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Prof. Mike Merrick

Department of Molecular Microbiology,
John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, UK

Email: mike.merrick@jic.ac.uk

I retired from my permanent position at the John Innes Centre in September 2015 and now hold an Emeritus fellowship in the Department of Molecular Microbiology. The pages below describe my continuing scientific interests and the work of my research group over the last decade or so.

Research Interests

Throughout my research career my interests focussed on bacterial nitrogen metabolism and the ways in which bacteria control all aspects of that metabolism in response to the availability of fixed nitrogen. Bacteria can use a wide range of organic and inorganic sources of nitrogen and they must therefore coordinate both the expression of genes and the activities of proteins required for nitrogen metabolism with the availability of nitrogen sources in their environment and with their intracellular nitrogen status (for reviews see: Merrick and Edwards, 1995; Arcondeguy et al, 2001; Huergo et al, 2013). The major research in my lab concerned the biology of the ubiquitous ammonium transport (Amt) proteins and of the signal transduction proteins of the PII family.

The transport of ammonium across cell membranes is a process of fundamental importance in almost all living organisms. The Amt proteins are ubiquitous, being found in eubacteria, archaebacteria, fungi, plants, nematode worms and insects. However closely related members of the Amt family are also present in higher animals, including humans: these Amt homologues are the Rhesus proteins. In my laboratory we developed the AmtB protein of Escherichia coli as a model which offers an excellent system to investigate questions of structure, function and signal transduction relating to Amt proteins (Merrick et al., 2006).

In most prokaryotes the coordination of gene expression and protein activity to control cellular N metabolism is achieved by the activities of the PII signal transduction proteins. These proteins have a remarkable ability to regulate the activities of transcription factors, enzymes and membrane proteins. They are also conserved within the plastids of higher plants.

B.Sc: Genetics, University of Birmingham, UK (1970)
Ph.D. Genetics, University of Birmingham, UK (1973)
Postdoc: John Innes Centre, Norwich UK (1973-76)
Research Scientist: Nitrogen Fixation Laboratory, University of Sussex, UK (1976 - 1995)
Project Leader: Dept. of Molecular Microbiology, John Innes Centre, Norwich, UK (1995 - 2012)
Associate Head of Department (2001 - Feb 2012)
Director of the Norwich Research Park Doctoral Training Partnership (2011 – 2015)
JIC Emeritus Fellow (Sep 2015 – present)

Ammonium Transport

The transport of ammonium across cell membranes is a process of fundamental importance in almost all living organisms. However the means by which ammonium enters cells was the subject of debate for many decades until genes encoding high-affinity ammonium transporters (Amt) were isolated in 1994 from both Saccharomyces cerevisae and Arabidopsis thaliana. The Amt family of proteins is unique and ubiquitous, being found in eubacteria, archaebacteria, fungi, plants, nematode worms and insects. In 1997 it was recognised that members of the Amt family are also present in higher animals including humans where their homologues are the Rhesus proteins.

The Amt and Rh protein family
The Amt/Rh protein family.

E. coli AmtB structure and function

The membrane topology of the E. coli Amt protein (AmtB) provides a model for the whole Amt family (Thomas, Mullins and Merrick, 2000). Bioinformatic data indicates that the majority of Amt proteins have eleven trans-membrane helices (TMH) with the N-terminus outside the membrane and the C-terminus inside. A subset of proteins, including E.coli AmtB, has an apparent additional twelfth TMH which has subsequently been shown to be a signal peptide (Thornton et al., 2006). The presence of this signal peptide appears to characterise Amt proteins in Gram –ve bacteria but its precise role in maturation of AmtB remains to be determined.

Purification and characterisation of E. coli AmtB showed it to be a stable trimer and this is almost certainly the case for all members of the Amt family (Blakey et al., 2002). The availability of purified AmtB facilitated the production of two-dimensional crystals that confirmed the trimeric nature of the protein (Conroy et al., 2004). Three dimensional crystals subsequently led to the solution of the X-ray structure of E. coli AmtB (Zheng et al., 2004; Khademi et al., 2004). The structure of AmtB strongly suggests that the protein functions as a channel (rather than a transporter), that mediates the flux of ammonia, NH3, through the conduction pore. Current models suggest that Amt proteins bind ammonium, NH4+, in the outer vestibule and subsequently deprotonate it. Whether the proton released also crosses the membrane or not remains to be determined (Javelle et al., 2006; Javelle et al., 2007, Javelle et al., 2008).

The E. Coli AmtB protein (Zheng et al., 2004)
The E. Coli AmtB protein.

Amt proteins and signal transduction

Amt proteins have also been implicated in cellular responses to ammonium availability (i.e. ammonium sensing) in a variety of organisms, including bacteria such as Azospirillum brasilense, fungi such as Saccharomyces cerevisiae and Ustilago maydis, and the slime mould Dictyostelium discoideum.

In bacteria the amtB gene is almost invariably transcriptionally linked to a second gene, glnK, that encodes a signal transduction protein (GlnK) belonging to the PII family (Arcondeguyet al.,2000). The conserved linkage of these two genes is strongly suggestive of a functional interaction between their products (Thomas, Coutts and Merrick, 2000) and indeed we have shown that in N-sufficient GlnK is sequestered to the membrane in an AmtB-dependent fashion (Coutts et al., 2002; Javelle et al., 2004). The AmtB-GlnK complex can be purified (Durand and Merrick, 2006) and its X-ray structure has been solved (Conroy et al., 2007). This structure demonstrates that binding of GlnK to AmtB physically blocks the ammonia conduction channel thereby controlling ammonia influx into the cell. This interaction is likely to be conserved throughout prokaryotes.

