The Mechanism of Amino Acid Activation: the Work of Mahlon Hoagland

Enzymatic Carboxyl Activation of Amino Acids(Hoagland, M. B., Keller, E. B., and Zamecnik, P. C. (1956) J. Biol. Chem. 218, 345–358)Mahlon Bush Hoagland was born in Boston, Massachusetts in 1921. He attended Harvard University and graduated in 1943. Knowing that he wanted to be a surgeon, Hoagland then enrolled at Harvard Medical School. However, he was diagnosed with tuberculosis, and his poor health prevented him from becoming a surgeon when he received his M.D. in 1948. Instead, he accepted a research position at Massachusetts General Hospital. In 1953, he became a postdoctoral fellow with Journal of Biological Chemistry (JBC) Classic author Fritz Lipmann (1) at Huntington Laboratories (also at Massachusetts General Hospital), and a year later, he moved to an adjoining laboratory to work on protein synthesis with JBC Classic author Paul Zamecnik (2).Open in a separate windowMahlon HoaglandInspired by Lipmann''s insights into acyl activation mechanisms, Hoagland used a cell-free system created by Zamecnik that carried out net peptide bond formation using ¹⁴C-amino acids (3) to uncover the mechanism of amino acid activation. As reported in the JBC Classic reprinted here, he isolated an enzyme fraction that, in the presence of ATP and amino acids, catalyzed the first step in protein synthesis: the formation of aminoacyl adenylates or activated amino acids. Using data from analysis of this fraction, Hoagland presented a scheme for amino acid activation in his Classic paper.A few years later, Zamecnik and Hoagland discovered a molecule that is essential for protein synthesis: tRNA. This discovery is the subject of the Zamecnik Classic (2).After the discovery of tRNA, Hoagland spent the next year (1957–1958) at Cambridge University''s Cavendish laboratories working with Francis Crick. During that year he traveled to France to visit the Institute Pasteur in Paris. Experiments begun at the Institute would, by 1960, lead to the discovery of messenger RNA (mRNA).When he returned to the United States, Hoagland was appointed associate professor of microbiology at Harvard Medical School. He remained there until 1967 when he accepted a position as professor at Dartmouth Medical School. In 1970, he became the director of the Worcester Foundation for Experimental Biology, a Massachusetts research institute founded by his father. He retired in 1985 and currently lives in Thetford, Vermont.Hoagland has received several awards and honors in recognition of his contributions to science. These include the 1976 Franklin Medal, the 1982 and 1996 Book Awards from the American Medical Writers Association, and membership in the American Academy of Arts and Sciences and the National Academy of Sciences.     

Yasutomi Nishizuka's Discovery of Protein Kinase C

Studies on a Cyclic Nucleotide-independent Protein Kinase and Its Proenzyme in Mammalian Tissues. I. Purification and Characterization of an Active Enzyme from Bovine Cerebellum (Takai, Y., Kishimoto, A., Inoue, M., and Nishizuka, Y. (1977) J. Biol. Chem. 252, 7603–7609)Direct Activation of Calcium-activated, Phospholipid-dependent Protein Kinase by Tumor-promoting Phorbol Esters (Castagna, M., Takai, Y., Kaibuchi, K., Sano, K., Kikkawa, U., and Nishizuka, Y. (1982) J. Biol. Chem. 257, 7847–7851)Yasutomi Nishizuka (1932–2004) was born in Ashiya-city, Japan. He attended Kyoto University and obtained his M.D. in 1957 and his Ph.D. in 1962, working with Journal of Biological Chemistry (JBC) Classic author Osamu Hayaishi (1). He then spent a year as a postdoctoral fellow at Rockefeller University with Fritz Lipmann (also featured in a JBC Classic (2)) before returning to Kyoto University to resume work with Hayaishi. During this time, Nishizuka studied the biosynthesis of nicotinamide adenine dinucleotide (NAD), the involvement of GTP in ribosomal protein translation, and ADP-ribosylation by diphtheria toxin.Open in a separate windowYasutomi NishizukaIn 1969, Nishizuka accepted the position of full professor and head of the department of biochemistry at the Kobe University School of Medicine. There, Nishizuka became interested in the role of protein kinases in the regulation of cell functions. This led to his discovery of a novel protein kinase, which he published in the first paper reprinted here as the JBC Classic. As Nishizuka reported in that paper, he and his colleagues partially purified the kinase from bovine cerebellum. They found that the enzyme was capable of phosphorylating histone and protamine and that it probably was produced from its precursor protein by a limited proteolytic reaction. The detailed properties of the proenzyme and its conversion to active protein kinase were reported in a subsequent JBC paper (3). Nishizuka named this new enzyme “protein kinase C (PKC).”A paper published by Nishizuka two years later in the JBC (4) showed that PKC was activated without limited proteolysis by a membrane-associated factor in the presence of a low concentration of Ca²⁺. In 1980, he published another paper in the JBC (5) showing that the membrane-associated factor was diacylglycerol, which suggested that the lipid could be a novel second messenger generated by receptor-stimulated phosphoinositide hydrolysis. Nishizuka validated this idea by showing that treating platelets with a combination of a Ca²⁺ ionophore and membrane-permeant short chain diacylglycerol mimicked stimulation by the aggregating agent thrombin (6). This discovery was a major advance in the understanding of cell signaling.Nishizuka and his colleagues then discovered that PKC is the biological target of tumor-promoting phorbol esters. At that time, it was well known that croton oil augmented carcinogenesis when it was applied at weekly intervals to the skin of mice in conjunction with a very dilute solution of benz[a]pyrene in acetone. The oil contained phorbol ester, a powerful tumor promoter, and caused a wide variety of cellular responses that were similar to those seen with hormones. Nishizuka speculated that the phorbol ester was producing diacylglycerol to activate PKC. However, upon further investigation, he realized that the phorbol ester contained a diacylglycerol-like structure and thus might activate PKC directly. In a series of experiments, published in the second JBC Classic reprinted here, Nishizuka was able to show that the phorbol ester activated PKC directly. This discovery showed that PKC was important for cell proliferation and cancer. It also established the use of phorbol esters as crucial tools for the manipulation of PKC activation in intact cells, eventually allowing the elucidation of the wide range of cellular processes regulated by this enzyme.This research laid the foundation for an enormous number of studies on the complex PKC family, many of them from Nishizuka''s group.In 1975, Nishizuka became president of the University of Kobe, a position that he held until 2001. He received numerous awards and honors for his research, including the Gairdner Foundation International Award (1988), the Alfred P. Sloan Jr. Prize (1988), the Japan Order of Culture (1988), the Albert Lasker Basic Medical Research Award (1989), the Kyoto Prize (1992), the Wolf Prize in Medicine (1995), the Jimenez Diaz Award (1995), and the Schering Prize (1995). He also served as a foreign member and honorary fellow of various academies, including the National Academies of Science, the Royal Society, l''Academie des Sciences, die Deutsche Akademie der Naturforscher Leopoldina, le Real Academia de Ciencias, the Asiatic Society, and the Japan Academy.¹     

