bluuebunny/crossref_metadata_2025 huggingface dataset:
Complexities in ETS-Domain Transcription Factor Function and Regulation: Lessons from the TCF (Ternary Complex Factor) Subfamily
Authors: Sharrocks A. D.
Published: January 2005

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.
Hypersensitive mousetraps, α1-antitrypsin deficiency and dementia
Authors: Lomas D. A. , Lourbakos A. , Cumming S.-A. , Belorgey D.
Published: January 2005

α1-Antitrypsin functions as a ‘mousetrap’ to inhibit its target proteinase, neutrophil elastase. The common severe Z deficiency variant (Glu342 → Lys) destabilizes the mousetrap to allow a sequential protein-protein interaction between the reactive-centre loop of one molecule and β-sheet A of another. These loop-sheet polymers accumulate within hepatocytes to form inclusion bodies that are associated with juvenile cirrhosis and hepatocellular carcinoma. The lack of circulating protein predisposes the Z α1-antitrypsin homozygote to emphysema. Loop-sheet polymerization is now recognized to underlie deficiency variants of other members of the serine proteinase inhibitor (serpin) superfamily, i.e. antithrombin, C1 esterase inhibitor and α1-anti-chymotrypsin, which are associated with thrombosis, angio-oedema and emphysema respectively. Moreover, we have shown recently that the same process in a neuron-specific protein, neuroserpin, underlies a novel inclusion-body dementia, known as familial encephalopathy with neuroserpin inclusion bodies. Our understanding of the structural basis of polymerization has allowed the development of strategies to prevent the aberrant protein-protein interaction in vitro. This must now be achieved in vivo if we are to treat the associated clinical syndromes.
Role of newly synthesized fibronectin in vascular smooth muscle cell migration on matrix-metalloproteinase-degraded collagen
Authors: Stringa E. , White D. , Tuan R. S. , Knauper V. , Gavrilovic J.
Published: January 2005

The migration of vascular smooth muscle cells (VSMC) is known to be a key process in the development of a number of vascular lesions, although the precise mechanisms involved have still to be elucidated. In the present study, the production of endogenous fibronectins by VSMC migrating across intact and matrix-metalloproteinase-degraded collagen type I has been explored. Cellular fibronectin seems to play a role in the enhanced migration seen when VSMC are exposed to degraded collagen and platelet-derived growth factor-BB. VSMC were found to synthesize both exon IIIA-containing fibronectin (which predominated) and exon IIIB-containing fibronectin. When these cells were exposed to substrates consisting of recombinant exon IIIA-or exon IIIB-containing fibronectin, rates of migration were not elevated above those seen with undegraded collagen. Endogenous fibronectin production may thus be necessary, but not sufficient, for VSMC migration over degraded collagenous substrates.
Modulation of extracellular matrix using adenovirus vectors
Authors: Richards C. D. , Kerr C. , Tong L. , Langdon C.
Published: January 2005

Metabolism of the extracellular matrix (ECM) is a complex process that becomes disregulated in disease states characterized by chronic inflammation of joints, as is seen in rheumatoid arthritis or fibrosis of the lung. The participation of certain cytokines in this process is generally accepted (transforming growth factor-β induces fibrosis), while the roles of other cytokines are less clear. Oncostatin M (OSM) is a member of the interleukin-6/leukaemia inhibitory factor (or gp130) cytokine family, and its participation in inflammation and the regulation of ECM metabolism is supported by a number of activities identified in vitro, including regulation of matrix metallo-proteinase-1 and tissue inhibitor of metalloproteinases-1. Local overexpression of transforming growth factor-β has been shown to be fibrogenic in mouse lung, whereas local OSM over-expression via intra-articular administration has been shown to induce a pannus-like inflammatory response in the synovium of mouse knee joints. Here we examine the effects of OSM in the context of those of transforming growth factor-β using an established adenovirus vector that expresses mOSM (AdmOSM). We administered the virus intra-nasally into Balb/C mice to achieve high expression of OSM in the lung, and examined the effects at various time points. AdmOSM resulted in a vigorous inflammatory response by day 7 which was characterized by an elevation of neutrophil and mononuclear cell numbers and a marked increase in collagen deposition. These data support the use of such systems to study the ECM in vivo, and indicate a potential role for OSM in inflammatory responses that can modulate steady-state ECM deposition in Balb/C mice.
Statins for the prevention of vein graft stenosis: a role for inhibition of matrix metalloproteinase-9
Authors: Porter K. E. , Turner N. A.
Published: January 2005

Saphenous vein (SV) grafts are commonly used to bypass coronary arteries that are diseased due to atherosclerosis. However, the development of intimal hyperplasia in such grafts can lead to patency-threatening stenosis and re-occlusion of the vessel. The proliferation and migration of smooth muscle cells (SMC) play key roles in the development of intimal hyperplasia, and an agent that inhibits both of these processes therefore has therapeutic potential. A prerequisite for SMC proliferation and migration in vivo is degradation of the basement membrane, achieved by secretion of the matrix-degrading gelatinases matrix metalloproteinase-2 (MMP-2) and MMP-9. Statins are cholesterol-lowering drugs that also have direct effects on SMC function. Here we report that neointima formation in organ-cultured human SV segments is inhibited by simvastatin, an effect that is associated with reduced MMP-9 activity. Additionally, our work shows that simvastatin not only inhibits proliferation, but importantly also inhibits invasion (migration through a matrix barrier), of cultured human SV SMC. Thus simvastatin treatment appears to inhibit neointima formation as a result of combined inhibition of SMC proliferation and invasion. The potential intracellular mechanisms by which statins affect SMC proliferation and migration, and thus attenuate intimal hyperplasia, are discussed, with particular emphasis on the role of MMP-9.
Functions and interplay of the tRNA-binding sites of the ribosome
Authors: Márquez V. , Wilson D. N. , Nierhaus K. H.
Published: January 2005

