scholarly journals The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources

2021 ◽  
Author(s):  
Maria Victoria Ferretti ◽  
Rania A Hussien ◽  
Miguel A Ballicora ◽  
Alberto A Iglesias ◽  
Carlos M Figueroa ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
De Novo ◽  
Metagenomic Data ◽  
Oxygenic Photosynthesis ◽  
Phylogenetic Position ◽  
Free Living ◽  
Adp Glucose Pyrophosphorylase ◽  
Essential Enzyme ◽  
The One ◽  
Allosteric Mechanisms

Until recently, all members of the cyanobacterial phylum were considered capable of performing oxygenic photosynthesis. This view has been questioned after the discovery of a group of presumed non-photosynthetic cyanobacteria named Melainabacteria. Using metagenomic data, we identified sequences encoding putative ADP-glucose pyrophosphorylase (EC 2.7.7.27, ADP-GlcPPase) from free-living and intestinal Melainabacteria. These genes were de novo synthesized and overexpressed in Escherichia coli. The purified recombinant proteins from the free-living and the intestinal Melainabacteria showed ADP-GlcPPase activity, with Vmax values of 2.3 and 7.1 U/mg, respectively. Both enzymes had similar affinities towards ATP (S0.5 ~0.3 mM) although the one from the intestinal source displayed a 6-fold higher affinity for glucose-1P. Both recombinant ADP-GlcPPases were sensitive to allosteric activation by glucose-6P (A0.5 ~0.3 mM), and to inhibition by Pi and ADP (I0.5 between 0.2 to 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. To the best of our knowledge, this is the first biochemical characterization of an active enzyme from Melainabacteria, offering further data to discussions regarding their phylogenetic position. This work contributes to a better understanding regarding the evolution of allosteric mechanisms in ADP-GlcPPases, an essential enzyme for the synthesis of glycogen in prokaryotes and starch in plants.

scholarly journals General synthetic strategy for regioselective ultrafast formation of disulfide bonds in peptides and proteins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shay Laps ◽  
Fatima Atamleh ◽  
Guy Kamnesky ◽  
Hao Sun ◽  
Ashraf Brik
Keyword(s):  
Drug Discovery ◽  
Disulfide Bonds ◽  
Unsolved Problem ◽  
De Novo ◽  
Therapeutic Potential ◽  
Selective Activation ◽  
One Pot ◽  
Synthetic Strategy ◽  
The One ◽  
Game Changer

AbstractDespite six decades of efforts to synthesize peptides and proteins bearing multiple disulfide bonds, this synthetic challenge remains an unsolved problem in most targets (e.g., knotted mini proteins). Here we show a de novo general synthetic strategy for the ultrafast, high-yielding formation of two and three disulfide bonds in peptides and proteins. We develop an approach based on the combination of a small molecule, ultraviolet-light, and palladium for chemo- and regio-selective activation of cysteine, which enables the one-pot formation of multiple disulfide bonds in various peptides and proteins. We prepare bioactive targets of high therapeutic potential, including conotoxin, RANTES, EETI-II, and plectasin peptides and the linaclotide drug. We anticipate that this strategy will be a game-changer in preparing millions of inaccessible targets for drug discovery.

Prospective enzymes for omega-3 PUFA biosynthesis found in endoparasitic classes within the phylum Platyhelminthes

2020 ◽  
Vol 94 ◽  
Author(s):  
D. Babaran ◽  
M.T. Arts ◽  
R.J. Botelho ◽  
S.A. Locke ◽  
J. Koprivnikar
Keyword(s):  
Parasite Species ◽  
De Novo ◽  
Genomic Data ◽  
Wide Distribution ◽  
Omega 3 ◽  
Free Living ◽  
Chain Pufa ◽  
Pufa Biosynthesis ◽  
Aquatic Food ◽  
Long Chain

