In Search of T. Rex’s Descendants using Bioinformatics!

While searching for genetics project ideas, I came across this interesting project on the Science Buddies website about how scientists were able to trace the closest living relatives of the scary Tyrannosaurus Rex dinosaur to a common species that usually ends up on our dinner plate! The project used the partial protein sequence identified from the dinosaur’s collagen and searched for similar sequences of living organisms stored in an online protein database called SwissProt using a program called BLAST. The idea is that if the sequences are similar, then these species would have a common ancestor with the T.Rex (Science Buddies Staff, 2020).

The story starts in 2000 when Bob Harmon and a crew from the Museum of the Rockies, based in Bozeman, Montana, discovering a well preserved T. Rex skeleton in a remote Montana canyon. Jack Horner, the famous paleontologist who was the inspiration behind the Jurassic Park movie character, Dr. Alan Grant, was the curator of paleontology at this museum. It was a 68 million year old female specimen and Dr. Mary Schweitzer found round microstructures in the fragments of it’s leg bone that looked like blood cells as well as collagen, a protein that is the building block of bones, muscles, blood vessels etc (Fields, 2006). It was thought that soft tissues like blood vessels, muscles etc. would decay over time, so there were some controversy regarding this discovery. However, by using mass spectrometry techniques on this sample, Dr. John Asara was able to detect seven collagen proteins (Dalton, 2009).

The DNA sequences identified by Dr. Asara are uploaded into freely accessible protein sequence databases like SwissProt, RCSB Protein Data Bank, etc. and can be searched and compared with other organisms’ protein sequences using online bioinformatics tools like BLAST. The protein sequence databases store informationa about the proteins, their structure, variants of the proteins, diseases caused etc. Similar databases store genetic information. BLAST or Basic Local Alignment Search Tool (also called the google of biological research) is a bioinformatics program that is used to search and compare protein or nucleotide sequence against a variety of squence databases. For example, the link between the SARS-Cov-2 coronavirus affecting humans in 2020 and the two coronaviruses found in bats and pangolins, RaTG13 and RmYN02 was found using a BLAST searches (Tao, Z., Qunfu, W., Zhigang, Z., 2020).

Using the steps in the Science Buddies website, I first searched for the Tyrannosaurus Rex collagen protein sequence using the National Center for Biotechnology Information (NCBI) search feature here. I selected “protein” in the “All Database” drop down and typed “Tyrannosaurus Rex” in the search box. It shows three results. I clicked on the first result with record name “Full=Collagen alpha-1 (I) chain”.

The record data is displayed with the source, the authors and the sequence at the bottom. The sequence can be downloaded as a file in FASTA format (FASTA is text based format used to represent DNA and protein sequences). An option to run BLAST from the record page is available on the right. I clicked the “Run BLAST” link.

The FASTA sequence is already populated in the “Enter accession number, gi, or FASTA sequence” box and the search tool is open under the “blastp” or Standard Protein BLAST tab. I entered a job title and selected “UniProtKB/Swiss-Prot(swissprot)” in the Search set Database drop down. The default algorithm is set to “blastp (protein-protein BLAST)” and clicked BLAST button after selecting “Show results in new window”.

I was surprised to find a number of significant alignments to common living organisms including the humble chicken (Gallus gallus) and another one that doesn’t end up on the dinner plate – the Norway rat (Rattus Norvegicus)! Here is the result of the search with the “Taxonomy” tab selected.

I learned a lot about the BLAST tool and sequences and I’m going to continue using this in other research work that I’ll be doing in the future, probably using Python programming. Stay tuned!

References

Science Buddies Staff. (2020, November 20). BLAST into the Past to Identify T. Rex’s Closest Living Relative. Retrieved from https://www.sciencebuddies.org/science-fair-projects/project-ideas/Genom_p018/genetics-genomics/t-rex-closest-living-relative

Fields, H. (2006, May 1). Dinosaur Shocker. Smithsonian Magazine. https://www.smithsonianmag.com/science-nature/dinosaur-shocker-115306469/

Dalton, R. (2009, April 20). Age-defying dinosaur collagen : Nature News. Nature. https://www.nature.com/news/2009/090430/full/news.2009.422.html

Tao, Z., Qunfu, W., Zhigang, Z. (2020, April 6). Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. ScienceDirect. https://www.sciencedirect.com/science/article/pii/S0960982220303602

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) “Basic local alignment search tool.” J. Mol. Biol. 215:403-410. PubMed

The UniProt Consortium, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D506–D515, https://doi.org/10.1093/nar/gky1049

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