Classification and phylogeny of the diapsid reptiles

Reptiles with two temporal openings in the skull are generally divided into two groups–the Lepidosauria (lizards, snakes, Sphenodon , 'eosuchians') and the Archosauria (crocodiles, thecodontians, dinosaurs, pterosaurs). Recent suggestions that these two are not sister-groups are shown to be unproven, whereas there is strong evidence that they form a monophyletic group, the Diapsida, on the basis of several synapomorphies of living and fossil forms. A cladistic analysis of skull and skeletal characters of all described Permo-Triassic diapsid reptiles suggests some significant rearrangements to commonly held views. The genus Petrolacosaurus is the sister-group of all later diapsids which fall into two large groups–the Archosauromorpha (Pterosauria, Rhynchosauria, Prolacertiformes, Archosauria) and the Lepidosauromorpha (Younginiformes, Sphenodontia, Squamata). The pterosaurs are not archosaurs, but they are the sister-group of all other archosauromorphs. There is no close relationship between rhynchosaurs and sphenodontids, nor between Prolacerta or Tanystropheus and lizards. The terms 'Eosuchia', 'Rhynchocephalia' and 'Protorosauria' have become too wide in application and they are not used. A cladistic classification of the Diapsida is given, as well as a phylogenetic tree which uses cladistic and stratigraphic data.     

Classification,distribution and phylogeny of the genus Ottelia

The genus Ottelia is one of the great genera of Hydrocharidaceae. About 25 species distributed in the Palaeotropics, extending from Africa through India and SE. Asia to Korea and Japan, Australia and New Caledonia, 1 species in Brazil; centres of specific devolopment are found in Central Africa and SE Asia. The present study is mainly based on the materials collected during the field explorations in the lakes of Yunnan and observations on the structure of the spathe and flowers, the variation of leaf of the plants cultivated in Kunming Bot. Garden. Instead of the wings of the spathe used by Dandy, by the characters such as uni-or bisexual flowers, this genus is divided into two subgenera, which by the number of the flowers in spathe and the number of the carpus in ovary again subdivided into 4 sections. They are as the following: A. Subg. Ottelia. Flowers bisexual. Sect. 1. Ottelia. Spathe with 1 flower; ovary with 6(—9) carpus. Sect. 2. Oligolobos (Gagnep.) Dandy. Spathe with many flowers; ovary with 3 carpus. B. Subg. Boottia (Wall.) Dandy. Flowers unisexual; the male spathe with 1-many flowers, the female spathe with many flowers. Sect. 3. Boottia. The male spathe with 1 flower; ovary with 9(—15) carpus. Sect. 4. Xystrolobos (Gagnep.) H. Li. The female spathe with (2-) many flowers; ovary with 3 or 9 carpus. The Chinense species of ottelia is in great need for revision. All of the species in China previousely described under Ottelia Pers, Boottia Wall., Oligolobos Gagnep, and Xystrolobos Gagen. are here combined into 3 species. They are O. alismoides, O. cordata, O. acuminata with 4 variaties. After a study of the geographic distribution and infer relation-ships among the floristic elements it has been proved that Ottelia is certainly an ancient genus, and the primitive types came into being and widely dispersed before the separation of Laurasia from Gondwana. During a considerable period of time the elements of the genus Ottelia in freshwater environment of different continents have been separately differentiated and evolved into more or less derived types. The structure of flowers in all of the asian species shows the following evolutionary tendenoes: 1. In this genus the plants with unisexual flowers have evolved from plants with bisexual flower; 2. In the groups with bisexual or unisexual flowers the number of stamens and styles reduced to 3-merous, but the number of flowers in spathe increased. So that the subgenus Ottelia is more primitive than the subgenus Bottia; While in the subgenus Ottelia O. alismoides is a more primitive than O. balansae and in the subgenus Boottia O. cordata is the most primitive, butO. alata seems to be the most advanced.     

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases

The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases.     

Biotechnological applications of hydrogenases

Hydrogenases have found use in a variety of biotechnological applications, including biohydrogen production, wastewater treatment, the prevention of microbial-induced corrosion and the generation and regeneration of NADP cofactors. In the future, advances in genome mining and screening techniques are likely to identify new hydrogenases for novel applications.     

Structure and mechanism of iron-only hydrogenases

The recent elucidation of the structures of iron-only hydrogenases from the microorganisms Clostridium pasteurianum and Desulfovibrio desulfuricans has revealed that the presumed site of reversible hydrogen oxidation exists as a unique, protein-associated organometallic prosthetic group. Details of the hydrogenase structures provide insight into the chemical mechanism of this highly evolved catalyst.     

