The seminar on Friday, October 16th will be presented by Dr. Jack Min. Dr.Min's talk is entitled "Prediction of Protein Subcellular Locations in Eukaryotes". For background reading, please see the cited articles in the Seminar Schedule. Please be sure to attend this presentation on the robust value of bioinformatics research.
Dr. Min presentation on prediction of protein subcellular locations in eukaryotes was captivating. Identification of protein subcellular location is an essential part of protein functional annotation. In order to understand gene products using the Gene Ontology program one must be conversant with the central dogma. The central dogma describe the processes from DNA- RNA- Proteins- Phenotype.
ReplyDeleteHis project dealt with the secretome. Secretome proteins are processed in the ER unlike other proteins synthesized in the ribosomes. He studied the enzymes in fungi that were responsible to breakdown cellulose from Canada forest residue producing bio-fuel.
FASTA format is the only accepted format in bioinformatics tool. He worked with tools such as UniProtK and Swiss- Prot database which contain high quality annotated and non-redundant protein sequence database. These tools show experimental data of protein subcellular locations. Tools used to predict accuracy of protein subcellular locations include SignalP, phobius, WolfPsort, targetP, TMHMM and PS-Scan. It is recommended to use more than one tool to increase accuracy.
Why are protein subcellular locations predictions simpler in prokaryotes?
Protein subcellular location prediction is more difficult in eukaryotes pathogens which are stained gram negative because gram negative bacteria have five major subcellular localization sites. These sites include the cytoplasm, periplasm, inner membrane, outer membrane and extracellular space. The subcellular location of a protein is important because it can provide information about its function. Unfortunately, the overall prediction accuracy for eukaryotes are in the 80 percentile range due to the high number of proteins. Studies have been trying to increase this percentage to reach the 90 percentile instead in order to analyze proteomic and genomic data. The study that I have cited below developed a multi modular PSORT-B which they intend for it to raise the prediction accuracy 14% higher than the highest reported prediction rate of 89%.
ReplyDeleteYu, C. S., Lin, C. J., & Hwang, J. K. (2004). Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein science : a publication of the Protein Society, 13(5), 1402–1406. https://doi.org/10.1110/ps.03479604
Eukaryotes have a much more complex subcellular makeup as compared to prokaryotes. Bacterial subcellular localization sites, for example, include the cytoplasm, periplasm, inner membrane, outer membrane and extracellular space.
ReplyDeleteProkaryotes have simpler cellular configurations than eukaryotes. In eukaryotes, proteins in the same subcellular area generally have similar functions. The complexity arises when you account for the variety of subcellular locations within a eukaryotic cell. Prokaryotes, on the other hand, are much simpler in their structure and makeup. This allows for more accurate, and much faster, protein localization.
ReplyDeleteI also enoyed Dr. Min's presentation on the prediction of protein subcellular locations in eukaryotes. Protein subcellular location predictions are much more simple in prokaryotes compared to eukaryotes because of the more simple subcellular makeup located in prokaryotes. Eukaryotes have more sites of subcelluar localization, so the prediction accuracy is not as high. Prokaryotes are more simple in their structure, so they are easier to predict with a high accuracy.
ReplyDeleteProkaryotes in general are simpler than eukaryotes. Structurally, eukaryotes are much more complex than prokaryotes. Prokaryotes lack membrane bound organelles and have one circular chromosome whereas eukaryotes have many membrane bound organelles and a nucleus containing chromosomes. Protein synthesis and modification occurs in different locations in the eukaryotic cell. Contrarily, protein transcription and translation occurs in the cytoplasm of prokaryotes. Therefore, eukaryotes have more protein subcellular locations than prokaryotes which makes protein subcellular location prediction in prokaryotes much easier.
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