Mammalian aldehyde oxidases: genetics, evolution and biochemistry

Mammalian aldehyde oxidases are a small group of proteins belonging to the larger family of molybdo-flavoenzymes along with xanthine oxidoreductase and other bacterial enzymes. The two general types of reactions catalyzed by aldehyde oxidases are the hydroxylation of heterocycles and the oxidation of aldehydes into the corresponding carboxylic acids. Different animal species are characterized by a different complement of aldehyde oxidase genes. Humans contain a single active gene, while marsupials and rodents are characterized by four such genes clustering at a short distance on the same chromosome. At present, little is known about the physiological relevance of aldehyde oxidases in humans and other mammals, although these enzymes are known to play a role in the metabolism of drugs and compounds of toxicological importance in the liver. The present article provides an overview of the current knowledge of genetics, evolution, structure, enzymology, tissue distribution and regulation of mammalian aldehyde oxidases. Received 30 August 2007; received after revision 2 November 2007; accepted 8 November 2007     

Hormones and vertebrate evolution

Résumé On sait que chez les vertébrés la structure moléculaire de certaines hormones, telles que les hormones thyroïdiennes, est restée sans changement pendant l'histoire évolutionnaire du groupe. L'auteur discute la fixation par les protochordés des iodures marqués, et la signification pour l'origine des hormones thyroïdiennes de la localisation des combinaisons organiques d'¹³¹I dans la tunique des urochordés et dans l'endostyle de ceux-ci et de l'amphioxus.Si on considère le groupe d'hormones avec molécules protéiques ou polypeptidiques, on trouve parmi elles des différences qui indiquent l'existence de quelques caractéristiques individuelles. Quant aux plus grandes molécules, elles diffèrent les unes des autres par les propriétés antigeniques et les poids moléculaires, peutêtre par rapport au développement de specificité protéique. Les plus petites molécules polypeptidiques, telles que les polypeptides hypothalamiques, montrent des différences en ce qui concerne les acides aminés. Ces variations sont accompagnées par des différences qui constituent en théorie une base pour l'évolution adaptive, mais il n'est pas facile de faire une corrélation entre elles et les caractères physiologiques des divers groupes.On doit donc admettre que le cours d'évolution ne dépend pas seulement des variations moléculaires des hormones, mais que des hormones déjà existantes sont utilisées pour établir de nouvelles fonctions. Pour comprendre alors la pleine signification des variations moléculaires des hormones, il faut chercher d'autres fonctions; on doit aussi étudier beaucoup d'autres espèces, surtout parmi les vertébrés inférieurs.     

Physiological functions of D-amino acid oxidases: from yeast to humans

D-Amino acid oxidase (DAAO) is a FAD-containing flavoenzyme that catalyzes the oxidative deamination of D-isomers of neutral and polar amino acids. This enzymatic activity has been identified in most eukaryotic organisms, the only exception being plants. In the various organisms in which it does occur, DAAO fulfills distinct physiological functions: from a catabolic role in yeast cells, which allows them to grow on D-amino acids as carbon and energy sources, to a regulatory role in the human brain, where it controls the levels of the neuromodulator D-serine. Since 1935, DAAO has been the object of an astonishing number of investigations and has become a model for the dehydrogenase-oxidase class of flavoproteins. Structural and functional studies have suggested that specific physiological functions are implemented through the use of different structural elements that control access to the active site and substrate/product exchange. Current research is attempting to delineate the regulation of DAAO functions in the contest of complex biochemical and physiological networks.     

Structure and function of type I copper in multicopper oxidases

The type I copper center in multicopper oxidases is constructed from 1Cys2His and weakly coordinating 1Met or the non-coordinating 1Phe/1Leu, and it exhibits spectral properties and an alkaline transition similar to those of the blue copper center in blue copper proteins. Since the type I copper center in multicopper oxidases is deeply buried inside the protein molecule, electron transfers to and from type I copper are performed through specific pathways: the hydrogen bond between an amino acid located at the substrate binding site and a His residue coordinating type I copper, and the His-Cys-His sequence connecting the type I copper center and the trinuclear copper center comprised of a type II copper and a pair of type III coppers. The intramolecular electron transfer rates can be tuned by mutating the fourth ligand of type I copper. Further, mutation at the Cys ligand gives a vacant type I copper center and traps the reaction intermediate during the four-electron reduction of dioxygen.     

Sonic hedgehog signaling pathway in vertebrate epithelial appendage morphogenesis: perspectives in development and evolution

Vertebrate epithelial appendages are elaborate topological transformations of flat epithelia into complex organs that either protrude out of external (integument) and internal (oral cavity, gut) epithelia, or invaginate into the surrounding mesenchyme. Although they have specific structures and diverse functions, most epithelial appendages share similar developmental stages, including induction, morphogenesis, differentiation and cycling. The roles of the SHH pathway are analyzed in exemplary organs including feather, hair, tooth, tongue papilla, lung and foregut. SHH is not essential for induction and differentiation, but is involved heavily in morphogenetic processes including cell proliferation (size regulation), branching morphogenesis, mesenchymal condensation, fate determination (segmentation), polarizing activities and so on. Through differential activation of these processes by SHH in a spatiotemporal-specific fashion, organs of different shape and size are laid down. During evolution, new links of developmental pathways may occur and novel forms of epithelial appendages may emerge, upon which evolutionary selections can act. Sites of major variations have progressed from the body plan to the limb plan to the epithelial appendage plan. With its powerful morphogenetic activities, the SHH pathway would likely continue to play a major role in the evolution of novel epithelial appendages.     

Release of oxidases from the roots of plants

Summary In this paper, we report on the isolation and purification of the oxidase released from the roots ofLactuca sativa seedlings. This is the first time that the release of oxidases from the roots of plants into their rhizosphere has been reported.     

