Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose

Conflicting reports have suggested that the silent information regulator 2 (SIR2) protein family employs NAD(+) to ADP-ribosylate histones [Tanny, J. C., Dowd, G. J., Huang, J., Hilz, H. & Moazed, D. (1999) Cell 99, 735-745; Frye, R. A. (1999) Biochem. Biophys. Res. Commun. 260, 273-279], deacetylate histones [Landry, J., Sutton, A., Tafrov, S. T., Heller, R. C., Stebbins, J., Pillus, L. & Sternglanz, R. (2000) Proc. Natl. Acad. Sci. USA 97, 5807-5811; Smith, J. S., Brachmann, C. B., Celic, I., Kenna, M. A., Muhammad, S., Starai, V. J., Avalos, J. L., Escalante-Semerena, J. C., Grubmeyer, C., Wolberger, C. & Boeke, J. D. (2000) Proc. Natl. Acad. Sci. USA 97, 6658-6663], or both [Imai, S., Armstrong, C. M., Kaeberlein, M. & Guarente, L. (2000) Nature (London) 403, 795-800]. Uncovering the true enzymatic function of SIR2 is critical to the basic understanding of its cellular function. Therefore, we set out to authenticate the reaction products and to determine the intrinsic catalytic mechanism. We provide direct evidence that the efficient histone/protein deacetylase reaction is tightly coupled to the formation of a previously unidentified acetyl-ADP-ribose product (1-O-acetyl-ADP ribose). One molecule of NAD(+) and one molecule of acetyl-lysine are readily catalyzed to one molecule of deacetylated lysine, nicotinamide, and 1-O-acetyl-ADP-ribose. A unique reaction mechanism involving the attack of enzyme-bound acetate or the direct attack of acetyl-lysine on an oxocarbenium ADP-ribose intermediate is proposed. We suggest that the reported histone/protein ADP-ribosyltransferase activity is a low-efficiency side reaction that can be explained through the partial uncoupling of the intrinsic deacetylation and acetate transfer to ADP-ribose.     

Book Reviews

Book reviewed in this article: WORK AND RETIREMENT: Stanley Parker. London: George Allen & Unwin. Australian agent: George Allen & Unwin Australia Pty. Ltd. A HANDBOOK OF ASSISTIVE DEVICES FOR THE HANDICAPPED ELDERLY: NEW HELP FOR INDEPENDENT LIVING: Joseph M. Bruer. HEALTH CARE OF THE ELDERLY: Tom Arie (ed) OUR ELDERS: Muir Gray and Gorden Wilcock ESTABLISHING A GERIATRIC SERVICE: edited by Davis CoakIey.     

Apparent mtDNA heteroplasmy in Alzheimer’s disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes

In an unprecedented finding, Davis et al. [Davis, R. E., Miller, S., Herrnstadt, C., Ghosh, S. S., Fahy, E., Shinobu, L. A., Galasko, D., Thal, L. J., Beal, M. F., Howell, N. & Parker, W. D., Jr. (1997) Proc. Natl. Acad. Sci. USA 94, 4526–4531] used an unusual DNA isolation method to show that healthy adults harbor a specific population of mutated mitochondrial cytochrome c oxidase (COX) genes that coexist with normal mtDNAs. They reported that this heteroplasmic population was present at a level of 10–15% in the blood of normal individuals and at a significantly higher level (20–30%) in patients with sporadic Alzheimer’s disease. We provide compelling evidence that the DNA isolation method employed resulted in the coamplification of authentic mtDNA-encoded COX genes together with highly similar COX-like sequences embedded in nuclear DNA (“mtDNA pseudogenes”). We conclude that the observed heteroplasmy is an artifact.     

Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities.

