scholarly journals Evolution of chlorophyll degradation is associated with plant transition to land

2021 ◽  
Author(s):  
Isabel Schumacher ◽  
Damian Menghini ◽  
Serguei Ovinnikov ◽  
Mareike Hauenstein ◽  
Nick Fankhauser ◽  
...  
Keyword(s):  
Large Scale ◽  
Biochemical Characterization ◽  
Parallel Evolution ◽  
Chlorophyll Degradation ◽  
Last Common Ancestor ◽  
Green Plants ◽  
Chlorophyll Catabolites ◽  
Stepwise Evolution ◽  
Colonization Of Land ◽  
Pigment Accumulation

AbstractColonization of land by green plants (Viridiplantae) some 500 million years ago was made possible by large metabolic and biochemical adaptations. Chlorophyll, the central pigment of photosynthesis, is highly photo-active. In order to mitigate deleterious effects of pigment accumulation, some plants have evolved a coordinated pathway to deal with chlorophyll degradation end-products, so-called phyllobilins. This pathway has been so far mostly unravelled in Arabidopsis thaliana. Here, large-scale comparative phylogenomic coupled to an innovative biochemical characterization strategy of phyllobilins allow a better understanding how such a pathway appeared in Viridiplantae. Our analysis reveals a stepwise evolution of the canonical pheophorbide a monooxygenase/phyllobilin pathway. It appears to have evolved gradually, first in chlorophyte’s chloroplasts, to ensure multicellularity by detoxifying chlorophyll catabolites, and in charophytes outside chloroplasts to allow adaptation of embryophytes to land. At least six out of the eight genes involved in the pathway were already present in the last common ancestor of green plants. This strongly suggests parallel evolution of distinct enzymes catalysing similar reactions in various lineages, particularly for the dephytylation step. Together, our study suggests that chlorophyll degradation accompanied the transition from water to land, and was therefore of great importance for plant diversification.

scholarly journals Evolution of central pattern generators and rhythmic behaviours

2016 ◽  
Vol 371 (1685) ◽  
pp. 20150057 ◽  
Author(s):  
Paul S. Katz
Keyword(s):  
Large Scale ◽  
Neural Circuits ◽  
Motor Pattern ◽  
Parallel Evolution ◽  
Central Pattern Generators ◽  
Neural Mechanism ◽  
Rhythmic Movements ◽  
Biological Organization ◽  
Gradual Evolution ◽  
Pattern Generators

Comparisons of rhythmic movements and the central pattern generators (CPGs) that control them uncover principles about the evolution of behaviour and neural circuits. Over the course of evolutionary history, gradual evolution of behaviours and their neural circuitry within any lineage of animals has been a predominant occurrence. Small changes in gene regulation can lead to divergence of circuit organization and corresponding changes in behaviour. However, some behavioural divergence has resulted from large-scale rewiring of the neural network. Divergence of CPG circuits has also occurred without a corresponding change in behaviour. When analogous rhythmic behaviours have evolved independently, it has generally been with different neural mechanisms. Repeated evolution of particular rhythmic behaviours has occurred within some lineages due to parallel evolution or latent CPGs. Particular motor pattern generating mechanisms have also evolved independently in separate lineages. The evolution of CPGs and rhythmic behaviours shows that although most behaviours and neural circuits are highly conserved, the nature of the behaviour does not dictate the neural mechanism and that the presence of homologous neural components does not determine the behaviour. This suggests that although behaviour is generated by neural circuits, natural selection can act separately on these two levels of biological organization.

scholarly journals Purification of a 100 kDa phospholipase A2 from spleen, lung and kidney: antiserum raised to pig spleen phospholipase A2 recognizes a similar form in bovine lung, kidney and platelets, and immunoprecipitates phospholipase A2 activity

1993 ◽  
Vol 294 (1) ◽  
pp. 261-270 ◽  
Author(s):  
D K Kim ◽  
J V Bonventre
Keyword(s):  
Arachidonic Acid ◽  
Phospholipase A2 ◽  
Large Scale ◽  
Biochemical Characterization ◽  
Tissue Injury ◽  
Rat Kidney ◽  
Deae Cellulose ◽  
Pla2 Activity ◽  
Purification Scheme ◽  
Pla2 Enzyme

