bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Organization of Cytoplasmic Ribosomal Protein Genes in the Arabidopsis Genome
Authors: Barakat Abdelali , Szick-Miranda Kathleen , Chang Ing-Feng , Guyot Romain , Blanc Guillaume , Cooke Richard , Delseny Michel , Bailey-Serres Julia 
Published: November 2008

Abstract
Eukaryotic ribosomes are made of two components, four ribosomal RNAs, and approximately 80 ribosomal proteins (r-proteins). The exact number of r-proteins and r-protein genes in higher plants is not known. The strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (Rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of Arabidopsis. By use of the numerous expressed sequence tag (EST) accessions and the complete genomic sequence of this species, we identified 249 genes (including some pseudogenes) corresponding to 80 (32 small subunit and 48 large subunit) cytoplasmic r-protein types. None of the r-protein genes are single copy and most are encoded by three or four expressed genes, indicative of the internal duplication of the Arabidopsis genome. The r-proteins are distributed throughout the genome. Inspection of genes in the vicinity of r-protein gene family members confirms extensive duplications of large chromosome fragments and sheds light on the evolutionary history of the Arabidopsis genome. Examination of large duplicated regions indicated that a significant fraction of the r-protein genes have been either lost from one of the duplicated fragments or inserted after the initial duplication event. Only 52 r-protein genes lack a matching EST accession, and 19 of these contain incomplete open reading frames, confirming that most genes are expressed. Assessment of cognate EST numbers suggests that r-protein gene family members are differentially expressed.
Characterization of a Functional Soluble Form of a Brassica napus Membrane-Anchored Endo-1,4-β-Glucanase Heterologously Expressed in Pichia pastoris
Authors: Mølhøj Michael , Ulvskov Peter , Dal Degan Florence 
Published: November 2008

Abstract
The Brassica napus gene,Cel16, encodes a membrane-anchored endo-1,4-β-glucanase with a deduced molecular mass of 69 kD. As for other membrane-anchored endo-1,4-β-glucanases, Cel16 consists of a predicted intracellular, charged N terminus (methionine1-lysine70), a hydrophobic transmembrane domain (isoleucine71-valine93), and a periplasmic catalytic core (lysine94-proline621). Here, we report the functional analysis of Δ1-90Cel16, the N terminally truncated Cel16, missing residues 1 through 90 and comprising the catalytic domain of Cel16 expressed recombinantly in the methylotrophic yeast Pichia pastoris as a soluble protein. A two-step purification protocol yielded Δ1-90Cel16 in a pure form. The molecular mass of Δ1-90Cel16, when determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was about 130 kD and about 60 kD after enzymatic removal of N-glycans, fitting the expected molecular mass of 59 kD. Δ1-90Cel16 was highly N glycosylated as compared with the native B. napus Cel16 protein. Δ1-90Cel16 had a pH optimum of 6.0. The activity of Δ1-90Cel16 was inhibited by EDTA and exhibited a strong dependence on calcium. Δ1-90Cel16 showed substrate specificity for low substituted carboxymethyl-cellulose and amorphous cellulose. It did not hydrolyze crystalline cellulose, xyloglycan, xylan, (1→3),(1→4)-β-d-glucan, the highly substituted hydroxyethylcellulose, or the oligosaccharides cellotriose, cellotetraose, cellopentaose, or xylopentaose. Size exclusion analysis of Δ1-90Cel16-hydrolyzed carboxymethylcellulose showed that Δ1-90Cel16 is a true endo-acting glucanase.
Responses of Photosynthetic Electron Transport in Stomatal Guard Cells and Mesophyll Cells in Intact Leaves to Light, CO2, and Humidity
Authors: Lawson Tracy , Oxborough Kevin , Morison James I.L. , Baker Neil R. 
Published: November 2008