The ribosome translates the genetic information of an mRNA molecule into a sequence of amino acids. The ribosome utilizes tRNAs to connect elements of the RNA and protein worlds during protein synthesis, i.e. an anticodon as a unit of genetic information with the corresponding amino acid as a building unit of proteins. Three tRNA-binding sites are located on the ribosome, termed the A, P and E sites. In recent years the tRNA-binding sites have been localized on the ribosome by three different techniques, small-angle neutron scattering, cryo-electron microscopy and X-ray analyses of 70 S crystals. These high-resolution glimpses into various ribosomal states together with a large body of biochemical data reveal an intricate interplay between the tRNAs and the three ribosomal binding sites, providing an explanation for the remarkable features of the ribosome, such as the ability to select the correct ternary complex aminoacyl-tRNA · EF-Tu · GTP out of more than 40 extremely similar tRNA complexes, the precise movement of the tRNA2 · mRNA complex during translocation and the maintenance of the reading frame.
Tissue plasminogen activator as a key effector in neurobiology and neuropathology
Authors: Teesalu T. , Kulla A. , Asser T. , Koskiniemi M. , Vaheri A.
Published: January 2005

Tissue plasminogen activator (tPA) is expressed by many types of neurons in the developing and adult rodent brain. We have now mapped tPA transcripts and protein in the human central nervous system using tissue arrays and find widespread expression, in particular in neocortical mantle, thalamus, amygdala, and hippocampal pyramidal neurons. The abundant presence of tPA protein in cellular vesicles implies that its acute release, e.g. upon ischaemic stroke or trauma, could play a role in neuronal damage. We also found in patients with multiple sclerosis (MS), and to a lesser extent patients with leukaemia and encephalitis, prominently elevated tPA activity in the cerebrospinal fluid and in MS in neurons in the proximity of areas of demyelination elevated tPA mRNA and antigen levels. In addition, we observed up-regulation of tPA expression in a mouse model of MS, experimental autoimmune encephalomyelitis. Accumulating evidence implies roles for tPA in normal neural function, as well as in neurodestructive processes in humans, such as occur in MS and brain tumours and warrant further studies on expression of tPA and its regulatory molecules in neurodegenerative diseases.
Coagulation cascade proteases and tissue fibrosis
Authors: Chambers R. C. , Laurent G. J.
Published: January 2005

Fibrotic disorders of the liver, kidney and lung are associated with excessive deposition of extracellular matrix proteins and ongoing coagulation-cascade activity. In addition to their critical roles in blood coagulation, thrombin and the immediate upstream coagulation proteases, Factors Xa and VIIa, influence numerous cellular responses that may play critical roles in subsequent inflammatory and tissue repair processes in vascular and extra-vascular compartments. The cellular effects of these proteases are mediated via proteolytic activation of a novel family of cell-surface receptors, the protease-activated receptors (PAR-1, −2, −3 and −4). Although thrombin is capable of activating PAR-1, −3 and −4, there is accumulating in vitro evidence that the profibrotic effects of thrombin are predominantly mediated via PAR-1. Factor Xa is capable of activating PAR-1 and PAR-2, but its mitogenic effects for fibroblasts are similarly mediated via PAR-1. These proteases do not exert their profibrotic effects directly, but act via the induction of potent fibrogenic mediators, such as platelet-derived growth factor and connective tissue growth factor. In vivo studies using proteolytic inhibitors, PAR-1 antagonists and PAR-1-deficient mice have provided evidence that coagulation proteases play a key role in tissue inflammation and in a number of vascular pathologies associated with hyperproliferation of smooth muscle cells. More recently, coagulation proteases have also been shown to play a role in the pathogenesis of fibrosis but the relative contribution of their cellular versus their procoagulant effects awaits urgent evaluation in vivo. These studies will be informative in determining the potential application of PAR-1 antagonists as antifibrotic agents.
Energetics of muscle contraction: the whole is less than the sum of its parts
Authors: Kushmerick M. J. , Conley K. E.
Published: January 2005