Cryogenic and Laser Photoexcitation Studies Identify Multiple Roles for Active Site Residues in the Light-driven Enzyme Protochlorophyllide Oxidoreductase

The light-activated enzyme NADPH-protochlorophyllide oxidoreductase (POR) catalyzes the trans addition of hydrogen across the C-17–C-18 double bond of protochlorophyllide (Pchlide), a key step in chlorophyll biosynthesis. Similar to other members of the short chain alcohol dehydrogenase/reductase family of enzymes, POR contains a conserved Tyr and Lys residue in the enzyme active site, which are implicated in a proposed reaction mechanism involving proton transfer from the Tyr hydoxyl group to Pchlide. We have analyzed a number of POR variant enzymes altered in these conserved residues using a combination of steady-state turnover, laser photoexcitation studies, and low temperature fluorescence spectroscopy. None of the mutations completely abolished catalytic activity. We demonstrate their importance to catalysis by defining multiple roles in the overall reaction pathway. Mutation of either residue impairs formation of the ground state ternary enzyme-substrate complex, pointing to a key role in substrate binding. By analyzing the most active variant (Y193F), we show that Tyr-193 participates in proton transfer to Pchlide and stabilizes the Pchlide excited state, enabling hydride transfer from NADPH to Pchilde. Thus, in addition to confirming the probable identity of the proton donor in Pchlide reduction, our work defines additional roles for these residues in facilitating hydride transfer through stabilization of the ground and excited states of the ternary enzyme complex.The light-driven enzyme protochlorophyllide oxidoreductase (POR)³ (EC 1.3.1.33) catalyzes the trans addition of hydrogen across the C-17–C-18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide) (see Fig. 1A) (1). This reaction is a key step in the synthesis of chlorophyll and leads to profound changes in the morphological development of photosynthetic organisms through modification and reorganization of plastid membranes (2, 3). In addition to POR, nonflowering land plants, algae, and cyanobacteria possess a light-independent Pchlide reductase, which consists of three separate subunits and allows these organisms to produce chlorophyllide in the dark (4). Together with DNA photolyase (5), POR is one of only two enzymes studied so far that exhibit a direct, natural requirement for light and because mixing strategies are no longer required to initiate the reaction, it is possible to trigger catalysis on very fast time scales and at cryogenic temperatures. Consequently, POR has proven to be an excellent model system for studying the role of protein dynamics in driving enzyme catalysis (1).Open in a separate windowFIGURE 1.The light-driven reduction of Pchlide. A, the trans addition of hydrogen across the C-17–C-18 double bond of Pchlide to form chlorophyllide (Chlide) in the chlorophyll biosynthesis pathway is catalyzed by the light-driven enzyme POR. B, shown is a three-dimensional model of the POR-catalyzed reaction based on the structural homology model of POR (26) and the proposed mechanism of hydride and proton transfer (8). Upon activation by light, a hydride is transferred to the C-17 position of Pchlide from the pro-S face of NADPH (shown in yellow), and the proton at the C-18 position is derived from Tyr-193 (shown in cyan). The conserved Lys-197 residue (shown in magenta) is proposed to decrease the pK_a of the Tyr to facilitate the proton transfer reaction.In the POR catalytic cycle, a ternary enzyme-NADPH-Pchlide complex is formed. Following light activation of this complex, a hydride ion is transferred from the pro-S face of NADPH to the C-17 atom of Pchlide (6, 7). The valence of the C-18 atom is satisfied by proton transfer, which is suggested to originate from an active site tyrosine residue (8). The catalytic cycle of POR has been analyzed through the trapping of intermediates at cryogenic temperatures. Following the initial light-driven reaction (9), there are a series of subsequent (slower) dark reactions (10, 11). The light-driven step involves hydride transfer from NADPH to form a charge transfer complex, which then facilitates protonation of the pigment intermediate during the first of the “dark” reactions (12). Moreover, through laser activation of catalysis, we have shown that both of these H-transfer reactions proceed by quantum mechanical tunneling coupled to motions in the enzyme-substrate complex on the submicrosecond time scale (13). The final dark steps in the reaction cycle involve a series of ordered product release and cofactor binding steps linked to conformational changes in the enzyme (10, 11, 14). Ultrafast measurements have uncovered spectral changes on the picosecond timescale that are likely to represent conformational changes prior to Pchlide reduction (15–19). Previous excitation of POR with a laser pulse leads to a more efficient conformation of the active site and an enhancement in the catalytic efficiency of the enzyme (18).POR is a member of a large family of enzymes known as short chain dehydrogenases/reductases (SDR). These are single domain NAD(P)⁺- or NAD(P)H-binding oxidoreductases that exist generally as dimers or tetramers (20). A number of SDR enzymes (e.g. carbonyl reductase, alcohol dehydrogenase, and dihydrofolate reductase) have been good model systems for studying the dynamics linked to enzyme catalysis (21–23). This family of enzymes has been amenable to studies of biological H-tunneling (24–26), and in particular the unique light-activated properties of POR make it an excellent system for studying mechanisms of H-transfer and dynamics in this family of enzymes.Structures of several SDR family members are available, and these have enabled the construction of a homology model of POR from Synechocystis (27). This model comprises a central parallel β-sheet of seven β-strands, surrounded by nine α-helices, with an additional unique 33-residue insertion between the fifth and sixth β-sheets. The NADPH cofactor binds within the N-terminal region of the enzyme, which contains a common nucleotide-binding motif with a tight βαβ fold, termed the Rossmann fold (27). Importantly, a Tyr and a Lys residue are both absolutely conserved throughout all members of the SDR family and are critical for catalysis in a number of enzymes (28–31). A common mechanism has been proposed for this group of enzymes, involving a Tyr-X-X-X-Lys motif. The Lys residue in this motif is presumed to facilitate proton donation from the Tyr hydroxyl group to substrate through favorable perturbation of the hydroxyl group pK_a (8, 31). In POR, multiple turnover assays have also indicated that these Tyr and Lys residues are important for activity (8, 32, 33), leading to a proposed mechanism that involves proton transfer from the conserved Tyr residue to the C-18 position of Pchlide (8) (Fig. 1B). The close proximity of the Lys residue is thought to allow the deprotonation step to occur at physiological pH by lowering the apparent pK_a of the phenolic group of the Tyr (8). However, confirmation of the exact role of these conserved residues has been compromised by the limited levels of activity observed in previous studies of the variant enzymes (8, 32, 33), and a detailed evaluation of the role of the active site Tyr and Lys residues on the chemical steps (i.e. hydride and proton transfer) has not been reported. We address this deficiency in the current work by analyzing a number of site-specific mutant forms altered at Tyr-193 and Lys-197 in a thermophilic POR from Thermosynechococcus elongatus BP-1. This was achieved using steady-state (multiple turnover) and laser photoexcitation (single turnover) methods and by trapping transient reaction intermediates by fluorescence spectroscopy performed at cryogenic temperatures.     

