MicroReview Control of translation initiation in Saccharomyces cerevisiae

The first observations regarding the control of translation initiation in the yeast Saccharomyces cerevisiae were made by Fred Sherman and his colleagues in 1971. Elegant genetic studies of the CYC1 gene resulted in the formulation of 'Sherman's Rules' for translation initiation as follows: (i) AUG is the only initiator codon. (ii) the most proximal AUG from the 5' end of a message will serve as the start site of translation; and (iii) if the upstream AUG codon is mutated then initiation begins at the next available AUG in the message. Hidden within these rules is the mechanism of eukaryotic translation initiation, as these very same rules were later shown to apply to higher eukaryotic organisms and were formulated into the scanning model. However, only in the past five years has yeast been taken seriously as an organism for studying the mechanism of eukaryotic translation initiation. The basis for this is that the yeast genes for at least four mammalian translation initiation factor homologues have been identified and the number is growing. Similar factors suggest similar mechanisms for translation initiation between yeast and mammals. For some translation initiation factors, the genetics of yeast has provided new insights into their function. A mechanism for regulating translation initiation in mammalian cells is now evident in yeast. It seems clear that the molecular genetics of yeast coupled with the available in vitro translation system will provide a wealth of information in the future regarding translational control and regulatory mechanisms. The purpose of this review is to summarize what is known about translational control in S. cerevisiae.     

Studies of the location and function of isoprenoid quinones in chlorosomes from green sulfur bacteria

The chlorosome antenna of the green sulfur bacterium Chlorobium tepidum essentially consists of aggregated bacteriochlorophyll (BChl) c enveloped in a glycolipid monolayer. Small amounts of protein and the isoprenoid quinones chlorobiumquinone (CK) and menaquinone-7 (MK-7) are also present. Treatment of isolated chlorosomes from Cb. tepidum with sodium dodecyl sulfate (SDS) did not affect the quinones, demonstrating that these are located in a site which is inaccessible to SDS, probably in the interior of the chlorosomes. About half of the quinones were removed by Triton X-100. The non-ionic character of Triton probably allowed it to extract components from within the chlorosomes. MK-10 in chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus was likewise found to be located in the chlorosome interior. The excitation transfer in isolated chlorosomes from Cb. tepidum is redox-regulated. We found a ratio of BChl c fluorescenceintensity under reducing conditions (Fred) to that under oxidizing conditions (Fox) of approximately 40. The chlorosomal BChl a fluorescence was also redox-regulated. When the chlorosomal BChl c–BChl c interactions were disrupted by 1-hexanol, the BChl c Fred/Fox ratiodecreased to approximately 3. When CK and MK-7 were extracted from isolated chlorosomes with hexane, the BChl c Fred/Fox ratio also decreased to approximately 3. A BChl c Fred/Fox ratio of 3–5 was furthermore observed in aggregates of pure BChl c and in chlorosomes from Cfx. aurantiacus which do not contain CK. We therefore suggest that BChl c aggregates inherently exhibit a small redox-dependent fluorescence (Fred/Fox 3) and that the large redox-dependent fluorescence observed in chlorobial chlorosomes (Fred/Fox 40) is CK-dependent.     

REVIEWS

Book reviewed in this article:
AAAS Atlas of Population and Environment, by Paul Harrison and Fred Pearce.     

The early days of DNA sequences

Fred Sanger was awarded the rare distinction of two Nobel Prizes for Chemistry, in 1958 and 1980. The first was for his work on the structure of proteins, particularly that of insulin, the latter for his contribution concerning the determination of nucleic acid sequences, the foundation work that ultimately led to The Human Genome Project.     

Chaperone-mediated autophagy: Dice's 'wild' idea about lysosomal selectivity

A little over 1 year ago, we lost a bright scientist and a dear colleague who, in his younger years, proposed the 'heretical' idea that lysosomes could selectively degrade cytosolic proteins. That scientist was J. Fred Dice, and his lifetime's discovery was the degradative pathway that we now know as chaperone-mediated autophagy.     

Apples, oranges and unknown fruit

For many microbiologists their ultimate goal is to understand microbial life at the whole-cell level. Here, Fred Neidhardt gives his view that attention must be paid to the growth conditions for this goal to be realized.     

The Empire of Things: Regimes of Value and Material Culture

The Empire of Things: Regimes of Value and Material Culture. Fred R. Myers, ed. Santa Fe, NM: SAR Press, 2001. 366 pp.     

San Nicol´s de Zurite: Religion and Daily Life of a Peruvian Andean Village in a Changing World

San Nicol´s de Zurite: Religion and Daily Life of. Peruvian Andean Village in. Changing World. Fred Spier. Amsterdam: VU University Press, 1995. 130 pp.     

