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https://www.readbyqxmd.com/read/29115926/co-expression-network-analysis-of-the-transcriptomes-of-rice-roots-exposed-to-various-cadmium-stresses-reveals-universal-cadmium-responsive-genes
#1
Mingpu Tan, Dan Cheng, Yuening Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
BACKGROUND: The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. RESULTS: We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment...
November 7, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28936722/kinetics-of-photosystem-ii-electron-transport-a-mathematical-analysis-based-on-chlorophyll-fluorescence-induction
#2
Agu Laisk, Vello Oja
The OJDIP rise in chlorophyll fluorescence during induction at different light intensities was mathematically modeled using 24 master equations describing electron transport through photosystem II (PSII) plus ordinary differential equations for electron budgets in plastoquinone, cytochrome f, plastocyanin, photosystem I, and ferredoxin. A novel feature of the model is consideration of electron in- and outflow budgets resulting in changes in redox states of Tyrosine Z, P680, and QA as sole bases for changes in fluorescence yield during the transient...
September 21, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28904074/mir408-regulates-grain-yield-and-photosynthesis-via-a-phytocyanin-protein
#3
Jin-Ping Zhang, Yang Yu, Yan-Zhao Feng, Yan-Fei Zhou, Fan Zhang, Yu-Wei Yang, Meng-Qi Lei, Yu-Chan Zhang, Yue-Qin Chen
Increasing grain yield is the most important object of crop breeding. Here, we report that the elevated expression of a conserved microRNA, OsmiR408, could positively regulate grain yield in rice (Oryza sativa) by increasing panicle branches and grain number. We further showed that OsmiR408 regulates grain yield by down-regulating its downstream target, OsUCL8, which is an uclacyanin (UCL) gene of the phytocyanin family. The knock down or knock out of OsUCL8 also increases grain yield, while the overexpression of OsUCL8 results in an opposite phenotype...
November 2017: Plant Physiology
https://www.readbyqxmd.com/read/28837661/contrasting-effects-of-copper-limitation-on-the-photosynthetic-apparatus-in-two-strains-of-the-open-ocean-diatom-thalassiosira-oceanica
#4
Anna A Hippmann, Nina Schuback, Kyung-Mee Moon, John P McCrow, Andrew E Allen, Leonard J Foster, Beverley R Green, Maria T Maldonado
There is an intricate interaction between iron (Fe) and copper (Cu) physiology in diatoms. However, strategies to cope with low Cu are largely unknown. This study unveils the comprehensive restructuring of the photosynthetic apparatus in the diatom Thalassiosira oceanica (CCMP1003) in response to low Cu, at the physiological and proteomic level. The restructuring results in a shift from light harvesting for photochemistry-and ultimately for carbon fixation-to photoprotection, reducing carbon fixation and oxygen evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28497192/redox-changes-of-ferredoxin-p700-and-plastocyanin-measured-simultaneously-in-intact-leaves
#5
Ulrich Schreiber
Properties and performance of the recently introduced Dual/KLAS-NIR spectrophotometer for simultaneous measurements of ferredoxin (Fd), P700, and plastocyanin (PC) redox changes, together with whole leaf chlorophyll a (Chl) fluorescence (emission >760, 540 nm excitation) are outlined. Spectral information on in vivo Fd, P700, and PC in the near-infrared region (NIR, 780-1000 nm) is presented, on which the new approach is based. Examples of application focus on dark-light and light-dark transitions, where maximal redox changes of Fd occur...
December 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28493482/emergence-of-cytochrome-bc-complexes-in-the-context-of-photosynthesis
#6
Daria V Dibrova, Daria N Shalaeva, Michael Y Galperin, Armen Y Mulkidjanian
The cytochrome bc (cyt bc) complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four-helical cytochrome b (cyt b) that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b6 f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven- or eight-helical cyt b with only two hemes (cyt bc1 -type complexes)...
September 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28406611/evaluation-of-p-13-c-15-n-cyano-phenylalanine-as-an-extended-time-scale-2d-ir-probe-of-proteins
#7
Amanda L Le Sueur, Sashary Ramos, Jonathan D Ellefsen, Silas Cook, Megan C Thielges
Two-dimensional infrared (2D IR) spectroscopy provides a powerful approach for the direct study of molecular dynamics with high spatial and temporal resolution. Its application for investigating specific locations in proteins requires the incorporation of IR probe groups with spectrally isolated absorptions to avoid the congestion inherent to protein spectra. This has motivated extensive efforts toward the development of new IR probes, but there remains a need for those that can extend the experimental time range, which is limited by their vibrational lifetimes...