Regulation of Translation by the Redox State of Elongation Factor G in the Cyanobacterium Synechocystis sp. PCC 6803

Elongation factor G (EF-G), a key protein in translational elongation, was identified as a primary target of inactivation by reactive oxygen species within the translational machinery of the cyanobacterium Synechocystis sp. PCC 6803 (Kojima, K., Oshita, M., Nanjo, Y., Kasai, K., Tozawa, Y., Hayashi, H., and Nishiyama, Y. (2007) Mol. Microbiol. 65, 936–947). In the present study, we found that inactivation of EF-G (Slr1463) by H₂O₂ was attributable to the oxidation of two specific cysteine residues and formation of a disulfide bond. Substitution of these cysteine residues by serine residues protected EF-G from inactivation by H₂O₂ and allowed the EF-G to mediate translation in a translation system in vitro that had been prepared from Synechocystis. The disulfide bond in oxidized EF-G was reduced by thioredoxin, and the resultant reduced form of EF-G regained the activity to mediate translation in vitro. Western blotting analysis showed that levels of the oxidized form of EF-G increased under strong light in a mutant that lacked NADPH-thioredoxin reductase, indicating that EF-G is reduced by thioredoxin in vivo. These observations suggest that the translational machinery is regulated by the redox state of EF-G, which is oxidized by reactive oxygen species and reduced by thioredoxin, a transmitter of reducing signals generated by the photosynthetic transport of electrons.Reactive oxygen species (ROS)² are produced as inevitable by-products of the light-driven reactions of photosynthesis. The superoxide radical, hydrogen peroxide (H₂O₂), and the hydroxyl radical are produced as a result of the photosynthetic transport of electrons, whereas singlet state oxygen (singlet oxygen) is produced by the transfer of excitation energy (1). Exposure of the photosynthetic machinery to strong light promotes the production of ROS and gives rise to oxidative stress (1).Strong light rapidly inactivates photosystem II (PSII). This phenomenon is referred to as photoinhibition (2–4), and it occurs when the rate of photodamage to PSII exceeds the rate of the repair of photodamaged PSII (5). The actions of ROS in the photoinhibition of PSII have been studied extensively, and several mechanisms for photoinhibition have been proposed (5). Recent studies of the effects of ROS on photodamage and repair have revealed that ROS act primarily by inhibiting the repair of photodamaged PSII and not by damaging PSII directly (5–9). Such studies have also shown that photodamage to PSII is an exclusively light-dependent event; photodamage is initiated by disruption of the manganese cluster of the oxygen-evolving complex upon absorption of light, in particular UV and blue light, with subsequent damage to the reaction center upon absorption of visible light by chlorophylls (10–12).Inhibition of the repair of PSII has been attributed to the suppression, by ROS, of the synthesis de novo of proteins that are required for the repair of PSII, such as the D1 protein, which forms a heterodimer with the D2 protein in the reaction center, in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis) (6, 7), in Chlamydomonas (13), and in plants (14, 15). Analysis of polysomes in Synechocystis has demonstrated that ROS inhibit the synthesis de novo of proteins primarily at the elongation step of translation, suggesting that some proteins involved in translational elongation might be the targets of inactivation by ROS (6, 7).A translation system in vitro was successfully prepared from Synechocystis, and biochemical investigations using this translation system have revealed that elongation factor G (EF-G), a GTP-binding protein that catalyzes the translocation of peptidyl-tRNA (16), is a primary target of inactivation by ROS (17). EF-G is reversibly inactivated by ROS in a redox-dependent manner; it is inactive in the oxidized form and active in the reduced form (17). Moreover, it has been proposed that changes in the activity of EF-G might depend on and be regulated by the redox states of cysteine residues within EF-G (17). However, the specific cysteine residues within EF-G that might be the targets of ROS and might be responsible for redox regulation remain to be determined.In the present study, we investigated the redox state of Slr1463, the EF-G that is phylogenetically closest to chloroplast EF-G among three homologs of EF-G in Synechocystis (17). We determined that two specific cysteine residues in the EF-G of Synechocystis were targets of oxidation by ROS. The resultant disulfide bond between the two cysteine residues was efficiently reduced by thioredoxin. In addition, we observed that EF-G was reduced by thioredoxin in vivo. Our findings revealed the mechanism of the ROS-induced inactivation of EF-G and suggested a mechanism for the redox regulation of translation by electrons generated during photosynthesis.     

