scholarly journals Episodic evolution of a eukaryotic NADK repertoire of ancient provenance

2018 ◽  
Author(s):  
Oliver Vickman ◽  
Albert J Erives
Keyword(s):  
Phylogenetic Analysis ◽  
Nicotinamide Adenine Dinucleotide ◽  
Reducing Power ◽  
Gene Repertoire ◽  
Biosynthetic Pathways ◽  
Nad Kinase ◽  
Evolutionary Transitions ◽  
Major Clade ◽  
Episodic Evolution ◽  
Almost All

NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic ("cyto") and mitochondrial ("mito") clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions.

scholarly journals Characterization of native and oxidized starches of two varieties of Peruvian carrot (Arracacia xanthorrhiza, B.) from two production areas of Paraná state, Brazil

2009 ◽  
Vol 52 (3) ◽  
pp. 701-713 ◽  
Author(s):  
Luciana Shizue Matsuguma ◽  
Luiz Gustavo Lacerda ◽  
Egon Schnitzler ◽  
Marco Aurélio da Silva Carvalho Filho ◽  
Célia Maria Landi Franco ◽  
...  
Keyword(s):  
Thermal Analysis ◽  
Reducing Power ◽  
Blue Color ◽  
Carboxyl Content ◽  
Modified Starches ◽  
Physicochemical Methods ◽  
Partial Degradation ◽  
Almost All ◽  
Production Areas

Two commercial varieties of Peruvian carrot ('Amarela de Carandaí' and 'Senador Amaral') were processed into flour, starch and bagasse and chemically evaluated. The starch was extracted, modified with H2O2 and characterized by the physicochemical methods. By using the methylene blue dyeing, the granules of the modified starches showed intense blue color. The carboxyl content, the reducing power and the amount of the water liberated from the pastes after the freeze-thawing were higher for the oxidized starches and their pastes were clearer than those of the native starches of the two varieties from the two production areas. The RVA viscoamylography showed that the modified starches had lower viscosities with differences between the varieties. In the thermal analysis, the temperatures of the pyrolysis were higher for the native (310.37, 299.08, 311.18 ºC) than for the modified starches (294.16, 296.65 e 293.29 ºC) for both the varieties. This difference could be related with the larger surface of the granules due to the partial degradation promoted by the chemical modification. In almost all results, the differences were evident between the varieties but not for the cultivation places.

scholarly journals Molecular Systematics and Patterns of Diversification in Pyrrhura (Psittacidae), with Special Reference to the Picta-Leucotis Complex

The Auk ◽  
2006 ◽  
Vol 123 (3) ◽  
pp. 660-680 ◽  
Author(s):  
Camila C. Ribas ◽  
Leo Joseph ◽  
Cristina Y. Miyaki
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Molecular Systematics ◽  
Neotropical Forests ◽  
The Third ◽  
Species Pairs ◽  
Age Variation ◽  
Mtdna Diversity ◽  
Almost All ◽  
Evolutionary Lineages

AbstractParakeets in the genus Pyrrhura occur in Amazonia and in almost all other major Neotropical forests. Their uneven distribution (with some widespread and several geographically restricted endemic taxa) and complex patterns of plum- age variation have long generated a confused taxonomy. Several taxonomically difficult polytypic species are usually recognized. Here, we present a mitochondrial DNA (mtDNA) phylogenetic analysis of Pyrrhura, with emphasis on the especially problematic picta-leucotis complex, to provide a more robust basis for interpreting the systematics and historical biogeography of the group. Our main findings are that (1) Pyrrhura can be divided into three main evolutionary lineages, one comprising P. cruentata, an Atlantic Forest endemic, the second comprising the picta-leucotis complex, and the third comprising the remaining species; (2) the traditionally recognized species P. picta and P. leucotis are not monophyletic; and (3) most of the species recognized by Joseph (2000, 2002) are diagnosable as independent evolutionary units, with the exception of the following species pairs: P. snethlageae and P. amazonum, P. leucotis and P. griseipectus, and P. roseifrons and P. peruviana. Other than P. cruentata, the two clades that constitute Pyrrhura appear to have radiated and evolved their present mtDNA diversity over short periods during the Plio-Pleistocene.Sistemática Molecular y Patrones de Diversificación en Pyrrhura (Psittacidae), con Énfasis en el Complejo Picta-Leucotis

scholarly journals New Chemical Probe Targeting Bacterial NAD Kinase

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4893
Author(s):  
David A. Clément ◽  
Clarisse Leseigneur ◽  
Muriel Gelin ◽  
Dylan Coelho ◽  
Valérie Huteau ◽  
...  
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Kinase Inhibitors ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Nicotinamide Adenine ◽  
Infection Model ◽  
Detailed Knowledge ◽  
Nad Kinase ◽  
Chemical Probe ◽  
Covalent Coupling