In recent host-guest studies, the helix-forming tendencies of amino acid residues have been quantified by three groups, each obtaining similar results [Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M. & Baldwin, R. L. (1990) Nature (London) 344, 268-270; O'Neil, K. T. & DeGrado, W. F. (1990) Science 250, 646-651; Lyu, P. C., Liff, M. I., Marky, L. A. & Kallenbach, N. R. (1990) Science 250, 669-673]. Here, we explore the hypothesis that these measured helix-forming propensities are due primarily to conformational restrictions imposed upon residue side chains by the helix itself. This proposition is tested by calculating the extent to which the bulky helix backbone "freezes out" available degrees of freedom in helix side chains. Specifically, for a series of apolar residues, the difference in configurational entropy, delta S, between each side chain in the unfolded state and in the alpha-helical state is obtained from a simple Monte Carlo calculation. These computed entropy differences are then compared with the experimentally determined values. Measured and calculated values are found to be in close agreement for naturally occurring amino acids and in total disagreement for non-natural amino acids. In the calculation, delta S(Ala) = 0. The rank order of entropy loss for the series of natural apolar side chains under consideration is Ala less than Leu less than Trp less than Met less than Phe less than Ile less than Tyr less than Val. Among these, none favor helix formation; Ala is neutral, and all remaining residues are unfavorable to varying degrees. Thus, applied to side chains, the term "helix preference" is a misnomer. While side chain-side chain interactions may modulate stability in some instances, our results indicate that the drive to form helices must originate in the backbone, consistent with Pauling's view of four decades ago [Pauling, L., Corey, R. B. & Branson, H. R. (1951) Proc. Natl. Acad. Sci. USA 37, 205-210].     

REVIEWS AND NOTICES OF BOOKS.

Y outh . Edited by T. N. Kelynaok, M.D. (Vol. IV. of the National Health Manuals.)
DREAMS AND MYTHS. By Dr. Karl Abraham of Berlin. Translated by W. A. White, M.D., of Washington.
P sycho -P athology of E veryday L ife . By Professor Dr. Sigmund Freud, LL.D. Authorized English edition, with Introduction by A. A. Brill, Ph.B., M.D., Chief of Clinic of Psychiatry, Columbia University, etc.
S ocial W ork IN L ondon , 1869 -1912. A History of the Charity Organization Society. By Helen Bosanquet, LL.D. (St. Andrews).
T he D octor's D ilemma , G etting M arried , and the S howing -UP OF B lanco P osnet . By Bernard Shaw.
S ocial C haos , AND T he W ay O ut . By Alfred Baker Read.
A rchives of N eurology and P sychiatry f rom the P athological L aboratory of the L ondon C ounty A sylums , C laybury , E ssex . Edited by Frederick Walker Mott, M.D., F.R.S., F.R.G.P., Director of the Laboratory and Pathologist to the London County Asylums. Vol. VI.     

Isolation and partial purification of an enzyme catalyzing the formation of O-xylosylzeatin in Phaseolus vulgaris embryos

An enzyme catalyzing the formation of a cytokinin metabolite, an O-pentosyl derivative of zeatin [Lee, Y. H., Mok, M. C., Mok, D. W. S., Griffin, D. A. & Shaw, G. (1985) Plant Physiol. 77, 635-641], was isolated from Phaseolus vulgaris embryos. Of all the potential pentose donors tested, UDP-xylose was the only substrate recognized by the enzyme. This indicates that the O-pentosyl derivatives previously obtained are O-xylosylzeatin and its ribonucleoside. The enzyme (UDP-xylose:zeatin O-xylosyltransferase, EC 2.4.2.-) has high affinity for trans-zeatin (K_m 2 μM) and dihydrozeatin (K_m 10 μM) but does not recognize cis-zeatin or ribosylzeatin. The molecular weight of the enzyme is approximately 50,000 and the pH optimum of the reaction is 8-8.5. Under comparable isolation and reaction conditions, similar enzyme activity could not be detected in P. lunatus embryos, confirming the genetic differences observed in vivo.     

