scholarly journals New insight into plant intramembrane proteases

2017 ◽  
Author(s):  
Małgorzata Adamiec ◽  
Lucyna Misztal ◽  
Robert Luciński
Keyword(s):  
Protein Turnover ◽  
Higher Plants ◽  
Protein Sequences ◽  
Higher Plant ◽  
Aspartic Proteases ◽  
Phylogenetic Relations ◽  
Intramembrane Proteases ◽  
Rhomboid Proteases ◽  
Zinc Metalloproteases ◽  
Insight Into

ABSTRACTThe process of proteolysis is a factor involved in control of the proper development of the plant and its responses to a changeable environment. Recent research has shown that proteases are not only engaged in quality control and protein turnover processes but also participate in the process which is known as regulated membrane proteolysis (RIP). Four families of integral membrane proteases, belonging to three different classes, have been identified: serine intramembrane proteases known as rhomboid proteases, site-2 proteases belonging to zinc metalloproteases, and two families of aspartic proteases: presenilins and signal peptide peptidases. The studies concerning intramembrane proteases in higher plants are, however, focused on Arabidopsis thaliana. The aim of the study was to identify and retrieve protein sequences of intramembrane protease homologs from other higher plant species and perform a detailed analysis of their primary sequences as well as their phylogenetic relations. This approach allows us to indicate several previously undescribed issues which may provide important directions for further research.

scholarly journals Using protein turnover to expand the applications of transcriptomics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marissa A. Smail ◽  
James K. Reigle ◽  
Robert E. McCullumsmith
Keyword(s):  
Protein Turnover ◽  
Half Life ◽  
Rna Expression ◽  
Protein Abundance ◽  
Life Data ◽  
Research Fields ◽  
Extended Application ◽  
Functional Implications ◽  
Transcriptomics Data ◽  
Insight Into

AbstractRNA expression and protein abundance are often at odds when measured in parallel, raising questions about the functional implications of transcriptomics data. Here, we present the concept of persistence, which attempts to address this challenge by combining protein half-life data with RNA expression into a single metric that approximates protein abundance. The longer a protein’s half-life, the more influence it can have on its surroundings. This data offers a valuable opportunity to gain deeper insight into the functional meaning of transcriptome changes. We demonstrate the application of persistence using schizophrenia (SCZ) datasets, where it greatly improved our ability to predict protein abundance from RNA expression. Furthermore, this approach successfully identified persistent genes and pathways known to have impactful changes in SCZ. These results suggest that persistence is a valuable metric for improving the functional insight offered by transcriptomics data, and extended application of this concept could advance numerous research fields.

Measurement of ferrochelatase activity using a novel assay suggests that plastids are the major site of haem biosynthesis in both photosynthetic and non-photosynthetic cells of pea (Pisum sativum L.)

2002 ◽  
Vol 362 (2) ◽  
pp. 423-432 ◽  
Author(s):  
Johanna E. CORNAH ◽  
Jennifer M. ROPER ◽  
Davinder Pal SINGH ◽  
Alison G. SMITH
Keyword(s):  
Ferrous Iron ◽  
Specific Activity ◽  
Higher Plants ◽  
Protoporphyrin Ix ◽  
Chlorophyll Synthesis ◽  
Marker Enzyme ◽  
Hexane Extraction ◽  
Higher Plant ◽  
Major Site ◽  
Haem Biosynthesis

Ferrochelatase is the terminal enzyme of haem biosynthesis, catalysing the insertion of ferrous iron into the macrocycle of protoporphyrin IX, the last common intermediate of haem and chlorophyll synthesis. Its activity has been reported in both plastids and mitochondria of higher plants, but the relative amounts of the enzyme in the two organelles are unknown. Ferrochelatase is difficult to assay since ferrous iron requires strict anaerobic conditions to prevent oxidation, and in photosynthetic tissues chlorophyll interferes with the quantification of the product. Accordingly, we developed a sensitive fluorimetric assay for ferrochelatase that employs Co2+ and deuteroporphyrin in place of the natural substrates, and measures the decrease in deuteroporphyrin fluorescence. A hexane-extraction step to remove chlorophyll is included for green tissue. The assay is linear over a range of chloroplast protein concentrations, with an average specific activity of 0.68nmol·min−1·mg of protein−1, the highest yet reported. The corresponding value for mitochondria is 0.19nmol·min−1·mg of protein−1. The enzyme is inhibited by N-methylprotoporphyrin, with an estimated IC50 value of ≈ 1nM. Using this assay we have quantified ferrochelatase activity in plastids and mitochondria from green pea leaves, etiolated pea leaves and pea roots to determine the relative amounts in the two organelles. We found that, in all three tissues, greater than 90% of the activity was associated with plastids, but ferrochelatase was reproducibly detected in mitochondria, at levels greater than the contaminating plastid marker enzyme, and was latent. Our results indicate that plastids are the major site of haem biosynthesis in higher plant cells, but that mitochondria also have the capacity for haem production.

