Noam Adir | Technion Israel Institute of Technology (original) (raw)

Papers by Noam Adir

Proceedings of the National Academy of Sciences, 2007

Using single-crystal x-ray diffraction, we found a formerly unknown twin form in calcite crystals... more Using single-crystal x-ray diffraction, we found a formerly unknown twin form in calcite crystals grown from solution to which a mollusc shell-derived 17-kDa protein, Caspartin, was added. This intracrystalline protein was extracted from the calcitic prisms of the Pinna nobilis shells. The observed twin form is characterized by the twinning plane of the (108)-type, which is in addition to the known four twin laws of calcite identified during 150 years of investigations. The established twin forms in calcite have twinning planes of the (001)-, (012)-, (104)-, and (018)-types. Our discovery provides additional evidence on the crucial role of biological macromolecules in biomineralization.

Acta Crystallographica Section A Foundations of Crystallography, 2005

PLOS ONE, 2015

Thylakoid membranes contain the redox active complexes catalyzing the light-dependent reactions o... more Thylakoid membranes contain the redox active complexes catalyzing the light-dependent reactions of photosynthesis in cyanobacteria, algae and plants. Crude thylakoid membranes or purified photosystems from different organisms have previously been utilized for generation of electrical power and/or fuels. Here we investigate the electron transferability from thylakoid preparations from plants or the cyanobacterium Synechocystis. We show that upon illumination, crude Synechocystis thylakoids can reduce cytochrome c. In addition, this crude preparation can transfer electrons to a graphite electrode, producing an unmediated photocurrent of 15 μA/cm2. Photocurrent could be obtained in the presence of the PSII inhibitor DCMU, indicating that the source of electrons is QA, the primary Photosystem II acceptor. In contrast, thylakoids purified from plants could not reduce cyt c, nor produced a photocurrent in the photocell in the presence of DCMU. The production of significant photocurrent (100 μA/cm2) from plant thylakoids required the addition of the soluble electron mediator DCBQ. Furthermore, we demonstrate that use of crude thylakoids from the D1-K238E mutant in Synechocystis resulted in improved electron transferability, increasing the direct photocurrent to 35 μA/cm2. Applying the analogous mutation to tobacco plants did not achieve an equivalent effect. While electron abstraction from crude thylakoids of cyanobacteria or plants is feasible, we conclude that the site of the abstraction of the electrons from the thylakoids, the architecture of the thylakoid preparations influence the site of the electron abstraction, as well as the transfer pathway to the electrode. This dictates the use of different strategies for production of sustainable electrical current from photosynthetic thylakoid membranes of cyanobacteria or higher plants.

Journal of structural biology, 2006

We have performed precise structural measurements on five different calcitic seashells by high-re... more We have performed precise structural measurements on five different calcitic seashells by high-resolution X-ray powder diffraction on a synchrotron beam line and by laboratory single crystal X-ray diffraction. The unit cell parameters a and c of biogenic calcite were found to be systematically larger than those measured in the non-biogenic calcite. The maximum lattice distortion (about 2.10(-3)) was detected along the c-axis. Under heat treatment above 200 degrees C, a pronounced lattice relaxation was observed, which allowed us to conclude that anisotropic lattice swelling in biogenic calcite is induced by organic macromolecules incorporated within the single crystal calcitic prisms during biomineralization. This conclusion is supported by the results of crystallization experiments in the presence of specific protein extracted from one of the shells.

Photosynthesis research, 2000

We have recently reported the crystallization of the reaction center of Photosystem II in the pre... more We have recently reported the crystallization of the reaction center of Photosystem II in the presence of detergent mixtures [Adir N (1999) Acta Crystallogr D Biol Crystallogr D55: 891-894]. We have used high performance liquid chromatography, dynamic light scattering, native gel electrophoresis and thermoluminescence measurements to characterize the interaction between these detergent mixtures and RC II, to try and understand their role in the crystallization process. Size exclusion HPLC and dynamic light scattering confirmed that the isolated RC II used for crystallization was exclusively monomeric. Dynamic light scattering measurements show that the detergent mixtures formed single micelles within a limited range of hydrodynamic radii. Both size exclusion HPLC and dynamic light scattering were used to follow the interaction between the detergent mixtures and monomeric RC II. These techniques revealed a decrease in the detergent mixture treated RC II particle size (with respect wi...