April 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28369912/multiparticle-brownian-dynamics-simulation-of-experimental-kinetics-of-cytochrome-bf-oxidation-and-photosystem-i-reduction-by-plastocyanin
#8
Ilya B Kovalenko, Olga S Knyazeva, Taras K Antal, Vladimir Y Ponomarev, Galina Yu Riznichenko, Andrei B Rubin
A model of electron transport from cytochrome f to photosystem I mediated by plastocyanin was designed on the basis of the multiparticle Brownian dynamics method. The model combines events which occur over a wide time range, including protein diffusion along the thylakoid membrane, long-distance interactions between proteins, formation of a multiprotein complex, electron transfer within a complex and complex dissociation. Results of the modeling were compared with the experimental kinetics measured in chloroplast thylakoids...
September 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28275891/connectivity-between-electron-transport-complexes-and-modulation-of-photosystem-ii-activity-in-chloroplasts
#9
Alexander N Tikhonov, Alexey V Vershubskii
In chloroplasts, photosynthetic electron transport complexes interact with each other via the mobile electron carriers (plastoquinone and plastocyanin) which are in surplus amounts with respect to photosystem I and photosystem II (PSI and PSII), and the cytochrome b 6 f complex. In this work, we analyze experimental data on the light-induced redox transients of photoreaction center P700 in chloroplasts within the framework of our mathematical model. This analysis suggests that during the action of a strong actinic light, even significant attenuation of PSII [for instance, in the result of inhibition of a part of PSII complexes by DCMU or due to non-photochemical quenching (NPQ)] will not cause drastic shortage of electron flow through PSI...
September 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28239191/the-rise-of-radicals-in-bioinorganic-chemistry
#10
Harry B Gray, Jay R Winkler
Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O2-reactive enzymes, raising the possibility that they play an antioxidant protective role...
October 2016: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/28199904/cyclic-electron-flow-may-provide-some-protection-against-psii-photoinhibition-in-rice-oryza-sativa-l-leaves-under-heat-stress
#11
Jemaa Essemine, Yi Xiao, Mingnan Qu, Hualing Mi, Xin-Guang Zhu
Previously we have shown that a quick down-regulation in PSI activity compares to that of PSII following short-term heat stress for two rice groups including C4023 and Q4149, studied herein. These accessions were identified to have different natural capacities in driving cyclic electron flow (CEF) around PSI; i.e., low CEF (lcef) and high CEF (hcef) for C4023 and Q4149, respectively. The aim of this study was to investigate whether these two lines have different mechanisms of protecting photosystem II from photodamage under heat stress...
April 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27859435/a-qm-mm-study-of-the-nature-of-the-entatic-state-in-plastocyanin
#12
Catherine A Hurd, Nicholas A Besley, David Robinson
Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory-based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27802305/structural-insights-into-the-nucleotide-binding-domains-of-the-p1b-type-atpases-hma6-and-hma8-from-arabidopsis-thaliana
#13
Hubert Mayerhofer, Emeline Sautron, Norbert Rolland, Patrice Catty, Daphné Seigneurin-Berny, Eva Pebay-Peyroula, Stéphanie Ravaud
Copper is a crucial ion in cells, but needs to be closely controlled due to its toxic potential and ability to catalyse the formation of radicals. In chloroplasts, an important step for the proper functioning of the photosynthetic electron transfer chain is the delivery of copper to plastocyanin in the thylakoid lumen. The main route for copper transport to the thylakoid lumen is driven by two PIB-type ATPases, Heavy Metal ATPase 6 (HMA6) and HMA8, located in the inner membrane of the chloroplast envelope and in the thylakoid membrane, respectively...
2016: PloS One
https://www.readbyqxmd.com/read/27769192/bioinformatic-identification-and-analysis-of-hydroxyproline-rich-glycoproteins-in-populus-trichocarpa
#14
Allan M Showalter, Brian D Keppler, Xiao Liu, Jens Lichtenberg, Lonnie R Welch
BACKGROUND: Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa)...
October 21, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27734239/modular-antenna-of-photosystem-i-in-secondary-plastids-of-red-algal-origin-a-nannochloropsis-oceanica-case-study
#15
David Bína, Zdenko Gardian, Miroslava Herbstová, Radek Litvín
Photosystem I (PSI) is a multi-subunit integral pigment-protein complex that performs light-driven electron transfer from plastocyanin to ferredoxin in the thylakoid membrane of oxygenic photoautotrophs. In order to achieve the optimal photosynthetic performance under ambient irradiance, the absorption cross section of PSI is extended by means of peripheral antenna complexes. In eukaryotes, this role is played mostly by the pigment-protein complexes of the LHC family. The structure of the PSI-antenna supercomplexes has been relatively well understood in organisms harboring the primary plastid: red algae, green algae and plants...