The E. coli AmtB – GlnK complex (Conroy et al., 2007)
X-ray structure of the E. coli AmtB/GlnK complex

In some cases the GlnK-AmtB complex plays a pivotal role in other nitrogen regulatory mechanisms within the cell. For example some nitrogen-fixing bacteria can reversibly inactivate the nitrogenase enzyme in response to extracellular ammonium. This process involves ADP-ribosylation of the NifH subunit of nitrogenase by the concerted efforts of inactivating (DraT) and activating (DraG) enzymes. In A. brasilense the activities of these enzymes is controlled by their interactions with two PII proteins, GlnB and GlnZ (the A. brasilense homologue or GinK) (Huergo et al., 2006a; Huergo et al., 2006b; Huergo et al., 2009). The DraG (dinitrogen-reductase activating glycohydrolase) protein is a monomer, and is the first ADP-ribosylhydrolase with a known biological substrate for which the crystal structure has been solved (Li et al., 2009). Under N-sufficient conditions (e.g. after ammonium shock) DraG is sequestered to the membrane by formation of a ternary complex with GlnZ and AmtB (Huergo et al., 2007; Rajendran et al., 2011). This reversible sequestration prevents DraG from interacting with nitrogenase thereby allowing DraT to inactivate NifH. The formation of this ternary complex between AmtB, GlnZ and DraG constitutes a novel mechanism of nitrogen regulation and it is conceivable that the activities of other GlnK targets could be regulated in a similar manner in other prokaryotes.


Lab Publications on ammonium transport

Wang J., Fulford T., Shao Q., Javelle A., Yang H., Zhu W., Merrick M. (2013) Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. PLoS ONE 8(5): e62745 (pdf file).

Radchenko, M.V., Thornton J. and Merrick M. (2010) Control of AmtB-GlnK complex formation by intracellular levels of ATP, ADP and 2-Oxoglutarate. J Biol Chem. 285(40): 31037-31045 (pdf file).

Truan, D., Huergo, L.F., Chubatsu, L.S., Merrick, M., Li, X.D. and Winkler, F.K. (2010) A new PII protein structure identifies the 2-oxoglutarate binding site. J Mol Biol. 400: 531-539 (pdf file).

Bao-zhen, L., Merrick, M., Su-mei, L., Hong-ying, L., Shu-wen, Z., Wei-ming, S. and Yan-hua, S. (2009) Molecular Basis and Regulation of Ammonium Transporter in Rice. Rice Science 16(4): 314-322 (pdf file).

Huergo, L.F., Merrick, M., Monteiro, R.A., Chubatsu, L.S., Steffens, M.B., Pedrosa, F.O. and Souza, E.M. (2009) In vitro interactions between the PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. J Biol Chem. 284: 6674-6682 (pdf file).

Li, X-D., Huergo, L.F., Gasperina, A., Pedrosa, F.O., Merrick, M. and Winkler, F.K. (2009) Crystal structure of dinitrogenase reductase activating glycohydrolase (DRAG) reveals conservation in the ADP-ribosylhydrolase fold and specific features in the ADP-ribose binding pocket. J. Mol. Biol. 390: 737-746 (pdf file).

Javelle, A., Lupo, D., Ripoche, P., Fulford, T., Merrick, M. and Winkler, F.K. (2008) Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB. Proc. Natl. Acad. Sci. USA. 105: 5040-5045 (pdf file).

Huergo, L.F., Merrick, M., Pedrosa, F.O., Chubatsu, L.S., Araujo, L.M. and Souza, E.M. (2007) Ternary complex formation between AmtB, GlnZ and the nitrogenase regulatory enzyme DraG reveals a novel facet of nitrogen regulation in bacteria. Mol. Microbiol. 66: 1523-1535. (pdf file)

Javelle, A., Lupo, D., Li, X-D., Merrick, M., Chami, M., Ripoche, P. and Winkler, F.K. (2007) Structural and mechanistic aspects of Amt/Rh proteins. J. Struct. Biol. 105: 5040-5045 (pdf file).

Conroy, M.J., Durand, A., Lupo, D., Li-X-D., Bullough, P.A., Winkler, F.K. and Merrick, M. (2007) The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc. Natl. Acad. Sci. USA. 104: 1213-1218 (pdf file).

Severi, E., Javelle, A. and Merrick, M. (2007) The conserved carboxy-terminal region of the ammonia channel AmtB plays a critical role in channel function. Mol. Memb. Biol. 24:161-171 (pdf file).

Javelle, A., Lupo, D., Zheng, L., Li, X-D., Winkler, F.K. and Merrick, M. (2006) An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance. J. Biol. Chem. 281: 39492-39498 (pdf file)

Huergo, L.F., Chubatsu, L.S., Souza, E.M., Pedrosa, F.O., Steffens, M.B.R. and Merrick, M. (2006) Interactions between PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. FEBS Letts. 580: 5232-5236 (pdf file)

Durand, A. and Merrick, M. (2006) In vitro analysis of the Escherichia coli AmtB-GlnK complex reveals a stoichiometric interaction and sensitivity to ATP and 2-oxoglutarate J. Biol. Chem 281: 29558-29567. (pdf file)

Merrick, M., Javelle, A., Durand, A., Severi, E., Thornton, J., Avent, N.D., Conroy, M.J. and Bullough, P.A. (2006) The Escherichia coliAmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins. Transfusion clinique et biologique 13: 97-102.(pdf file)

Thornton, J., Blakey, D., Scanlon, E. and Merrick, M. (2006) The ammonia channel protein AmtB from Escherichia coli is a polytopic membrane protein with a cleavable signal peptide. FEMS Microbiol. Letts. 258: 114-120 (request pdf file)

Huergo, L.F., Souza, E.M., Araujo, M.S., Pedrosa, F.O., Chubatsu, L.S., Steffens, M.B.R., and Merrick, M. (2006) ADP-ribosylation of dinitrogenase reductase in Azospirillum brasilense is regulated by AmtB-dependent membrane sequestration of DraG. Mol. Microbiol. 59: 326-337 (pdf file).

