\"Carotenoids are a distinctive, widespread class of molecules with diverse meta
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"Carotenoids are a distinctive, widespread class of molecules with diverse metabolic and ecological roles in organism (1). Variants of these colored compounds are synthesized with the same set of homologous enzymes, of which copies are distributed in many species of Bacteria, Archaea, Fungi, and plants. Animals require carotenoids for several functions, ranging from ornamentation to antioxidants and immune system modulators to precursors for visual pigments [e.g. (1-4)]. But animals obtain these compounds from food, and so far, no animal has been reported to make its own carotenoids. Here we report the presence and expression of carotenoid biosynthetic genes in aphids (Insecta: Hemiptera). Further, we show they underlie production of carotenoids and color, including a genetic color polymorphism affecting interactions with natural enemies (5). Phylogenetic analyses imply the ancestral transfer of these genes from a fungus to an ancestor of numerous modern aphid species." (Abstract from Moran & Jarvik 2010. Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science 328: 624-627) Modified version of Fig 1: QUESTIONS: A) One of the carotenoid biosynthesis proteins explored in this study was torulene, also known as carotene dehydrogenase. Search NCBI and find a carotene dehydrogenase protein sequence from this study. Briefly explain your search strategy (which database did you use? What search terms? Any other steps?) and how you were able to confirm from the results of your search that you had found the correct sequence data. (3 pts) 1. B) Write an R script to find the same sequence data. Include your R script file with this assignment. (2 pts)Explanation / Answer
The study explained that the catotenoid biosynthesis protein is from an aphid species and the protein is also known as torulene.
NCBI is a public repository of biological data which includes biological sequences.
a. From searching the term torulene in the NCBI website, the protein section shows 18 hits. From the hits the only two carotene dehydrogenase sequences are identified from Acyrthosiphon pisum (pea aphid) strain LSR1. The protein sequece are under the NCBI reference ID NP_001171302.1 (GenBank ID: ADF29294.1). Both the sequences are same under difference database accession IDs and the sequence are from pea aphid. The search is furthur confirmed that the sequences are from the authors (Moran,N.A. and Jarvik,T.).
b. R language is an interpreted language which uses command line interpreter.
The NCBI gives documentation for all their databases can be used through rentrez. Using helper functions in rentrez NCBI’s databases can be accessed.
First install the database for access and install the GitHub version and load the database.
Install.packages(“rentrez”)
Install.packages(“devtools”)
Devtools::install_github(“ropensci/rentrez”)
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