The Discovery and Characterization of Molybdopterin: the Work of K. V. Rajagopalan

Hepatic Sulfite Oxidase. A Functional Role for Molybdenum(Cohen, H. J., Fridovich, I., and Rajagopalan, K. V. (1971) J. Biol. Chem. 246, 374–382)Characterization of the Molybdenum Cofactor of Sulfite Oxidase, Xanthine, Oxidase, and Nitrate Reductase. Identification of a Pteridine as a Structural Component(Johnson, J. L., Hainline, B. E., and Rajagopalan, K. V. (1980) J. Biol. Chem. 255, 1783–1786)The Structure of the Molybdenum Cofactor. Characterization of Di(carboxamidomethyl)molybdopterin from Sulfite Oxidase and Xanthine Oxidase(Kramer, S. P., Johnson, J. L., Ribeiro, A. A., Millington, D. S., and Rajagopalan, K. V. (1987) J. Biol. Chem. 262, 16357–16363)K. V. Rajagopalan was born in 1930 in Udupi, a town in South India. He attended Presidency College in Madras (now called Chennai) and graduated with a B.Sc. in Chemistry in 1951. He then enrolled at the University of Madras to do graduate work in the biochemistry department and earned his Ph.D. in 1957. After graduating, Rajagopalan served as an assistant research officer at the Indian Council of Medical Research. Two years later, he started a postdoctoral fellowship in the biochemistry department at Duke University, working with Journal of Biological Chemistry (JBC) Classic author Philip Handler (1).Open in a separate windowK. V. RajagopalanRajagopalan''s initial research project at Duke, carried out in collaboration with JBC Classic author Irwin Fridovich (2), dealt with the competitive inhibition of several enzymes by urea and guanidine. Next, Rajagopalan moved on to studies of aldehyde oxidase and xanthine oxidase and noticed that both enzymes had unusual absorption spectra. Further investigation revealed that they both contained a molybdenum cofactor, something that had not been seen in any other mammalian proteins. Some of Rajagopalan''s electron paramagnetic resonance (EPR) studies on aldehyde oxidase can be found in the JBC Classic on Helmut Beinert (3).These early findings led to an interest in proteins containing molybdenum and formed the basis of Rajagopalan''s future research. In the first JBC Classic reprinted here, Rajagopalan, Fridovich, and Harvey J. Cohen report the discovery of another molybdenum-containing enzyme, sulfite oxidase. The paper documents the presence and function of molybdenum in sulfite oxidase and describes some aspects of its EPR signal. The paper was published along with two other papers (4, 5), which discussed the purification and properties of sulfite oxidase from bovine liver and the nature of its heme prosthetic group.By 1980, several more molecules had been added to the list of molybdenum-containing proteins, but the nature of the cofactor still remained elusive. This was, in part, due to the fact that the activated cofactor was extremely labile in the presence of oxygen and thus very hard to characterize. To circumvent this problem, Rajagopalan developed a method to isolate the oxidized, inactive form of the molybdenum cofactor from sulfite oxidase, xanthine oxidase, and nitrate reductase. His procedure and initial characterization are reported in the second JBC Classic reprinted here. In the paper, Rajagopalan and his colleagues also provided evidence that a pteridine moiety acted as a structural component of the cofactor.Continuing with this work, Rajagopalan was able to isolate two additional stable degradation products (6) and confirm that the molybdenum cofactor consisted of a complex between molybdenum and a unique pterin which he named molybdopterin.In the final JBC Classic reprinted here, Rajagopalan describes the successful isolation of a stable alkylated derivative of molybdopterin, camMPT, from sulfite oxidase and xanthine oxidase by a procedure involving treatment with iodoacetamide under mild denaturing conditions. Structural studies on the product confirmed that molybdopterin is a 6-alkylpterin with a 4-carbon side chain, which has an enedithiol at carbons 1′ and 2′, a hydroxyl at carbon 3′, and a terminal phosphate group.Today, Rajagopalan remains at Duke as James B. Duke Professor of Biochemistry, a position he assumed in 1995. It is interesting to note that, in 1969 when Handler left Duke to become the President of the National Academy of Sciences, he designated Rajagopalan as PI of his National Institutes of Health (NIH) grant. This has subsequently become the longest continuously funded NIH grant, currently in its 62nd year.     