BOOK REVIEW FOR GASTROENTEROLOGISTS

Book review in this article:
SURGICAL DISEASES OF THE PANCREAS: John M. Howard, M.D., F.A.C.S., Professor and Chairman, Department of Surgery, Hahnemann Medical College, and Surgeon in Chief, Hahnemann Hospital, Consultant in Surgery, Walter Reed Army Medical Center, Washington, D. C., etc. and George L. Jordan, Jr., M.D., M.S., F.A.C.S., Associate Professor in Surgery, Baylor University College of Medicine, Consultant in Surgery, Veterans Administration Hospital, Attending in Surgery, Methodist Hospital and Jefferson Davis Hospital, Houston, Texas     

REVIEWS AND NOTICES OF BOOKS.

T uberculosis Y ear -B ook and S anatoria A nnual . Edited by T. N. Kelynack, M.D. Vol. i. 1913-14.
A D aughter's I nheritance . By Mrs. G. S. Reaney.
A C linical M anual of M ental D iseases . By Francis X. Dercum, M.D., Ph.D., Professor of Nervous and Mental Diseases, Jefferson Medical College, Philadelphia.
T he MO ntessori P rinciples and P ractice . By E. P. Culverwell, M.A., Professor of Education, University of Dublin.
T he W eakest L ink . By Harold Begbie.
R ough -H ewers . By Agnes L. Neild.
T he B lood of the F athers : A P lay in F our A cts . By G. Frank Lydston
T he I deals and O rganization of a M edical S ociety . By Jamieson B. Hurry, M.A., M.D.
M edical E lectricity and L ight : A n E lementary T extbook for N urses . By Ettie Sayer, M.B., B.S.
T he P ress and its S tory : An Account of the Birth and Development of Journalism up to the Present Day, with the History of all the Leading Newspapers, Daily, Weekly, or Monthly, Secular and Religious, Past and Present; also the Story of their Production from Wood-Pulp to the Printed Sheet. By J. D. Symon, M.A., sometime Assistant-Editor of the Illustrated London News.
A ncient E ugenics : The Arnold Prize Essay for 1913. By Allen G. Roper, B.A.     

Short-lived chlorine-36 in a Ca- and Al-rich inclusion from the Ningqiang carbonaceous chondrite

Excesses of sulfur-36 in sodalite, a chlorine-rich mineral, in a calcium- and aluminum-rich inclusion from the Ningqiang carbonaceous chondrite linearly correlate with chorine/sulfur ratios, providing direct evidence for the presence of short-lived chlorine-36 (with a half-life of 0.3 million years) in the early solar system. The best inferred (36Cl/35Cl)o ratios of the sodalite are approximately 5 x 10(-6). Different from other short-lived radionuclides, chlorine-36 was introduced into the inclusion by solid-gas reaction during secondary alteration. The alteration reaction probably took place at least 1.5 million years after the first formation of the inclusion, based on the correlated study of the 26Al-26Mg systems of the relict primary minerals and the alteration assemblages, from which we inferred an initial ratio of (36Cl/35Cl)o > or = 1.6 x 10(-4) at the time when calcium- and aluminum-rich inclusions formed. This discovery supports a supernova origin of short-lived nuclides [Cameron, A. G. W., Hoeflich, P., Myers, P. C. & Clayton, D. D. (1995) Astrophys. J. 447, L53; Wasserburg, G. J., Gallino, R. & Busso, M. (1998) Astrophys. J. 500, L189-L193], but presents a serious challenge for local irradiation models [Shu, F. H., Shang, H., Glassgold, A. E. & Lee, T. (1997) Science 277, 1475-1479; Gounelle, M., Shu, F. H., Shang, H., Glassgold, A. E., Rehm, K. E. & Lee, T. (2001) Astrophys. J. 548, 1051-1070]. Furthermore, the short-lived 36Cl may serve as a unique fine-scale chronometer for volatile-rock interaction in the early solar system because of its close association with aqueous and/or anhydrous alteration processes.     