Phospholipase A2 (PLA2) plays a key role in the production of intracellular and extracellular chemical mediators such as arachidonic acid, eicosanoids and platelet-activating factor, which modulate membrane channel activity, signal transduction, are vasoactive and chemotactic, and are implicated in many pathophysiological mechanisms of inflammation and tissue injury. We previously identified, purified and characterized an arachidonic acid-selective cytosolic 100-110 kDa PLA2 from bovine platelets and rat kidney that is activated during cell stimulation. The purification schemes previously published resulted in low yields of enzyme, insufficient for extensive biochemical characterization. We report the purification of a large-molecular-mass (100 kDa) PLA2 from pig spleen, bovine kidney and bovine lung, using a novel large-scale purification scheme. The enzyme was purified to near homogeneity from an acidified extract obtained from 4.8 kg of pig spleen by sequential use of DEAE-cellulose anionic exchange, Butyl-Toyopearl hydrophobic chromatography and DEAE-5PW h.p.l.c., and further purified by non-denaturing PAGE. This purification scheme will permit the preparation of quantities of purified native enzyme sufficient to study its properties and regulation. To generate antiserum against the PLA2 enzyme, the 100 kDa protein was excised and electroeluted from SDS/PAGE gels of the active fractions after DEAE-5PW h.p.l.c., and this was used as antigen. This polyclonal antibody against pig spleen 100 kDa PLA2 protein reacted with 100 kDa bands in preparations partially purified from bovine platelets, kidney and lung as well as pig spleen, and immunoprecipitated PLA2 activity from these sources. The antibody also immunoprecipitated a 100 kDa protein from cytosolic fractions of cultured renal mesangial cells, human erythroleukaemia cells and human monocytic U937 cells. Considerable PLA2 activity was present in the immunoprecipitates. To our knowledge this antibody is unique in its ability to permit measurement of PLA2 activity in the immunoprecipitate itself, and will be a useful tool for the study of the regulation and the activation mechanisms of the native PLA2 enzyme.

scholarly journals Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity

2018 ◽  
Vol 7 (3) ◽  
pp. 27 ◽  
Author(s):  
Afshan Masood ◽  
Hicham Benabdelkamel ◽  
Assim Alfadda
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Large Scale ◽  
Protein Identification ◽  
Biochemical Characterization ◽  
Biological Fluids ◽  
Protein Composition ◽  
Cellular Protein ◽  
Human Obesity ◽  
Two Dimensional Gel Electrophoresis

Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.

scholarly journals Development and Evaluation of PCR Assays for the Detection of Paenibacillus larvae in Honey Samples: Comparison with Isolation and Biochemical Characterization

2003 ◽  
Vol 69 (3) ◽  
pp. 1504-1510 ◽  
Author(s):  
Tamás Bakonyi ◽  
Irmgard Derakhshifar ◽  
Elvira Grabensteiner ◽  
Norbert Nowotny
Keyword(s):  
Dna Extraction ◽  
Large Scale ◽  
Biochemical Characterization ◽  
Direct Detection ◽  
Extraction Methods ◽  
Proteinase K ◽  
Paenibacillus Larvae ◽  
Lower Sensitivity ◽  
Pcr Assays ◽  
Dna Extraction Methods

ABSTRACT PCR assays were developed for the direct detection of Paenibacillus larvae in honey samples and compared with isolation and biochemical characterization procedures. Different primer pairs, designed from the 16S rRNA and the metalloproteinase precursor gene regions, and different DNA extraction methods were tested and compared. The sensitivity of the reactions was evaluated by serial dilutions of DNA extracts obtained from P. larvae cultures. The specificity of the primers was assessed by analyzing related Paenibacillus and Bacillus strains isolated from honey. The PCR assays also amplified these related bacteria, but at lower sensitivity. In the next step, the PCR assays were applied to contaminated honey and other bee products originating from 15 countries. Lysozyme treatment followed by proteinase K digestion was determined to be the best DNA extraction method for P. larvae spores. The most sensitive primer pair detected P. larvae in 18 of 23 contaminated honey samples, as well as in pollen, wax, and brood. Honey specimens containing saprophyte bacilli and paenibacilli, but not P. larvae, were PCR negative. Although the isolation and biochemical identification method (BioLog) showed higher sensitivity and specificity, PCR proved to be a valuable technique for large-scale screening of honey samples for American foulbrood, especially considering its rapidity and moderate costs.