Abstract
High-resolution images of the chlorophyll fluorescence parameterF q ′/F m ′from attached leaves of commelina (Commelina communis) and tradescantia (Tradescantia albiflora) were used to compare the responses of photosynthetic electron transport in stomatal guard cell chloroplasts and underlying mesophyll cells to key environmental variables.F q ′/F m ′estimates the quantum efficiency of photosystem II photochemistry and provides a relative measure of the quantum efficiency of non-cyclic photosynthetic electron transport. Over a range of light intensities, values ofF q ′/F m ′were 20% to 30% lower in guard cell chloroplasts than in mesophyll cells, and there was a close linear relationship between the values for the two cell types. The responses ofF q ′/F m ′of guard and mesophyll cells to changes of CO2 and O2 concentration were very similar. There were similar reductions ofF q ′/F m ′of guard and mesophyll cells over a wide range of CO2concentrations when the ambient oxygen concentration was decreased from 21% to 2%, suggesting that both cell types have similar proportions of photosynthetic electron transport used by Rubisco activity. When stomata closed after a pulse of dry air,F q ′/F m ′of both guard cell and mesophyll showed the same response; with a marked decline when ambient CO2 was low, but no change when ambient CO2 was high. This indicates that photosynthetic electron transport in guard cell chloroplasts responds to internal, not ambient, CO2 concentration.
Protection against Heat Stress-Induced Oxidative Damage in Arabidopsis Involves Calcium, Abscisic Acid, Ethylene, and Salicylic Acid
Authors: Larkindale Jane , Knight Marc R. 
Published: November 2008

AbstractPlants, in common with all organisms, have evolved mechanisms to cope with the problems caused by high temperatures. We examined specifically the involvement of calcium, abscisic acid (ABA), ethylene, and salicylic acid (SA) in the protection against heat-induced oxidative damage in Arabidopsis. Heat caused increased thiobarbituric acid reactive substance levels (an indicator of oxidative damage to membranes) and reduced survival. Both effects required light and were reduced in plants that had acquired thermotolerance through a mild heat pretreatment. Calcium channel blockers and calmodulin inhibitors increased these effects of heating and added calcium reversed them, implying that protection against heat-induced oxidative damage in Arabidopsis requires calcium and calmodulin. Similar to calcium, SA, 1-aminocyclopropane-1-carboxylic acid (a precursor to ethylene), and ABA added to plants protected them from heat-induced oxidative damage. In addition, the ethylene-insensitive mutant etr-1, the ABA-insensitive mutant abi-1, and a transgenic line expressingnahG (consequently inhibited in SA production) showed increased susceptibility to heat. These data suggest that protection against heat-induced oxidative damage in Arabidopsis also involves ethylene, ABA, and SA. Real time measurements of cytosolic calcium levels during heating in Arabidopsis detected no increases in response to heat per se, but showed transient elevations in response to recovery from heating. The magnitude of these calcium peaks was greater in thermotolerant plants, implying that these calcium signals might play a role in mediating the effects of acquired thermotolerance. Calcium channel blockers and calmodulin inhibitors added solely during the recovery phase suggest that this role for calcium is in protecting against oxidative damage specifically during/after recovery.
AtREM1, a Member of a New Family of B3 Domain-Containing Genes, Is Preferentially Expressed in Reproductive Meristems
Authors: Franco-Zorrilla José M. , Cubas Pilar , Jarillo José A. , Fernández-Calvı́n Begoña , Salinas Julio , Martı́nez-Zapater José M. 
Published: November 2008

Abstract
We have isolated and characterized AtREM1, the Arabidopsis ortholog of the cauliflower (Brassica oleracea) BoREM1. AtREM1 belongs to a large gene family of more than 20 members in Arabidopsis. The deduced AtREM1 protein contains several repeats of a B3-related domain, and it could represent a new class of regulatory proteins only found in plants. Expression of AtREM1 is developmentally regulated, being first localized in a few central cells of vegetative apical meristems, and later expanding to the whole inflorescence meristem, as well as primordia and organs of third and fourth floral whorls. This specific expression pattern suggests a role in the organization of reproductive meristems, as well as during flower organ development.
Insertional Mutants of Chlamydomonas reinhardtii That Require Elevated CO2 for Survival
Authors: Van Kyujung , Wang Yingjun , Nakamura Yoshiko , Spalding Martin H. 
Published: November 2008