Conroy, M.J., Bullough, P.A., Merrick, M. and Avent, N.D. (2005) Modeling the human Rhesus proteins: implications for structure and function. Brit. J. Haematology 131: 534-551 (pdf file)

Javelle, A., Thomas, G., Marini, A-M., Krämer, R., and Merrick, M. (2005) In vivo functional characterisation of the E. coli ammonium channel AmtB: evidence for metabolic coupling of AmtB to glutamine synthetase. Biochem. J. 390: 215-222. (pdf file)

Javelle, A. and Merrick, M. (2005) Complex formation between AmtB and GlnK: an ancestral role in prokaryotic nitrogen control. Biochem. Soc. Trans. 33: 174-176. (pdf file)

Conroy, M.J., Jamieson, S.J., Blakey, D., Kaufmann, T., Engle, A., Fotiadis, D., Merrick, M. and Bullough, P.A. (2004) Electron and atomic force microscopy of the trimeric ammonium transporter AmtB. EMBO reports 5: 1153-1158. (pdf file)

von Wiren N. and Merrick, M.(2004) Regulation and function of ammonium carriers in bacteria, fungi and plants. Topics in Current Genetics 9: 95-120. (pdf file)

Javelle A., Severi E., Thornton J., and Merrick M. (2004) Ammonium sensing in E.coli : The role of the ammonium transporter AmtB and AmtB-GlnK complex formation J. Biol. Chem. 279: 8530-8538. (pdf file)

Blakey, D., Leech, A., Thomas, G.H., Coutts, G., Findlay, K. and Merrick, M.(2002) Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochem. J. 364: 527-535. (pdf file).

Coutts, G., Thomas, G., Blakey, D., and Merrick, M. (2002) Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. The EMBO Journal 21: 536-545 (pdf file).

Thomas, G.H., Mullins, J. G. L. and Merrick, M. (2000) Membrane topology of the Mep/Amt family of ammonium transporters. Molecular Microbiology 37: 331-344. (pdf file)

Thomas, G., Coutts, G. and Merrick, M. (2000) The glnKamtB operon: a conserved gene pair in prokaryotes. Trends in Genetics 16: 11-14. (pdf file)

Taté R., Cermola M., Riccio A., Iaccarino M., Merrick M., Favre R. and Patriarca E.J. (1999) The ectopic expression of the Rhizobium etli amtB gene affects the symbiosome differentiation process and nodule development. Molecular Plant-Microbe Interactions 12: 515-525.

Taté R., Riccio A., Merrick M. and Patriarca E.J. (1998) The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation. Molecular Plant-Microbe Interactions 11:188-198.

Rhesus proteins

Rhesus (Rh) proteins show significant similarity to Amt proteins and have also been demonstrated to also be capable of ammonium transport. The human Rh proteins (RhAG, RhCE, RhD) are found in the membranes of red blood cells and constitute a major class of blood group antigens. Their precise physiological role in the erythrocyte has yet to be established and indeed some investigators have argued that their function in the erythrocyte is to facilitate movement of CO2, rather than ammonia, across the cell membrane.

To study this question we carried out molecular dynamics simulations of the permeation of ammonia and carbon dioxide mediated by Rh50 from Nitrosomonas europaea. To assess the physiological relevance of NH3 and CO2 permeation across Rh50, we also computed potentials of mean force (PMFs) and permeabilities for NH3 and CO2 flux across Rh50 and compare them to permeation through a range of lipid membranes. We concluded that Rh50 is expected to enhance NH3 flux across dense membranes, such as membranes with a substantial cholesterol content, whereas the CO2 permeabilities of membranes are too high to allow significant Rh50-mediated CO2 flux (Hub et al., 2010).

Two non-erythroid Rh proteins (RhBG, RhCG) are also present in humans. These are expressed in the liver and kidney where they are proposed to play important roles in ammonium transport. In fish Rh proteins are found in not only in red blood cells, kidney and spleen but also in gills where they are thought to mediate ammonia excretion. Rh-like proteins are also found in nematodes, slime moulds and marine sponges and it seems likely that they could have a common role, namely the transport of ammonium, in all these organisms.

The human Rh erythrocyte complex had been proposed to be a tetramer but modelling of Rh proteins using the structure of E. coli AmtB as a starting point, led us to conclude that Rh proteins were also likely to be trimeric (Conroy et al., 2005). Recently genes encoding Rh proteins have been identified in some bacterial genomes. We have studied one of these, from an ammonia-oxidising bacterium Nitrosomonas europaea, and have solved the X-ray structure of the protein. NeRh50 is indeed a homotrimer which is structurally very similar to AmtB and when expressed in yeast it is able to facilitate ammonium uptake (Cherif-Zahar et al., 2007; Lupo et al., 2007). Solution of the crystal structure of Human Rh C glycoprotein (RhCG) by Stroud and co-workers in 2010 confirmed that it also forms a trimeric complex in which the subunits are very similar to AmtB but have an additional transmebrane helix at their N-terminus.

The Nitrosomonas europaea Rh50 protein (Lupo et al., 2007)
The structure of the Nitrosomonas europaea Rh50 protein.