International review of cytology, 2003

Initiation of meiosis in Saccharomyces cerevisiae is regulated by mating type and nutritional con... more Initiation of meiosis in Saccharomyces cerevisiae is regulated by mating type and nutritional conditions that restrict meiosis to diploid cells grown under starvation conditions. Specifically, meiosis occurs in MATa/MATalpha cells shifted to nitrogen depletion media in the absence of glucose and the presence of a nonfermentable carbon source. These conditions lead to the expression and activation of Ime 1, the master regulator of meiosis. IME1 encodes a transcriptional activator recruited to promoters of early meiosis-specific genes by association with the DNA-binding protein, Ume6. Under vegetative growth conditions these genes are silent due to recruitment of the Sin3/Rpd3 histone deacetylase and Isw2 chromatin remodeling complexes by Ume6. Transcription of these meiotic genes occurs following histone acetylation by Gcn5. Expression of the early genes promote entry into the meiotic cycle, as they include genes required for premeiotic DNA synthesis, synapsis of homologous chromosom...

The Journal of biological chemistry, Jan 11, 2003

A novel fraction of c-phycocyanin from the thermophilic cyanobacterium Thermosynechcoccus vulcanu... more A novel fraction of c-phycocyanin from the thermophilic cyanobacterium Thermosynechcoccus vulcanus, with an absorption maxima blue-shifted to 612 nm (PC612), has been purified from allophycocyanin and crystallized. The crystals belong to the P63 space group with cell dimensions of 153 A x 153 A x 59 A with a single (alphabeta) monomer in the asymmetric unit, resulting in a solvent content of 65%, and diffract to 2.7 A. The PC612 crystal structure has been determined by molecular replacement and refined to a crystallographic R-factor of 20.9% (Rfree = 27.8%). The crystal packing in this form shows that the PC612 form of phycocyanin does not associate into hexamers and that its association with adjacent trimers in the unit cell is very different from that found in a previously determined structure of the normal form of T. vulcanus phycocyanin, which absorbs at 620 nm. Analysis of the PC612 structure shows that the alpha subunits, which typically form the interface between two trimers ...

Normophosphatemic familial tumoral calcinosis (NFTC) is an autosomal recessive disorder character... more Normophosphatemic familial tumoral calcinosis (NFTC) is an autosomal recessive disorder characterized by calcium deposition in skin and mucosae and associated with unremitting pain and life-threatening skin infections. A homozygous missense mutation (p.K1495E), resulting in SAMD9 protein degradation, was recently shown to cause NFTC in five families of Jewish-Yemenite origin. In this study, we evaluated another Jewish-Yemenite NFTC kindred. All patients were compound heterozygous for two mutations in SAMD9: K1495E and a previously unreported nonsense mutation, R344X, predicted to result in a markedly truncated molecule. Screening of unaffected population-matched controls revealed heterozygosity for K1495E and R344X only in individuals of Jewish-Yemenite ancestry, but not in more than 700 control samples of other origins, including 93 non-Jewish Yemenite. These data may be suggestive of positive selection, considering the rarity of NFTC and the small size of the Jewish-Yemenite population; alternatively, they may reflect genetic drift or the effect of a population-specific modifier trait. Calcifications in NFTC generally develop over areas subjected to repeated trauma and are associated with marked inflammatory manifestations, indicating that SAMD9 may play a role in the inflammatory response to tissue injury. We therefore assessed the effect of cellular stress and tumor necrosis factor-alpha (TNF-alpha), a potent pro-inflammatory cytokine, on SAMD9 gene expression. Whereas exogenous hydrogen peroxide and heat shock did not affect SAMD9 transcription, osmotic shock was found to markedly upregulate SAMD9 expression. In addition, incubation of endothelial cells with TNF-alpha caused a dose-related, p38-dependant increase in SAMD9 expression. These data link NFTC and SAMD9 to the TNF-alpha signaling pathway, suggesting a role for this system in the regulation of extra-osseous calcification.

Journal of Biological Chemistry, 2000

Fibroblast growth factors (FGFs) mediate a multitude of physiological and pathological processes ... more Fibroblast growth factors (FGFs) mediate a multitude of physiological and pathological processes by activat- ing a family of tyrosine kinase receptors (FGFRs). Each FGFR binds to a unique subset of FGFs and ligand bind- ing specificity is essential in regulating FGF activity. FGF-7 recognizes one FGFR isoform known as the FGFR2 IIIb isoform or keratinocyte growth factor re- ceptor (KGFR),