REVIEWS AND NOTICES OF BOOKS

Book Reviews in this article.
T he C ycle of L ife according to M odern S cience . By C. W. Saleeby, M.D.
T he T reatment of N eurasthenia . By A. Proust and Gilbert Ballet.
U p from the S lums . By Owen Kildare.
H ow to D eal with the U nemployed . By Mary Higgs.
P ractical H ints for T ravelers in the N ear E ast . By E. A. Reynolds-Ball, F.R.G.S.
E nglish M edicine in the A nglo -S axon T imes . By Joseph Frank Payne, M.D.
A S parrow , a M ouse , and a M an : A S tudy in S olitude . By George H. R. Dabbs, M.D.
T he F ood of the G ods , and H ow it came to E arth . By H. G. Wells.
E x C athedrac : E ssays on I nsanity . By T. Claye Shaw, M.D., F.R.C.P.
C linical L ectures on M ental D iseases . By T. S. Clouston, M.D., F.R.C.P.
T he P roblem of the M ilk -S upply . By F. Lawson Dodd, M.R.C.S. Eng., L.R.C.P. Lond., L.D.S., D.P.H. Lond.
C linical L ectures on N eurasthenia . By Thomas D. Savill, M.D.
A n I ntroduction to D ermatology . By Norman Walker, M.D.
A nesthetics and their A dministration : A Text-book for Medical and Dental Practitioners and Students. By Frederic W. Hewitt, M.A., M.D.
A B oy's C ontrol and S elf -E xpression . By Eustace Miles, M.A.     

REVIEWS AND NOTICES OF BOOKS

Book Review in this Articles
T he A lcohol C ase : T he S umming-up . By Father Power, S.J., B.A.
T he P rinciples of A nthropology and S ociology in their R elation to C riminal P rocedure . By Maurice Parmelee, M.A.
H uman S peech : A S tudy in the P urposive A ction of L iving M atter . By N. C. Macnamara, F.R.C.S.
M endel's P rinciples of H eredity . By W. Bateson, M.A., F.R.S., V.M.H.
C hristian R eunion . By Frank Spence.
D rugs and the D rug H abit . By Harrington Sainsbury, M.D., F.R.C.P.
P arenthood and R ace C ulture . An Outline of Eugenics. By Caleb Williams Saleeby, M.D., Ch.B., F.Z.S., F.R.S.E.
P eace and H appiness . By the Right Hon.
T he L aw of C hildren and Y oung P ersons (in relation to penal offences), including the C hildren A ct , 1908. By L. A. Atherley Jones, K.C., M.P., and Hugh H. L. Bellot, D.C.L.
Y our C hild's H ealth . By John Grimshaw, M.D., B.S., D.P.H
W astage of C hild -L ife as E xemplified by C onditions in L ancashire . By J. Johnston, M.D.
H ints and H elps : A M anual of I ncidental T emperance T eaching . By Charles Wakely.
H ealth and C ommon S ense . By Woods Hutchinson, A.M., M.D.
P rinciples and M ethods of P hysical E ducation and H ygiene . By W. P. Welpton, B.Sc.
T he M odern C hild . Compiled by Hervey Elwes. With a foreword by L. Allen Harker.
T he P oor L aw R eport of 1909. By Helen Bosanquet.     

Aniracetam reduces glutamate receptor desensitization and slows the decay of fast excitatory synaptic currents in the hippocampus.

