Representing phylogenetic tree at atomic level (C,H,N,O,S) instead of protein sequences
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7.7 years ago
Naresh ▴ 60

Hi,

To construct phylogenetic tree, we usually consider genes or protein sequences. I have a idea to represent the phylogenetic tree one step down at its atomic level instead of protein sequences.

Please share me your opinions, whether representing phylogenetic tree at atomic levels instead of protein sequence will make any sense .

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Hi Naresh,

This is not your first post about working on the atomic level instead of protein sequences, and I must admit that I still don't get it. You have been asking questions like this for months now... I assume converting the 20 amino acids each to their atomic components shouldn't be too hard, so that cannot be the problem. Right? I also wonder about the biological hypothesis of working on the atomic level rather than on the protein level. Aren't aminoacids the most basic functional elements of proteins? What information does the atomic level add to this?

In addition, perhaps I miss something, but I don't see the added value of representing protein sequences on the atomic level rather than on the protein level, given that the atomic level is completely dependent on the protein level (ignoring transient post-translational modifications) and as such doesn't add new information to the tree.

Don't see this as critique, but I'm just wondering...

Cheers, Wouter

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Hi Wouter, Thank you for your valuable comments. I don't take it as critique. I take this in a positive way. Converting the 20 amino acids each of their atomic components is not the problem now. I have done it.

Background info: we have taken around 1000 genes and made a phylogenetic tree using archateryx tool - we relied on the taxonomy offered by NCBI and reconstructed the taxonomic tree from publically available database dumps (Ref. Arne Kutzner et al., Genomics, 2015). data unpublished. At gene level, they found some similarity between bacteria and fungi., They wanted to study even at atomic level to show the same results. so that at end, they can say that both at gene level and atomic level - we can say that bacteria and fungi show similarity.

according to me. we cannot study the species at atomic level - because of the physiological variability which is dependable on C,H,N,O,S variability also. I don't know how to convince my boss who is asking me to study at atomic level to represent the phylogenetic tree.

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Essentially, when calculating a phylogenetic tree you are comparing similarities and dissimilarities between the species. So if you compare on the protein level, you compare the amino acid structure. But how do you do this on the atomic level? Do you want to compare the number of C,H,N,O,S in each species? Or do you use a primary sequence/structure? Both of these are directly dependent on the amino acid sequence (again ignoring post translational modifications). Can you give me the atomic level of a small protein or peptide as an example?

You are talking about C,H,N,O,S variability, which is a dynamic property of the organism (the levels change constantly due to exchange with environment). However, phylogenetic trees based on protein structure are static and non-dependent on environment. I'm not sure this makes biological sense.

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Yes. Even i know this does not make any biological sense.

My boss wants me to study assimilation and metabolism of various species like Bacteria, Fungi, Protozoa, animals & Plants. How C,H,N,O,S are getting assimilated and metabolised in various species like Bacteria, Fungi, Protozoa, animals & Plants.

If i study this - Can i make sense to represent the phylogenetic tree at atomic level instead of protein sequences.

Please guide me.

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For me this sounds a bit like a non sense. You can play around with the CHNSO composition of your organisms under different conditions. You can use these data to see similarity amongst organisms and conditions, for example performing a cluster analysis. Then you could compare the topology of the dendrogram with the topology of the phylogenetic tree obtained using nucleotide or protein sequences. Anyway, it sounds like your project so maybe you have to come out with your own approach/ideas.

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