From a78834231ed82dd0ca70bc144ea7baed70df3ac8 Mon Sep 17 00:00:00 2001 From: Lomagome <70604815+Lomagome@users.noreply.github.com> Date: Mon, 5 Oct 2020 22:47:04 -0400 Subject: [PATCH 1/3] Update README.md --- README.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index cb997131..c652011b 100644 --- a/README.md +++ b/README.md @@ -24,11 +24,20 @@ OK, here we go. ## Introduction and Goals -The goal of my project is to answer the question, What is...? +The goal of my project is to answer the question, do proteases and chaperones evolve at a similar rate? +This question is prompted by a recent study available on bioRxiv on proteome expansion across the tree of life (Rebeaud et al., 2020). They write extensively about the evolution of chaperones and co-chaperones, but say little about proteases. However, it has been well-catalogued that chaperones and proteases play different (but arguably equally important) roles in maintaining proteostasis in a cell (Gottesman et al., 1997). Furthermore, the network of chaperones and proteases that make up protein quality control (PQC) networks are necessary for cell tolerance of perturbations, and, acting as a mechanism of robustness are thus a driving force of evolution. + + +https://www.biorxiv.org/content/10.1101/2020.06.08.140319v2 +http://genesdev.cshlp.org/content/11/7/815.full.pdf The methods I will use to do this are... +I will need to download sequence data for certain PQC genes, align them, and construct a phylogenetic tree. I'm wondering if I can create a tree where each edge represents a specific PQC protein. I imagine I would have to collect a lot of sequences of this homologous protein across species and then create some kind of average estimate of its placement with respect to other proteins. I can create the tree using R and iqtree with the methods we have used in class thus far. I can also use R to estimate and compare evolutionary rates of time based on the phylogenies I create. However, I have no idea how I will organize my collection of homologous protein sequences into one input to map on a tree. + + +For the purpose of this project, the data I will use are publicly available at NCBI. Some of the most well-studied PQC systems are in E. coli (GroEL, GroES, Lon) so I think that would be a good place to start. However, I would love some input on how far I should expand this question (to other bacteria, other microbes, all animals?) -The data I will use are (my own data/ data publicly available at YYY/ simulations) +I will be limited by what is publicly available, but I hope to implement the methods I learn in this project on my own sequence data as my thesis progresses. This will ultimately be sequence data from nearshore bacterial communities in the Long Island Sound. ## Methods From 08ebb05100424dfe3e73a84161834bd75e8534d7 Mon Sep 17 00:00:00 2001 From: Lomagome <70604815+Lomagome@users.noreply.github.com> Date: Mon, 5 Oct 2020 22:55:52 -0400 Subject: [PATCH 2/3] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index c652011b..c601aa49 100644 --- a/README.md +++ b/README.md @@ -32,8 +32,7 @@ https://www.biorxiv.org/content/10.1101/2020.06.08.140319v2 http://genesdev.cshlp.org/content/11/7/815.full.pdf The methods I will use to do this are... -I will need to download sequence data for certain PQC genes, align them, and construct a phylogenetic tree. I'm wondering if I can create a tree where each edge represents a specific PQC protein. I imagine I would have to collect a lot of sequences of this homologous protein across species and then create some kind of average estimate of its placement with respect to other proteins. I can create the tree using R and iqtree with the methods we have used in class thus far. I can also use R to estimate and compare evolutionary rates of time based on the phylogenies I create. However, I have no idea how I will organize my collection of homologous protein sequences into one input to map on a tree. - +I will need to download sequence data for certain PQC genes, align them, and construct a phylogenetic tree. I'm wondering if I can create a tree where each edge represents a specific PQC protein. I imagine I would have to collect a lot of sequences of this homologous protein across species and then create some kind of average estimate of its placement with respect to other proteins. I can create the tree using R and iqtree with the methods we have used in class thus far. I can also use R to estimate and compare evolutionary rates of time based on the phylogenies I create. However, I'm not sure yet how I will organize my collection of homologous protein sequences into one input to map on a tree. For the purpose of this project, the data I will use are publicly available at NCBI. Some of the most well-studied PQC systems are in E. coli (GroEL, GroES, Lon) so I think that would be a good place to start. However, I would love some input on how far I should expand this question (to other bacteria, other microbes, all animals?) From e7e79e53912f00365f49949a3f0b3e7d4f07d4d8 Mon Sep 17 00:00:00 2001 From: Lomagome <70604815+Lomagome@users.noreply.github.com> Date: Tue, 6 Oct 2020 22:05:12 -0400 Subject: [PATCH 3/3] Update README.md --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c601aa49..78265ba4 100644 --- a/README.md +++ b/README.md @@ -20,21 +20,20 @@ Some guidelines and tips: OK, here we go. -# Title of my project +# Comparing Evolution Rates of Protein Quality Control Genes ## Introduction and Goals -The goal of my project is to answer the question, do proteases and chaperones evolve at a similar rate? +The goal of my project is to answer the question, "Do proteases and chaperones evolve at a similar rate?" This question is prompted by a recent study available on bioRxiv on proteome expansion across the tree of life (Rebeaud et al., 2020). They write extensively about the evolution of chaperones and co-chaperones, but say little about proteases. However, it has been well-catalogued that chaperones and proteases play different (but arguably equally important) roles in maintaining proteostasis in a cell (Gottesman et al., 1997). Furthermore, the network of chaperones and proteases that make up protein quality control (PQC) networks are necessary for cell tolerance of perturbations, and, acting as a mechanism of robustness are thus a driving force of evolution. - https://www.biorxiv.org/content/10.1101/2020.06.08.140319v2 http://genesdev.cshlp.org/content/11/7/815.full.pdf The methods I will use to do this are... -I will need to download sequence data for certain PQC genes, align them, and construct a phylogenetic tree. I'm wondering if I can create a tree where each edge represents a specific PQC protein. I imagine I would have to collect a lot of sequences of this homologous protein across species and then create some kind of average estimate of its placement with respect to other proteins. I can create the tree using R and iqtree with the methods we have used in class thus far. I can also use R to estimate and compare evolutionary rates of time based on the phylogenies I create. However, I'm not sure yet how I will organize my collection of homologous protein sequences into one input to map on a tree. +I will need to download sequence data for certain PQC genes, align them, and construct a phylogenetic tree. I'm wondering if I can create a tree where each edge represents a specific PQC protein gene. I imagine I would have to collect a lot of sequences of orthologous PQC genes across species and then create some kind of average estimate of its placement with respect to other proteins. I can create the tree using R and iqtree with the methods we have used in class thus far. I can also use R to estimate and compare evolutionary rates of time based on the phylogenies I create. However, I'm not sure yet how I will organize my collection of homologous protein sequences into one input to map on a tree. -For the purpose of this project, the data I will use are publicly available at NCBI. Some of the most well-studied PQC systems are in E. coli (GroEL, GroES, Lon) so I think that would be a good place to start. However, I would love some input on how far I should expand this question (to other bacteria, other microbes, all animals?) +For the purpose of this project, the data I will use are publicly available at NCBI. Some of the most well-studied PQC systems are in E. coli (GroEL, GroES, Lon) so I think that would be a good place to start. However, I would love some input on how far I should expand this question (to other bacteria, other microbes, all animals?) I think it would be really cool to include archaea, since I imagine many extremophiles rely heavily on PQC proteins to keep them alive in gnarly environments! If my study focused on bacteria, maybe archaea could be an outgroup? I will be limited by what is publicly available, but I hope to implement the methods I learn in this project on my own sequence data as my thesis progresses. This will ultimately be sequence data from nearshore bacterial communities in the Long Island Sound.