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Summer school

Project name
Regulatory role of ribose-phosphate isomerase isoenzymes in central carbon metabolism of cyanobacterium Synechocystis PCC 6803
Leader
MSc. Anushree Bachhar
Description of the activities of the project
  • Synechocystis PCC 6803 is a model organism and a mixotrophic cyanobacterium. There are many isozymes (enzymes with the same roles but different properties) in the sequenced genome of Synechocystis but the function of many isozymes is still unknown. If we look at the case of ribose phosphate isomerase (RPI), which catalyses interconversion of ribose 5-phosphate to ribulose 5-phosphate within the Calvin cycle, there are two annotated RPIs for Synechocystis, RPI A (slr0194) and RPI B (ssl 2153). However, the position of RPI in the metabolic network does not provide any hints regarding the role and need of multiple RPIs. Furthermore, there is a possibility that the annotation of one of RPI might be incorrect.
  • There are experimental techniques which could help us to test if both annotated RPIs have indeed the function of RPI. However, even in the positive answer, the results would not likely to answer the question, “why are there two RPIs?” Fortunately, instead of spending resources and often limited time of scientific equipment in wet labs, one can employ the computational methods of Systems biology as the initial step of analysis.
  • Firstly, we will run a bioinformatic analysis of RPIs in Synechocystis, analysing the occurrence of RPI isozymes in other organisms and their similarity by comparing primary structure. Then, we will implement the second RPI in the kinetic model of Synechocystis and run various tests aiming to answer the benefits of existence of two RPIs. The test will run in MATLAB and will analysis the response to different growth conditions (levels of CO2 and glucose) as well as simulating the fluctuation of the environment.
    • Through the project, the student will learn:
    • basics of bioinformatics, including the creation of phylogenetic tree
    • kinetic modelling of metabolism
    • various omics integration
    • working with MATLAB
    • how the metabolism and isoenzymes work in a prokaryotic organism.
  • The project outcome will be an improved understanding of how the metabolic regulation is influenced by isoenzymes, particularly the role(s) of ribose-phosphate isomerases within Synechocystis 6803.
Students
  • Number of students - 1
  • high school students students - NO
  • university students - YES
  • Prepositions (what should the students know): at least one of these: Basic knowledge of biochemistry (what is enzyme and gene expression), basic experience with any programming language

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