The process of reversible phosphorylation: the work of Edmond H. Fischer

Edmond H. Fischer was awarded the 1992 Nobel Prize in Physiology or Medicine for his joint research with Edwin G. Krebs on reversible protein phosphorylation. The two Classics reprinted here relate some of Fischer and Krebs'' early discoveries in their phosphorylase researchPhosphorylase Activity of Skeletal Muscle Extracts (Krebs, E. G., and Fischer, E. H. (1955) J. Biol. Chem. 216, 113–120)Conversion of Phosphorylase b to Phosphorylase a in Muscle Extracts (Fischer, E. H., and Krebs, E. G. (1955) J. Biol. Chem. 216, 121–132)Edmond H. Fischer was born in Shanghai, China in 1920. He was sent to boarding school in Switzerland at age 7, and in 1935, he entered Geneva''s Collège de Calvin. There, he became friends with his classmate Wilfried Haudenschild, and together, they decided that one of them should go into the sciences and the other into medicine so they could cure the world of all ills. Fischer chose science.Open in a separate windowEdmond H. FischerJust before the start of World War II, Fischer completed high school and entered the School of Chemistry at the University of Geneva. He earned two Licences ès Sciences, one in biology, the other in chemistry, and 2 years later, he was awarded a Diploma of “Ingénieur Chimiste.” For his thesis, he worked with Kurt H. Meyer on the purification of amylase from hog and human pancreas, as well as saliva and several strains of bacteria.In 1950, Fischer went to the United States to do a postdoctoral fellowship with Paul Karrer at CalTech. However, when he arrived in Pasadena he received a letter from Journal of Biological Chemistry (JBC) Classic author Hans Neurath (1), chairman of the department of biochemistry at the University of Washington, offering him an assistant professorship in his department. Fischer visited Seattle and accepted the offer, in part because the surrounding mountains, forests, and lakes reminded him of his native Switzerland.Within 6 months of his arrival, Fischer started working on glycogen phosphorylase with Edwin G. Krebs, who was featured in a previous JBC Classic (2). Krebs had trained with JBC Classic authors Carl and Gerty Cori who had discovered that muscle phosphorylase exists in two forms, phosphorylase a, which was easily crystallized and was active without the addition of AMP, and phosphorylase b, a more soluble protein, which was inactive without AMP (3). They believed that AMP served some kind of co-factor function for the enzyme, facilitating its transition between the two forms.However, in Geneva, Fischer had purified potato phosphorylase, which had no AMP requirement. Because it seemed unlikely that muscle phosphorylase but not potato phosphorylase would require AMP as a co-factor, Fischer and Krebs decided to try to elucidate the role of AMP in the phosphorylase reaction. They never discovered what the nucleotide was doing (this problem was solved several years later when Jacques Monod proposed his allosteric model for the regulation of enzymes), but they did discover that muscle phosphorylase was regulated by an enzyme-catalyzed phosphorylation-dephosphorylation reaction.The two JBC Classics reprinted here relate some of Fischer and Krebs'' early discoveries in their phosphorylase research. In the first Classic, the pair performed experiments to determine whether environmental temperature affects the phosphorylase content of skeletal muscle. They were unable to detect any temperature effects, but they did make the surprising discovery that the muscle extracts contained mainly phosphorylase b rather than phosphorylase a. The pair concluded that “If resting muscle contains mainly phosphorylase b… then pronounced activation of the phosphorylase reaction under various conditions is possible.”The second JBC Classic was printed back-to-back with the first. In it, Krebs and Fischer examine the requirements for the phosphorylase conversion and present evidence that the conversion of phosphorylase b to a in cell-free muscle extracts requires a nucleotide containing high energy phosphate and a divalent metal ion. However, they state that “whether this implies that during conversion there is a direct phosphorylation of the enzyme or the formation of an ‘active’ intermediate cannot be stated at this time. It is also possible that the function of ATP is concerned with the synthesis of a prosthetic group.”Similar work was being carried out on liver phosphorylase at approximately the same time by Earl Sutherland. As discussed in a previous JBC Classic (4), Sutherland discovered the second messenger cyclic AMP (cAMP), which he showed promoted the phosphorylation and activation of phosphorylase. The way in which cAMP promoted phosphorylase activation was eventually elucidated when Krebs and Fischer discovered phosphorylase kinase, which was responsible for phosphorylating phosphorylase. Phosphorylase kinase itself existed in a highly activated phosphorylated form and a less active nonphosphorylated form.As a result of the significance of their studies, Krebs and Fischer were awarded the 1992 Nobel Prize in Physiology or Medicine “for their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism.”In addition to the Nobel Prize, Fischer has received many awards and honors in recognition of his contributions to science. These include the Werner Medal from the Swiss Chemical Society, the Lederle Medical Faculty Award, the Prix Jaubert from the University of Geneva, and jointly with Krebs, the Senior Passano Award and the Steven C. Beering Award from Indiana University. Fischer was elected to the American Academy of Arts and Sciences in 1972 and to the National Academy of Sciences in 1973.¹     

Comparison of Gas Chromatography and Mineralization Experiments for Measuring Loss of Selected Polychlorinated Biphenyl Congeners in Cultures of White Rot Fungi

Two methods were used to compare the biodegradation of six polychlorinated biphenyl (PCB) congeners by 12 white rot fungi. Four fungi were found to be more active than Phanerochaete chrysosporium ATCC 24725. Biodegradation of the following congeners was monitored by gas chromatography: 2,3-dichlorobiphenyl, 4,4′-dichlorobiphenyl, 2,4′,5-trichlorobiphenyl (2,4′,5-TCB), 2,2′,4,4′-tetrachlorobiphenyl, 2,2′,5,5′-tetrachlorobiphenyl, and 2,2′,4,4′,5,5′-hexachlorobiphenyl. The congener tested for mineralization was 2,4′,5-[U-¹⁴C]TCB. Culture supernatants were also assayed for lignin peroxidase and manganese peroxidase activities. Of the fungi tested, two strains of Bjerkandera adusta (UAMH 8258 and UAMH 7308), one strain of Pleurotus ostreatus (UAMH 7964), and Trametes versicolor UAMH 8272 gave the highest biodegradation and mineralization. P. chrysosporium ATCC 24725, a strain frequently used in studies of PCB degradation, gave the lowest mineralization and biodegradation activities of the 12 fungi reported here. Low but detectable levels of lignin peroxidase and manganese peroxidase activity were present in culture supernatants, but no correlation was observed among any combination of PCB congener biodegradation, mineralization, and lignin peroxidase or manganese peroxidase activity. With the exception of P. chrysosporium, congener loss ranged from 40 to 96%; however, these values varied due to nonspecific congener binding to fungal biomass and glassware. Mineralization was much lower, ≤11%, because it measures a complete oxidation of at least part of the congener molecule but the results were more consistent and therefore more reliable in assessment of PCB biodegradation.