Lab Publications on Rhesus proteins

Hub J. S., Winkler F.K., Merrick M. and de Groot B.L. (2010) Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes. Journal of the American Chemical Society. 132(38): 13251-13263. (pdf file)

Lupo, D., Li, X-D., Durand, A., Tomizaki, T., Cherif-Zahar, B., Matassi, G., Merrick, M. and Winkler, F. (2007) The 1.3 Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. Proc. Natl. Acad. Sci. USA. 104: 19303-19308. (pdf file)

Cherif-Zahar, B., Durand, A., Schmidt, I., Matic, I., Merrick, M. and Matassi, G. (2007) Evolution and Functional Characterisation of the RH50 Gene from the Ammonia-Oxidizing Bacterium Nitrosomonas europaea. J. Bacteriol. 189:, 9090-9100. (pdf file)

Javelle, A., Lupo, D., Li, X-D., Merrick, M., Chami, M., Ripoche, P. and Winkler, F.K. (2007) Structural and mechanistic aspects of Amt/Rh proteins. J. Struct. Biol.158: 472-481 (pdf file)

Merrick, M., Javelle, A., Durand, A., Severi, E., Thornton, J., Avent, N.D., Conroy, M.J. and Bullough, P.A. (2006) The Escherichia coliAmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins. Transfusion clinique et biologique 13: 97-102.(pdf file)

Conroy, M.J., Bullough, P.A., Merrick, M. and Avent, N.D. (2005) Modeling the human Rhesus proteins: implications for structure and function. Brit. J. Haematology 131: 534-551 (pdf file)

PII proteins and signal transduction

PII proteins are now recognized as one of the most widely distributed signal transduction proteins in nature, being ubiquitous in bacteria, archaea and plants (Arcondeguy et al., 2001). Many bacteria and archaea encode multiple PII proteins, whereas only a single copy is present in the cyanobacteria and in plants.

PII proteins function by protein–protein interaction, whereby they have been shown to control the activities of a wide range of targets, including enzymes, transcription factors and membrane transport proteins. These targets are almost invariably involved in cellular nitrogen metabolism, and hence PII proteins are considered to be pivotal regulators of nitrogen metabolism in most prokaryotes. More recently, it has also been proposed that their functions may extend to the co-ordination of nitrogen and carbon metabolism and to sensing of cellular energy status. The key to the sensory properties of the PII proteins is their ability to bind the effector molecules 2-OG (2-oxoglutarate) and ATP or ADP.

The structure of the E. coli PII protein GlnK
Fig. 1 The structure of the E. coli PII protein GlnK

PII proteins are homotrimers with 12–13 kDa subunits that display a highly conserved structure. The trimer is a compact cylindrically shaped molecule from which three long exposed loops (the T-loops) protrude (Figure 1). The T-loops are significantly conserved in sequence, but are structurally very flexible and can adopt various conformations. They are vital for PII interactions with many of their targets and are also often sites of reversible covalent modification. In addition to the T-loops, PII proteins are also characterized by three lateral inter-subunit clefts, within which are two smaller loops (the B- and C-loops) (Figure 1). PII proteins have been divided into three subfamilies, encoded by the genes glnB, glnK and nifI (Arcondeguy et al., 2001). GlnB and GlnK are closely related and are often encoded in the same organism. A considerable number of X-ray structures have been solved for both GlnB and GlnK. NifI proteins are more distantly related: they occur in nitrogen-fixing archaea and function in regulating nitrogen fixation; however, no structures of NifI proteins have been solved.

PII proteins have two modes of signal perception. The first which is apparently conserved in all PII proteins, consists of the binding of effector molecules ATP, ADP, and 2-oxoglutarate (2-OG). ATP or ADP binds in the lateral clefts between the subunits, where the B- and T-loops from one subunit and the C-loop from another contribute to a nucleotide-binding pocket (Figure 2; Conroy et al., 2007, Truan et al., 2010). The binding site for 2-OG was identified from a crystal structure of Azospirillum brasilense GlnZ, (a GlnK homologue) co-crystallised with 2-OG (Truan et al., 2010). Both ATP and 2-OG bind in the lateral clefts, where they participate in the coordination of a Mg2+ ion (Figure 2). This is consistent with the observation that MgATP binding is synergistic with the binding of 2-OG.

A. Binding of 2-OG, MgATP to GlnZ;  B. Binding of ADP to GlnK
Fig. 2 A. Binding of 2-OG, MgATP to GlnZ; B. Binding of ADP to GlnK

In vivo studies of the cellular pools of these effectors suggest that fluctuation in the 2-OG pool is the key determinant of the behaviour of PII proteins (Radchenko et al., 2010). High 2-OG favours binding of MgATP and a relatively disordered T-loop conformation, whereas low 2-OG leads to ATP being replaced by ADP in the nucleotide-binding cleft and a concomitant change in the T-loop to a more ordered conformation (Truan et al., 2010).

The role of ATP/ADP binding has been ascribed by some authors to an “energy-status” sensing mechanism for PII proteins. However an alternative model has been proposed following the report of a 2-OG dependent ATPase activity in E. coli GlnK (Radchenko et al, 2013). In this model the ATPase activity drives the conformational change that occurs following a drop in the intracellular 2-OG level.

Many, but not all, PII proteins are subject to covalent modification through the action of the bifunctional enzyme (GlnD) that covalently modifies PII by uridylylation or deuridylylation of Tyr51 in the T-loop. GlnD activity is regulated by the cellular glutamine pool; hence, the modification state of PII reflects the cellular glutamine status. In some organisms PII modification is by adenylylation (Streptomycetes) or phosphorylation (Cyanobacteria). The role of covalent modification has been reviewed recently (Merrick, 2015; Radchenko et al, 2014).

PII proteins typically interact with their targets through T-loop contacts (Figure 3; for review see Radchenko et al., 2011) as typified by the interaction of GlnK with AmtB (Conroy et al., 2007).

Structures of PII complexes:  A. GlnK-AmtB; B. PII-NAGK; C. PII-PipX
Fig. 3 Structures of PII complexes: A. GlnK-AmtB; B. PII-NAGK; C. PII-PipX

However we have recently shown that the interaction of Azospirillum brasilense GlnZ with the DraG protein is not through the T-loops (Rajendran et al., 2011), thereby allowing GlnZ to form a ternary AmtB-GlnZ-DraG complex (Figure 4).