Abstract The free-living infectious stages of macroparasites, specifically, the cercariae of trematodes (flatworms), are likely to be significant (albeit underappreciated) vectors of nutritionally important polyunsaturated fatty acids (PUFA) to consumers within aquatic food webs, and other macroparasites could serve similar roles. In the context of de novo omega-3 (n-3) PUFA biosynthesis, it was thought that most animals lack the fatty acid (FA) desaturase enzymes that convert stearic acid (18:0) into ɑ-linolenic acid (ALA; 18:3n-3), the main FA precursor for n-3 long-chain PUFA. Recently, novel sequences of these enzymes were recovered from 80 species from six invertebrate phyla, with experimental confirmation of gene function in five phyla. Given this wide distribution, and the unusual attributes of flatworm genomes, we conducted an additional search for genes for de novo n-3 PUFA in the phylum Platyhelminthes. Searches with experimentally confirmed sequences from Rotifera recovered nine relevant FA desaturase sequences from eight species in four genera in the two exclusively endoparasite classes (Trematoda and Cestoda). These results could indicate adaptations of these particular parasite species, or may reflect the uneven taxonomic coverage of sequence databases. Although additional genomic data and, particularly, experimental study of gene functionality are important future validation steps, our results indicate endoparasitic platyhelminths may have enzymes for de novo n-3 PUFA biosynthesis, thereby contributing to global PUFA production, but also representing a potential target for clinical antihelmintic applications.

scholarly journals Natural variation in yolk fatty acids, but not androgens, predicts offspring fitness in a wild bird

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Lucia Mentesana ◽  
Martin N. Andersson ◽  
Stefania Casagrande ◽  
Wolfgang Goymann ◽  
Caroline Isaksson ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Polyunsaturated Fatty Acids ◽  
Maternal Effects ◽  
Natural Variation ◽  
De Novo ◽  
Natural Populations ◽  
Egg Laying ◽  
Interactive Effects ◽  
Free Living ◽  
Offspring Fitness

Abstract Background In egg-laying animals, mothers can influence the developmental environment and thus the phenotype of their offspring by secreting various substances into the egg yolk. In birds, recent studies have demonstrated that different yolk substances can interactively affect offspring phenotype, but the implications of such effects for offspring fitness and phenotype in natural populations have remained unclear. We measured natural variation in the content of 31 yolk components known to shape offspring phenotypes including steroid hormones, antioxidants and fatty acids in eggs of free-living great tits (Parus major) during two breeding seasons. We tested for relationships between yolk component groupings and offspring fitness and phenotypes. Results Variation in hatchling and fledgling numbers was primarily explained by yolk fatty acids (including saturated, mono- and polyunsaturated fatty acids) - but not by androgen hormones and carotenoids, components previously considered to be major determinants of offspring phenotype. Fatty acids were also better predictors of variation in nestling oxidative status and size than androgens and carotenoids. Conclusions Our results suggest that fatty acids are important yolk substances that contribute to shaping offspring fitness and phenotype in free-living populations. Since polyunsaturated fatty acids cannot be produced de novo by the mother, but have to be obtained from the diet, these findings highlight potential mechanisms (e.g., weather, habitat quality, foraging ability) through which environmental variation may shape maternal effects and consequences for offspring. Our study represents an important first step towards unraveling interactive effects of multiple yolk substances on offspring fitness and phenotypes in free-living populations. It provides the basis for future experiments that will establish the pathways by which yolk components, singly and/or interactively, mediate maternal effects in natural populations.

scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

Divisional morphogenesis in the marine ciliate Holosticha warreni (Ciliophora: Hypotrichida)

2000 ◽  
Vol 80 (5) ◽  
pp. 785-788 ◽  
Author(s):  
Xiaozhong Hu ◽  
Weibo Song ◽  
Alan Warren
Keyword(s):  
Coastal Waters ◽  
De Novo ◽  
Cortical Development ◽  
Impregnation Method ◽  
Marine Ciliate ◽  
Group Type ◽  
Generation Mode ◽  
The One