Understanding muscle energetics is a problem in optimizing supply of ATP to the demands of ATPases. The complexity of reactions and their fluxes to achieve this balance is greatly reduced by recognizing constraints imposed by the integration of common metabolites at fixed stoichiometry among modular units. ATPase is driven externally. Oxidative phosphorylation and glycogenolysis are the suppliers. We focus on their regulation which involves different controls, but reduces to two principles that enable facile experimental analysis of the supply and demand fluxes. The ratio of concentration of phospho-creatine (PCr) to ATP, not their individual values, sets the range of achievable concentrations of ADP in resting and active muscle (at fixed pH) in different cell types. This principle defines the fraction of available flux of oxidative phosphorylation utilized (at fixed enzyme activities). Then the kinetics of PCr recovery defines the kinetics of oxygen supply and substrate utilization. The second principle is the constancy of PCr and H+ (lactate) production by glycogenolysis due to the coupling of ATPase and glycolysis. This principle enables glycogenolytic flux to be measured from intracellular proton loads. Further simplification occurs because the magnitude of the interacting fluxes and metabolite concentrations are specified within narrow limits when both the resting and active fluxes are quantified. Thus there is a small set of rules for assessing and understanding the thermodynamics and kinetics of muscle energetics.
Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era
Authors: Davies G. J. , Henrissat B.
Published: January 2005

Simple and complex carbohydrates have been described as ‘the last frontier of molecular and cell biology’. The enzymes that are required for the synthesis and degradation of these compounds provide an enormous challenge in the post-genomic era. This reflects both the extreme chemical and functional diversity of sugars and the difficulties in characterizing both the substrates and the enzymes themselves. The vast myriad of enzymes involved in the synthesis, modification and degradation of oligosaccharides and polysaccharides is only just being unveiled by genomic sequencing. These so-called ‘carbohydrate-active enzymes’ lend themselves to classification by sensitive sequence similarity detection methods. The modularity, often extremely complex, of these enzymes must first be dissected and annotated before high throughput characterization or ‘structural genomics’ approaches may be employed. Once achieved, modular analysis also permits collation of a detailed ‘census’ of carbohydrate-active enzymes for a whole organism or throughout an ecosystem. At the structural level, improvements in X-ray crystallography have opened up a three-dimensional understanding of the way these enzymes work. The mechanisms of many of the glycoside hydrolase families are becoming clearer, yet glycosyltransferases are only slowly revealing their secrets. What is clear from the genomic and structural data is that if we are to harness the latent power of glycogenomics, scientists must consider distant sequence relatives revealed by the sequence families or other sensitive detection methods.
On the relationship between affinity for molecular hydrogen and the physiological directionality of hydrogenases
Authors: van Haaster D.J. , Hagedoorn P.-L. , Jongejan J.A. , Hagen W.R.
Published: February 2005

The physiological significance of the generic reaction H2↔2[H] is not always clear because hydrogenases may function in the breakdown of molecular hydrogen or in its synthesis or in both directions. Fe-hydrogenases have nevertheless been most often associated with proton reduction and NiFe-hydrogenases with hydrogen oxidation. A re-determination of the KM of H2 oxidation by Pyrococcus furiosus NiFe-hydrogenase-I and by Desulfovibrio vulgaris Fe-hydrogenase suggests that affinity for hydrogen has been seriously underestimated and that the kinetics of hydrogen activation in relation to the directionality of hydrogenases should be re-evaluated.
A semi-empirical molecular orbital scheme to study electron transfer in iron–sulphur proteins
Authors: Sundararajan M. , McNamara J.P. , Mohr M. , Hillier I.H. , Wang H.
Published: February 2005

We describe the use of the semi-empirical molecular orbital method PM3 (parametric method 3) to study the electronic structure of iron–sulphur proteins. We first develop appropriate parameters to describe models of the redox site of rubredoxins, followed by some preliminary calculations of multinuclear iron systems of relevance to hydrogenases.
Non-standard structures of the Ni-Fe cofactor in the regulatory and the NAD-reducing hydrogenases from Ralstonia eutropha
Authors: Löscher S. , Burgdorf T. , Buhrke T. , Friedrich B. , Dau H. , Haumann M.
Published: February 2005

Spectroscopy on two oxygen-insensitive Ni-Fe hydrogenases from Ralstonia eutropha (NAD-reducing, soluble hydrogenase; hydrogen sensor, regulatory hydrogenase) reveals non-standard catalytic behaviour and unique structures of their Ni-Fe cofactors. Possible mechanistic implications are briefly discussed.
Transcriptional regulation of the uptake [NiFe]hydrogenase genes in Rhodobacter capsulatus
Authors: Vignais P.M. , Elsen S. , Colbeau A.
Published: February 2005

Transcription of the hupSL genes, which encode the uptake [NiFe]hydrogenase of Rhodobacter capsulatus, is specifically activated by H2. Three proteins are involved, namely the H2-sensor HupUV, the histidine kinase HupT and the transcriptional activator HupR. hupT and hupUV mutants have the same phenotype, i.e. an increased level of hupSL expression (assayed by phupS::lacZ fusion) in the absence of H2; they negatively control hupSL gene expression. HupT can autophosphorylate its conserved His217, and in vitro phosphotransfer to Asp54 of its cognate response regulator, HupR, was demonstrated. The non-phosphorylated form of HupR binds to an enhancer site (5′-TTG-N5-CAA) of phupS localized at −162/−152 nt and requires integration host factor to activate fully hupSL transcription. HupUV is an O2-insensitive [NiFe]hydrogenase, which interacts with HupT to regulate the phosphorylation state of HupT in response to H2 availability. The N-terminal domain of HupT, encompassing the PAS domain, is required for interaction with HupUV. This interaction with HupT, leading to the formation of a (HupT)2–(HupUV)2 complex, is weakened in the presence of H2, but incubation of HupUV with H2 has no effect on the stability of the heterodimer/tetramer, HupUV–(HupUV)2, equilibrium. HupSL biosynthesis is also under the control of the global two-component regulatory system RegB/RegA, which controls gene expression in response to redox. RegA binds to a site close to the −35 promoter recognition site and to a site overlapping the integration host factor DNA-binding site (5′-TCACACACCATTG, centred at −87 nt) and acts as a repressor.
The hydrogenases of Thiocapsa roseopersicina
Authors: Kovács K.L. , Kovács Á.T. , Maróti G. , Mészáros L.S. , Balogh J. , Latinovics D. , Fülöp A. , Dávid R. , Dorogházi E. , Rákhely G.
Published: February 2005