Aniracetam is a nootropic drug that has been shown to selectively enhance quisqualate receptor-mediated responses in Xenopus oocytes injected with brain mRNA and in hippocampal pyramidal cells [Ito, I., Tanabe, S., Kohda, A. & Sugiyama, H. (1990) J. Physiol. (London) 424, 533-544]. We have used patch clamp recording techniques in hippocampal slices to elucidate the mechanism for this selective action. We find that aniracetam enhances glutamate-evoked currents in whole-cell recordings and, in outside-out patches, strongly reduces glutamate receptor desensitization. In addition, aniracetam selectively prolongs the time course and increases the peak amplitude of fast synaptic currents. These findings indicate that aniracetam slows the kinetics of fast synaptic transmission and are consistent with the proposal [Trussell, L. O. & Fischbach, G. D. (1989) Neuron 3, 209-218; Tang, C.-M., Dichter, M. & Morad, M. (1989) Science 243, 1474-1477] that receptor desensitization governs the strength of fast excitatory synaptic transmission in the brain.     

Glutaredoxin homolog encoded by vaccinia virus is a virion-associated enzyme with thioltransferase and dehydroascorbate reductase activities.

Glutaredoxins (GRXs), also known as thioltransferases, use glutathione as a cofactor for reduction of disulfides in prokaryotes and eukaryotes. We demonstrate that the vaccinia virus O2L open reading frame encodes a functional GRX, as predicted by Johnson et al. [Johnson, G. P., Goebel, S. J., Perkus, M. E., Davis, S. W., Winslow, J. P. & Paoletti, E. (1991) Virology 181, 378-381] from sequence homology. The 12-kDa protein product of the O2L open reading frame was synthesized after viral DNA replication, coincident with a major increase in cytoplasmic glutathione-dependent thioltransferase activity. The protein was associated with purified vaccinia virions and was not released by treatment with a nonionic detergent unless dithiothreitol was added. The virion-derived protein, as well as a recombinant form expressed in Escherichia coli, exhibited thioltransferase and dehydroascorbate reductase activities indicative of a functional GRX. The postreplicative synthesis of vaccinia virus GRX and its association with virions suggest that the enzyme may have novel roles in the virus growth cycle.     

Incorporating structure to predict microRNA targets

MicroRNAs (miRNAs) are a recently discovered set of regulatory genes that constitute up to an estimated 1% of the total number of genes in animal genomes, including Caenorhabditis elegans, Drosophila, mouse, and humans [Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. (2001) Science 294, 853-858; Lai, E. C., Tomancak, P., Williams, R. W. & Rubin, G.M. (2003) Genome Biol. 4, R42; Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. (2001) Science 294, 858-862; Lee, R. C. & Ambros, V. (2001) Science 294, 862-8644; and Lee, R. C., Feinbaum, R. L. & Ambros, V. (1993) Cell 115, 787-798]. In animals, miRNAs regulate genes by attenuating protein translation through imperfect base pair binding to 3' UTR sequences of target genes. A major challenge in understanding the regulatory role of miRNAs is to accurately predict regulated targets. We have developed an algorithm for predicting targets that does not rely on evolutionary conservation. As one of the features of this algorithm, we incorporate the folded structure of mRNA. By using Drosophila miRNAs as a test case, we have validated our predictions in 10 of 15 genes tested. One of these validated genes is mad as a target for bantam. Furthermore, our computational and experimental data suggest that miRNAs have fewer targets than previously reported.     

The first step in vision occurs in femtoseconds: complete blue and red spectral studies.

Femtosecond transient absorption measurements of the cis-trans isomerization of the visual pigment rhodopsin clarify the interpretation of the dynamics of the first step in vision. We present femtosecond time-resolved spectra as well as kinetic measurements at specific wavelengths between 490 and 670 nm using 10-fs probe pulses centered at 500 and 620 nm following a 35-fs pump pulse at 500 nm. The expanded spectral window beyond that available (500-570 nm) in our previous study [Schoenlein, R. W., Peteanu, L. A., Mathies, R. A. & Shank, C. V. (1991) Science 254, 412-415] provides the full differential absorption spectrum of the photoproduct as a function of delay time after photolysis. The high time-resolution data presented here contradict an alternative interpretation of the rhodopsin photochemistry offered by Callender and co-workers [Yan, M., Manor, D., Weng, G., Chao, H., Rothberg, L., Jedju, T. M., Alfano, R. R. & Callender, R. H. (1991) Proc. Natl. Acad. Sci. USA 88, 9809-9812]. Our results confirm that the red-shifted (lambda max approximately 570 nm) photo-product of the isomerization reaction is fully formed within 200 fs. Subsequent changes in the differential spectra between 200 fs and 6 ps are attributed to a combination of dynamic ground-state processes such as intramolecular vibrational energy redistribution, vibrational cooling, and conformational relaxation.     