有瓣蝇类分类、系统发育及演化

有瓣蝇类(Calyptratae)隶属于昆虫纲(Insecta)四大超适应辐射类群之一的双翅目(Diptera),占双翅目已知物种多样性的近20%。有瓣蝇类分布广泛,生物学习性极为多样,在维系生态系统稳定中发挥着重要作用,是媒介、法医、传粉和天敌昆虫学研究领域的热点类群,也是探究双翅目系统演化及其成功适应辐射的关键类群。为了还原有瓣蝇类的演化历史,许多著名昆虫学者先后对该类昆虫开展过不同层面的研究。有瓣蝇类的单系性得到了普遍支持,并被分为3个总科——虱蝇总科(Hippoboscoidea)、蝇总科(Muscoidea)和狂蝇总科(Oestroidea),其中单系的狂蝇总科与多系的蝇总科聚为一支,再与虱蝇总科成为姐妹群。在科级阶元水平,蝠蝇科(Streblidae)(虱蝇总科)、花蝇科(Anthomyiidae)(蝇总科)、丽蝇科(Calliphoridae)(狂蝇总科)、邻寄蝇科(Rhinophoridae)(狂蝇总科)等类群的单系性仍有待验证,且新的科仍在不断被建立［如粉蝇科(Polleniidae)、乌鲁鲁蝇科(Ulurumyiidae)］,因此,有瓣蝇类科级系统发育关系仍不十分明晰。已有研究对虱蝇总科虱蝇科(Hippoboscidae)、蝠蝇科、蛛蝇科(Nycteribiidae),蝇总科蝇科(Muscidae)、粪蝇科(Scathophagidae),狂蝇总科麻蝇科(Sarcophagidae)、狂蝇科(Oestridae)胃蝇亚科(Gasterophilinae)的演化历史进行研究,明确了起源与扩散、寄主转移、取食策略等关键生物学习性的演化历史。但由于部分关键类群生活史信息的缺失,以及尚未有效解决的系统发育关系,有瓣蝇类演化历史仍有许多待解之谜。本文综述了有瓣蝇类分类、系统发育及演化研究进展,是在系统学研究进入系统发育基因组学时代后对该类群相关研究进展的首次全面总结。     

Molecular biology of microbial hydrogenases

Hydrogenases (H2ases) are metalloproteins. The great majority of them contain iron-sulfur clusters and two metal atoms at their active center, either a Ni and an Fe atom, the [NiFe]-H2ases, or two Fe atoms, the [FeFe]-H2ases. Enzymes of these two classes catalyze the reversible oxidation of hydrogen gas (H2 <--> 2 H+ + 2 e-) and play a central role in microbial energy metabolism; in addition to their role in fermentation and H2 respiration, H2ases may interact with membrane-bound electron transport systems in order to maintain redox poise, particularly in some photosynthetic microorganisms such as cyanobacteria. Recent work has revealed that some H2ases, by acting as H2-sensors, participate in the regulation of gene expression and that H2-evolving H2ases, thought to be involved in purely fermentative processes, play a role in membrane-linked energy conservation through the generation of a protonmotive force. The Hmd hydrogenases of some methanogenic archaea constitute a third class of H2ases, characterized by the absence of Fe-S cluster and the presence of an iron-containing cofactor with catalytic properties different from those of [NiFe]- and [FeFe]-H2ases. In this review, we emphasise recent advances that have greatly increased our knowledge of microbial H2ases, their diversity, the structure of their active site, how the metallocenters are synthesized and assembled, how they function, how the synthesis of these enzymes is controlled by external signals, and their potential use in biological H2 production.     

Multiple forms of bacterial hydrogenases

Ackrell, B. A. C. (University of Hawaii, Honolulu), R. N. Asato, and H. F. Mower. Multiple forms of bacterial hydrogenases. J. Bacteriol. 92:828-838. 1966.-Extracts of certain bacterial species have been shown by disc electrophoresis on polyacrylamide gel to contain multiple hydrogenase systems. The hydrogenase enzymes comprising these systems have different electrophoretic mobilities and produce a band pattern that is unique for each bacterial species. Of 20 bacterial species known to possess hydrogenase activity and which were examined by this technique, only the activities of Clostridium tetanomorphum and C. thermosaccharolyticum could be attributed, at pH 8.3, to a single hydrogenase enzyme. This multiplicity of hydrogenase forms was found both in bacteria which contain mostly soluble hydrogenases and in those where the hydrogenase is predominantly associated with particulate material. When solubilization of this particulate material could be effected, at least two solubilized hydrogenases were released, and, of these, one would have the same electrophoretic properties (i.e., R(F)) as one of the soluble hydrogenases already present in small amounts within the cell. Different growth conditions for various types of bacteria, such as the nitrogen source, the degree of aeration, and photosynthetic versus aerobic growth in the dark, as well as the conditions under which the cells were stored, markedly affected the hydrogenase activity of the cells, but not their hydrogenase band pattern. The disc electrophoresis technique proved to be 10 times more sensitive than the manometric technique in detecting hydrogenase activity.     