Polychlorinated biphenyls (PCBs) are produced by chlorination of biphenyl, resulting in up to 209 different congeners. Commercial mixtures range from light oily fluids to waxes, and their physical properties make them useful as heat transfer fluids, hydraulic fluids, solvent extenders, plasticizers, flame retardants, organic diluents, and dielectric fluids (1, 21). Approximately 24 million lb are in the North American environment (19). The stability and hydrophobic nature of these compounds make them a persistent environmental hazard.To date, bacterial transformations have been the main focus of PCB degradation research. Aerobic bacteria use a biphenyl-induced dioxygenase enzyme system to attack less-chlorinated congeners (mono- to hexachlorobiphenyls) (1, 5, 7, 8, 22). Although more-chlorinated congeners are recalcitrant to aerobic bacterial degradation, microorganisms in anaerobic river sediments reductively dechlorinate these compounds, mainly removing the meta and para chlorines (1, 6, 10, 33, 34).The degradation of PCBs by white rot fungi has been known since 1985 (11, 18). Many fungi have been tested for their ability to degrade PCBs, including the white rot fungi Coriolus versicolor (18), Coriolopsis polysona (41), Funalia gallica (18), Hirneola nigricans (35), Lentinus edodes (35), Phanerochaete chrysosporium (3, 11, 14, 17, 18, 35, 39, 41–43), Phlebia brevispora (18), Pleurotus ostreatus (35, 43), Poria cinerescens (18), Px strain (possibly Lentinus tigrinus) (35), and Trametes versicolor (41, 43). There have also been studies of PCB metabolism by ectomycorrhizal fungi (17) and other fungi such as Aspergillus flavus (32), Aspergillus niger (15), Aureobasidium pullulans (18), Candida boidinii (35), Candida lipolytica (35), Cunninghamella elegans (16), and Saccharomyces cerevisiae (18, 38). The mechanism of PCB biodegradation has not been definitively determined for any fungi. White rot fungi produce several nonspecific extracellular enzymes which have been the subject of extensive research. These nonspecific peroxidases are normally involved in lignin degradation but can oxidize a wide range of aromatic compounds including polycyclic aromatic hydrocarbons (37). Two peroxidases, lignin peroxidase (LiP) and Mn peroxidase (MnP), are secreted into the environment of the fungus under conditions of nitrogen limitation in P. chrysosporium (23, 25, 27, 29) but are not stress related in fungi such as Bjerkandera adusta or T. versicolor (12, 30).Two approaches have been used to determine the biodegradability of PCBs by fungi: (i) loss of the parent congener analyzed by gas chromatography (GC) (17, 32, 35, 42, 43) and (ii) mineralization experiments in which the ¹⁴C of the universally labeled ¹⁴C parent congener is recovered as ¹⁴CO₂ (11, 14, 18, 39, 41). In the first method, the loss of a peak on a chromatogram makes it difficult to decide whether the PCB is being partly degraded, mineralized, adsorbed to the fungal biomass, or bound to glassware, soil particles, or wood chips. Even when experiments with killed-cell and abiotic controls are performed, the extraction efficiency and standard error can make data difficult to interpret. For example, recoveries can range anywhere from 40 to 100% depending on the congener used and the fungus being investigated (17). On the other hand, recovery of significant amounts of ¹⁴CO₂ from the cultures incubated with a ¹⁴C substrate provides definitive proof of fungal metabolism. There appears to be only one report relating data from these two techniques (18), and in that study, [U-¹⁴C]Aroclor 1254, rather than an individual congener, was used.In this study, we examined the ability of 12 white rot fungal strains to metabolize selected PCB congeners to determine which strains were the most active degraders. Included in this group was P. chrysosporium ATCC 24725, a strain used extensively in PCB studies (3, 14, 18, 35, 39, 41–43). Six PCB congeners were selected to give a range of chlorine substitutions and therefore a range of potential biodegradability which was monitored by GC. One of the chosen congeners was ¹⁴C labeled and used in studies to compare the results from a mineralization method with those from the GC method.     

In Vitro Characterization of a Recombinant Blh Protein from an Uncultured Marine Bacterium as a ��-Carotene 15,15��-Dioxygenase