Putative AmtB-GlnZ-DraG complex derived by superimposition of the E. coli AmtB-GlnK structure with the A. brasilense GlnZ-DraG structure. (AmtB - orange; GlnZ – blue; DraG – green)
Fig. 4 Putative AmtB-GlnZ-DraG complex derived by superimposition of the E. coli AmtB-GlnK structure with the A. brasilense GlnZ-DraG structure. (AmtB - orange; GlnZ – blue; DraG – green)


Publications relating to PII proteins and signal transduction

Inaba, J., J. Thornton, L. F. Huergo, R. A. Monteiro, G. Klassen, F. O. Pedrosa, M. Merrick, and E. M. de Souza. (2015) Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense. Microbiol.Res. 171:65-72.

Merrick, M. (2015) Post-translational modification of PII signal transduction proteins. Front Microbiol. 5:763.

Radchenko, M. V., J. Thornton, and M. Merrick. (2014) Association and dissociation of the GlnK-AmtB complex in response to cellular nitrogen status can occur in the absence of GlnK post-translational modification. Front Microbiol. 5:731.

Radchenko, M. V., J. Thornton, and M. Merrick. (2013) PII signal transduction proteins are ATPases whose activity is regulated by 2-oxoglutarate. Proc.Natl.Acad.Sci.U.S.A 110:12948-12953

Huergo L. F., Chandra G., Merrick M. (2013) PII signal transduction proteins: nitrogen regulation and beyond. FEMS Microbiology Reviews, 37, 251-283 (pdf file).

Huergo L. F., Pedrosa F. O., Muller-Santos M., Chubatsu L. S., Monteiro R. A., Merrick M., Souza E. M. (2012) PII signal transduction proteins: pivotal players in post-translational control of nitrogenase activity. Microbiology 158: 176-190 (pdf file).

Rajendran C., Gerhardt E.C.M., Bjelic S., Gasperina A., Scarduelli M., Pedrosa F.O., Chubatsu L.S., Merrick M., Souza E.M., Winkler F.K., Huergo L.F., Li X.D. (2011) Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction. PNAS 108(48): E1254-1263

Radchenko, M. and Merrick M. (2011) The role of effector molecules in signal transduction by Pll proteins. Biochem. Soc. Trans. 39: 189-194 (pdf file).

Truan, D., Huergo, L.F., Chubatsu, L.S., Merrick, M., Li, X.D. and Winkler, F.K. (2010) A new PII protein structure identifies the 2-oxoglutarate binding site. J Mol Biol. 400: 531-539 (pdf file).

Huergo, L.F., Merrick, M., Monteiro, R.A., Chubatsu, L.S., Steffens, M.B., Pedrosa, F.O. and Souza, E.M. (2009) In vitro interactions between the PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. J Biol Chem. 284: 6674-6682 (pdf file).

Huergo L.F., Chubatsu L.S., Souza E.M., Pedrosa F.O., Steffens M.B.R. and Merrick M. (2006) Interactions between PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. FEBS Letts. 580: 5232-5236 (pdf file)

Coutts, G., Thomas, G., Blakey, D., and Merrick, M. (2002) Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. The EMBO Journal 21: 536-545 (pdf file).

Arcondeguy, T., Jack, R. and Merrick, M. (2001) The PII signal transduction proteins: pivotal players in microbial nitrogen control. Microbiol. Mol. Biol. Reviews 65: 80-105. (pdf file)

Ercolano, E., Mirabella, R., Merrick, M. and Chiurazzi, M. (2001) The Rhizobium leguminosarum glnB gene is down-regulated during symbiosis. Mol. Gen. Genet. 264: 555-564. (pdf file)

Thomas, G.H., Mullins, J. G. L. and Merrick, M. (2000) Membrane topology of the Mep/Amt family of ammonium transporters. Molecular Microbiology 37: 331-344. (pdf file)

Arcondeguy, T., van Heeswijk, W.C., and Merrick, M. (1999). Studies on the roles of GlnK and GlnB in regulating Klebsiella pneumoniae NifL-dependent nitrogen control. FEMS Microbiol.Lett. 180: 263-270. (pdf file)

Former group members

Mr Jeremy Thornton (2002-2012)
Jeremy.Thornton@jic.ac.uk

Dr Martha Radchenko (2007-2011)
marta.radchenko@rosalindfranklin.edu

Dr Steve Pullan (2006-2009)
http://uk.linkedin.com/pub/steven-pullan/4a/23/797

Mr Alexandre Decorps (2005-2009)

Dr Juliana Inaba (2008)
https://br.linkedin.com/pub/juliana-inaba/97/20a/5b2/en

Dr Kolja Szymanski (2007-2008)

Dr Luciano Huergo (2006)
http://www.researchgate.net/profile/Luciano_Huergo 

Dr Elizabeth Scanlon (2004-2007)
https://uk.linkedin.com/in/elizabethscanlon

Dr Anne Durand (2004-2006)
http://www.cgm.cnrs-gif.fr/spip.php?article141&lang=fr

Dr Tim Fulford (2003-2006)

Dr Arnaud Javelle (2002-2005)
http://www.strath.ac.uk/staff/javellearnauddr/

Dr Emmanuele Severi (2002-2005)
https://uk.linkedin.com/pub/emmanuele-severi/13/107/a50

Dr Graham Coutts (1999-2002)
http://www.ls.manchester.ac.uk/people/profile/?alias=couttsg

Dr Gavin Thomas (1998-2000)
http://www.york.ac.uk/biology/research/biochemistry-biophysics/gavin-h-thomas/

Dr Tania Arcondeguy (1997-2000)