Activation and active sites of nickel-containing hydrogenases

Hydrogenases that contain nickel and iron-sulphur clusters also have a regulatory mechanism, by which exposure to oxidants such as oxygen prevents their reaction with hydrogen. Treatment with reducing agents then causes reactivation. In some hydrogenases from Desulfovibrio species, there is evidence that there are at least two different deactivated states, which differ in their rates of reductive reactivation. The membrane-bound hydrogenase of D. desulfuricans, Norway strain, the periplasmic hydrogenase of D. gigas and the membrane-bound hydrogenase of Alcaligenes eutrophus can be isolated in a state (termed "Unready") which requires up to several hours for full activation by hydrogen. By contrast the soluble hydrogenases of D. desulfuricans and A. eutrophus can be reactivated relatively rapidly. In all of these enzymes, with the exception of the latter one, the existence of the activated and deactivated states can be correlated with different ESR-detectable forms of nickel. The possible functions of nickel and [Fe-4S] clusters in catalysis are discussed.     

Membrane targeting and translocation of bacterial hydrogenases

Periplasmic or membrane-bound bacterial hydrogenases are generally composed of a small subunit and a large subunit. The small subunit contains a peculiar N-terminal twin-arginine signal peptide, whereas the large subunit lacks any known targeting signal for export. Genetic and biochemistry data support the assumption that the large subunit is cotranslocated with the small subunit across the cytoplasmic membrane. Indeed, the signal peptide carried by the small subunit directs both the small and the large subunits to the recently identified Mtt/Tat pathway, independently of the Sec machinery. In addition, the twin-arginine signal peptide of hydrogenase is capable of directing protein import into the thylakoidal lumen of chloroplasts via the homologous deltapH-driven pathway, which is independent of the Sec machinery. Therefore, the translocation of hydrogenase shares characteristics with the deltapH-driven import pathway in terms of Sec-independence and requirement for the twin-arginine signal peptide, and with protein import into peroxisomes in a "piggyback" fashion.     

Dynamic electrochemical experiments on hydrogenases

Photosynthesis Research - A powerful approach for studying hydrogenases, applying a suite of dynamic electrochemical techniques known as protein film electrochemistry, is trailblazing fresh...     

Oxygen-tolerant hydrogenases in hydrogen-based technologies

To develop a viable H2 technology, production of H2 has to be significantly enlarged by using renewable resources. One option of generating H2 is the photosynthetic conversion of sunlight and water directly to H2 and O2. Photosystems and hydrogenases are currently being exploited for the design of efficient H2-producing systems that require highly active and O2-tolerant biocatalysts. This communication focuses on two challenging features: hydrogenases that produce H2 in the presence of O2, and direct electron transfer between photosystem I (PS I) and hydrogenase. The latter is accomplished by connecting both modules through a protein fusion or a synthetic molecular wire. These are first steps toward a photosynthetic microbial cell or a semi-synthetic system that may be employed in future H2-based technologies.     

The hydrogenases and formate dehydrogenases ofEscherichia coli

Escherichia coli has the capacity to synthesise three distinct formate dehydrogenase isoenzymes and three hydrogenase isoenzymes. All six are multisubunit, membrane-associated proteins that are functional in the anaerobic metabolism of the organism. One of the formate dehydrogenase isoenzymes is also synthesised in aerobic cells. Two of the formate dehydrogenase enzymes and two hydrogenases have a respiratory function while the formate dehydrogenase and hydrogenase associated with the formate hydrogenlyase pathway are not involved in energy conservation. The three formate dehydrogenases are molybdo-selenoproteins while the three hydrogenases are nickel enzymes; all six enzymes have an abundance of iron-sulfur clusters. These metal requirements alone invoke the necessity for a profusion of ancillary enzymes which are involved in the preparation and incorporation of these cofactors. The characterisation of a large number of pleiotropic mutants unable to synthesise either functionally active formate dehydrogenases or hydrogenases has led to the identification of a number of these enzymes. However, it is apparent that there are many more accessory proteins involved in the biosynthesis of these isoenzymes than originally anticipated. The biochemical function of the vast majority of these enzymes is not understood. Nevertheless, through the construction and study of defined mutants, together with sequence comparisons with homologous proteins from other organisms, it has been possible at least to categorise them with regard to a general requirement for the biosynthesis of all three isoenzymes or whether they have a specific function in the assembly of a particular enzyme. The identification of the structural genes encoding the formate dehydrogenase and hydrogenase isoenzymes has enabled a detailed dissection of how their expression is coordinated to the metabolic requirement for their products. Slowly, a picture is emerging of the extremely complex and involved path of events leading to the regulated synthesis, processing and assembly of catalytically active formate dehydrogenase and hydrogenase isoenzymes. This article aims to review the current state of knowledge regarding the biochemistry, genetics, molecular biology and physiology of these enzymes.     

