John Innes Centre site search
Alison Smith
Department of Metabolic Biology
Alison Smith

Control of starch metabolism in leaves:

During the night, plants are dependent for growth and maintenance on the mobilisation of stores of carbon acquired via photosynthesis during the previous day.  In the model plant Arabidopsis, and many other diverse species, these stores are in the form of starch. In the Arabidopsis leaf about 40% of the carbon assimilated during photosynthesis is used immediately by the plant, and the other half is stored as starch for use during the night.



Starch granules in Arabidopsis leaf chloroplasts at the end of the day.








Mobilisation of starch reserves at night occurs at an essentially linear rate, and almost all of the reserves are used up at dawn when photosynthesis can resume again.  This pattern of starch accumulation and mobilisation over the course of a day is vital for the normal growth of the plant. Plants in which this pattern is disrupted by mutations or by unpredictable environmental changes grow less well than normal plants in predictable conditions. This is because shortage of carbon during the night leads to symptoms of starvation and to temporary slowing or cessation of growth.




The pattern of starch accumulation and mobilisation in an Arabidopsis rosette grown with 12 h light, 12 h dark. Starch reserves last until dawn. If the night is unexpectedly extended after starch is exhausted, growth stops and “starvation” genes are expressed.






We wish to understand:

  • The pathway by which starch is degraded
  • The control of starch degradation at night
  • The control of partitioning of newly-assimilated carbon into starch during the day

Our major collaborators include:

  • Sam Zeeman and colleagues, ETH, Zurich
  • Martin Steup and colleagues, University of Potsdam
  • Jychian Chen and colleagues, Academia Sinica, Taipei
  • Mark Stitt and colleagues, Max-Planck Institute for Molecular Plant Physiology, Postdam-Golm
  • Rob Field and colleagues, John Innes Centre
  • Cristobal Uauy and colleagues, John Innes Centre
  • Martin Howard and colleagues, John Innes Centre

The starch degradation pathway

The pathway has been elucidated by the work of several labs including our own.
Starch granules are degraded by two sorts of hydrolytic enzymes: β-amylases and the debranching ezyme ISOAMYLASE3 (ISA3). The action of these enzymes is facilitated by the phosphorylation and hence hydration of the granule surface by glucan water dikinases (GWD and PWD) followed by dephosphorylation by glucan phosphate phosphatases (SEX4 and LSF2) to permit to permit full hydrolysis of the starch polymers.
 The chief product of granule hydrolysis is maltose, which is exported from the chloroplast into the cytosol via the transporter MEX1. Hydrolysis also produces maltotriose, which is disproportionated via the glucanotransferase DPE1 to give longer chains that can be attacked by β-amylases and glucose which can be exported from the chloroplast into the cytosol.
In the cytosol, maltose is metabolised via the glucanotransferase DPE2. The reducing glucose residue of maltose is released as free glucose; the non-reducing glucose residue is putatively transferred to a complex polysaccharide called soluble heteroglycan (SHG). This glucosyl residue is then converted to glucose 1-phosphate by a cytosolic glucan phosphorylase. Free glucose produced in the pathway is phosphorylated by hexokinase to glucose 6-phosphate. The hexose phosphates are then used in cellular metabolism or converted to sucrose for export to other parts of the plant.



Current model of starch degradation in Arabidopsis leaves (see Smith 2012)










Current research in the Smith lab includes:

The precise role and importance of the glucan, water dikinase GWD
The precise role and importance of the glucanotransferase DPE2

Recent relevant publications:

Fulton DC, Stettler M, Mettler T, Vaughan CK, Li J, Franscisco P, Gil M, Reinhold H, Eicke S, Messerli G, Dorken G, Halliday K, Smith AM, Smith SM, Zeeman, S.C. (2008) β-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active 7-amylases in Arabidopsis chloroplasts. Plant Cell 20, 1040-1058
Kötting O, Santelia D, Edner C, Eicke S, Marthaler T, Gentry MS, Comparot-Moss S, Chen J, Smith, AM, Steup M, Ritte G, Zeeman SC (2009) STARCH-EXCESS4 is a laforin-like phosphoglucan phosphatase required for starch degradation in Arabidopsis thaliana. Plant Cell 21, 334-346
Comparot-Moss S, Kötting O, Stettler M, Edner C, Graf A, Weise SE, Streb S,  Lue WL, MacLean D, Mahlow S, Ritte G, Steup M, Chen J, Zeeman SC, Smith AM (2010) A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves. Plant Physiol 152, 685-697
Zeeman SC, Kossmann J, Smith AM (2010) Starch; its metabolism, evolution and biotechnological modification in plants. Ann Rev Plant Biol 61, 209-234
Smith AM (2012) Starch in the Arabidopsis plant. Starch/Staerke 61, 421-434