scholarly journals Electronic Structure of Tyrosyl D Radical of Photosystem II, as Revealed by 2D-Hyperfine Sublevel Correlation Spectroscopy

2021 ◽  
Vol 7 (9) ◽  
pp. 131
Author(s):  
Maria Chrysina ◽  
Georgia Zahariou ◽  
Nikolaos Ioannidis ◽  
Yiannis Sanakis ◽  
George Mitrikas
Keyword(s):  
Electronic Structure ◽  
Photosystem Ii ◽  
Water Oxidation ◽  
Spinacia Oleracea ◽  
Higher Plants ◽  
Correlation Spectroscopy ◽  
Oxygen Evolving Complex ◽  
Higher Plant ◽  
Proton Coupled Electron Transfer ◽  
S Oxidation

The biological water oxidation takes place in Photosystem II (PSII), a multi-subunit protein located in thylakoid membranes of higher plant chloroplasts and cyanobacteria. The catalytic site of PSII is a Mn4Ca cluster and is known as the oxygen evolving complex (OEC) of PSII. Two tyrosine residues D1-Tyr161 (YZ) and D2-Tyr160 (YD) are symmetrically placed in the two core subunits D1 and D2 and participate in proton coupled electron transfer reactions. YZ of PSII is near the OEC and mediates electron coupled proton transfer from Mn4Ca to the photooxidizable chlorophyll species P680+. YD does not directly interact with OEC, but is crucial for modulating the various S oxidation states of the OEC. In PSII from higher plants the environment of YD• radical has been extensively characterized only in spinach (Spinacia oleracea) Mn- depleted non functional PSII membranes. Here, we present a 2D-HYSCORE investigation in functional PSII of spinach to determine the electronic structure of YD• radical. The hyperfine couplings of the protons that interact with the YD• radical are determined and the relevant assignment is provided. A discussion on the similarities and differences between the present results and the results from studies performed in non functional PSII membranes from higher plants and PSII preparations from other organisms is given.

scholarly journals Origins of the new influenza A(H1N1) virus: time to take action

2009 ◽  
Vol 14 (22) ◽  
Author(s):  
G M Nava ◽  
M S Attene-Ramos ◽  
J K Ang ◽  
M Escorcia
Keyword(s):  
Influenza A ◽  
H1n1 Virus ◽  
Phylogenetic Analyses ◽  
Protein Sequences ◽  
Interspecies Transmission ◽  
Genetic Evolution ◽  
Protein Homology ◽  
Influenza A H1n1 ◽  
Insight Into

To gain insight into the possible origins of the 2009 outbreak of new influenza A(H1N1), we performed two independent analyses of genetic evolution of the new influenza A(H1N1) virus. Firstly, protein homology analyses of more than 400 sequences revealed that this virus most likely evolved from recent swine viruses. Secondly, phylogenetic analyses of 5,214 protein sequences of influenza A(H1N1) viruses (avian, swine and human) circulating in North America for the last two decades (from 1989 to 2009) indicated that the new influenza A(H1N1) virus possesses a distinctive evolutionary trait (genetic distinctness). This appears to be a particular characteristic in pig-human interspecies transmission of influenza A. Thus these analyses contribute to the evidence of the role of pig populations as “mixing vessels” for influenza A(H1N1) viruses.

scholarly journals Genetic fine-structure of the GA-1 locus in the higher plant Arabidopsis thaliana (L.) Heynh

1983 ◽  
Vol 41 (1) ◽  
pp. 57-68 ◽  
Author(s):  
M. Koornneef ◽  
J. Van Eden ◽  
C. J. Hanhart ◽  
A. M. M. De Jongh
Keyword(s):  
Arabidopsis Thaliana ◽  
Fine Structure ◽  
Higher Plants ◽  
Wild Type ◽  
Higher Plant ◽  
Selfed Progeny ◽  
Intragenic Deletion ◽  
Genetic Length ◽  
Genetic Fine Structure ◽  
Half Diallel

SUMMARYNon-germinating gibberellin (GA) responsive mutants are a powerful tool to study genetic fine structure in higher plants. Nine alleles (EMS-and fast neutron-induced) of the ga-1 locus of Arabidopsis thaliana were tested in a complete half-diallel. No wild type ‘recombinants’ were found in the selfed progeny of 9 homoallelic combinations (in total 3 × 105 plants); in the progenies from the 36 selfed hetero allelics the wild type frequency ranged from zero to 6·6 × 10−4. These frequencies allowed the construction of an internally consistent map for five different sites representing eight alleles. The ninth allele covered three sites and thus behaved like an intragenic deletion. The estimate of the total genetic length of the ga-1 locus was 0·07 cM. The order of the sites was also clearly reflected by the association with proximal outside markers. On the assumption that wild type gametes predominantly arise from reciprocal events, it was shown that a cross-over within the ga-1 locus leads to positive interference in the adjacent region.The results are discussed with respect to the mutagen used, the frequencies found in other plant and Drosophila genes, and the possible occurrence of gene conversion.