Codon optimization was used to synthesize the blh gene from the uncultured marine bacterium 66A03 for expression in Escherichia coli. The expressed enzyme cleaved β-carotene at its central double bond (15,15′) to yield two molecules of all-trans-retinal. The molecular mass of the native purified enzyme was ∼64 kDa as a dimer of 32-kDa subunits. The K_m, k_cat, and k_cat/K_m values for β-carotene as substrate were 37 μm, 3.6 min⁻¹, and 97 mm⁻¹ min⁻¹, respectively. The enzyme exhibited the highest activity for β-carotene, followed by β-cryptoxanthin, β-apo-4′-carotenal, α-carotene, and γ-carotene in decreasing order, but not for β-apo-8′-carotenal, β-apo-12′-carotenal, lutein, zeaxanthin, or lycopene, suggesting that the presence of one unsubstituted β-ionone ring in a substrate with a molecular weight greater than C₃₅ seems to be essential for enzyme activity. The oxygen atom of retinal originated not from water but from molecular oxygen, suggesting that the enzyme was a β-carotene 15,15′-dioxygenase. Although the Blh protein and β-carotene 15,15′-monooxygenases catalyzed the same biochemical reaction, the Blh protein was unrelated to the mammalian β-carotene 15,15′-monooxygenases as assessed by their different properties, including DNA and amino acid sequences, molecular weight, form of association, reaction mechanism, kinetic properties, and substrate specificity. This is the first report of in vitro characterization of a bacterial β-carotene-cleaving enzyme.Vitamin A (retinol) is a fat-soluble vitamin and important for human health. In vivo, the cleavage of β-carotene to retinal is an important step of vitamin A synthesis. The cleavage can proceed via two different biochemical pathways (1, 2). The major pathway is a central cleavage catalyzed by mammalian β-carotene 15,15′-monooxygenases (EC 1.14.99.36). β-Carotene is cleaved by the enzyme symmetrically into two molecules of all-trans-retinal, and retinal is then converted to vitamin A in vivo (3–5). The second pathway is an eccentric cleavage that occurs at double bonds other than the central 15,15′-double bond of β-carotene to produce β-apo-carotenals with different chain lengths, which are catalyzed by carotenoid oxygenases from mammals, plants, and cyanobacteria (6). These β-apo-carotenals are degraded to one molecule of retinal, which is subsequently converted to vitamin A in vivo (2).β-Carotene 15,15′-monooxygenase was first isolated as a cytosolic enzyme by identifying the product of β-carotene cleavage as retinal (7). The characterization of the enzyme and the reaction pathway from β-carotene to retinal were also investigated (4, 8). The enzyme activity has been found in mammalian intestinal mucosa, jejunum enterocytes, liver, lung, kidney, and brain (5, 9, 10). Molecular cloning, expression, and characterization of β-carotene 15,15′-monooxygenase have been reported from various species, including chickens (11), fruit flies (12), humans (13), mice (14), and zebra fishes (15).Other proteins thought to convert β-carotene to retinal include bacterioopsin-related protein (Brp) and bacteriorhodopsin-related protein-like homolog protein (Blh) (16). Brp protein is expressed from the bop gene cluster, which encodes the structural protein bacterioopsin, consisting of at least three genes as follows: bop (bacterioopsin), brp (bacteriorhodopsin-related protein), and bat (bacterioopsin activator) (17). brp genes were reported in Haloarcula marismortui (18), Halobacterium sp. NRC-1 (19), Halobacterium halobium (17), Haloquadratum walsbyi, and Salinibacter ruber (20). Blh protein is expressed from the proteorhodopsin gene cluster, which contains proteorhodopsin, crtE (geranylgeranyl-diphosphate synthase), crtI (phytoene dehydrogenase), crtB (phytoene synthase), crtY (lycopene cyclase), idi (isopentenyl diphosphate isomerase), and blh gene (21). Sources of blh genes were previously reported in Halobacterium sp. NRC-1 (19), Haloarcula marismortui (18), Halobacterium salinarum (22), uncultured marine bacterium 66A03 (16), and uncultured marine bacterium HF10 49E08 (21). β-Carotene biosynthetic genes crtE, crtB, crtI, crtY, ispA, and idi encode the enzymes necessary for the synthesis of β-carotene from isopentenyl diphosphate, and the Idi, IspA, CrtE, CrtB, CrtI, and CrtY proteins have been characterized in vitro (23–28). Blh protein has been proposed to catalyze or regulate the conversion of β-carotene to retinal (29, 30), but there is no direct proof of the enzymatic activity.In this study, we used codon optimization to synthesize the blh gene from the uncultured marine bacterium 66A03 for expression in Escherichia coli, and we performed a detailed biochemical and enzymological characterization of the expressed Blh protein. In addition, the properties of the enzyme were compared with those of mammalian β-carotene 15,15′-monooxygenases.     

Aberrant Expression of Dynein light chain 1 (DYNLT1) is Associated with Human Male Factor Infertility*

DYNLT1 is a member of a gene family identified within the t-complex of the mouse, which has been linked with male germ cell development and function in the mouse and the fly. Though defects in the expression of this gene are associated with male sterility in both these models, there has been no study examining its association with spermatogenic defects in human males. In this study, we evaluated the levels of DYNLT1 and its expression product in the germ cells of fertile human males and males suffering from spermatogenic defects. We screened fertile (n = 14), asthenozoospermic (n = 15), oligozoospermic (n = 20) and teratozoospermic (n = 23) males using PCR and Western blot analysis. Semiquantitative PCR indicated either undetectable or significantly lower levels of expression of DYNLT1 in the germ cells from several patients from across the three infertility syndrome groups, when compared with that of fertile controls. DYNLT1 was localized on head, mid-piece, and tail segments of spermatozoa from fertile males. Spermatozoa from infertile males presented either a total absence of DYNLT1 or its absence in the tail region. Majority of the infertile individuals showed negligible levels of localization of DYNLT1 on the spermatozoa. Overexpression of DYNLT1 in GC1-spg cell line resulted in the up-regulation of several cytoskeletal proteins and molecular chaperones involved in cell cycle regulation. Defective expression of DYNLT1 was associated with male factor infertility syndromes in our study population. Proteome level changes in GC1-spg cells overexpressing DYNLT1 were suggestive of its possible function in germ cell development. We have discussed the implications of these observations in the light of the known functions of DYNLT1, which included protein trafficking, membrane vesiculation, cell cycle regulation, and stem cell differentiation.The t-complex of the mouse occupies the proximal half of chromosome 17 and contains genes which have profound effects on spermatogenesis. Multiple mutations in several loci in the t-complex appear to interact to cause complete male sterility (1, 2). Tctex-1 (t-complex testis expressed-1), lately renamed as dynein light chain 1 (Dynlt1)¹, is identified as a candidate gene involved in male sterility in mice (1) and maps to the t-complex in mice (3). Dynlt1 is a member of a multigene family which is virtually germ cell-specific and is eightfold over expressed in t-homozygotes and 200-fold higher in testis than in other adult tissues (1). The human homologue of the mouse Dynlt1 is located on chromosome 6q25.2–25.3. The amino acid sequence shows a high degree of similarity to the predicted product of the Dynlt1 gene of the mouse t complex (4).DYNLT1 gene encodes a 14 kDa protein constituting the inner arm L1 of cytoplasmic and flagellar dynein complexes (5, 6). DYNLT1 is localized to Golgi complexes as well (7). DYNLT1 protein is present in sperm tails and oocytes (8, 9). A wide range of cellular events are brought about by cytoplasmic dynein and its association with the accessory intermediate, light intermediate, and light chain subunits. These subunits define the interaction of cytoplasmic dynein motor complex with other molecules (10). DYNLT1 is involved in cargo binding (11), lymphocyte division (8), vesicle transport (12–14), and human embryo implantation (15). DYNLT1 is known to undergo phosphorylation during apical delivery of rhodopsin (16) and during its interaction with the bone morphogenetic receptor type II (BMPRII) (17). DYNLT1 can function in dynein-independent fashion as a cell fate regulator by its interaction with G-protein β γ subunit regulating initial neurite sprouting (18), axonal specification, and elongation of hippocampal neurons in culture (11, 19). GEF-H1 is bound to microtubules by DYNLT1 and its release without microtubule depolymerization is mediated through the interaction of DYNLT1 with G proteins (20). DYNLT1 is a novel marker for neural progenitors in adult brain (21). DYNLT1 regulatory element was identified which selectively marked nestin⁺/GFAP⁺/Sox2⁺ neural stem-like cells in developing and adult brain (22). The genetic knockdown of DYNLT1 in radial precursors promoted neurogenesis (23). The use of GFP placed under the control of DYNLT1 promoter to mark adult neural stem cells and thus allowing the insertion of any nucleotide sequence selectively into neural progenitors has been patented (24).DYNLT1 is reported to have functional roles in non-murine germ cells as well. DYNLT1 was found to be essential during spermatid differentiation in Drosophila (10) and a mouse DYNLT1 homolog was identified in the dynein light chain of sea urchin sperm flagella (25, 26). However, the expression of DYNLT1 in human testicular germ cells and its association, if any, with human male factor subfertility are not yet evaluated. This study evaluates the association between DYNLT1expression and spermatogenesis in infertile human males and the possible function of DYNLT1 in spermatogonial cell division and differentiation.     