Dr Emma Southern (1996-1999)
http://uk.linkedin.com/pub/emma-thompson/30/814/985

Dr Rachel Jack (1994-1998)

Dr Rob Edwards (1991-1994)
https://edwards.sdsu.edu/research/

Dr Wyatt Paul (1986-1989)
wyatt.paul@biogemma.com

Dr Andreas Holtel (1984-1988)
https://be.linkedin.com/pub/andreas-holtel/39/23b/87a/en

Dr Stuart MacFarlane (1983-1986)
http://www.scri.ac.uk/staff/StuartMacFarlane

Dr Ariel Álvarez Morales (1980-1983)
https://mx.linkedin.com/pub/ariel-alvarez-morales/9a/420/77b/en

Dr. Guadalupe Espin (1978-1981)
http://www.ibt.unam.mx/server/PRG.base?tipo:doc,dir:PRG.curriculum,par:espin

Lab Publications since 1993

Inaba, J., J. Thornton, L. F. Huergo, R. A. Monteiro, G. Klassen, F. O. Pedrosa, M. Merrick, and E. M. de Souza. (2015) Mutational analysis of GlnB residues critical for NifA activation in Azospirillum brasilense. Microbiol.Res. 171:65-72.

Merrick, M. (2015) Post-translational modification of PII signal transduction proteins. Front Microbiol. 5:763.

Radchenko, M. V., J. Thornton, and M. Merrick. (2014) Association and dissociation of the GlnK-AmtB complex in response to cellular nitrogen status can occur in the absence of GlnK post-translational modification. Front Microbiol. 5:731.

Radchenko, M. V., J. Thornton, and M. Merrick. (2013) PII signal transduction proteins are ATPases whose activity is regulated by 2-oxoglutarate. Proc.Natl.Acad.Sci.U.S.A 110:12948-12953

Wang, J., T. Fulford, Q. Shao, A. Javelle, H. Yang, W. Zhu, and M. Merrick. (2013) Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. PLoS.One. 8:e62745.

Huergo L. F., Chandra G., Merrick M. (2013) PII signal transduction proteins: nitrogen regulation and beyond. FEMS Microbiology Reviews, 37, 251-283 (pdf file).

Huergo L. F., Pedrosa F. O., Muller-Santos M., Chubatsu L. S., Monteiro R. A., Merrick M., Souza E. M. (2012) PII signal transduction proteins: pivotal players in post-translational control of nitrogenase activity. Microbiology 158: 176-190 (pdf file).

Rajendran C., Gerhardt E.C.M., Bjelic S., Gasperina A., Scarduelli M., Pedrosa F.O., Chubatsu L.S., Merrick M., Souza E.M., Winkler F.K., Huergo L.F., Li X.D. (2011) Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction. PNAS 108(48): E1254-1263 (pdf file).

Pullan S.T., Chandra G., Bibb M.J. and Merrick M. (2011) Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. BMC Genomics 12: 175 (pdf file).

Radchenko, M. and Merrick M. (2011) The role of effector molecules in signal transduction by Pll proteins. Biochem. Soc. Trans. 39: 189-194 (pdf file).

Hub J. S., Winkler F.K., Merrick M. and de Groot B.L. (2010) Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes. Journal of the American Chemical Society 132(38): 13251-13263 (pdf file).

Radchenko, M.V., Thornton J. and Merrick M. (2010) Control of AmtB-GlnK complex formation by intracellular levels of ATP, ADP and 2-Oxoglutarate. J Biol Chem. 285(40): 31037-31045 (pdf file).

Truan, D., Huergo, L.F., Chubatsu, L.S., Merrick, M., Li, X.D. and Winkler, F.K. (2010) A new PII protein structure identifies the 2-oxoglutarate binding site. J Mol Biol. 400: 531-539 (pdf file).

Bao-zhen, L., Merrick, M., Su-mei, L., Hong-ying, L., Shu-wen, Z., Wei-ming, S. and Yan-hua, S. (2009) Molecular Basis and Regulation of Ammonium Transporter in Rice. Rice Science 16(4): 314-322 (pdf file)

Gorla, P., Pandey, J.P., Parthasarathy, S., Merrick, M. and Siddavattam, D. (2009) Organophosphate hydrolase in Brevundimonas diminuta is targeted to the periplasmic face of the inner membrane by the twin arginine translocation (Tat) pathway. J. Bacteriol. 191: 6292-6299. (pdf file)

Li, X-D., Huergo, L.F., Gasperina, A., Pedrosa, F.O., Merrick, M. and Winkler, F.K. (2009) Crystal structure of dinitrogenase reductase activating glycohydrolase (DRAG) reveals conservation in the ADP-ribosylhydrolase fold and specific features in the ADP-ribose binding pocket. J. Mol. Biol. 390: 737-746 (pdf file).

Huergo, L.F., Merrick, M., Monteiro, R.A., Chubatsu, L.S., Steffens, M.B., Pedrosa, F.O. and Souza, E.M. (2009) In vitro interactions between the PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. J Biol Chem. 284: 6674-6682 (pdf file).

Javelle, A., Lupo, D., Ripoche, P., Fulford, T., Merrick, M. and Winkler, F.K. (2008) Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB. Proc. Natl. Acad. Sci. USA. 105: 5040-5045 (pdf file).

Khajamohiddin, S., Repalle, E.J., Pinjari, A.B., Siddavattam, D. and Merrick, M. (2008) Biodegradation of aromatic compounds: An overview of meta-fission product hydrolases. Critical Reviews in Microbiology 34: 13-31.

