SysMO Sulfolobus (Schleper)-WesterhoffManchester

Lead Research Organisation: University of Manchester
Department Name: Chem Eng and Analytical Science

Abstract

Most living organisms are rather robust vis-à-vis a great number of changes in their environment. Mammals and birds achieve much of this robustness by having different organs and cells process different tasks in a highly coordinated fashion. Unicellular microrganisms may derive much of their robustness from intracellular networks. This is somewhat understood for two of the three domains of Life, but not yet at all for the most recently discovered life form, i.e. Archaea. Yet it is these Archaea that are subject to the most extreme challenges from the environment as some of them live in hyperthermal vents or in salt and are subject to sudden and extreme variations. Only recently, the science has been developed that analyzes how intracellular networks generate important properties that are absent from the components of those networks. In much the same way groups of people can be much more effective than the same number of people all operating individually.) This 'Systems Biology' will here be deployed and tuned to analyze mechanisms of robustness in one of the most extreme Archae that is presently amenable to such studies, i.e. Sulfolobus solfataricus. The research program brings together much of the most appropriate expertise from four European countries. It will focus in the robustness of perhaps the most vital and massive biochemical functions of all organisms, i.e. their main carbon and energy metabolism. It wll look at perhaps the most pervasive perturbations cells of microorganisms experience, i.e. variations in temperature. A computer 'replica' of central carbon and energy metabolism will be made. Both in well-coordinated experiments and in the computer replica the various mechanisms through which the organisms achieve robustness will be identified and quantified. The extent, to which the mechanisms can stand in for each other should one of them be eliminated, will be determined. This new aspect of Systems Biology will suggest new ways to design drugs againt parasytic cells, where adaptation of those cells is taken into account. The understanding achieved will also help develop these organisms as perhaps ideal biological factories for chemicals, including energy-fuel that needs to be harvested from extreme environments.

Technical Summary

Even slight differences between the rates of individual reactions in major metabolic pathways should cause rapid accumulation or depletion of intermediates with potentially deleterious effects. With a change in temperature, the rates of individual reactions in metabolic pathways must therefore change by precisely the same extent. Organisms could adapt by (i) having identical temperature coefficients of the enzymes, (ii) metabolic regulation, (iii) adjusting Vmax's (e.g. through enzyme phosphorylation), (iv) adjusting translation or protein stability, (v) adjusting transcription or mRNA stability, (vi) rerouting the metabolic flow, (vii) formation of compatible solutes, (viii) export of 'overflow' metabolites or (ix) going into dormancy. We propose to quantify each of these adaptations in a systems biology approach. The issue should be most acute for thermophiles. This research programme will therefore study the central carbohydrate metabolism (CCM) of Sulfolobus and its regulation under temperature variation. The archaeal CCM has pathways and enzymes that differ from their bacterial or eukaryotic counterparts. Details of regulation and energetic of the CCM will be revealed while we will assemble the data required for integration of genomic, transcriptomic, proteomic, metabolomic, kinetic and biochemical information on the effects of temperature changes. The focus shall be on a part of the CCM, i.e. the unusual, branched Entner-Doudoroff (ED) pathway for glucose and galactose uptake and catabolism to pyruvate. The required data accuracy will be achieved by combining the expertise of a number of specialized laboratories in different European countries. Our long term goal is to use our proposed Analysis, Modelling and Experimental Design Platform as a nucleus for building a sufficiently precise replica for this part of the living cell ('a Silicon Cell') to enable computation of life, particularly its robustness to changes in temperature, at the system level.

Publications

10 25 50
 
Description We discovered two new hypotheses (or principles of function that needed to be validated for this particular organism): (i) the existence of so-called black and grey holes in the metabolism of organisms and (ii) a possible function for the presence of GAPN in thermophylic organisms. We constructed a kinetic model for the main pathway for carbon and energy metabolism with particular focus on the part between GAP and PEP. We found various places where futile cycling might occur
Exploitation Route The findings have been and are being taken forward in multiple projects that followed upon this project, many in the group of Prof Siebers in Duisburg Germany. Some of these proceed in a further collaboration between her and my group.
Sectors Chemicals,Education,Energy,Manufacturing, including Industrial Biotechology,Other

 
Description The findings have been used in various follow up projects. Multiple of these proceed in the group of Prof Siebers in Duisburg Germany. Some proceed in my own group. Use of the findings should further come form companies using this organism in bio-production, thereby using our mathematical models and discoveries to increase productivity.
First Year Of Impact 2011
Sector Education,Environment,Manufacturing, including Industrial Biotechology
Impact Types Economic

 
Title Candidate pathway finding 
Description Steatosis or fatty liver disease is an important disease sometimes leading to hepatocarcinoma. Most researchers engaged in genomics are searching for so-called candidate genes in their data, which then should identify single-gene causes and single target strategies. We have developed a way to identify/examine 'candidate pathways'. More inn general, the portfolio of projects ahs led to a great increase in number of detailed kinetic models of metabolic pathways (as reported in JWS-Online). these are now of great use for other organisms and the same pathways or other pathways in the same organisms. All these models are also of use for the development of the Infrastructure Systems Biology Europe (ISBE). 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2016 
Provided To Others? Yes  
Impact This is now used in multiple research projects. Through JWS online and BioModels our models are used by many. 
 
Title S. Solfataricus lower glycolysis model 
Description Kinetic model for the lower half of glycolysis in S solfataricus (an Archaeon) 
Type Of Material Computer model/algorithm 
Year Produced 2014 
Provided To Others? Yes  
Impact Used by other academic researchers 
URL https://jws2.sysmo-db.org/models/kouril1/
 
Description Siebers 
Organisation University Duisburg-Essen
Country Germany 
Sector Academic/University 
PI Contribution Modelling
Collaborator Contribution Data
Impact Publications Grant applications
Start Year 2006
 
Description Snoep 
Organisation University of Stellenbosch
Country South Africa 
Sector Academic/University 
PI Contribution Ideas, models, data
Collaborator Contribution Ideas, models, data management
Impact Publications Models Grant proposals
 
Description VU Amsterdam 
Organisation Free University of Amsterdam
Country Netherlands 
Sector Academic/University 
PI Contribution Expertise, information, data
Collaborator Contribution Expertise, information, data
Impact Publications Grant proposals Learned students Understanding of Biology