Looking at DNA through the Electron Microscope: the Work of Jack Griffith

Electron Microscopic Visualization of the RecA Protein-mediated Pairing and Branch Migration Phases of DNA Strand Exchange(Register, J. C., 3rd, Christiansen, G., and Griffith, J. (1987) J. Biol. Chem. 262, 12812–12820)Formation of DNA Loop Replication Fork Generated by Bacteriophage T7 Replication Proteins(Park, K., Debyser, Z., Tabor, S., Richardson, C. C., and Griffith, J. (1998) J. Biol. Chem. 273, 5260–5270)Jack D. Griffith was born in Logan, Utah, in 1942. He attended Occidental College in Los Angeles and received his B.A. in physics in 1964. Griffith then enrolled at the California Institute of Technology where he worked with Journal of Biological Chemistry (JBC) Classic author James Bonner (1) studying chromosome structure with electron microscopy (EM).Open in a separate windowJack GriffithIn the late 1960s, scientists were using a technique called metal shadow casting to visualize molecules via EM. The method involved spraying a layer of metal on the molecule. Because the sample was slightly raised, it got coated with more metal than its supporting film, which allowed the molecule''s outline to be seen with an electron microscope. A variation on the technique in which the sample was coated with denatured protein was used to visualize DNA. This provided a good way to look at the shape of DNA, but the specific proteins bound to the DNA were obscured by the thick coating. For his Ph.D. work, Griffith developed the EM technology needed to directly visualize bare DNA and DNA-protein complexes. His methods involved carefully controlled rotary shadow casting with tungsten and mounting the DNA on very thin carbon films.After graduating in 1969, Griffith did a 1-year postdoctoral fellowship with Benjamin Siegel at Cornell University and a 3-year fellowship with JBC Classic author Arthur Kornberg (2) at Stanford University. Using the methods Griffith developed at Caltech, Griffith, Kornberg, and Joel A. Huberman published a paper showing an EM image of Escherichia coli DNA polymerase I bound to DNA (3). This was not only the first EM image of DNA bound to a known protein, but it also showed that electron microscopy had the potential to provide quantitative information about macromolecular assemblies involving DNA.Griffith stayed at Stanford as a research scientist until 1978 when he became an associate professor at the Lineberger Comprehensive Cancer Center and the Department of Microbiology and Immunology at the University of North Carolina at Chapel Hill. At UNC, he designed a research program in which he used EM and biochemical tools to study DNA. The two JBC Classics reprinted here demonstrate some of those studies.In the first Classic, Griffith and his colleagues investigated the role of the E. coli RecA protein in homologous recombination. RecA catalyzes this process by promoting pairing and strand exchange between homologous DNA molecules. The scientists used EM to follow reactions in three homologous DNA pairs: supertwisted double-stranded (ds) DNA and linear single-stranded (ss) DNA; linear dsDNA and circular ssDNA; and linear dsDNA and colinear ssDNA. They found that all three reactions undergo a three-step pathway. First, the RecA protein-ssDNA filament makes contact with a homologous dsDNA (joining). Second, both DNA partners are at least partially enveloped within the nucleoprotein filament, and if the DNA topology is favorable, exchange of DNA strands then ensues (envelopment/exchange). Finally, upon completion of strand exchange, this complex is resolved and the products are released.In the second Classic, Griffith teamed with JBC Classic author Charles C. Richardson (4) and used EM to examine the architecture of the DNA and DNA-protein intermediates involved in replication reactions employing the T7 replication proteins. This study showed the first direct evidence of the presence of a DNA loop at the replication fork and provided a long sought after proof of the Alberts trombone model of looping of the lagging strand during replication. One of Griffith and Richardson''s co-authors on this paper, Stanley Tabor, is the son of long time JBC editor Herbert Tabor.Griffith remains at the University of North Carolina at Chapel Hill as Kenan Distinguished Professor of Microbiology and Immunology and Biochemistry. He has received many honors and awards for his contributions to science including the Ellison Senior Scholar Award (2001–2005), the ASBMB Herbert A. Sober Award (2002), the Grand Gold Medal of Comenius University, Slovak Republic (2006), and the Glenn Foundation Award (2007). He was also elected to the American Association for the Advancement of Science (2001) and the American Academy of Arts and Sciences (2005) and served on the Journal of Biological Chemistry editorial board from 2002 to 2007.