scholarly journals Deep sequencing of mitochondrial DNA and characterization of a novel POLG mutation in a patient with arPEO

2020 ◽  
Vol 6 (1) ◽  
pp. e391
Author(s):  
Carola Hedberg-Oldfors ◽  
Bertil Macao ◽  
Swaraj Basu ◽  
Christopher Lindberg ◽  
Bradley Peter ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Muscle Biopsy ◽  
Deep Sequencing ◽  
Large Scale ◽  
Biochemical Characterization ◽  
Late Onset ◽  
Novel Mutation ◽  
Progressive External Ophthalmoplegia ◽  
Oxidase Deficiency

ObjectiveTo determine the pathogenicity of a novel POLG mutation in a man with late-onset autosomal recessive progressive external ophthalmoplegia using clinical, molecular, and biochemical analyses.MethodsA multipronged approach with detailed neurologic examinations, muscle biopsy analyses, molecular genetic studies, and in vitro biochemical characterization.ResultsThe patient had slowly progressive bilateral ptosis and severely reduced horizontal and vertical gaze. Muscle biopsy showed slight variability in muscle fiber size, scattered ragged red fibers, and partial cytochrome c oxidase deficiency. Biallelic mutations were identified in the POLG gene encoding the catalytic A subunit of POLγ. One allele carried a novel mutation in the exonuclease domain (c.590T>C; p.F197S), and the other had a previously characterized null mutation in the polymerase domain (c.2740A>C; p.T914P). Biochemical characterization revealed that the novel F197S mutant protein had reduced exonuclease and DNA polymerase activities and confirmed that T914P was inactive. By deep sequencing of mitochondrial DNA (mtDNA) extracted from muscle, multiple large-scale rearrangements were mapped and quantified.ConclusionsThe patient's phenotype was caused by biallelic POLG mutations, resulting in one inactive POLγA protein (T914P) and one with decreased polymerase and exonuclease activity (F197S). The reduction in polymerase activity explains the presence of multiple pathogenic large-scale deletions in the patient's mtDNA.

scholarly journals Elevated Expression of a Functional Suf Pathway in the E.coli BL21(DE3) Cell Line Enhances Recombinant Production of an Iron-Sulfur Cluster Containing Protein

2019 ◽  
Author(s):  
Elliot I. Corless ◽  
Erin L. Mettert ◽  
Patricia J. Kiley ◽  
Edwin Antony
Keyword(s):  
Large Scale ◽  
Biochemical Characterization ◽  
Protein A ◽  
Fold Increase ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
E Coli ◽  
Iron Sulfur ◽  
Elevated Expression ◽  
Operon Expression

ABSTRACTStructural and spectroscopic analysis of iron-sulfur [Fe-S] cluster-containing proteins is often limited by the occupancy and yield of recombinantly produced proteins. Here we report that Escherichia coli BL21(DE3), a strain routinely used to overexpress [Fe-S] cluster-containing proteins, has a nonfunctional Suf pathway, one of two E. coli [Fe-S] cluster biogenesis pathways. We confirmed that BL21(DE3) and commercially available derivatives carry a deletion that results in an inframe fusion of sufA and sufB genes within the sufABCDSE operon. We show that this fusion protein accumulates in cells but is - inactive in [Fe-S] biogenesis. Restoration of an intact Suf pathway combined with enhanced suf operon expression led to a remarkable (~3-fold) increase in the production of the [4Fe-4S] cluster-containing BchL protein, a key component of the dark-operative protochlorophyllide oxido-reductase complex. These results show that this engineered ‘SufFeScient’ derivative of BL21(DE3) is suitable for enhanced large-scale synthesis of an [Fe-S] cluster-containing protein.IMPORTANCELarge quantities of recombinantly overexpressed iron-sulfur cluster-containing proteins are necessary for their in-depth biochemical characterization. Commercially available E. coli strain BL21(DE3) and its derivatives have a mutation that inactivates the function of one of the two native pathways (Suf pathway) responsible for cluster biogenesis. Correction of the mutation, combined with sequence changes that increase Suf expression can increase yield and cluster occupancy of [Fe-S] cluster-containing enzymes, facilitating the biochemical analysis of this fascinating group of proteins.

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