The purple sulphur phototrophic bacterium, Thiocapsa roseopersicina BBS, contains several NiFe hydrogenases. One of these enzymes (HynSL) is membrane associated, remarkably stable and can be used for practical applications. HupSL is also located in the photosynthetic membrane, its properties are similar to other known Hup-type NiFe hydrogenases. A third hydrogenase activity was located in the soluble fraction and was analogous to the NAD-reducing hydrogenases of cyanobacteria. The hoxEFUYH genes are transcribed together. HoxE is needed for the in vivo electron flow to and from the soluble hydrogenase. Some of the accessory genes were identified using random mutagenesis, and sequencing of the T. roseopersicina genome is in progress. The HupD, HynD and HoxW gene products corresponded to the proteases processing the C-termini of the three NiFe hydrogenases respectively. HypF and HupK mutants displayed significant in vivo H2 evolution, which could be linked to the nitrogenase activity for the ΔhypF and to the bidirectional Hox activity in the ΔhupK strain. Both HypC proteins are needed for the biosynthesis of each NiFe hydrogenase. The hydrogenase expression is regulated at the transcriptional level through distinct mechanisms. The expression of hynSL is up-regulated under anaerobic conditions with the participation of an FNR (fumarate and nitrate reduction regulator)-type protein, FnrT. Although the genes encoding a typical H2 sensor (hupUV) and a two-component regulator (hupR and hupT) are present in T. roseopersicina, the system is cryptic in the wild-type BBS strain. The hupR gene was identified in the gene cluster downstream from hupSL. Introduction of actively expressed hupT repressed the hupSL gene expression as expected by analogy with other bacteria.
Molecular characterization of uptake hydrogenase in Frankia
Authors: Leul M. , Mattsson U. , Sellstedt A.
Published: February 2005

A molecular characterization of uptake hydrogenase in Frankia was performed by using two-dimensional gel electrophoresis, matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry, PCR amplification and Southern blotting. A polypeptide of approx. 60 kDa was recognized in Frankia UGL011102, AVCI1 and KB5 on the two-dimensional gel by blotting with Ralstonia eutropha (Hox G) antibody. Further analysis by MS resulted in a peptide ‘fingerprint’, which was similar to the membrane-bound hydrogenase 2 large subunit (HYD2) in Escherichia coli. In addition, a 127 bp PCR fragment could also be amplified from Frankia AVCI1, which gave a 76% similarity with the large subunit of hydrogenase in, e.g., Azotobacter chrococcum, Bradyrhizobium japonicum and Rhizobium leguminosarum. Although immunological similarity between the small subunit of Frankia hydrogenase and that of other organisms has not yet been found, a PCR product of 500 bp could be amplified from the local source of Frankia, the analysis of which gave 69 and 67% identity with the small subunit of hydrogenases in B. japonicum and R. leguminosarum respectively. A Southern-blot analysis further indicated evidence for the presence of the small hydrogenase subunit in other Frankia strains, i.e. KB5, AvcI1 and CcI3.
Hydrogenase electrodes for fuel cells
Authors: Karyakin A.A. , Morozov S.V. , Karyakina E.E. , Zorin N.A. , Perelygin V.V. , Cosnier S.
Published: February 2005

Considering crucial problems that limit use of platinum-based fuel cells, i.e. cost and availability, poisoning by fuel impurities and low selectivity, we propose electrocatalysis by enzymes as a valuable alternative to noble metals. Hydrogenase electrodes in neutral media achieve hydrogen equilibrium potential (providing 100% energy conversion), and display high activity in H2 electrooxidation, which is similar to that of Pt-based electrodes in sulphuric acid. In contrast with platinum, enzyme electrodes are highly selective for their substrates, and are not poisoned by fuel impurities. Hydrogenase electrodes are capable of consuming hydrogen directly from microbial media, which ensures their use as fuel electrodes in treatment of organic wastes.
Applications of bacterial hydrogenases in waste decontamination, manufacture of novel bionanocatalysts and in sustainable energy
Authors: Macaskie L.E. , Baxter-Plant V.S. , Creamer N.J. , Humphries A.C. , Mikheenko I.P. , Mikheenko P.M. , Penfold D.W. , Yong P.
Published: February 2005