American Journal of Human Genetics, 2008

Journal of Molecular Biology, 2005

The MntC protein is the periplasmic solute-binding protein component of the high-affinity mangane... more The MntC protein is the periplasmic solute-binding protein component of the high-affinity manganese ATP-binding cassette-type transport system in the cyanobacterium Synechocytis PCC sp. 6803. We have determined the structure of recombinant MntC at 2.9 Aresolution by X-ray crystallography using a combination of multi-wavelength anomalous diffraction and molecular replacement. The presence of Mn2C in the metal ion-binding

Photochem. Photobiol. Sci., 2015

To improve the energy conversion efficiency of solar organic cells, the clue may lie in the devel... more To improve the energy conversion efficiency of solar organic cells, the clue may lie in the development of devices inspired by an efficient light harvesting mechanism of some aquatic photosynthetic microorganisms that are adapted to low light intensity. Consequently, we investigated the pathways of excitation energy transfer (EET) from successive light harvesting pigments to the low energy level inside the phycobiliprotein antenna system of Acaryochloris marina, a cyanobacterium, using a time resolved absorption difference spectroscopy with a resolution time of 200 fs. The objective was to understand the actual biochemical process and pathways that determine the EET mechanism. Anisotropy of the EET pathway was calculated from the absorption change trace in order to determine the contribution of excitonic coupling. The results reveal a new electron energy relaxation pathway of 14 ps inside the phycocyanin component, which runs from phycocyanin to the terminal emitter. The bleaching of the 660 nm band suggests a broader absorption of the terminal emitter between 660 nm and 675 nm. Further, there are trimer depolarization kinetics of 450 fs and 500 fs in high and low ionic strength, respectively, which arise from the relaxation of the β84 and α84 in adjacent monomers of phycocyanin. Under conditions of low ionic strength buffer solution, the evolution of the kinetic amplitude during the depolarization of the trimer is suggestive of trimer conservation within the phycocyanin hexamer. The anisotropy values were 0.38 and 0.40 in high and in low ionic strength, respectively, indicating that there is no excitonic delocalization in the high energy level of phycocyanin hexamers.

Journal of Investigative Dermatology, 2014

Journal of Biological Chemistry, 2003

A novel fraction of c-phycocyanin from the thermo- philic cyanobacterium Thermosynechcoccus vulca... more A novel fraction of c-phycocyanin from the thermo- philic cyanobacterium Thermosynechcoccus vulcanus, with an absorption maxima blue-shifted to 612 nm (PC612), has been purified from allophycocyanin and crystallized. The crystals belong to the P63 space group with cell dimensions of 153 Å 153 Å 59 Å with a single () monomer in the asymmetric unit, resulting in a solvent content

Advances in Photosynthesis and Respiration, 2005

Photoinhibition is a state of physiological stress that occurs in all oxygen evolving photosynthe... more Photoinhibition is a state of physiological stress that occurs in all oxygen evolving photosynthetic organisms exposed to light. The primary damage occurs within the reaction center of Photosystem II (PS II). While irreversible photoinduced damage to PS II occurs at all light intensities, the efficiency of photosynthetic electron transfer decreases markedly only when the rate of damage exceeds the rate of its repair, which requires de novo PS II protein synthesis. Photoinhibition has been studied for over a century using a large variety of biochemical, biophysical and genetic methodologies. The discovery of the light induced turnover of a protein, encoded by the plastid psbA gene (the D1 protein), later identified as one of the photochemical reaction center II proteins, has led to the elucidation of the underlying mechanism of photoinhibition and to a deeper understanding of the PS II 'life cycle.' Abbreviations: bRC -bacterial reaction center; Chl -chlorophyll; DCIP -dichlorophenol-indophenol; DCMU -3-(3,4, dichlorophenyl) 1,1-dimethylurea; EMBO -European Molecular Biology Organization; kDa -kilo Dalton, apparent; LMW -low molecular weight proteins of PS II; NASA -National Aeronautics Space Agency; pD1 precursor -carboxy-terminal unprocessed D1 protein; Pheo -the primary PS II electron acceptor; Pheo .−.pheophytin anion radical; PI -photoinhibition; PS I, PS II -photosystem I and II respectively; Q A -Q B -Q A .− -Q B .− -the primary and secondary electron acceptors quinones of PS II in the oxidized and semiquinone radical form, respectively; RCII -photosystem II reaction center; S 2 -S 3 -the oxidation states of the manganese cluster of PS II donor side that has lost one or two electrons, respectively; Y Z , Y Z .− -the tyrosine 161 of the D1 protein in the neutral and anion radical form, respectively Participants at the EMBO (European Molecular Biology Organization) Workshop on Photosystem II Dynamics held in Jerusalem, Israel, 1987. First row (left to right): Aviah Zilberstein, Franklin Callahan, Anastasios Melis, the late Philip Thornber, Itzhak Ohad and Marvin Edelman (organizers); Shmuel Malkin and Mordechai Avron are the last two in this row. Second row, (left to right): (last). Third row (left to right): Aaron Kaplan (2nd), Joseph Hirschberg (3rd), Bruce M. Greenberg (6th, behind and on the left of N. Murata), Paul Mathis (7th, behind O Canaani), Gunnar Oquist (wearing glasses), Jonathan Gressel (behind N. Adir); John Bennett is behind and between S. Golden and E. Tobin; Achim Trebst and Gernot Renger (last two). Last row (left to right): Victor Gaba (behind and to the left of B. Greenberg), Wim Vermaas (beard and glasses), Hartmut Michel (behind C. Critchley), Judith St. John (right to J. Gressel), John Gray (behind S. Golden), Bertil Andersson and Jim Barber (last). Photo provided by Itzhak Ohad.