Nicotinamide adenine dinucleotide (NAD) kinases are essential and ubiquitous enzymes involved in the tight regulation of NAD/nicotinamide adenine dinucleotide phosphate (NADP) levels in many metabolic pathways. Consequently, they represent promising therapeutic targets in cancer and antibacterial treatments. We previously reported diadenosine derivatives as NAD kinase inhibitors with bactericidal activities on Staphylococcus aureus. Among them, one compound (namely NKI1) was found effective in vivo in a mouse infection model. With the aim to gain detailed knowledge about the selectivity and mechanism of action of this lead compound, we planned to develop a chemical probe that could be used in affinity-based chemoproteomic approaches. Here, we describe the first functionalized chemical probe targeting a bacterial NAD kinase. Aminoalkyl functional groups were introduced on NKI1 for further covalent coupling to an activated SepharoseTM matrix. Inhibitory properties of functionalized NKI1 derivatives together with X-ray characterization of their complexes with the NAD kinase led to identify candidate compounds that are amenable to covalent coupling to a matrix.

scholarly journals Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum

2011 ◽  
Vol 77 (22) ◽  
pp. 7984-7997 ◽  
Author(s):  
Daniel Amador-Noguez ◽  
Ian A. Brasg ◽  
Xiao-Jiang Feng ◽  
Nathaniel Roquet ◽  
Joshua D. Rabinowitz
Keyword(s):  
Amino Acids ◽  
Clostridium Acetobutylicum ◽  
Reducing Power ◽  
Tca Cycle ◽  
Content Type ◽  
Isotope Tracers ◽  
Metabolic Fluxes ◽  
The Tca Cycle ◽  
Concentration Changes ◽  
Almost All

ABSTRACTThe fermentation carried out by the biofuel producerClostridium acetobutylicumis characterized by two distinct phases. Acidogenesis occurs during exponential growth and involves the rapid production of acids (acetate and butyrate). Solventogenesis initiates as cell growth slows down and involves the production of solvents (butanol, acetone, and ethanol). Using metabolomics, isotope tracers, and quantitative flux modeling, we have mapped the metabolic changes associated with the acidogenic-solventogenic transition. We observed a remarkably ordered series of metabolite concentration changes, involving almost all of the 114 measured metabolites, as the fermentation progresses from acidogenesis to solventogenesis. The intracellular levels of highly abundant amino acids and upper glycolytic intermediates decrease sharply during this transition. NAD(P)H and nucleotide triphosphates levels also decrease during solventogenesis, while low-energy nucleotides accumulate. These changes in metabolite concentrations are accompanied by large changes in intracellular metabolic fluxes. During solventogenesis, carbon flux into amino acids, as well as flux from pyruvate (the last metabolite in glycolysis) into oxaloacetate, decreases by more than 10-fold. This redirects carbon into acetyl coenzyme A, which cascades into solventogenesis. In addition, the electron-consuming reductive tricarboxylic acid (TCA) cycle is shutdown, while the electron-producing oxidative (clockwise) right side of the TCA cycle remains active. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources (carbon and reducing power) from biomass production into solvent production.

scholarly journals Controlling Rhizoctonia Damping-off of Chinese Mustard by Using Endomycorrhizal Rhizoctonia spp. Isolated from Orchid Mycorrhizae

Plant Disease ◽  
2016 ◽  
Vol 100 (1) ◽  
pp. 85-91 ◽  
Author(s):  
Jr-Hau Jiang ◽  
Si-Loi Tam ◽  
Takeshi Toda ◽  
Lung-Chung Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Rhizoctonia Solani ◽  
Disease Severity ◽  
Anastomosis Group ◽  
Effective Strategy ◽  
Damping Off ◽  
Binucleate Rhizoctonia ◽  
Orchid Mycorrhizae ◽  
Almost All ◽  
Test Plants

