I need to compare two organisms to figure out if they're related but one of the organism is not well studied and only a part of its expansion segment is sequenced. Is it useful to compare the expansion segments of various organisms to build a tree?
The 40S subunit is the small subunit of eukaryotic 80S ribosomes. It is structurally and functionally related to the 30S subunit of 70S prokaryotic ribosomes. The 40S subunit contains the decoding center which monitors the complementarity of tRNA and mRNA in protein translation. It is the target of most eukaryotic initiation factors and also interacts with the internal ribosome entry site. The core of the 40S subunit is formed by the 18S ribosomal RNA (abbreviated 18S rRNA), which is homologous to the prokaryotic 16S rRNA. This rRNA core is decorated with dozens of proteins The phylogenic alignment of homologous L35 protein suggests that human large subunit ribosomal protein L35 carries a 54 aa eukaryotic expansion segment.
Dear Rathnavel
rRNA generally has the property of folding as you will know I guess, so paired regions can be differentiated from unpaired.
In a consequence the molecule forms a complex tertiary structure, with the exposed outer parts taking over the main functions of the ribosome.
In eucaryotic rRNAs core regions (the parts that are in the centre of the molecule) are usually much more conserved with respect to both Primary sequence and length Variation, when compared to divergent Domains. Since the latter often Show significant length Variation, they are likewise referred to as Expansion segments.
For a rough overview you can see this at
http://en.wikipedia.org/wiki/Eukaryotic_Ribosome_(80S)
It makes sense to compare Expansion segments among organisms, and there is plenty of literature where People did so. Just be Aware that depending on the Variation you will have in your organisms, the Problems of alignment will increase with increasing length Variation. Alignment strategies taking secondary structure into account may prevent you from getting ambiguous alignments.
Greetings
Nikola
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