Isocitrate dehydrogenase gene duplication and fixed heterophenotype in the cultivated soybeanGlycine max

Summary Isocitrate dehydrogenase (E.C. 1.1.1.42) gene duplication was demonstrated in the self-pollinated soybean (Glycine max) by means of starch-gel electrophoresis. This finding explains the heterogeneity and/or fixed heterophenotype observed in some soybean cultivars.     

Structure, function and evolution of antifreeze proteins

Antifreeze proteins bind to ice crystals and modify their growth. These proteins show great diversity in structure, and they have been found in a variety of organisms. The ice-binding mechanisms of antifreeze proteins are not completely understood. Recent findings on the evolution of antifreeze proteins and on their structures and mechanisms of action have provided new understanding of these proteins in different contexts. The purpose of this review is to present the developments in contrasting research areas and unite them in order to gain further insight into the structure and function of the antifreeze proteins. Received 2 September 1998; received after revision 21 October 1998; accepted 2 November 1998     

A note on the evolution of the transducer mechanism of the vertebrate retinal rod

Summary The Ca²⁺-gating mechanism that is the key component of membrane excitability in Paramecium has recently been localized on the cilia of this animal. Such a finding shows how the change in Ca²⁺ permeability (which is the probable consequence of the photoisomerization of rhodopsin) of the discs of the outer segments of the retinal rods could have evolved.     

Recent progress in intein research: from mechanism to directed evolution and applications

Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.     

New norsesquiterpene aldehyde and sesquiterpene hemiacetal from the seed ofPolygonum hydropiper

Summary A new norsesquiterpene aldehyde, polygonal and a new sesquiterpene hemiacetal, isodrimeninol having drimane skeleton have been isolated from the seed ofPolygonum hydropiper, and their structures have been established to be1 and5. Polygonal showed pungency and plant growth inhibitory activity.     

The opsins of the vertebrate retina: insights from structural,biochemical, and evolutionary studies

The vertebrate retina contains several classes of visual pigments responsible for such diverse functions as image- and nonimage-forming vision, the entrainment of circadian cycles, and the pupilary light response. With vision being vital to the survival of many species, the elucidation of the structural and biochemical properties of visual pigments has been the focus of a large body of research that has led to rapid advances in the field of photoreception. In this review, the current understanding of the structure, function, biochemistry, and evolution of the opsins that make up the photopigments in the vertebrate retina will be reviewed. These include the rod and cone opsins, melanopsin, RGR, peropsin, and VA-opsin. The goal is to highlight important questions that have been answered and to define some of the remaining questions in the field that will provide future directions for research.     

Significant differential gene duplication without ancestral tetraploidy in a genus of mexican fish

Summary A comparison of the protein products of 20–25 structural gene loci among the known species of the goodeid fish genusSkiffia suggests that at least 4 loci (16–20%) have undergone species-specific duplications (or, in 1 case, apparent loss) during the evolution of the genus. The species are clearly diploids, and the data therefore indicate that even a large proportion of differentially duplicated loci within a group of related fish species is not critical evidence of common tetraploid ancestry. Differential duplication of structural gene loci may be an important component of the genetic differences that separate congeneric conventional diploid species.Supported by NSF grants DEB76-20958 (BJT), DEB77-03257 (EMR) and DEB77-17315 (RRM).     

Distinct but parallel evolutionary patterns between alcohol and aldehyde dehydrogenases: addition of fish/human betaine aldehyde dehydrogenase divergence

Alcohol dehydrogenases (ADHs) of the MDR type (medium-chain dehydrogenases/reductases) have diverged into two evolutionary groups in eukaryotes: a set of 'constant' enzymes (class III) typical of basal enzymes, and a set of 'variable' enzymes (remaining classes) suggesting 'evolving' forms. The variable set has larger overall variability, different segment variability, and variability also in functional segments. Using a major aldehyde dehydrogenase (ALDH) from cod liver and fish ALDHs deduced from the draft genome sequence of Fugu rubripes (Japanese puffer fish), we found that ALDHs form more complex patterns than the ADHs. Nevertheless, ALDHs also group into 'constant' and 'variable' sets, have separate segment variabilities, and distinct functions. Betaine ALDH (class 9 ALDH) is 'constant,' has three segments of variability, all non-functional, and a limited fish/human divergence, reminiscent of the ADH class III pattern. Enzymatic properties of fish betaine ALDH were also determined. Although all ALDH patterns are still not known, overall patterns are related to those of ADH, and group separations may be distinguished. The results can be interpreted functionally, support ALDH isozyme distinctions, and assign properties to the multiplicities of the ADH and ALDH enzymes.     

Blood-forming tissues in orthopteran insects: An analogue to vertebrate hemopoietic organs

Résumé Des cellules sanguines différenciées sont produites tout au long de la vic larvaire et imaginale des Insectes Orthoptères par des tissus hématopoïétiques spécialisés. Nos études morphologiques et expérimentales soulignent l'analogie que présentent ces tissus avec les organes hématopoïétiques des Vertébrés, à la fois sur le plan structural et sur la plan fonctionnel.     

Current topics in genome evolution: Molecular mechanisms of new gene formation

Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. These shared functional domains, however, are differentially shuffled among evolutionary lineages to produce an increasing number of domain architectures. Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events. Received 18 October 2006; received after revision 18 November 2006; accepted 28 November 2006     

Conserved eukaryotic transposable elements and the evolution of gene regulation

Multiple remnants of transposable elements preserved in cis-regulatory modules may represent a record of mutations that were critical to the evolution of gene regulation and speciation. Received 13 August 2007; received after revision 8 October 2007; accepted 23 October 2007