Abstract
Aquatic photosynthetic organisms live in quite variable conditions of CO2 availability. To survive in limiting CO2conditions, Chlamydomonas reinhardtii and other microalgae show adaptive changes, such as induction of a CO2-concentrating mechanism, changes in cell organization, increased photorespiratory enzyme activity, induction of periplasmic carbonic anhydrase and specific polypeptides (mitochondrial carbonic anhydrases and putative chloroplast carrier proteins), and transient down-regulation in the synthesis of Rubisco. The signal for acclimation to limiting CO2 in C. reinhardtii is unidentified, and it is not known how they sense a change of CO2 level. The limiting CO2 signals must be transduced into the changes in gene expression observed during acclimation, so mutational analyses should be helpful for investigating the signal transduction pathway for low CO2 acclimation. Eight independently isolated mutants of C. reinhardtiithat require high CO2 for photoautotrophic growth were tested by complementation group analysis. These mutants are likely to be defective in some aspects of the acclimation to low CO2because they differ from wild type in their growth and in the expression patterns of five low CO2-inducible genes (Cah1, Mca1, Mca2,Ccp1, and Ccp2). Two of the new mutants formed a single complementation group along with the previously described mutant cia-5, which appears to be defective in the signal transduction pathway for low CO2 acclimation. The other mutations represent six additional, independent complementation groups.
Exceptional Sensitivity of Rubisco Activase to Thermal Denaturation in Vitro and in Vivo
Authors: Salvucci Michael E. , Osteryoung Katherine W. , Crafts-Brandner Steven J. , Vierling Elizabeth 
Published: November 2008

AbstractHeat stress inhibits photosynthesis by reducing the activation of Rubisco by Rubisco activase. To determine if loss of activase function is caused by protein denaturation, the thermal stability of activase was examined in vitro and in vivo and compared with the stabilities of two other soluble chloroplast proteins. Isolated activase exhibited a temperature optimum for ATP hydrolysis of 44°C compared with ≥60°C for carboxylation by Rubisco. Light scattering showed that unfolding/aggregation occurred at 45°C and 37°C for activase in the presence and absence of ATPγS, respectively, and at 65°C for Rubisco. Addition of chemically denatured rhodanese to heat-treated activase trapped partially folded activase in an insoluble complex at treatment temperatures that were similar to those that caused increased light scattering and loss of activity. To examine thermal stability in vivo, heat-treated tobacco (Nicotiana rustica cv Pulmila) protoplasts and chloroplasts were lysed with detergent in the presence of rhodanese and the amount of target protein that aggregated was determined by immunoblotting. The results of these experiments showed that thermal denaturation of activase in vivo occurred at temperatures similar to those that denatured isolated activase and far below those required to denature Rubisco or phosphoribulokinase. Edman degradation analysis of aggregated proteins from tobacco and pea (Pisum sativum cv “Little Marvel”) chloroplasts showed that activase was the major protein that denatured in response to heat stress. Thus, loss of activase activity during heat stress is caused by an exceptional sensitivity of the protein to thermal denaturation and is responsible, in part, for deactivation of Rubisco.
Differential Regulation of mRNA Levels of Acyl Carrier Protein Isoforms in Arabidopsis
Authors: Bonaventure Gustavo , Ohlrogge John B. 
Published: November 2008

Abstract
All higher plants express several different acyl carrier protein (ACP) isoforms in a tissue-specific manner. We provide evidence that expression of mRNA for the most abundant ACP isoform in Arabidopsis leaves (ACP4) is increased severalfold by light, whereas mRNA levels for ACP isoforms 2 and 3 are independent of light. The presence of GATA-like motifs in the upstream region of theAcl1.4 gene (encoding for ACP4) and the similarity in light-mediated induction to ferredoxin-A mRNA suggests a direct role of light in Acl1.4 gene activation. Polyribosomal analysis indicated that light also affects the association of ACP transcripts with polysomes, similarly to mRNAs encoding ferredoxin-A. ACP2, ACP3, and ACP4 mRNA levels were also examined in Arabidopsis cell suspension culture and were found to be differentially controlled by metabolic and/or growth derived signals. Comparison of 5′-untranslated regions (UTRs) of ACP mRNAs of diverse plant species revealed two motifs that have been conserved during evolution, a CTCCGCC box and C-T-rich sequences. Fusions of the 5′-UTR sequences of ACP1 and ACP2 to luciferase and expression in transgenic plants indicated that the ACP1 leader contributes to preferential expression in seeds, whereas the ACP2 5′-UTR favored expression in roots. The deletion of 58 bp containing the conserved motifs of the ACP1 5′-UTR resulted in 10- to 20-fold lower gene expression in leaf and seed tissues of transgenic Arabidopsis plants.
Unraveling the Effects of Plant Hydraulics on Stomatal Closure during Water Stress in Walnut
Authors: Cochard Hervé , Coll Lluis , Le Roux Xavier , Améglio Thierry 
Published: November 2008

