris, 2001) involves a random coupling model. This method proposes that formation occurs through coupling of individual monolignols to the growing lignin polymer in a somewhat random fashion through radical mediated interactions. The second and more controversial of the two, is through a dirigent protein model. Dirigent proteins help to dictate the stereochemistry of a compound during formation. This dirigent control suggests then that lignification might occur under strict regulation that controls the formation of individual bonds to the growing lignin polymer 7.