Inoculation of hypovirulent Rhizoctonia spp. has been recognized as an effective strategy for protecting plants against damping-off caused by pathogenic Rhizoctonia spp. In this study, endomycorrhizal Rhizoctonia spp. isolated from fungal pelotons in orchid plants were used for controlling Rhizoctonia damping-off of Chinese mustard. According to phylogenetic analysis and anastomosis group (AG) determination, the virulence of three isolates of multinucleate Rhizoctonia solani in AG-6; eight isolates of binucleate Rhizoctonia in AG-A, AG-B, AG-G, AG-P, and AG-R; and two isolates of binucleate R. repens were evaluated using test plants. All isolates, except that in AG-R, caused low disease severity in 10-day-old radish (0.10 to 0.61), cucumber (0.28 to 0.54), and Chinese mustard (0.18 to 0.65). By contrast, pathogenic isolates in AG-4 killed almost all test plants with symptoms of collapsed hypocotyl and wilted leaves (0.88 to 0.96). Of the 13 endomycorrhizal Rhizoctonia isolates assessed, AG-P isolates Cno10-3 and CalS1-2 provided 91 and 100% protection, respectively, against R. solani AG-4 in 26-day-old Chinese mustard. This study revealed that endomycorrhizal Rhizoctonia spp. in orchid have the potential to biologically control damping-off of Chinese mustard.

Cladistic analysis of the Early Cambrian olenelloid trilobites

1998 ◽  
Vol 72 (1) ◽  
pp. 59-78 ◽  
Author(s):  
Bruce S. Lieberman
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Intraspecific Variability ◽  
Evolutionary Relationships ◽  
Early Cambrian ◽  
New Genera ◽  
Phylogenetic Structure ◽  
Major Clade ◽  
Lateral Margins

A phylogenetic analysis was used to determine evolutionary relationships within the Early Cambrian superfamily Olenelloidea Walcott, 1890. Phylogenetic patterns within the suborder Olenellina Walcott, 1890, which contains the Olenelloidea and the Fallotaspidoidea Hupé, 1953, are also discussed. The Olenelloidea are monophyletic, and synapomorphies uniting them include the condition of the ocular lobes where they intersect the frontal lobe of the glabella, and the condition of the lateral margins of the glabellar lobes. In contrast, taxa formerly assigned to the Fallotaspidoidea are shown to represent a paraphyletic grade of several genera, some more closely related to the Olenelloidea, and some more closely related to the Redlichiina Richter, 1933. Seventy-nine exoskeletal characters were coded for 26 taxa within the Olenellina. These included 22 ingroup Olenelloidea and four outgroup taxa that have traditionally been assigned to the Fallotaspidoidea. When subjected to parsimony analysis these character data yielded a single most parsimonious cladogram that provides an hypothesis of relationship for the generic clades within the superfamily. Two new genera are recognized herein, Fritzolenellus and Lochmanolenellus. It has been argued that genetic flexibility was so great and trilobite morphology was so plastic in the Early Cambrian that suprageneric classification of Early Cambrian trilobites is precluded. Although levels of intraspecific variability may have been slightly higher in the Early Cambrian relative to the mid Paleozoic, based on the extent of polymorphic character codings, it was not so high as to obviate attempts at recovering phylogenetic structure in a major clade of Early Cambrian taxa. In addition, the consistency index recovered by this analysis is not unduly low for a phylogenetic database of this size. The phylogenetic analysis also has bearing on patterns of allometric heterochrony, which have often been held to be significant in Early Cambrian trilobites. The paedomorphic retention of advanced genal spines into the adult probably evolved at least four times. Three of the episodes can be best described as neoteny, the fourth, as progenesis. Finally, based on the phylogeny, it is likely that rates of speciation in trilobites may have been two to three times higher in the Early Cambrian than in the mid Paleozoic.

scholarly journals Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

2015 ◽  
Vol 89 (13) ◽  
pp. 6585-6594 ◽  
Author(s):  
Dorine Gaëlle Reteno ◽  
Samia Benamar ◽  
Jacques Bou Khalil ◽  
Julien Andreani ◽  
Nicholas Armstrong ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Open Reading Frames ◽  
Gene Repertoire ◽  
Significant Similarity ◽  
Content Type ◽  
Genes Encoding ◽  
Giant Viruses ◽  
Almost All

ABSTRACTGiant viruses are protist-associated viruses belonging to the proposed orderMegavirales; almost all have been isolated fromAcanthamoebaspp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage fromVermamoebavermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy.IMPORTANCEBy usingVermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the familyAsfarviridae. Moreover, the faustovirus gene repertoire is ≈3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).

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