Abstract
The objectives of the study were to identify the relevant hydraulic parameters associated with stomatal regulation during water stress and to test the hypothesis of a stomatal control of xylem embolism in walnut (Juglans regia× nigra) trees. The hydraulic characteristics of the sap pathway were experimentally altered with different methods to alter plant transpiration (E plant) and stomatal conductance (g s). Potted trees were exposed to a soil water depletion to alter soil water potential (Ψsoil), soil resistance (R soil), and root hydraulic resistances (R root). Soil temperature was changed to alter R root alone. Embolism was created in the trunk to increase shoot resistance (R shoot). Stomata closed in response to these stresses with the effect of maintaining the water pressure in the leaf rachis xylem (P rachis) above −1.4 MPa and the leaf water potential (Ψleaf) above −1.6 MPa. The same dependence of E plant andg s on P rachis or Ψleaf was always observed. This suggested that stomata were not responding to changes in Ψsoil,R soil, R root, orR shoot per se but rather to their impact onP rachis and/or Ψleaf. Leaf rachis was the most vulnerable organ, with a thresholdP rachis for embolism induction of −1.4 MPa. The minimum Ψleaf values corresponded to leaf turgor loss point. This suggested that stomata are responding to leaf water status as determined by transpiration rate and plant hydraulics and thatP rachis might be the physiological parameter regulated by stomatal closure during water stress, which would have the effect of preventing extensive developments of cavitation during water stress.
Environmental Regulation of Lateral Root Initiation in Arabidopsis
Authors: Malamy Jocelyn E. , Ryan Katherine S. 
Published: November 2008

Abstract
Plant morphology is dramatically influenced by environmental signals. The growth and development of the root system is an excellent example of this developmental plasticity. Both the number and placement of lateral roots are highly responsive to nutritional cues. This indicates that there must be a signal transduction pathway that interprets complex environmental conditions and makes the “decision” to form a lateral root at a particular time and place. Lateral roots originate from differentiated cells in adult tissues. These cells must reenter the cell cycle, proliferate, and redifferentiate to produce all of the cell types that make up a new organ. Almost nothing is known about how lateral root initiation is regulated or coordinated with growth conditions. Here, we report a novel growth assay that allows this regulatory mechanism to be dissected in Arabidopsis. When Arabidopsis seedlings are grown on nutrient media with a high sucrose to nitrogen ratio, lateral root initiation is dramatically repressed. Auxin localization appears to be a key factor in this nutrient-mediated repression of lateral root initiation. We have isolated a mutant, lateral root initiation 1 (lin1), that overcomes the repressive conditions. This mutant produces a highly branched root system on media with high sucrose to nitrogen ratios. The lin1 phenotype is specific to these growth conditions, suggesting that thelin1 gene is involved in coordinating lateral root initiation with nutritional cues. Therefore, these studies provide novel insights into the mechanisms that regulate the earliest steps in lateral root initiation and that coordinate plant development with the environment.
Aluminum Toxicity Is Associated with Mitochondrial Dysfunction and the Production of Reactive Oxygen Species in Plant Cells
Authors: Yamamoto Yoko , Kobayashi Yukiko , Devi S. Rama , Rikiishi Sanae , Matsumoto Hideaki 
Published: November 2008

AbstractPotential mechanisms of Al toxicity measured as Al-induced inhibition of growth in cultured tobacco cells (Nicotiana tabacum, nonchlorophyllic cell line SL) and pea (Pisum sativum) roots were investigated. Compared with the control treatment without Al, the accumulation of Al in tobacco cells caused instantaneously the repression of mitochondrial activities [monitored by the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and the uptake of Rhodamine 123] and, after a lag of about 12 h, triggered reactive oxygen species (ROS) production, respiration inhibition, ATP depletion, and the loss of growth capability almost simultaneously. The presence of an antioxidant, butylated hydroxyanisol, during Al treatment of SL cells prevented not only ROS production but also ATP depletion and the loss of growth capability, suggesting that the Al-triggered ROS production seems to be a cause of ATP depletion and the loss of growth capability. Furthermore, these three late events were similarly repressed in an Al-tolerant cell line (ALT301) isolated from SL cells, suggesting that the acquisition of antioxidant functions mimicking butylated hydroxyanisol can be a mechanism of Al tolerance. In the pea root, Al also triggered ROS production, respiration inhibition, and ATP depletion, which were all correlated with inhibition of root elongation. Taken together, we conclude that Al affects mitochondrial functions, which leads to ROS production, probably the key critical event in Al inhibition of cell growth.
Isolation and Functional Analysis of Homogentisate Phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis
Authors: Collakova Eva , DellaPenna Dean 
Published: November 2008

