Elucidation of the bacterial sphingolipid biosynthetic pathway in Sphingomonas wittichii

Lead Research Organisation: University of St Andrews
Department Name: Chemistry


Cells are made of membranes which are composed of chemicals called 'lipids' - these contain hydrophobic (water hating) and hydrophilic (water loving) parts. Membranes have to be strong to keep cell contents in but also be able to let molecules in (nutrients, metals, salts) - as well as keeping toxic materials out and expelling waste. They must also stop water flooding in and bursting the cell by increased osmotic pressure. Cells have evolved different membranes with different chemical composition. Mammals have complicated membranes and they generate 100s of different lipids. Similarly, yeast, plants and viruses have species-specific lipids. Bacteria too have unique and unusual lipids - they also play important roles in the immune response and inflammation. Mammals have evolved to recognise their own lipids as 'self' but can expertly detect foreign lipids from pathogenic bacteria, fungi and viruses. Once detected, the mammalian cell can mount an effective immune response to kill the invader. This then begs the question, if a bacterium has evolved to have lipids similar to a human's - how do we tell them apart? Looking more closely at the lipids themselves our project will focus on a special branch of interesting lipids called 'sphingolipids'. They were discovered >100 years ago in human brains by John Thudichum who knew that they played an important role in brain chemistry. It took until the 1930s for Herbert Carter to work out the chemistry of the sphingolipids - a polar, water soluble head and a fatty acid non-polar tail. They were found to be made from the common amino acid L-serine and a long carbon (>C16) chain. Scientists have long wondered about how sphingolipids are made inside the cell from common building blocks and then transported to the outside - this must happen very quickly when the cells are rapidly growing and dividing. Also, sphingolipids are dangerous - too many or too little in one cell can be lethal so the amounts are delicately controlled in a way we still don't fully understand. To uncover the chemical details and explore the enzymes involved we and other scientists are studying sphingolipid biosynthesis in humans, plants, yeast and bacteria. We have chosen an interesting bacterium Sphingomonas wittichii because it is not harmful to man - in fact it can degrade toxins to harmless molecules. These Sphingomonas are highly unusual because they make sphingolipids that resemble our own to some extent. We will explore how Sphingomonas makes sphingolipids by carefully characterising the genes that encode the enzymes that carry out the initial conversion of serine and the fatty acid, through the complex 2nd and 3rd steps, and beyond. We are helped because the Department of Energy (USA) have already sequenced the Sphingomonas wittichii genome and predict it to have >5000 genes. However, we do not know which ones are involved in sphingolipid biosynthesis. We will use chemical, biochemical, genetic and molecular biology methods to help us understand each step. We have already made a start and found an unusual small protein (~80 amino acids long) that we think links sphingolipid and fatty acid biosynthesis. Most of the work will be carried out in Edinburgh but we will also work with Jim Naismith in St.Andrews who can determine the 3D structure of a protein, as well as a genetics expert in the USA, Teresa Dunn. Our teamwork will put us ahead of our competitors. By the end of the grant we will have determined the basic roadmap of bacterial sphingolipid biosynthesis and be able to begin to compare it with the map in humans, plants and yeast. We'll obtain insight into how these species evolved to make the same sphingolipid and begin to understand how each controls the amount in each cell. Whilst we carry out the work we will make sure we give seminars to experts and the general public telling them what we've found out and will also publish in highly-rated international journals that will benefit UK science.

Technical Summary

Sphingolipids (SLs) and their glycosylated forms (GSLs) are essential components of eukaryotic membranes and are also potent signalling molecules. They are composed of a long chain base and a polar head group. They are found in humans, plants, yeasts and some bacteria. The first step in SL biosynthesis in all organisms is the coupling the amino acid L-serine with a long chain fatty acid thioester substrate. This is catalysed by a pyridoxal 5'-phosphate (PLP) cofactor dependent enzyme, serine palmitoyltransferase (SPT). It produces the 1st intermediate ketodihydrosphingosine (KDS), CO2 and CoASH. SPTs from eukaryotes are heterodimeric membrane bound enzymes but in bacteria such as Sphingomonas they are soluble cytoplasmic enzymes. We were the first to characterise the high resolution x-ray structure of a bacterial SPT and we have used it to model the human enzyme. The SL biosynthetic pathways in various organisms are complicated and the enzymes tightly controlled but detailed structural analysis is lacking. In this project we will continue our breakthrough SL biosynthesis work on a model bacterial system - Sphingomonas wittichii whose genome sequence is known. We will use chemical, biochemical and genetic tools to identify and characterise the early steps in the pathway. We have already identified a potential novel link between SL and fatty acid synthesis - we discovered a small acyl carrier protein (ACP) that may complex with the SPT to make KDS. Thereafter the KDS product is streospecifically reduced by a reductase using a NAD(P) cofactor then N-acylated to form a ceramide. We will complement these methods with tools from yeast genetics to search for bacterial homologs. We will conclude with a preliminary study of how sugars are attached to the SL core to generate GSLs and identify any kinases. Our work will provide the first insight into SL biosynthesis in this kingdom of life and allow a comparison with the SL pathway in higher organisms.

Planned Impact

The impact is the same as the Edinburgh (lead) component.


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Lowther J (2012) Structural, mechanistic and regulatory studies of serine palmitoyltransferase. in Biochemical Society transactions

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Wadsworth JM (2013) The chemical basis of serine palmitoyltransferase inhibition by myriocin. in Journal of the American Chemical Society

Description We have determined the structure of the complex of this enzyme. This has allowed a deeper insight into the mechanism and into what goes wrong in the Hereditary Sensory and Autonomic Neuropathy disease. We have taken this work forward to work on the human enzyme, we have been able to purify this integral membrane protein complex.
Exploitation Route They might be used to help treat patients with this disease.
Sectors Healthcare

Description They are leading to an improved understanding of the disease.
First Year Of Impact 2014
Sector Healthcare
Impact Types Societal

Title Protein complex 
Description We have determined an important complex of the SPT enzyme 
Type Of Technology New Material/Compound 
Year Produced 2012 
Impact No actual Impacts realised to date 
Description Schools visits 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Each year I host visits to my lab from local secondary school (10's of pupils) and I also give a talk to visiting school pupils on science (approx 50 pupils).

Some of the children seemed to appreciate that chemistry was important in biology.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014
Description Training and workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Between 20 to 50 pupils per year visit St Andrews and as part of this, they are exposed to structural biology.

Teachers report increased enthusiasm for biomedical science
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010,2011,2012,2013
Description workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Helped in the training of post-graduate students in structural biology at the following meetings.
CCP4/ZCAM workshop, Zaragoza, Spain March 2012
CCP4/ APS workshop, Argonne, USA, June 2012
CCP4/APS workshop, Argonne, USA, June 2013
CCP4/CeBEM workshop, Montevideo, Uruguay, April 2013

Widespread use of UK authored software.
Year(s) Of Engagement Activity 2013,2014
URL http://www.ccp4.ac.uk