Painting Culture: The Making of an Aboriginal High Art

Painting Culture: The Making of an Aboriginal High Art. Fred R. Myers. Durham, NC: Duke University Press, 2002. 410 pp.     

Complexity revisited

I look back at my 1996 book Complexity and the Function of Mind in Nature, responding to papers by Pamela Lyon, Fred Keijzer and Argyris Arnellos, and Matt Grove.     

Singapore signalling: the 2012 hedgehog pathway cocktail

The 'Hedgehog Signalling in Development Evolution and Disease' conference took place in Biopolis, Singapore, in March 2012. Organized by Phil Ingham with help from Xinhua Lin, Mary-Ann Price and Fred de Sauvage, it brought leading researchers together to discuss the latest findings and exchange ideas on every aspect of hedgehog signalling.     

Book Reviews

Oxygen Free Radicals in Tissue Damage Editors Merrill Tarr and Fred Samson Birkhauser, Boston, 1993

Free Radicals in Medicine edited by K.H. Cheeseman and T.F. Slater British Medical Bulletin volume 49 no. 3 Churchill-Livingstone 1993     

REVIEWS

Book reviewed in this article:
Propagation of Horticultural Plants. Guy W. Adriance Fred. R. Brison.
Diseases of Bulbs. W. C. Moore.
Destructive and Useful Insects: their habits and control. C. L. Metcalf W. P. Flint.     

Cytokines: making the right choice

Fred Finkelmon and Joseph Urban propose that optimal host defense against different classes of parasite depends upon induction of different sets of immune effector mechanisms, which are, in turn, dependent upon secretion of different sets of cytokines. The authors suggest that hosts identify characteristics common to parasites of a given type as those triggers that stimulate secretion of the proper cytokine set.     

Camphor Pathway Redux: Functional Recombinant Expression of 2,5- and 3,6-Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453 with Their Cognate Flavin Reductase Catalyzing Baeyer-Villiger Reactions

Whereas the biochemical properties of the monooxygenase components that catalyze the oxidation of 2,5-diketocamphane and 3,6-diketocamphane (2,5-DKCMO and 3,6-DKCMO, respectively) in the initial catabolic steps of (+) and (−) isomeric forms of camphor (CAM) metabolism in Pseudomonas putida ATCC 17453 are relatively well characterized, the actual identity of the flavin reductase (Fred) component that provides the reduced flavin to the oxygenases has hitherto been ill defined. In this study, a 37-kDa Fred was purified from a camphor-induced culture of P. putida ATCC 17453 and this facilitated cloning and characterization of the requisite protein. The active Fred is a homodimer with a subunit molecular weight of 18,000 that uses NADH as an electron donor (K_m = 32 μM), and it catalyzes the reduction of flavin mononucleotide (FMN) (K_m = 3.6 μM; k_cat = 283 s⁻¹) in preference to flavin adenine dinucleotide (FAD) (K_m = 19 μM; k_cat = 128 s⁻¹). Sequence determination of ∼40 kb of the CAM degradation plasmid revealed the locations of two isofunctional 2,5-DKCMO genes (camE_25–1 for 2,5-DKCMO-1 and camE_25–2 for 2,5-DKCMO-2) as well as that of a 3,6-DKCMO-encoding gene (camE₃₆). In addition, by pulsed-field gel electrophoresis, the CAM plasmid was established to be linear and ∼533 kb in length. To enable functional assessment of the two-component monooxygenase system in Baeyer-Villiger oxidations, recombinant plasmids expressing Fred in tandem with the respective 2,5-DKCMO- and 3,6-DKCMO-encoding genes in Escherichia coli were constructed. Comparative substrate profiling of the isofunctional 2,5-DCKMOs did not yield obvious differences in Baeyer-Villiger biooxidations, but they are distinct from 3,6-DKCMO in the stereoselective oxygenations with various mono- and bicyclic ketone substrates.     

Chaperone-mediated autophagy: The heretofore untold story of J. Fred “Paulo” Dice

The best-characterized process of autophagy is macroautophagy. Many an article or talk has started with the phrase “…macroautophagy, hereafter referred to as autophagy.” This one will be different because we are going to learn more about the person most responsible for increasing our understanding of chaperone-mediated autophagy, or CMA, J. Fred Dice.     

Representations of Art and Arts of Representation

The Traffic in Culture: Refiguring Art and Anthropology. George E. Marcus and Fred R. Myers. eds. Berkeley: University of California Press, 1995. 380 pp.
The Death of Authentic Primitive Art and Other Tales of Progress. Shelly Errington. Berkeley: University of California Press, 1998. 309 pp.     