The cortical development of the marine hypotrichous ciliate Holosticha warreni, found in coastal waters near Qingdao, China, was investigated using the protargol impregnation method. In the proter, disorganization of the parental adoral zone of membranelles and undulating membranes contributes to the formation of its oral primordia which replace the parental buccal apparatus completely. Cirral anlagen in both division parts derive from the breaking of primary primordia. Most midventral cirri join in the formation of these primordia which occurs de novo separately from the oral primordia. Each of the 11 to 13 oblique streaks divides into three segments (new cirri) while the last two anlagen produce four each. Two frontoterminal cirri derive from the posteriormost anlage. The marginal rows develop from the parental structure. The generation mode of dorsal kineties is of the ‘one group type’ without forming caudal cirri.

Biochemical characterization of Plasmodium falciparum CTP:phosphoethanolamine cytidylyltransferase shows that only one of the two cytidylyltransferase domains is active

2013 ◽  
Vol 450 (1) ◽  
pp. 159-167 ◽  
Author(s):  
Sweta Maheshwari ◽  
Marina Lavigne ◽  
Alicia Contet ◽  
Blandine Alberge ◽  
Emilie Pihan ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Cellular Localization ◽  
Biochemical Characterization ◽  
De Novo ◽  
Membrane Lipids ◽  
Polyclonal Antibodies ◽  
Homology Modelling ◽  
Site Directed Mutagenesis ◽  
Recombinant Enzymes ◽  
Parasite Life Cycle

The intra-erythrocytic proliferation of the human malaria parasite Plasmodium falciparum requires massive synthesis of PE (phosphatidylethanolamine) that together with phosphatidylcholine constitute the bulk of the malaria membrane lipids. PE is mainly synthesized de novo by the CDP:ethanolamine-dependent Kennedy pathway. We previously showed that inhibition of PE biosynthesis led to parasite death. In the present study we characterized PfECT [P. falciparum CTP:phosphoethanolamine CT (cytidylyltransferase)], which we identified as the rate-limiting step of the PE metabolic pathway in the parasite. The cellular localization and expression of PfECT along the parasite life cycle were studied using polyclonal antibodies. Biochemical analyses showed that the enzyme activity follows Michaelis–Menten kinetics. PfECT is composed of two CT domains separated by a linker region. Activity assays on recombinant enzymes upon site-directed mutagenesis revealed that the N-terminal CT domain was the only catalytically active domain of PfECT. Concordantly, three-dimensional homology modelling of PfECT showed critical amino acid differences between the substrate-binding sites of the two CT domains. PfECT was predicted to fold as an intramolecular dimer suggesting that the inactive C-terminal domain is important for dimer stabilization. Given the absence of PE synthesis in red blood cells, PfECT represents a potential antimalarial target opening the way for a rational conception of bioactive compounds.

Observing microscopic phases of lichen life cycles on transparent substrata placed in situ

2005 ◽  
Vol 37 (5) ◽  
pp. 373-382 ◽  
Author(s):  
William B. SANDERS
Keyword(s):  
Life Cycle ◽  
Developmental Stages ◽  
Life Cycles ◽  
Potential Significance ◽  
Free Living ◽  
Lichen Community ◽  
One Year ◽  
The One ◽  
Observation Period

The utility of plastic cover slips as a substratum for in situ study of lichen developmental stages is further explored in a neotropical foliicolous lichen community and in a European temperate corticolous community. Twenty-one months after placement in the tropical forest, the cover slips bore foliicolous lichen thalli with several species producing characteristic ascocarps and ascospores, indicating the suitability of the substratum for completion of the life cycle of these lichens. On cover slips placed within the temperate corticolous community, lichen propagules anchored to the substratum with relatively short attachment hyphae but did not develop further within the one year observation period. Intimately intermixed microbial communities of short-celled, mainly pigmented fungi and chlorophyte algae developed upon the transparent substratum. Among the algae, Trebouxia cells, often in groups showing cell division and without associated lichenizing hyphae, were commonly observed. The potential significance of the free-living populations in the life cycle of Trebouxia and in those of Trebouxia-associated lichen fungi is discussed.

