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581.
René TJM van der Heijden Berend Snel Vera van Noort Martijn A Huynen 《BMC bioinformatics》2007,8(1):83
Background
Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. 相似文献582.
ATG genes encode proteins that are required for macroautophagy, the Cvt pathway and/or pexophagy. Using the published Atg protein sequences, we have screened protein and DNA databases to identify putative functional homologs (orthologs) in 21 fungal species (yeast and filamentous fungi) of which the genome sequences were available. For comparison with Atg proteins in higher eukaryotes, also an analysis of Arabidopsis thaliana and Homo sapiens databases was included. This analysis demonstrated that Atg proteins required for non-selective macroautophagy are conserved from yeast to man, stressing the importance of this process in cell survival and viability. The A. thaliana and human genomes encode multiple proteins highly similar to specific fungal Atg proteins (paralogs), possibly representing cell type-specific isoforms. The Atg proteins specifically involved in the Cvt pathway and/or pexophagy showed poor conservation, and were generally not present in A. thaliana and man. Furthermore, Atg19, the receptor of Cvt cargo, was only detected in Saccharomyces cerevisiae. Nevertheless, Atg11, a protein that links receptor-bound cargo (peroxisomes, the Cvt complex) to the autophagic machinery was identified in all yeast species and filamentous fungi under study. This suggests that in fungi an organism-specific form of selective autophagy may occur, for which specialized Atg proteins have evolved. 相似文献
583.
584.
Maria C. Rubio Laura Calvo‐Begueria Mercedes Díaz‐Mendoza Mohamed Elhiti Marten Moore Manuel A. Matamoros Euan K. James Isabel Díaz Carmen Prez‐Rontom Irene Villar Violeta C. Sein‐Echaluce Kim H. Hebelstrup Karl‐Josef Dietz Manuel Becana 《The Plant journal : for cell and molecular biology》2019,100(1):38-54
Symbiotic hemoglobins provide O2 to N2‐fixing bacteria within legume nodules, but the functions of non‐symbiotic hemoglobins or phytoglobins (Glbs) are much less defined. Immunolabeling combined with confocal microscopy of the Glbs tagged at the C‐terminus with green fluorescent protein was used to determine their subcellular localizations in Arabidopsis and Lotus japonicus. Recombinant proteins were used to examine nitric oxide (NO) scavenging in vitro and transgenic plants to show S‐nitrosylation and other in vivo interactions with NO and abscisic acid (ABA) responses. We found that Glbs occur in the nuclei, chloroplasts and amyloplasts of both model plants, and also in the cytoplasm of Arabidopsis cells. The proteins show similar NO dioxygenase activities in vitro, are nitrosylated in Cys residues in vivo, and scavenge NO in the stomatal cells. The Cys/Ser mutation does not affect NO dioxygenase activity, and S‐nitrosylation does not significantly consume NO. We demonstrate an interaction between Glbs and ABA on several grounds: Glb1 and Glb2 scavenge NO produced in stomatal guard cells following ABA supply; plants overexpressing Glb1 show higher constitutive expression of the ABA responsive genes Responsive to ABA (RAB18), Responsive to Dehydration (RD29A) and Highly ABA‐Induced 2 (HAI2), and are more tolerant to dehydration; and ABA strongly upregulates class 1 Glbs. We conclude that Glbs modulate NO and interact with ABA in crucial physiological processes such as the plant's response to dessication. 相似文献
585.
Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X = Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to approximately 70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO. 相似文献
586.
Levin Simon A. Anderies John M. Adger Neil Barrett Scott Bennett Elena M. Cardenas Juan Camilo Carpenter Stephen R. Crpin Anne-Sophie Ehrlich Paul Fischer Joern Folke Carl Kautsky Nils Kling Catherine Nyborg Karine Polasky Stephen Scheffer Marten Segerson Kathleen Shogren Jason van den Bergh Jeroen Walker Brian Weber Elke U. Wilen James 《Ecosystems》2022,25(3):697-711
Ecosystems - The increasing frequency of extreme events, exogenous and endogenous, poses challenges for our societies. The current pandemic is a case in point; but "once-in-a-century"... 相似文献
587.
Kim Cuddington Z. Tasker Hull Warren J. S. Currie Marten A. Koops 《Theoretical Ecology》2015,8(3):333-347
Mate-finding difficulties in small populations are often postulated to create strong demographic Allee effects that increase the probability of extinction of native species or, similarly, decrease the probability that non-native species will successfully invade. Many species make use of a restricted number of mating locations, detectable from long-distance, that are not selected for habitat reasons (e.g., hilltopping in butterflies). This ‘landmarking’ strategy may specifically address the problem of overcoming mate-finding difficulties. Using a variant of the birthday problem, we demonstrate that populations which locate a restricted number of mate-finding sites using landmark features may have high probability of successful mating even at very low population densities. Therefore, a strong Allee threshold, if it exists, may be very small, and non-native species that make use of this strategy may have a very good chance of population establishment at low density. 相似文献
588.
Plasmids were constructed which contained two expression units encoding single-chain insulin precursors. Surprisingly, the total amount of insulin precursor produced was similar to that produced from plasmids containing a single expression unit. In this system, therefore, two expression cassettes can be brought to compete for the limited ability of the yeast cell for synthesis and secretion. Using genes encoding B(1-29)-A(1-21) and B(1-29)-Ala-Ala-Lys-A-(1-21), the slightly different precursors could be quantified individually after separation by high-performance liquid chromatography from the culture supernatant. The two-cassette system allowed a sensitive and well controlled comparison of parameters important for optimal expression of a heterologous gene in Saccharomyces cerevisiae. The system was used to compare two promoter constructions and also to evaluate the position of expression cassettes in the plasmid. Finally the codon usage in the gene to be expressed was found to influence its ability to compete for expression. 相似文献
589.
Female redhead ducks (Aythya americana) exhibit one of the highest
frequenciesof facultative parasitic egg laying, extending reproductive
choiceswithin a season beyond nesting only. The occurrence of alternative
strategieson a population level within and among years and the factorsthat
influence choices are not well documented or understood.We developed a
dynamic state variable model to predict reproductivestrategy choice and the
influence of female age, body mass,food availability, and host availability
on strategy choice.The model predicts a general distribution of strategy
choiceby body mass and a strong influence of both age and host availability
onstrategy choice. As body mass increases, females choose morecostly
reproductive strategies from nonbreeding to parasitizingto nesting to a dual
strategy, which is defined as a parasiticallylaid clutch of eggs followed by
another clutch laid in the females'own nest. Comparatively, food availability
only influenced strategychoice by slightly increasing the use of more costly
strategies.Predictions of strategy choice by body mass reflect relationships
similarto those proposed by others. Previous studies of the influenceof food
availability on observed parasitic frequencies producedmixed and often
conflicting results. We propose that femaleredheads are assessing the host
environment before making reproductivechoices and food availability functions
to fine tune this assessmentby encouraging or discouraging more costly
strategies at a lowerbody mass. 相似文献
590.
Dirk Gottschling Hartmut Seliger Gema Tarrasón Jaume Piulats Marten Wiersma Ramon Eritja 《Letters in Peptide Science》2000,7(1):35-39
The preparation of peptide nucleic acids (PNA)carrying a c-myc tag-peptide sequence isdescribed. These PNA-peptide chimeras have higheraffinity to complementary DNA than unmodifiedoligonucleotides. Moreover, they can be used asnonradioactive probes with sensitivity similar toother nonradioactive methods. 相似文献