Optical properties of the adaxial and abaxial faces of leaves. Chlorophyll fluorescence, absorption and scattering coefficients.

Emission fluorescence spectra were obtained for the adaxial and abaxial faces of dicotyledonous (Ficus benjamina L., Ficus elastica, Gardenia jasminoides and Hedera helix) and monocotyledonous leaves (Gladiolus spp. and Dracaena cincta bicolor). After correction by light-re-absorption processes, using a previously published physical model, the adaxial faces of dicotyledons showed a fluorescence ratio Fred/Ffar-red rather lower than the respective values for the abaxial faces. Monocotyledons and shade-adapted-plants showed similar values for the corrected fluorescence ratio for both faces. Even when differences in experimental fluorescence emission from adaxial and abaxial leaves in dicotyledons are mostly due to light re-absorption processes, the residual dissimilarity found after application of the correction model would point to the fact that fluorescence re-absorption is not the only responsible for the observed disparity. It was concluded that light re-absorption processes does not account entirely for the differences in the experimental emission spectra between adaxial and abaxial leaves. Differences that remains still present after correction might be interpreted in terms of a different photosystem ratio (PSII/PSI). Experiments at low temperature sustained this hypothesis. In dicotyledons, light reflectance for adaxial leaves was found to be lower than for the abaxial ones. It was mainly due to an increase in the scattering coefficient for the lower leaf-side. The absorption coefficient values were slightly higher for the upper leaf-side. During senescence of Ficus benjamina leaves, the scattering coefficient increased for both the upper and lower leaf-sides. With senescence time the absorption coefficient spectra broadened while the corrected fluorescence ratio (Fred/Ffar-red) decreased for both faces. The results pointed to a preferential destruction of photosystem II relative to photosystem I during senescence.     

Book notices

ATLAS OF ENTOMOPATHOGENIC FUNGI. By Robert A. Samson, Harry C. Evans and Jean-Paul Latge.
THE GENETICS OF SOCIAL EVOLUTION. Edited by Michael D. Breed and Robert E. Page, Jr.
THE MONARCH BUTTERFLIES: INTERNATIONAL TRAVELLERS. By Fred A. Urquhart.     

SOLVING TAXONOMIC AND NOMENCLATURAL PROBLEMS IN PACIFIC GIGARTINACEAE (RHODOPHYTA) USING DNA FROM TYPE MATERIAL

Molecular data obtained by a procedure for extracting PCR-amplifiable nuclear and chloroplast DNA from old and formalin-fixed red algal herbarium specimens were used to elucidate problems in the systematics of Pacific Gigartinaceae. Correspondence between nucleotide sequences of the internal transcribed spacer 1 region or the RUBISCO spacer from type specimens and modern collections supports the following conclusions. (1) The type of Fucus cordatus Turner, now Iridaea cordata (Turner) Bory, came from the southern hemisphere (probably from Isla de los Estados, Argentina) rather than from Banks Island, B.C., Canada. (2) The type of Iridaea heterocarpa P. et R. [Mazzaella heterocarpa (P. et R.) Fred.] represents the tetrasporangial phase of a species of Chondrus, possibly C. crispus Stackh. (3) The types of Iridaea lilacina P. et R., I. phyllocarpa P. et R., and Iridophycus furcatum S. et G. represent a single species from Alaska, Mazzaella phyllocarpa (P. et R.) Perest., currently but incorrectly called M. heterocarpa. (4) The type of Iridophycus oregonum Doty represents the tetrasporangial phase of the species from southern Alaska to southern California known incorrectly as M. heterocarpa. (5) Mazzaella splendens (S. et G.) Fred. is more closely related to M. linearis (S. et G.) Fred. than it is to M. flaccida (S. et G.) Fred. (6) Iridophycus coriaceum S. et G. is conspecific with M. splendens, whereas Rhodoglossum coriaceum E.Y. Dawson is an independent species: Mazzaella coriacea (E.Y. Dawson) Hughey. (7) Iridaea cornucopiae P. et R. is conspecific with Mazzaella laminarioides (Bory) Fred., and the type probably came from Chile rather than from the North Pacific. (8) Plants attributed to Iridaea cornucopiae in Pacific North America are referable to Mazzaella parksii (S. et G.) comb. nov. (9) Rhodoglossum parvum G. M. Smith et Hollenb. is an independent species: Mazzaella parva (G. M. Smith et Hollenb.) comb. nov. (10) Grateloupia squarrulosa S. et G., Grateloupia johnstonii S. et G., and Gigartina pectinata E.Y. Dawson represent a single species: Chondracanthus squarrulosus (S. et G.) comb. nov.