Bacterial hydrogenases have been harnessed to the removal of heavy metals from solution by reduction to less soluble metal species. For Pd(II), its bioreduction results in the deposition of cell-bound Pd(0)-nanoparticles that are ferromagnetic and have a high catalytic activity. Hydrogenases can also be used synthetically in the production of hydrogen from sugary wastes through breakdown of formate produced by fermentation. The Bio-H2 produced can be used to power an electrical device using a fuel cell to provide clean electricity. Production of hydrogen from confectionery wastes by one organism (Escherichia coli) can be used as the electron donor for the production of Bio-Pd0 from soluble Pd(II) by a second organism. The resulting Bio-Pd0 can then be used as a bioinorganic catalyst in the remediation of Cr(VI)-contaminated solutions or polychlorinated biphenyls at the expense of Bio-H2, as a hydrogenation catalyst for industry or as a component of a fuel cell electrode.
Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase
Authors: Cohen J. , Kim K. , Posewitz M. , Ghirardi M.L. , Schulten K. , Seibert M. , King P.
Published: February 2005

The [Fe]-hydrogenase enzymes are highly efficient H2 catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H2 catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O2 inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O2 and H2 diffusion in CpI ([Fe]-hydrogenase I from Clostridium pasteurianum). Our preliminary results suggest that H2 diffuses more easily and freely than O2, which is restricted to a small number of allowed pathways to and from the active site. These O2 pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.
Use of molecular hydrogen as an energy substrate by human pathogenic bacteria
Authors: Maier R.J.
Published: February 2005

Molecular hydrogen is produced as a fermentation by-product in the large intestine of animals and its production can be correlated with the digestibility of the carbohydrates consumed. Pathogenic Helicobacter species (Helicobacter pylori and H. hepaticus) have the ability to use H2 through a respiratory hydrogenase, and it was demonstrated that the gas is present in the tissues colonized by these pathogens (the stomach and the liver respectively of live animals). Mutant strains of H. pylori unable to use H2 are deficient in colonizing mice compared with the parent strain. On the basis of available annotated gene sequence information, the enteric pathogen Salmonella, like other enteric bacteria, contains three putative membrane-associated H2-using hydrogenase enzymes. From the analysis of gene-targeted mutants it is concluded that each of the three membrane-bound hydrogenases of Salmonella enterica serovar Typhimurium are coupled with an H2-oxidizing respiratory pathway. From microelectrode probe measurements on live mice, H2 could be detected at approx. 50 μM levels within the tissues (liver and spleen), which are colonized by Salmonella. The half-saturation affinity of whole cells of these pathogens for H2 is much less than this, so it is expected that the (H2-utilizing) hydrogenase enzymes be saturated with the reducing substrate in vivo. All three enteric NiFe hydrogenase enzymes contribute to virulence of the bacterium in a typhoid fever-mouse model, and the combined removal of all three hydrogenases resulted in a strain that is avirulent and (in contrast with the parent strain) one that is not able to pass the intestinal tract to invade liver or spleen tissue. It is proposed that H2 utilization and specifically its oxidation, coupled with a respiratory pathway, is required for energy production to permit growth and maintain efficient virulence of a number of pathogenic bacteria during infection of animals. These would be expected to include the Campylobacter jejuni, a bacterium closely related to Helicobacter, as well as many enteric bacteria (Escherichia coli, Shigella and Yersinia species).
Nar1p, a conserved eukaryotic protein with similarity to Fe-only hydrogenases, functions in cytosolic iron-sulphur protein biogenesis
Authors: Balk J. , Pierik A.J. , Aguilar Netz D.J. , Mühlenhoff U. , Lill R.
Published: February 2005

The genome of the yeast Saccharomyces cerevisiae encodes the essential protein Nar1p that is conserved in virtually all eukaryotes and exhibits striking sequence similarity to bacterial iron-only hydrogenases. Previously, we have shown that Nar1p is an Fe-S protein and that assembly of its co-factors depends on the mitochondrial Fe-S cluster biosynthesis apparatus. Using functional studies in vivo, we demonstrated that Nar1p has an essential role in the maturation of cytosolic and nuclear, but not of mitochondrial, Fe-S proteins [Balk, Pierik, Aguilar Netz, Mühlenhoff and Lill (2004) EMBO J. 23, 2105–2115]. Here we provide further spectroscopic evidence that Nar1p possesses two Fe-S clusters. We also show that Nar1p is required for Fe-S cluster assembly on the P-loop NTPase Nbp35p, another newly identified component of the cytosolic Fe-S protein assembly machinery. These data suggest a complex biochemical pathway of extra-mitochondrial Fe-S protein biogenesis involving unique eukaryotic proteins.
[NiFe]-Hydrogenase maturation endopeptidase: structure and function
Authors: Theodoratou E. , Huber R. , Böck A.
Published: February 2005

Hydrogenase maturation endopeptidases catalyse the terminal step in the maturation of the large subunit of [NiFe]-hydrogenases. They remove a C-terminal extension from the precursor of the subunit, triggering a conformational switch that results in the bridging of the Fe and Ni atoms of the metal centre via the thiolate of a cysteine residue and in closure of the centre. This review summarizes what is known about the structure of the protein, its substrate specificity and its possible reaction mechanism.
The enigma of Paracoccus pantotrophus cytochrome cd1 activation
Authors: Zajicek R.S. , Ferguson S.J.
Published: February 2005