Huergo, L.F., Merrick, M., Pedrosa, F.O., Chubatsu, L.S., Araujo, L.M. and Souza, E.M. (2007) Ternary complex formation between AmtB, GlnZ and the nitrogenase regulatory enzyme DraG reveals a novel facet of nitrogen regulation in bacteria. Mol. Microbiol. 66: 1523-1535. (pdf file)

Lupo, D., Li, X-D., Durand, A., Tomizaki, T., Cherif-Zahar, B., Matassi, G., Merrick, M. and Winkler, F. (2007) The 1.3 Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. Proc. Natl. Acad. Sci. USA. 104: 19303-19308. (pdf file)

Cherif-Zahar, B., Durand, A., Schmidt, I., Matic, I., Merrick, M. and Matassi, G. (2007) Evolution and Functional Characterisation of the RH50 Gene from the Ammonia-Oxidizing Bacterium Nitrosomonas europaea. J. Bacteriol. 189:, 9090-9100. (pdf file)

Javelle, A., Lupo, D., Li, X-D., Merrick, M., Chami, M., Ripoche, P. and Winkler, F.K. (2007) Structural and mechanistic aspects of Amt/Rh proteins. J. Struct. Biol.158: 472-481 (pdf file)

Conroy, M.J., Durand, A., Lupo, D., Li-X-D., Bullough, P.A., Winkler, F.K. and Merrick, M. (2007) The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc. Natl. Acad. Sci. USA. 104: 1213-1218 (pdf file).

Severi, E., Javelle, A. and Merrick, M. (2007) The conserved carboxy-terminal region of the ammonia channel AmtB plays a critical role in channel function. Mol. Memb. Biol. 24: 161-171 (pdf file).

Khajamohiddin, S., Pakala, S.B., Chakka, D.P., Merrick, M., Bhaduri, A., Sowdhamini, R. and Siddavattam, S. (2006) A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551. Biochem. Biophys. Res. Comm. 351: 675-681 (pdf file).

Javelle, A., Lupo, D., Zheng, L., Li, X-D., Winkler, F.K. and Merrick, M. (2006) An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance. J. Biol. Chem. 281: 39492-39498 (pdf file)

Huergo L.F., Chubatsu L.S., Souza E.M., Pedrosa F.O., Steffens M.B.R. and Merrick M. (2006) Interactions between PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense. FEBS Letts. 580: 5232-5236 (pdf file)

Pakala S.B., Gorla P., Pinjari A.B., Krovidi R.K., Baru R., Yanamandra M., Merrick M. and Siddavattam D. (2006) Biodegradation of methyl parathion and p-nitrophenol: Evidence for the presence of a p-nitrophenol 2–hydroxylase in a Gram-negative Serratia sp. strain DS001. App. Microbiol. Biotechnol. (pdf file).

Durand, A. and Merrick, M. (2006) In vitro analysis of the Escherichia coli AmtB-GlnK complex reveals a stoichiometric interaction and sensitivity to ATP and 2-oxoglutarate J. Biol. Chem281: 29558-29567. (pdf file).

Merrick, M., Javelle, A., Durand, A., Severi, E., Thornton, J., Avent, N.D., Conroy, M.J. and Bullough, P.A. (2006) The Escherichia coliAmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins. Transfusion clinique et biologique 13: 97-102.(pdf file)

Thornton, J., Blakey, D., Scanlon, E. and Merrick, M. (2006) The ammonia channel protein AmtB from Escherichia coli is a polytopic membrane protein with a cleavable signal peptide. FEMS Microbiol. Letts. 258: 114-120 (pdf file)

Siddavatam, D., Raju, E.R., Emmanuel Paul, P.V. and Merrick, M. (2006) Overexpression of parathion hydrolase in Escherichia coli stimulates the synthesis of outer membrane porin OmpF. Pesticide Biochem. Physiol. 86: 146-150. (pdf file)

Huergo, L.F., Souza, E.M., Araujo, M.S., Pedrosa, F.O., Chubatsu, L.S., Steffens, M.B.R., and Merrick, M. (2006) ADP-ribosylation of dinitrogenase reductase in Azospirillum brasilense is regulated by AmtB-dependent membrane sequestration of DraG. Mol. Microbiol. 59: 326-337 (pdf file).

Conroy, M.J., Bullough, P.A., Merrick, M. and Avent, N.D. (2005) Modeling the human Rhesus proteins: implications for structure and function. Brit. J. Haematology 131: 534-551 (pdf file)

Manvathi, B., Pakala, S.B., Gorla, P., Merrick, M. and Siddavattam, D. (2005) Influence of zinc and cobalt on expression and activity of parathion hydrolase from Flavobacterium sp. ATCC27551. Pesticide Biochem. Physiol. 83: 37-45. (pdf file)

Javelle, A., Thomas, G., Marini, A-M., Krämer, R., and Merrick, M. (2005) In vivo functional characterisation of the E. coli ammonium channel AmtB: evidence for metabolic coupling of AmtB to glutamine synthetase. Biochem. J. 390: 215-222. (pdf file)

Javelle, A. and Merrick, M. (2005) Complex formation between AmtB and GlnK: an ancestral role in prokaryotic nitrogen control. Biochem. Soc. Trans. 33: 174-176. (pdf file)

Conroy, M.J., Jamieson, S.J., Blakey, D., Kaufmann, T., Engle, A., Fotiadis, D., Merrick, M. and Bullough, P.A. (2004) Electron and atomic force microscopy of the trimeric ammonium transporter AmtB. EMBO reports 5: 1153-1158. (pdf file)

Merrick, M.J. (2004) Nitrogen control of nitrogen fixation in free-living diazotrophs. In "Genetics and Regulation of Nitrogen Fixing Bacteria" eds: W. Klipp, B. Maepohl, J.R. Gallon and W.E. Newton. (pdf file)

von Wiren N. and Merrick, M. (2004) Regulation and function of ammonium carriers in bacteria, fungi and plants. Topics in Current Genetics 9: 95-120. (pdf file)

Javelle A., Severi E., Thornton J., and Merrick M. (2004) Ammonium sensing in E.coli : The role of the ammonium transporter AmtB and AmtB-GlnK complex formation J. Biol. Chem. 279: 8530-8538. (pdf file)

Siddavattam D., Khajamohiddin S., Manavathi B., Pakala S.B. and Merrick, M. (2003) Transposon-like organisation of the plasmid-borne organophosphate degradation (opd) gene cluster found in Flavobacterium sp. App. Env. Microbiol. 69: 2533-2539.(pdf file)

Blakey, D., Leech, A., Thomas, G.H., Coutts, G., Findlay, K. and Merrick, M. (2002) Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochem. J. 364: 527-535. (pdf file).