The control of starch degradation

The rate of starch degradation during the night is under precise control, so that starch is exhausted at but not before dawn. The flexibility and subtlety of this control is illustrated when plants are subjected to an unexpected early night. Starch degradation is immediately adjusted to a rate lower than that on previous nights, so that starch reserves once again last until dawn.
starch content













In order to implement this adjustment correctly, information about starch content at the onset of night (S) must be integrated with information about the length of time until dawn (T). We have established that information about the length of time until dawn is supplied by the circadian clock, and that this sort of adjustment of flux through the starch degradation pathway is made at the post-translational level. Thus far, we know very little about how the clock influences the pathway or how the amount of starch in the leaf is “measured” in order to set the rate of degradation. 

Current research in the Smith lab includes:

  • A mutant screen designed to identify genes necessary for correct adjustment of the rate of starch degradation.
  • Study of GWD to determine whether this is the major point at which flux through the pathway is controlled.
  • A systems approach to understand the relationship between the circadian clock, starch metabolism and growth. This is the work of an EU FP7 consortium “TiMet”, coordinated by Andrew Millar (University of Edinburgh).
  • A mathematical modelling approach to provide information about the likely properties of S and T, to aid in their identification. This is collaboration with modeller Martin Howard and Antonio Scialdone in JIC’s Computational and Systems Biology Department.
  • Screening of other crop and model species, to obtain a broader picture of the control of carbon availability in leaves at night.

Recent relevant publications:

Smith AM, Stitt M (2007) Coordination of carbon supply and plant growth. Plant Cell Env 30, 1128-1149
Graf A, Schlereth A, Stitt M, Smith AM (2010) Circadian control of carbohydrate availability for growth in Arabidopsis plants at night.  Proc Natl Acad Sci USA 107, 9458-9463
Vriet C, Welham T, Brachmann A, Pike M, Pike J, Perry J, Parniske M, Sato S, Tabata S, Smith AM, Wang, TL (2010) A suite of Lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism. Plant Physiol 154, 643-655
Graf A, Smith AM (2011) Starch and the clock: the dark side of plant productivityTrends Plant Sci 16, 169-175
Crumpton-Taylor M, Grandison S, Png KMY, Bushby AJ, Smith AM (2012) Control of starch granule numbers in Arabidopsis chloroplasts. Plant Physiol 158, 905-916


The control of partitioning of carbon into starch

The proportion of the carbon assimilated during photosynthesis that is stored as starch depends on both short- and long-term factors. In the short term, changes in the rate of photosynthesis or the rate of synthesis of sucrose and its export from the leaf bring about changes in the rate of starch synthesis. Thus if the rate of sucrose synthesis exceeds demand for sucrose, the rate of starch synthesis is increased. Conversely if the rate of photosynthesis falls, the rate of starch synthesis decreases so that the rate of sucrose synthesis is maintained. The mechanisms that bring about this short-term control of partitioning are well understood, and involve modulation of the rate of starch synthesis at the level of the enzyme ADPglucose pyrophosphorylase (AGPase) in response to changes in the rate of sucrose synthesis.
In contrast, very little is known about the longer-term control of partitioning. It is clear that information about the anticipated length of the night is used to set the proportion of newly-assimilated carbon that is stored as starch. Thus plants grown in short days partition a higher proportion of newly-assimilated carbon into starch than plants grown in long days. However, the underlying mechanisms are not understood.

Current research in the Smith lab includes:

  • Investigation of AGPase as a target for mechanisms that control partitioning according to daylength
  • Screens of clock and photoperiod mutants to identify upstream components necessary for the adjustment of partitioning according to day length. Both projects are under the umbrella of the EU FP7 consortium “TiMet”, timetcoordinated by Andrew Millar (University of Edinburgh).