The light-induced inactivation of the photochemical reaction center II (RCII) of oxygenic chlorop... more The light-induced inactivation of the photochemical reaction center II (RCII) of oxygenic chloroplasts (pho- toinhibition) was investigated in cells and isolated thy- lakoids of the green alga Chlamydomonas reinhardtii. The process is resolved into a reversible conforma- tional change followed by an irreversible modification of RCII Dl protein. The light-induced changes in viuo persisted in isolated thylakoids. The first step

THE PLANT CELL ONLINE, 2001

Divergent architecture of shoot models in flowering plants reflects the pattern of production of ... more Divergent architecture of shoot models in flowering plants reflects the pattern of production of vegetative and reproductive organs from the apical meristem. The SELF-PRUNING ( SP ) gene of tomato is a member of a novel CETS family of regulatory genes ( CEN , TFL1 , and FT ) that controls this process. We have identified and describe here several proteins that interact with SP (SIPs) and with its homologs from other species: a NIMA-like kinase (SPAK), a bZIP factor, a novel 10-kD protein, and 14-3-3 isoforms. SPAK, by analogy with Raf1, has two potential binding sites for 14-3-3 proteins, one of which is shared with SP. Surprisingly, overexpression of 14-3-3 proteins partially ameliorates the effect of the sp mutation. Analysis of the binding potential of chosen mutant SP variants, in relation to conformational features known to be conserved in this new family of regulatory proteins, suggests that associations with other proteins are required for the biological function of SP and that ligand binding and protein-protein association domains of SP may be separated. We suggest that CETS genes encode a family of modulator proteins with the potential to interact with a variety of signaling proteins in a manner analogous to that of 14-3-3 proteins.

The ISME Journal, 2007

Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photo... more Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photosynthetic productivity in the open ocean. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages that infect these cyanobacteria suggests new paradigms for the regulation, function and evolution of photosynthesis in the vast pelagic ecosystem. Reports on the prevalence and expression of phage photosynthesis genes, and evolutionary data showing a potential recombination of phage and host genes, suggest a model in which phage photosynthesis genes help support photosynthetic activity in their hosts during the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psbA genes in surface water along the global ocean sampling transect are of phage origin, and that the phage genes are undergoing an independent selection for distinct D1 proteins. Furthermore, we show that different viral psbA genes are expressed in the environment.

Proceedings of the National Academy of Sciences, 2004

Relating thermodynamic parameters to structural and biochemical data allows a better understandin... more Relating thermodynamic parameters to structural and biochemical data allows a better understanding of substrate binding and its contribution to catalysis. The analysis of the binding of carbohydrates to proteins or enzymes is a special challenge because of the multiple interactions and forces involved. Isothermal titration calorimetry (ITC) provides a direct measure of binding enthalpy (⌬H a) and allows the determination of the binding constant (free energy), entropy, and stoichiometry. In this study, we used ITC to elucidate the binding thermodynamics of xylosaccharides for two xylanases of family 10 isolated from Geobacillus stearothermophilus T-6. The change in the heat capacity of binding (⌬C p ‫؍‬ ⌬H͞⌬T) for xylosaccharides differing in one sugar unit was determined by using ITC measurements at different temperatures. Because hydrophobic stacking interactions are associated with negative ⌬C p, the data allow us to predict the substrate binding preference in the binding subsites based on the crystal structure of the enzyme. The proposed positional binding preference was consistent with mutants lacking aromatic binding residues at different subsites and was also supported by tryptophan fluorescence analysis.