Coutts, G., Thomas, G., Blakey, D., and Merrick, M. (2002) Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. The EMBO Journal 21: 536-545 (pdf file).

Arcondeguy, T., Jack, R. and Merrick, M. (2001) The PII signal transduction proteins: pivotal players in microbial nitrogen control. Microbiol. Mol. Biol. Reviews 65: 80-105. (pdf file)

Ercolano, E., Mirabella, R., Merrick, M. and Chiurazzi, M. (2001) The Rhizobium leguminosarum glnB gene is down-regulated during symbiosis. Mol. Gen. Genet. 264: 555-564. (pdf file)

Thomas, G.H., Mullins, J. G. L. and Merrick, M. (2000) Membrane topology of the Mep/Amt family of ammonium transporters. Molecular Microbiology 37: 331-344. (pdf file)

Spinosa, M., Riccio, A., Mandrich, L., Manco, G., Lamberti, A., Iaccarino, M., Merrick M., and Patriarca, E.J. (2000) Inhibition of glutamine synthetase II expression by the product of the gstI gene. Molecular Microbiology 37: 443-452. (pdf file)

Arcondeguy, T., Lawson, D. and Merrick, M. (2000) Two residues in the T-loop of GlnK determine NifL-dependent nitrogen control of nifgene expression. J. Biol. Chem. 275:38452-38456. (pdf file).

Southern, E. and Merrick, M. (2000) The role of Region II in the RNA polymerase sigma factor sigma N (sigma 54). Nucleic Acids Research 28: 2563-2570. (pdf file)

Thomas, G., Coutts, G. and Merrick, M. (2000) The glnKamtB operon: a conserved gene pair in prokaryotes. Trends in Genetics 16: 11-14. (pdf file)

Arcondeguy, T., van Heeswijk, W.C., and Merrick, M. (1999). Studies on the roles of GlnK and GlnB in regulating Klebsiella pneumoniae NifL-dependent nitrogen control. FEMS Microbiol.Lett. 180: 263-270. (pdf file)

Taté, R., Cermola, M., Riccio, A., Iaccarino, M., Merrick, M., Favre, R. and Patriarca, E.J. (1999) The ectopic expression of the Rhizobium etli amtB gene affects the symbiosome differentiation process and nodule development. Molecular Plant-Microbe Interactions 12: 515-525. (pdf file)

Jack, R., de Zamaroczy, M. and Merrick, M. (1999) The signal transduction protein GlnK is required for NifL-dependent nitrogen control of nif gene expression in Klebsiella pneumoniae. J. Bacteriol 181: 1156-1162. (pdf file)

Taté, R., Riccio, A., Merrick, M. and Patriarca, E.J. (1998) The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation. Molecular Plant-Microbe Interactions 11: 188-198. (pdf file)

Juty, N.S., Moshiri, F., Merrick, M., Anthony, C. and Hill, S. (1997) The Klebsiella pneumoniae cytochrome bd' terminal oxidase complex and its role in microaerobic nitrogen fixation. Microbiol 143: 2673-2683. (pdf file)

Reizer, J., Reizer, A., Merrick, M.J., Plunkett, III G., Rose, D.J. and Saier, Jr. M.H. (1996) Novel phosphotransferase-encoding genes revealed by Analysis of the Escherichia coli genome: a chimeric gene encoding an Enzyme I homologue that possesses a putative sensory transduction domain. Gene 181: 103-108.

Spratt, B.G., Zhou, J., Taylor, M. and Merrick, M.J. (1996) Monofunctional biosynthetic peptidoglycan transglycosylases. Mol.Microbiol.19: 639-640.

Taylor, M., Butler, R., Chambers, S., Casimiro, M., Badii, F. and Merrick, M. (1996) The RpoN box motif of the RNA polymerase sigma factor sigmaN plays a role in promoter recognition. Mol.Microbiol. 22: 1045-1054.

Edwards, R. and Merrick, M. (1995) The role of uridylytransferase in the control of Klebsiella pneumoniae nif gene regulation. Mol.Gen.Genet. 247: 189-198.

Merrick, M.J. and Edwards, R.A. (1995) Nitrogen control in bacteria. Microbiol.Revs. 59: 604-622. (pdf file)

Merrick, M.J. and Taylor, M.S. (1994) Studies on the role of open-reading frames linked to the sigma factor gene rpoN in K.pneumonaiae. In Proceedings of the 1st European Nitrogen Fixation Conference (Edited by Kiss G.B. and Endre G.), p. 287. Officina Press, Szeged.

Merrick, M.J. (1994) Nitrogen fixation: regulation of gene expression. In The Encyclopedia of Molecular Biology (Edited by Kendrew J.), p. 731. Blackwell, Oxford.

Rieder, G., Merrick, M.J., Castorph, H. and Kleiner, D. (1994) Function of the hisF and hisH gene products in histidine biosynthesis. J.Biol.Chem. 269: 14386-14390.

Merrick, M.J. (1993) In a class of its own - the RNA polymerase sigma factor sigma54 (sigma N). Mol.Microbiol. 10: 903-909.