Paracoccus pantotrophus cytochrome cd1 nitrite reductase is isolated under aerobic conditions from anaerobically grown cells in an inactive form. This state requires reductive activation to make it catalytically competent for nitrite reduction. In this work, we discuss the methods of this reductive activation and its consequences for the cell.
The role of ResA in type II cytochrome c maturation
Authors: Crow A. , Le Brun N.E. , Oubrie A.
Published: February 2005

Numerous bacterial proteins involved in the nitrogen cycle, and other processes, require c-type haem as a cofactor. c-type cytochromes are formed by covalent attachment of haem to the conserved CXXCH motif. Here, we briefly review what is presently known about cytochrome c maturation in Bacillus subtilis with particular emphasis on the crystal structures of ResA.
Nitrate and nitrite transport in Escherichia coli
Authors: Jia W. , Cole J.A.
Published: February 2005

Two polytopic membrane proteins, NarK and NarU, are involved in nitrate and nitrite uptake and nitrite extrusion by Escherichia coli. A third polytopic membrane protein, NirC, functions only in nitrite transport. During exponential growth, the quantity of NarU in membrane fractions was <0.01% of the quantity of NarK. During the stationary phase of growth, the ratio of NarU to NarK increased to 0.1%. However, in the exponential phase of growth, the strain expressing only NarK transports and reduces nitrate and nitrite at a rate only slightly higher than that of the strain expressing only NarU, indicating that, in a NarK+ strain, the rate of nitrate reduction is not limited by the rate of nitrate transport. By measuring nitrate and nitrite transport abilities of strains expressing only narK or expressing both narK and nirC, we hypothesized that NarK might function as a primary nitrate–nitrite antiporter. After nitrate is imported by NarK and reduced to nitrite, some nitrite is expelled from the cell and then reimported for reduction to ammonia. Two highly conserved positively charged residues, Arg-87 and Arg-303 of NarU, were shown by site-directed mutagenesis to play a key role in anion transport. This result indicates that NarU might form a single channel for nitrate and nitrite transport.
Nitrogen assimilation and nitrogen control in cyanobacteria
Authors: Flores E. , Herrero A.
Published: February 2005

Nitrogen sources commonly used by cyanobacteria include ammonium, nitrate, nitrite, urea and atmospheric N2, and some cyanobacteria can also assimilate arginine or glutamine. ABC (ATP-binding cassette)-type permeases are involved in the uptake of nitrate/nitrite, urea and most amino acids, whereas secondary transporters take up ammonium and, in some strains, nitrate/nitrite. In cyanobacteria, nitrate and nitrite reductases are ferredoxin-dependent enzymes, arginine is catabolized by a combination of the urea cycle and arginase pathway, and urea is degraded by a Ni2+-dependent urease. These pathways provide ammonium that is incorporated into carbon skeletons through the glutamine synthetase–glutamate synthase cycle, in which 2-oxoglutarate is the final nitrogen acceptor. The expression of many nitrogen assimilation genes is subjected to regulation being activated by the nitrogen-control transcription factor NtcA, which is autoregulatory and whose activity appears to be influenced by 2-oxoglutarate and the signal transduction protein PII. In some filamentous cyanobacteria, N2 fixation takes place in specialized cells called heterocysts that differentiate from vegetative cells in a process strictly controlled by NtcA.
Microbial reduction of selenate and nitrate: common themes and variations
Authors: Watts C.A. , Ridley H. , Dridge E.J. , Leaver J.T. , Reilly A.J. , Richardson D.J. , Butler C.S.
Published: February 2005

A number of biochemically distinct systems have been characterized for the microbial reduction of the oxyanions, selenate (SeO42−) and nitrate (NO3−). Two classes of molybdenum-dependent nitrate reductase catalyse the respiratory-linked reduction of nitrate (NO3−) to nitrite (NO2−). The main respiratory nitrate reductase (NAR) is membrane-anchored, with its active site facing the cytoplasmic compartment. The other enzyme (NAP) is water-soluble and located in the periplasm. In recent years, our understanding of each of these enzyme systems has increased significantly. The crystal structures of both NAR and NAP have now been solved and they provide new insight into the structure, function and evolution of these respiratory complexes. In contrast, our understanding of microbial selenate (SeO42−) reduction and respiration is at an early stage; however, similarities to the nitrate reductase systems are emerging. This review will consider some of the common themes and variations between the different classes of nitrate and selenate reductases.
Detoxification of nitric oxide by the flavorubredoxin of Salmonella enterica serovar Typhimurium
Authors: Mills P.C. , Richardson D.J. , Hinton J.C.D. , Spiro S.
Published: February 2005

Salmonella possesses multiple enzymes that utilize NO as a substrate, and could therefore contribute to the organism's ability to resist nitrosative killing by macrophages. Flavorubredoxin is an oxygen-sensitive enzyme that reduces NO to nitrous oxide. The Salmonella enterica serovar Typhimurium norV gene encoding flavorubredoxin was disrupted and the NO sensitivity of the mutant was determined. The norV mutant showed a greater sensitivity to NO than wild-type S. Typhimurium, but did recover growth after a transient inhibition. The mutant phenotype suggests that multiple enzymes are employed by S. Typhimurium to detoxify NO under anaerobic conditions, one of which is flavorubredoxin.
Tracking nitrate reducers and denitrifiers in the environment
Authors: Philippot L.
Published: February 2005

