John Innes Centre

Fundamental Cellular Processes

The aim of this theme of our research is to understand, at the molecular level, fundamental cellular processes in tractable model bacterial systems.  The knowledge accrued in this way can subsequently be used to inform the more strategic research programmes both at JIC and elsewhere.  Our studies of fundamental cell processes encompass a wide range of disciplines including microbial physiology, biochemistry, molecular genetics, structural biology and computational biology. Current major topics within this research theme are:

Environmental signalling in bacteria

Group leader:  

Prof. Ray Dixon

The ability of bacteria to respond to a multitude of environmental signals and integrate these signals to trigger adaptive responses provides a successful strategy for survival in rapidly changing environments.

Domain structure of NorR and structural model of the NO-sensing GAF domain Domain structure of NorR and structural model of the NO-sensing GAF domain

Understanding the molecular mechanisms by which these signals are perceived and integrated is the main aim of our work. We are analysing multi-protein signalling complexes in which interactions are modulated by redox changes, ligand binding and covalent modification.

Our major emphasis is on signal transduction cascades that regulate nitrogen fixation genes in response to oxygen, carbon and fixed nitrogen status. We also study a specific class of prokaryotic transcription factors that use energy from nucleotide hydrolysis to drive the process of transcription initiation. These bacterial enhancer binding proteins interact at a distance with RNA polymerase holoenzyme containing an unusual sigma factor, sigma54. One such protein under study (in collaboration with Stephen Spiro, Dallas, USA) is NorR, a nitric oxide responsive transcriptional activator that controls expression of genes required for NO detoxification. Enhancer binding proteins contain a variety of sensory modules that probably contribute to the adaptability and unique physiological diversity of many bacteria.

Nitrogen control

Group leader:

Prof. Mike Merrick

X-ray crystal structure of the E. coli AmtB protein (space fill) complexed with the cytoplasmic signal transduction protein GlnK (ribbons) which regulates ammonium influx.

X-ray crystal structure of the E. coli AmtB protein (space fill) complexed with the cytoplasmic signal transduction protein GlnK (ribbons) which regulates ammonium influx.

Bacteria can use a wide range of organic and inorganic sources of nitrogen and they must therefore coordinate the expression of genes required for nitrogen metabolism with the availability of nitrogen sources in their environment and with their intracellular nitrogen status.   Whilst different species of prokaryotes vary considerably in the range of nitrogen sources that they can utilise there are a number of fundamental mechanisms that are ubiquitous both with regard to nitrogen assimilation and to gene regulation in response to the availability of fixed nitrogen. 

The preferred source of nitrogen for most bacteria is ammonium and a major focus of our research is on the biology of the ubiquitous ammonium transport (Amt) proteins.  The Amt proteins are found in eubacteria, archaebacteria, fungi, plants, nematode worms and insects.  They are also present in higher animals including humans where their homologues are the Rhesus proteins. 

We are studying the Escherichia coli AmtB protein as a model which offers an excellent system to investigate questions of structure, function and signal transduction relating to these proteins. Recent work has included elucidation of the mechanism by which ammonium flux into the bacterial cell is controlled and the first determination of the structure of a Rhesus protein.