March 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/27620972/conservation-of-core-complex-subunits-shaped-the-structure-and-function-of-photosystem-i-in-the-secondary-endosymbiont-alga-nannochloropsis-gaditana
#16
Alessandro Alboresi, Clotilde Le Quiniou, Sathish K N Yadav, Martin Scholz, Andrea Meneghesso, Caterina Gerotto, Diana Simionato, Michael Hippler, Egbert J Boekema, Roberta Croce, Tomas Morosinotto
Photosystem I (PSI) is a pigment protein complex catalyzing the light-driven electron transport from plastocyanin to ferredoxin in oxygenic photosynthetic organisms. Several PSI subunits are highly conserved in cyanobacteria, algae and plants, whereas others are distributed differentially in the various organisms. Here we characterized the structural and functional properties of PSI purified from the heterokont alga Nannochloropsis gaditana, showing that it is organized as a supercomplex including a core complex and an outer antenna, as in plants and other eukaryotic algae...
January 2017: New Phytologist
https://www.readbyqxmd.com/read/27524487/maternal-enodls-are-required-for-pollen-tube-reception-in-arabidopsis
#17
Yingnan Hou, Xinyang Guo, Philipp Cyprys, Ying Zhang, Andrea Bleckmann, Le Cai, Qingpei Huang, Yu Luo, Hongya Gu, Thomas Dresselhaus, Juan Dong, Li-Jia Qu
During the angiosperm (flowering-plant) life cycle, double fertilization represents the hallmark between diploid and haploid generations [1]. The success of double fertilization largely depends on compatible communication between the male gametophyte (pollen tube) and the maternal tissues of the flower, culminating in precise pollen tube guidance to the female gametophyte (embryo sac) and its rupture to release sperm cells. Several important factors involved in the pollen tube reception have been identified recently [2-6], but the underlying signaling pathways are far from being understood...
September 12, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27493208/identification-of-two-conserved-residues-involved-in-copper-release-from-chloroplast-pib-1-atpases
#18
Emeline Sautron, Cécile Giustini, ThuyVan Dang, Lucas Moyet, Daniel Salvi, Serge Crouzy, Norbert Rolland, Patrice Catty, Daphné Seigneurin-Berny
Copper is an essential transition metal for living organisms. In the plant model Arabidopsis thaliana, half of the copper content is localized in the chloroplast, and as a cofactor of plastocyanin, copper is essential for photosynthesis. Within the chloroplast, copper delivery to plastocyanin involves two transporters of the PIB-1-ATPases subfamily: HMA6 at the chloroplast envelope and HMA8 in the thylakoid membranes. Both proteins are high affinity copper transporters but share distinct enzymatic properties...
September 16, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27417715/the-role-of-electrostatic-interactions-in-the-process-of-diffusional-encounter-and-docking-of-electron-transport-proteins
#19
I B Kovalenko, S S Khrushchev, V A Fedorov, G Yu Riznichenko, A B Rubin
Electrostatic interaction of plastocyanin and cytochrome f in the process of protein-protein complex formation was investigated by computer simulation methods. It was shown that long-range electrostatic interaction promotes energetically favorable mutual orientation of protein molecules at distances between their cofactors shorter than 5 nm. At distances shorter than 3 nm, these electrostatic interactions lead to a significantly detectable increase in the rate of convergence of the cofactors.
May 2016: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27368165/thylakoid-membrane-model-of-the-chl-a-fluorescence-transient-and-p700-induction-kinetics-in-plant-leaves
#20
N E Belyaeva, A A Bulychev, G Yu Riznichenko, A B Rubin
A new Thylakoid model is presented, which describes in detail the electron/proton transfer reactions between membrane protein complexes including photosystems II and I (PSII, PSI), cytochrome (Cyt) b 6 f, mobile plastoquinone PQ pool in the thylakoid membrane, plastocyanin in lumen and ferredoxin in stroma, reduction of NADP via FNR and cyclic electron transfer. The Thylakoid model parameters were fitted both to Chl fluorescence induction data (FI) and oxido-reductions of P700 (ΔA 810) measured from 20 μs up to 20 s in pea leaves...
December 2016: Photosynthesis Research
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