The ability to respire nitrate when oxygen is limited has been described in taxonomically diverse microorganisms including members of the α-, β-, γ- and ε-proteobacteria, high and low GC Gram-positive bacteria and even Archaea. Respiratory nitrate reduction is the first step of the denitrification pathway, which is important since it is the main biological process responsible for the return of fixed nitrogen to the atmosphere, thus completing the nitrogen cycle. During the last decade, considerable knowledge has been accumulated on the biochemistry and genetics of the nitrate reductases. In this paper, we summarize the recent progress in molecular approaches for studying the ecology of the nitrate-reducing community in the environment.
Nitrate respiration in the actinomycete Streptomyces coelicolor
Authors: van Keulen G. , Alderson J. , White J. , Sawers R.G.
Published: February 2005

Streptomyces coelicolor is an obligate aerobic, filamentous soil-dwelling bacterium. Remarkably, the genome of S. coelicolor has three copies of the narGHJI operon that encodes respiratory nitrate reductase. This review summarizes our current views on the requirements for multiple nitrate reductases in S. coelicolor.
Transport regulation by the serum- and glucocorticoid-inducible kinase SGK1
Authors: Lang F. , Vallon V. , Grahammer F. , Palmada M. , Böhmer C.
Published: February 2005

The serum- and glucocorticoid-inducible kinase SGK1 is an ubiquitously expressed kinase with the ability to regulate a variety of transport systems. Recent observations point to a role of SGK1 in the regulation of diverse physiological functions such as epithelial transport and cardiac and neuronal excitability. At least partially through its effect on transport, SGK1 contributes to a number of pathophysiological conditions including metabolic syndrome and fibrosing disease.
Glucose sensing via the protein kinase A pathway in Schizosaccharomyces pombe
Authors: Hoffman C.S.
Published: February 2005

The fission yeast Schizosaccharomyces pombe primarily detects glucose via a cAMP-signalling pathway. Components of this pathway include the Git3 G-protein-coupled receptor and a heterotrimeric G-protein, from which the Gpa2 Gα subunit activates adenylate cyclase (Git2/Cyr1). Three additional proteins, Git1, Git7 and Git10 are required to generate a cAMP response even in a strain expressing an activated form of Gpa2, which is capable of bypassing the loss of the GPCR and Gβγ dimer. Therefore, Git1, Git7 and Git10 either act in a G-protein-independent manner or are required to stabilize or assemble a functional signalling complex. Although prior data suggested that the Cgs2 cAMP phosphodiesterase (PDE) does not regulate the cAMP response, we now have evidence that along with adenylate cyclase regulation, PDE activation is important for limiting the response to glucose. Finally, regulation of protein kinase A activation appears to involve both traditional post-translational regulation of the function of the components of the cAMP pathway and glucose-dependent transcriptional regulation of some of these cAMP pathway genes.
Development and use of fluorescent nanosensors for metabolite imaging in living cells
Authors: Fehr M. , Okumoto S. , Deuschle K. , Lager I. , Looger L.L. , Persson J. , Kozhukh L. , Lalonde S. , Frommer W.B.
Published: February 2005

To understand metabolic networks, fluxes and regulation, it is crucial to be able to determine the cellular and subcellular levels of metabolites. Methods such as PET and NMR imaging have provided us with the possibility of studying metabolic processes in living organisms. However, at present these technologies do not permit measuring at the subcellular level. The cameleon, a fluorescence resonance energy transfer (FRET)-based nanosensor uses the ability of the calcium-bound form of calmodulin to interact with calmodulin binding polypeptides to turn the corresponding dramatic conformational change into a change in resonance energy transfer between two fluorescent proteins attached to the fusion protein. The cameleon and its derivatives were successfully used to follow calcium changes in real time not only in isolated cells, but also in living organisms. To provide a set of tools for real-time measurements of metabolite levels with subcellular resolution, protein-based nanosensors for various metabolites were developed. The metabolite nanosensors consist of two variants of the green fluorescent protein fused to bacterial periplasmic binding proteins. Different from the cameleon, a conformational change in the binding protein is directly detected as a change in FRET efficiency. The prototypes are able to detect various carbohydrates such as ribose, glucose and maltose as purified proteins in vitro. The nanosensors can be expressed in yeast and in mammalian cell cultures and were used to determine carbohydrate homeostasis in living cells with subcellular resolution. One future goal is to expand the set of sensors to cover a wider spectrum of metabolites by using the natural spectrum of bacterial periplasmic binding proteins and by computational design of the binding pockets of the prototype sensors.
Glucose modulation of cell size in yeast
Authors: Vanoni M. , Rossi R.L. , Querin L. , Zinzalla V. , Alberghina L.
Published: February 2005

Saccharomyces cerevisiae cells grown in glucose have larger average size than cells grown in ethanol. Besides, yeast must reach a carbon source-modulated critical cell size in order to enter S phase at Start. This control is of outmost physiological relevance, since it allows us to coordinate cell growth with cell cycle progression and it is responsible for cell size homeostasis. The cell sizer mechanism requires the overcoming of two sequential thresholds, involving Cln3 and Far1, and Clb5,6 and Sic1, respectively. When both thresholds are non-functional, carbon source modulation of cell size at Start is completely abolished. Since inactivation of extracellular glucose sensing through deletion of either the GPR1 or the GPA2 gene causes a marked, but partial, reduction in the ability to modulate cell size and protein content at Start, it is proposed that both extracellular and intracellular glucose signalling is required for properly setting the cell sizer in glucose media.
CD36-dependent fatty acid uptake regulates expression of peroxisome proliferator activated receptors
Authors: Drover V.A. , Abumrad N.A.
Published: February 2005