Iron hydrogenases and the evolution of anaerobic eukaryotes

Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic protozoa scattered throughout the eukaryotic tree. Hydrogenases also play a central role in the hydrogen and syntrophic hypotheses for eukaryogenesis. Here, we show that sequences related to iron-only hydrogenases ([Fe] hydrogenases) are more widely distributed among eukaryotes than reports of hydrogen production have suggested. Genes encoding small proteins which contain conserved structural features unique to [Fe] hydrogenases were identified on all well-surveyed aerobic eukaryote genomes. Longer sequences encoding [Fe] hydrogenases also occur in the anaerobic eukaryotes Entamoeba histolytica and Spironucleus barkhanus, both of which lack hydrogenosomes. We also identified a new [Fe] hydrogenase sequence from Trichomonas vaginalis, bringing the total of [Fe] hydrogenases reported for this organism to three, all of which may function within its hydrogenosomes. Phylogenetic analysis and hypothesis testing using likelihood ratio tests and parametric bootstrapping suggest that the [Fe] hydrogenases in anaerobic eukaryotes are not monophyletic. Iron-only hydrogenases from Entamoeba, Spironucleus, and Trichomonas are plausibly monophyletic, consistent with the hypothesis that a gene for [Fe] hydrogenase was already present on the genome of the common, perhaps also anaerobic, ancestor of these phylogenetically distinct eukaryotes. Trees where the [Fe] hydrogenase from the hydrogenosomal ciliate Nyctotherus was constrained to be monophyletic with the other eukaryote sequences were rejected using a likelihood ratio test of monophyly. In most analyses, the Nyctotherus sequence formed a sister group with a [Fe] hydrogenase on the genome of the eubacterium Desulfovibrio vulgaris. Thus, it is possible that Nyctotherus obtained its hydrogenosomal [Fe] hydrogenase from a different source from Trichomonas for its hydrogenosomes. We find no support for the hypothesis that components of the Nyctotherus [Fe] hydrogenase fusion protein derive from the mitochondrial respiratory chain.     

Immunological relationship among hydrogenases.

We examined the immunological cross-reactions of 11 different hydrogenase antigens with 9 different hydrogenase antibodies. Included were antibodies and antigens of both subunits of the hydrogenases of Bradyrhizobium japonicum and Thiocapsa roseopersicina. The results showed a strong relationship among the Ni-Fe dimeric hydrogenases. The two subunits of Ni-Fe dimeric hydrogenases appeared immunologically distinct: specific interactions occurred only when antibodies to the 60- and 30-kilodalton subunits reacted with the 60- and 30-kilodalton-subunit antigens. The interspecies cross-reactions suggested that at least one conserved protein region exists among the large subunits of these enzymes, whereas the small subunits are less conserved. Antibodies to the Fe-only bidirectional hydrogenase of Clostridium pasteurianum reacted with the Desulfovibrio vulgaris bidirectional hydrogenase. Surprisingly, antibodies to the clostridial uptake hydrogenase did not react with any of the Fe-only bidirectional hydrogenases but did react with several of the Ni-Fe dimeric hydrogenases. The two hydrogenases from C. pasteurianum were found to be quite different immunologically. The possible relationship of these findings to the structure and catalytic functions of hydrogenase are discussed.     

Localization and stability of hydrogenases from aerobic hydrogen bacteria

Alcaligenes eutrophus strains H 16, B 19, G 27 and N9A contained two different hydrogenases. One enzyme catalyzed the reduction of NAD by hydrogen and was strictly localized in the soluble cell fraction, while the second enzyme was found to be particulate and unable to react with NAD.All other tested strains, Alcaligenes paradoxus SA 29, Pseudomonas facilis, P. palleronii RH 2, Pseudomonas sp. strain GA 3, Paracoccus denitrificans, Aquaspirillum autotrophicum SA 32, and Corynebacterium autotrophicum 14g and 7C contained only a single enzyme exclusively bound to membranes. This was established using fractional centrifugation, indicator enzyme systems, gentle methods of cell disintegration and discontinuous sucrose density gradient centrifugation. In cell-free extracts obtained by rough disruption (sonication) of cells, hydrogenase was associated to particles of different size and sedimentation velocity. A partial solubilization of hydrogenase caused by sonication was observed with P. facilis.Without exception, the particulate hydrogenases were found (1) to be unable to reduce pyridine nucleotides, and (2) to reduce methylene blue at an extremely high activity. The eminent reaction rate of 34 moles H₂ oxidized per min and mg protein has been determined in particle suspensions of Pseudomonas sp. strain GA 3. All hydrogenases were stable during storage under hydrogen atmosphere, except the soluble enzyme from A. eutrophus H 16 which was shown to be more stable under aerobic conditions.