On extended x-ray absorption fine structure studies of hemoglobin

Results of extended x-ray absorption fine structure (EXAFS) studies of the iron atom in deoxygenated hemoglobin are reviewed. It is shown that the iron-porphinato nitrogen distance has been determined to be 2.06 +/- 0.01 A by two independent investigations [Eisenberger, P.M., Shulman, R.G., Kincaid, B. M., Brown, G. S. & Ogawa, S. (1978) Nature (London) 274, 30-34 and Perutz, M.F., Hasnain, S.S., Duke, P.J., Sessler, J.L. & Hahn, J.E. (1982) Nature (London) 295, 535-538]. Difficulties experienced by Perutz et al. in using this distance to calculate the iron's distance above the plane by triangulation are shown to be due to ignoring differences between ferrous and ferric hemes. It is concluded that the iron is 0.2 +/- 0.1 0.2 A above the plane of the nitrogens as originally shown by Eisenberger et al.     

BOOK REVIEWS

Book reviewed in this article:
SHOCK AND ALLIED FORMS OF FAILURE OF THE CIRCULATION. H. A. Davis, M.D., C.M., F.A.C.S.
MAJOR ENDOCRINE DISORDERS. S. Leonard Simpson, M.A., M.D., F.R.C.P.
VENOUS THROMBOSIS AND PULMONARY EMBOLISM. Harold Neuhof, M.D.     

REVIEWS AND NOTICES OF BOOKS

R eport of and M inutes of E vidence taken before the D epartmental C ommittee appointed to inquire into the O peration of the L aw relating to I nebriates , and to their D etention in R eformatories and R etreats , with A ppendixes A nd I ndexes .
T he B ible of N ature . By J. Arthur Thomson, M.A.
T he T axation of the L iquor T rade . By Joseph Rowntree and Arthur Sherwell, M.P.
A lcohol and the H uman B ody : An Introduction to the Study of the Subject, and a Contribution to National Health. By Sir Victor Horsley, F.R.S., F.R.C.S., M.B., B.S., end Mary D. Sturge, M.D.
A S ystem of D iet and D ietetics . Edited by G. A. Sutherland, M.D., F.R.C.P.
T he U nbmployable and U nemployed . By Percy Alden, M.P., and Edward E. Hayward, M.
S weating . By Edward Cadbury and George Swam, MA.
C hild -L ife and L abour . By Margaret Alden, M.D.
S chool R eports and S chool E fficiency . By David H. Snedden, Ph.D., and William H. Allen, Ph.D.
T homas H ealing , L over of C hildren , T eacher of T eachers . By Rev. C. Arnold Healing.
T he B oy's own R eciter . Edited by George Andrew Hutchison
T he G irl's own R eciter . Edited by Charles Peters.
M others in C ouncil , or T alks in M others M eetings . By Ellen M. McDougall.
A lmoners of the K ing . By Thomas Durley.
L ife's O rchestra .
L ife's C olours .
T he A nimals S unday R est . Pp. 2E, with 13 illustrations. Prim 1s. net. By Hallie Killick
P roblems of to - day . By Andrew Carnegie.
T he O rnaments of the M inisters . By the Rev. Percy Dearmer, M.A.
C hurch B ells . By H. B. Walters, M.A., F.S.A.
T he A rchitectural H istory of the C hristian C hurch . By A. G. Hill, M.A., F.S.A.