CD36 is an important regulator of lipid metabolism in vivo due to its role in the facilitated uptake of long-chain FAs (fatty acids). CD36-deficient mice display reduced TAG (triacylglycerol) in muscle, but elevated hepatic TAG. Also, insulin sensitivity is enhanced peripherally, while it appears impaired in the liver [Goudriaan, Dahlmans, Teusink, Ouwens, Febbraio, Maassen, Romijn, Havekes, and Voshol (2003) J. Lipid. Res. 44, 2270–2277; and Hajri, Han, Bonen and Abumrad (2002) J. Clin. Invest. 109, 1381–1389]. Tissues such as muscle, which normally express high levels of CD36, shift to high glucose utilization in CD36 deficiency [Hajri, Han, Bonen and Abumrad (2002) J. Clin. Invest. 109, 1381–1389], so we hypothesized that this shift must involve adaptive changes in the PPAR (peroxisome-proliferator-activated receptor) transcription factors which regulate FA metabolism. To test this, we examined mRNA levels for the three PPAR isoforms in tissues of WT (wild-type) and CD36-deficient mice following the administration of saline, glucose or olive oil by intragastric gavage. Compared with WT mice, CD36-null mice had 5–10-fold increased PPAR mRNA in adipose tissue in the basal state, and did not exhibit diet-induced changes. Correlations between adipose PPAR mRNA abundance and plasma lipids were observed in WT mice, but not in CD36-null mice. The opposite was true for hepatic PPAR mRNA levels, which correlated with plasma FA, TAG and/or glucose only in CD36-null mice. No significant differences were observed in PPAR mRNA levels in the intestine, where CD36 does not impact on FA uptake. The data suggest that CD36 and the PPARs are components of the FA-sensing machinery to respond to changes in FA flux in a tissue-specific manner.
The calcium-sensing receptor as a nutrient sensor
Authors: Riccardi D. , Maldonado-Perez D.
Published: February 2005

Critical to cell fate in many cell types is the ability to sense and respond to acute changes in free ionized extracellular calcium concentration ([Ca2+]o). Such tight control is mediated by the activation of a protein known as the extracellular-calcium-sensing receptor (CaR). CaR belongs to the ‘family C’ of G-protein-coupled receptors and was the first G-protein-coupled receptor to be identified to have an inorganic cation, calcium, as its ligand. While calcium is the physiological agonist of the receptor, several other polyvalent cations and polycations can also modulate CaR function as do certain L-aromatic amino acids, polyamines, salinity and pH. This feature renders the CaR uniquely capable of generating cell- and tissue-specific responses, and of integrating inputs deriving from changes in the Ca2+o concentration with signals deriving from the local metabolic environment. Here we address the role of the CaR in physiology and disease, the range of CaR modulators and the potential roles of the CaR as a metabolic sensor in a variety of physiological (and pathological) scenarios.
Quantum-mechanical studies of NMR properties of solutes in liquid crystals: A new strategy to determine orientational order parameters
Authors: Pavanello Michele , Mennucci Benedetta , Ferrarini Alberta
Published: February 2005

We present a quantum-mechanical method to calculate the tensorial NMR magnetic properties of molecules in liquid crystals. The method exploits a density functional description for the solute and the integral equation formalism version of the polarizable continuum model to include the effects of the dielectric anisotropy of the solvent on the wave function of the solute molecule and on its response to an applied magnetic field. Taking into account the dependence of the calculated molecular tensors on the solute orientation, we have derived the necessary expressions to relate such tensors to the spectral observables. These equations are then used to determine order parameters by calculating the nuclear shieldings of various solutes in the nematic ZLI-1167. Comparisons with experimental data of the same parameters are finally presented.
Application of the constrained fluid λ-integration path to the calculation of high temperature Au(110) surface free energies
Authors: Grochola Gregory , Snook Ian K. , Russo Salvy P.
Published: February 2005

Recently a method termed constrained fluid λ-integration was proposed for calculating the free energy difference between bulk solid and liquid reference states via the construction of a reversible thermodynamic integration path; coupling the two states in question. The present work shows how the application of the constrained fluid λ-integration concept to solid/liquid slab simulation cells makes possible a generally applicable computer simulation methodology for calculating the free energy of any surface and/or surface defect structure, including surfaces requiring variations in surface atom or density number, such as the (1×5) Au(100) or (1×2) missing row Au(110) reconstructed surfaces or excess adatom/vacancy/step populated surfaces. We evaluate the methodology by calculating the free energy of various disordered high temperature Au(110) embedded atom method surfaces constrained to differing excess surface atom numbers [including those corresponding to the (1×2) missing row reconstructed surface] and obtained the interesting result that at 1000K (as distinct from lower temperatures) the free energy difference between these surfaces is reduced to zero; a result which is consistent with an expected order-disorder phase transition for the Au(110) surface at such high temperatures.