Structural Biochemistry/Nematode RNA

=Nematodes= Nematodes are one of the most diverse phylums of all animals. Half of the 28,000 different species of nematodes are parasitic. Nematodes, a type of roundworm, have tubular digestive systems with openings at both ends. Found in nearly all parts of the world, nematodes have adapted to almost all ecosystems, characterized by varying levels of water salinity, temperature, and altitude. Not only have they adapted, nematodes have evolved to outnumber other animals that coexist in the same ecosystems. For example, nematodes constitute 90% of all life on the seafloor.

Although some nematodes are completely dependent on other types of animals for reproduction, some of the strategies used by nematodes seem rather advanced. For example, the parasitic tetradonematid nematode is hypothesized to induce fruit mimicry in tropical ants. Infected ants develop bright red gasters, tend to be more sluggish, and walk with their gasters in a conspicuous elevated position. These changes likely cause frugivorous birds to confuse the infected ants for berries and eat them. Parasite eggs passed in the bird's feces are subsequently collected by foraging Cephalotes atratus and are fed to their larvae, thus completing the tetradonematid life cycle.

The genomes of nematodes are distinct from other metazoans
RNA regulation is an important and pervasive process, made possible by both RNA molecules and RNA-binding proteins. RNA molecules function as regulators and targets in diverse pathways pertinent to the proper decoding of the genome. RNA-binding proteins act as effectors of RNA stability and translation efficiency, guide transcripts to defined locations within the cell, control the fidelity of gene decoding, and function as cofactors to promote the activity of functional and structural RNA molecules.

Caenorhabditis elegans is a model organism
The facile genetics of the nematode Caenorhabditis elegans make it a useful observational model organism for the study of RNA regulatory mechanisms. The function of specific genes in this organism can be disrupted in a relatively straightforward manner by RNA interference (RNAi). The use of RNAi allows researchers to determine the function of specific genes, by silencing their functions in certain ways. In another important application, it was discovered that this organism showed behavioral responses to nicotine, including acute response, tolerance, withdrawal, and sensitization.

Nematodes contain an expanded genome
A surprising discovery based on the laboratory study of C. elegans is that the genome of nematodes contains an expansion of putative RNA-binding proteins relative to other metazoans. The RNA-binding protein Pumilio has 11 homologs in, while it has only two homologs in humans. The CCCH-type tandem zinc finger (TZF) family, which includes the mammalian protein tristetraprolin (TTP) has 16 homologs in roundworms. Lastly, there exists 27 Argonaute homologs in nematodes.

A homologous trait is any characteristic of organisms that is derived from a common ancestor. Paralogs are homologs present in the same species, and usually differ in function. Paralogs arise from gene duplication. Orthologs are homologs present in different species, and usually are similar in function. Orthologs usually arise from speciation when one species diverges into two separate species. Homology among proteins, DNA, and RNA is often concluded on the basis of sequence similarity. It is more effective to compare amino acid sequences than nucleotide base sequences because there are 20 distinct amino acids and only 4 distinct nucleotide bases.

Forward and reverse genetic experiments have provided data, which highlight the basis for the expansion of nematode homologs. Specifically, the data indicate that the RNA-binding family expansions may play roles in germline development, gametogenesis, and early embryogenesis.

The PUF family of RNA-binding proteins
The founding members of the PUF family of RNA-binding proteins are Pumilio and FBF, which together maintain the population of progenitor cells in the distal region of the germline. This group promotes the cellular switch from spermatogenesis to oogenesis at the onset of adulthood. During the transition from mitosis to meiosis when the single-celled state becomes a syncytial region, the meiotic nuclei recellularize. Spermatocytes are formed first during the L4 larval stage and stored in the spermatheca, which are then converted to oocytes.

PUF-8 and PUF-9 are biochemically similar to enzymes, in that one of their RNA-binding properties includes a high level of specificity. For instance, the eight nucleotide (5’-UGURNNAUA-3’) that is recognized by the PUF domains differs by a single nucleotide from the nucleotide NRE (Nanos Response Element). NRE is only a single nucleotide shorter than FBE, yet the FBR is discriminated by the two PUF elements more than 30-fold.

The nematode TZF binding specificity is different than the nematode PUF binding specificity. MEX-5 is a TZF protein that binds with a high affinity but relaxed specificity to any uridine rich sequence. The relaxed specificity means that TZF binds to both uridine rich sequences and polyuridine, while TTP binds more that 80-fold more tightly to AREs than polyuridine.

Conclusion
The function of RNA-binding proteins, like all proteins, is dictated by their structure. Novel function of RNA-binding protein families, with a common domain characterized by a new binding specificity, is a based on structural changes. Biochemistry and genetics serves as a basis for the identification of critical sequence elements and structural changes, yet fails to provide a mechanistic explanation of how these elements directly relate to novel function. Evidently, further research is necessary in the area of structural studies in an RNA-binding family.