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

The higher plant PII signal transduction protein: structure, function and properties

2007 ◽  
Vol 85 (6) ◽  
pp. 533-537 ◽  
Author(s):  
Greg B.G. Moorhead ◽  
Tony S. Ferrar ◽  
Yan M. Chen ◽  
Yutaka Mizuno ◽  
Catherine S. Smith ◽  
...  
Keyword(s):  
Higher Plants ◽  
Structural Features ◽  
Signaling Proteins ◽  
Higher Plant ◽  
Binding Partner ◽  
Signal Transduction Protein ◽  
Metabolic Sensor ◽  
Nitrogen Sensing ◽  
Over 40 Years

The PII carbon/nitrogen sensing protein was discovered in Escherichia coli (Migula 1895) Castellani and Chalmers 1919, over 40 years ago. Orthologues have been discovered in three kingdoms of life making it one of the most ancient and conserved signaling proteins known. Recent advances in the field have established its primary binding partner in plants as N-acetyl glutamate kinase and the crystal structure has revealed features unique to plants that likely contribute to its function in vivo. Here, we review the properties, function, and novel structural features of this chloroplast-localized metabolic sensor of higher plants.

Photoreduction of NADP+ in Photosystem II of Higher Plants: Requirement for Manganese

1992 ◽  
Vol 47 (1-2) ◽  
pp. 57-62 ◽  
Author(s):  
Suleyman I. Allakhverdiev ◽  
Vyacheslav V. Klimov
Keyword(s):  
Photosystem Ii ◽  
Higher Plants ◽  
Complete Removal ◽  
Reaction Centers ◽  
Higher Plant ◽  
Ps Ii ◽  
Alternate Pathway ◽  
Manganese Extraction ◽  
Quinone Acceptor ◽  
Reduced State

Abstract The effects of reversible manganese extraction on NADP+ photoreduction were studied with higher plant subchloroplast preparations of photosystem II (PS II). Under anaerobic conditions, when the reaction centers (RCs) of PS II are “closed” (i.e. in the state [P680 Pheo] QA), and in the presence of ferredoxin-ferredoxin-NADP+ reductase, NADP+ reduction is observed at a rate of 0.8 -1.1 nmol/mg × chlorophyll × h. After complete removal of manganese from PS II, the rate of NADP+ reduction is reduced 40 - 50-fold. Upon the addition of Mn at a concentration of approx. 4 Mn atoms per reaction center, the NADP+ reduction is restored up to 85 -90% of the initial value. When half of this amount of Mn is combined with about 40 times of the equivalent concentration of other divalent ions (Ca2+, Sr2+, Mg2+ etc.) the reaction is also reactivated. Dinoseb (10-6 m) an inhibitor of electron transfer in PS II prevents NADP+ photoreduction. It is concluded that under conditions when the first quinone acceptor, QA, is in its reduced state (QA-) electrons are transferred from reduced pheophytin (Pheo·̅) to NADP+, indicating that PS II can reduce NADP+ without the participation of PS I. On the basis of these and literature data, an alternate pathway for electron phototransfer in PS II reaction centers of higher plants is suggested. Some problems concerning the Z-scheme are discussed.

scholarly journals Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicky Atkinson ◽  
Yuwei Mao ◽  
Kher Xing Chan ◽  
Alistair J. McCormick
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Recent Work ◽  
Single Phase ◽  
Inorganic Carbon ◽  
Higher Plants ◽  
Initial Step ◽  
Operating Efficiency ◽  
Higher Plant ◽  
Spontaneous Condensation ◽  
Concentrating Mechanism

AbstractPhotosynthetic CO2 fixation in plants is limited by the inefficiency of the CO2-assimilating enzyme Rubisco. In most eukaryotic algae, Rubisco aggregates within a microcompartment known as the pyrenoid, in association with a CO2-concentrating mechanism that improves photosynthetic operating efficiency under conditions of low inorganic carbon. Recent work has shown that the pyrenoid matrix is a phase-separated, liquid-like condensate. In the alga Chlamydomonas reinhardtii, condensation is mediated by two components: Rubisco and the linker protein EPYC1 (Essential Pyrenoid Component 1). Here, we show that expression of mature EPYC1 and a plant-algal hybrid Rubisco leads to spontaneous condensation of Rubisco into a single phase-separated compartment in Arabidopsis chloroplasts, with liquid-like properties similar to a pyrenoid matrix. This work represents a significant initial step towards enhancing photosynthesis in higher plants by introducing an algal CO2-concentrating mechanism, which is predicted to significantly increase the efficiency of photosynthetic CO2 uptake.

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