scholarly journals Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes

2012 ◽  
Vol 78 (15) ◽  
pp. 5288-5296 ◽  
Author(s):  
Yu-Wei Wu ◽  
Mina Rho ◽  
Thomas G. Doak ◽  
Yuzhen Ye
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Human Subjects ◽  
Human Microbiome ◽  
Metagenomic Data ◽  
De Bruijn Graph ◽  
Content Type ◽  
Gene Cassettes ◽  
Dental Diseases ◽  
Normal Human

ABSTRACTThe NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of oral spirochetes implicated in dental diseases in normal human individuals, using recombination sites associated with the chromosomal integron inTreponemagenomes, taking advantage of the multiple copies of the integron recombination sites (repeats) in the genomes, and using a targeted assembly approach that we have developed. We find that integron-containingTreponemaspecies are present in ∼80% of the normal human subjects included in the HMP. Further, we are able tode novoassemble the integron gene cassettes using our constrained assembly approach, which employs a unique application of the de Bruijn graph assembly information; most of these cassette genes were not assembled in whole-metagenome assemblies and could not be identified by mapping sequencing reads onto the known referenceTreponemagenomes due to the dynamic nature of integron gene cassettes. Our study significantly enriches the gene pool known to be carried byTreponemachromosomal integrons, totaling 826 (598 97% nonredundant) genes. We characterize the functions of these gene cassettes: many of these genes have unknown functions. The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes.

scholarly journals Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Elisabeth Hehenberger ◽  
Javier del Campo ◽  
Noriko Okamoto ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Phylogenetic Position ◽  
Rrna Gene ◽  
Ancestral State ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Free Living ◽  
Surface Ocean ◽  
Lsu Rrna Gene ◽  
Important Host ◽  
Copepod Eggs

ABSTRACTSpores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

scholarly journals Three ways to develop clinical guidelines. ADAPTE and AGREE GRS procedures

2019 ◽  
Vol 65 (3) ◽  
pp. 197-203
Author(s):  
Olga Yu. Rebrova
Keyword(s):  
Clinical Guidelines ◽  
De Novo ◽  
Professional Association ◽  
Professional Organization ◽  
Medical Community ◽  
Highly Qualified ◽  
National Medical ◽  
Multi Stage ◽  
Adaptation Procedure ◽  
The One

Development of de novo clinical guidelines (CG) is a complex process that requires highly qualified personnel, an extended amount of time (from 1 to 3 years), and, consequently, substantial funding. In many countries there are limits to these resources, and so, as an alternative to the development of actual de novo CG, the expert community has developed simplified ways of preparing CG: adoption and adaptation. Adoption is the easiest option – it is simply translation of clinical guidelines developed by a credible foreign professional association into the native language. In this case, of course, translated guidelines should be attributed accurately as a translation, without claiming additional authorship by a local professional association. It may be stated that the local professional organization has discussed and approved the translated document. It is also possible to post comments. Another way – adaptation – is to adjust the CG, developed in one country, to the conditions and features of the healthcare system in another country. Adaptation is fundamentally more difficult than adoption. An adaptation procedure has been developed by ADAPTE, an international group of experts. Their detailed procedure, complete with commentaries, is freely available. The key stage of the multi-stage adaptation procedure is the assessment of the methodological quality of the adapted CG using the AGREE II questionnaire or its simplified version, AGREE GRS. An assessment of the relevance, consistency, acceptability and applicability of the CG is also performed. In situations of a pronounced shortage of resources, adoption of the CG is preferable, while under less constrained conditions – adaptation of the CG. Development of de novo CG in the context of an unlimited exchange of information seems inappropriate and unnecessarily costly. The compromise is an adaptation that serves, on the one hand, to significantly save various types of resources, and, on the other, to promote the methodology of evidence-based medicine in the national medical community.

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