Abstract
Tocopherols, collectively known as vitamin E, are lipid-soluble antioxidants synthesized exclusively by photosynthetic organisms and are required components of mammalian diets. The committed step in tocopherol biosynthesis involves condensation of homogentisic acid and phytyl diphosphate (PDP) catalyzed by a membrane-bound homogentisate phytyltransferase (HPT). HPTs were identified fromSynechocystis sp. PCC 6803 and Arabidopsis based on their sequence similarity to chlorophyll synthases, which utilize PDP in a similar prenylation reaction. HPTs from both organisms used homogentisic acid and PDP as their preferred substrates in vitro but only Synechocystis sp. PCC 6803 HPT was active with geranylgeranyl diphosphate as a substrate. Neither enzyme could utilize solanesyl diphosphate, the prenyl substrate for plastoquinone-9 synthesis. In addition, disruption of Synechocystis sp. PCC 6803 HPT function causes an absence of tocopherols without affecting plastoquinone-9 levels, indicating that separate polyprenyltransferases exist for tocopherol and plastoquinone synthesis in Synechocystis sp. PCC 6803. It is surprising that the absence of tocopherols in this mutant had no discernible effect on cell growth and photosynthesis.
Arabidopsis Seedling Growth, Storage Lipid Mobilization, and Photosynthetic Gene Expression Are Regulated by Carbon:Nitrogen Availability
Authors: Martin Thomas , Oswald Oliver , Graham Ian A. 
Published: November 2008

Abstract
The objective of the current work was to establish the degree to which the effects of carbon and nitrogen availability on Arabidopsis seedling growth and development are due to these nutrients acting independently or together. Growth of seedlings on low (0.1 mm) nitrogen results in a significant reduction of seedling and cotyledon size, fresh weight, chlorophyll, and anthocyanin content but a slight increase in endogenous sugars. The addition of 100 mm sucrose (Suc) to the nitrogen-depleted growth media results in a further reduction in cotyledon size and chlorophyll content and an overall increase in anthocyanins and endogenous sugars. Storage lipid breakdown is almost completely blocked in seedlings grown on low nitrogen and 100 mm Suc and is significantly inhibited when seedlings are grown on either low nitrogen or high Suc. Carbohydrate repression of photosynthetic gene expression can only be observed under low nitrogen conditions. Low (0.1 mm) nitrogen in the absence of exogenous carbohydrate results in a significant decrease in chlorophyll a/b-binding proteinand ribulose bisphosphate carboxylase small subunit gene transcript levels. Thus, carbon to nitrogen ratio rather than carbohydrate status alone appears to play the predominant role in regulating various aspects of seedling growth including storage reserve mobilization and photosynthetic gene expression.
A Slow Maturation of a Cysteine Protease with a Granulin Domain in the Vacuoles of Senescing Arabidopsis Leaves
Authors: Yamada Kenji , Matsushima Ryo , Nishimura Mikio , Hara-Nishimura Ikuko 
Published: November 2008

Abstract
Arabidopsis RD21 is a cysteine protease of the papain family. Unlike other members of the papain family, RD21 has a C-terminal extension sequence composed of two domains, a 2-kD proline-rich domain and a 10-kD domain homologous to animal epithelin/granulin family proteins. The RD21 protein was accumulated as 38- and 33-kD proteins in Arabidopsis leaves. An immunoblot showed that the 38-kD protein had the granulin domain, whereas the 33-kD protein did not. A pulse-chase experiment with Bright-Yellow 2 transformant cells expressing RD21 showed that RD21 was synthesized as a 57-kD precursor and was then slowly processed to make the 33-kD mature protein via the 38-kD intermediate. After a 12-h chase, the 38-kD intermediate was still detected in the cells. These results indicate that the N-terminal propeptide was first removed from the 57-kD precursor, and the C-terminal granulin domain was then slowly removed to yield the 33-kD mature protein. Subcellular fractionation of the Bright-Yellow 2 transformant showed that the intermediate and mature forms of RD21 were localized in the vacuoles. Under the acidic conditions of the vacuolar interior, the intermediate was found to be easily aggregated. The intermediate and the mature protein were accumulated in association with leaf senescence. Taken together, these results indicate that the intermediate of RD21 was accumulated in the vacuoles as an aggregate, and then slowly matured to make a soluble protease by removing the granulin domain during leaf senescence.