bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual Intracellular Localization and Targeting of Aminoimidazole Ribonucleotide Synthetase in Cowpea
Authors: Goggin Danica Erin , Lipscombe Richard , Fedorova Elena , Millar A. Harvey , Mann Anthea , Atkins Craig Anthony , Smith Penelope Mary Collina 
Published: March 2003

Abstract
De novo purine biosynthesis is localized to both mitochondria and plastids isolated from Bradyrhizobium sp.-infected cells of cowpea (Vigna unguiculata L. Walp) nodules, but several of the pathway enzymes, including aminoimidazole ribonucleotide synthetase (AIRS [EC 6.3.3.1], encoded by Vupur5), are encoded by single genes. Immunolocalization confirmed the presence of AIRS protein in both organelles. Enzymatically active AIRS was purified separately from nodule mitochondria and plastids. N-terminal sequencing showed that these two isoforms matched the Vupur5 cDNA sequence but were processed at different sites following import; the mitochondrial isoform was five amino acids longer than the plastid isoform. Electrospray tandem mass spectrometry of a trypsin digest of mitochondrial AIRS identified two internal peptides identical with the amino acid sequence deduced from Vupur5 cDNA. Western blots of proteins from mitochondria and plastids isolated from root tips showed a single AIRS protein present at low levels in both organelles. 35S-AIRS protein translated from aVupur5 cDNA was imported into isolated pea (Pisum sativum) leaf chloroplasts in vitro by an ATP-dependent process but not into import-competent mitochondria from several plant and non-plant sources. Components of the mature protein are likely to be important for import because the N-terminal targeting sequence was unable to target green fluorescent protein to either chloroplasts or mitochondria in Arabidopsis leaves. The data confirm localization of the protein translated from the AIRS gene in cowpea to both plastids and mitochondria and that it is cotargeted to both organelles, but the mechanism underlying import into mitochondria has features that are yet to be identified.
Proteome Analysis. Novel Proteins Identified at the Peribacteroid Membrane from Lotus japonicus Root Nodules
Authors: Wienkoop Stefanie , Saalbach Gerhard 
Published: March 2003

Abstract
The peribacteroid membrane (PBM) forms the structural and functional interface between the legume plant and the rhizobia. The model legume Lotus japonicus was chosen to study the proteins present at the PBM by proteome analysis. PBM was purified from root nodules by an aqueous polymer two-phase system. Extracted proteins were subjected to a global trypsin digest. The peptides were separated by nanoscale liquid chromatography and analyzed by tandem mass spectrometry. Searching the nonredundant protein database and the green plant expressed sequence tag database using the tandem mass spectrometry data identified approximately 94 proteins, a number far exceeding the number of proteins reported for the PBM hitherto. In particular, a number of membrane proteins like transporters for sugars and sulfate; endomembrane-associated proteins such as GTP-binding proteins and vesicle receptors; and proteins involved in signaling, for example, receptor kinases, calmodulin, 14-3-3 proteins, and pathogen response-related proteins, including a so-called HIR protein, were detected. Several ATPases and aquaporins were present, indicating a more complex situation than previously thought. In addition, the unexpected presence of a number of proteins known to be located in other compartments was observed. Two characteristic protein complexes obtained from native gel electrophoresis of total PBM proteins were also analyzed. Together, the results identified specific proteins at the PBM involved in important physiological processes and localized proteins known from nodule-specific expressed sequence tag databases to the PBM.
Phytochromes B, D, and E Act Redundantly to Control Multiple Physiological Responses in Arabidopsis
Authors: Franklin Keara A. , Praekelt Uta , Stoddart Wendy M. , Billingham Olivia E. , Halliday Karen J. , Whitelam Garry C. 
Published: March 2003

Abstract
Phytochrome-mediated perception of the ratio of red to far-red wavelengths in the ambient light environment is fundamental to plant growth and development. Such monitoring enables plants to detect neighboring vegetation and initiate avoidance responses, thus conferring considerable selective advantage. The shade avoidance syndrome in plants is characterized by elongation growth and early flowering, responses that are fully induced by end-of-day far-red light treatments. Elucidating the roles of individual phytochromes in mediating responses to red to far-red has however always been confounded by synergistic and mutually antagonistic coactions between family members. The creation of triple and quadruple mutants in Arabidopsis, deficient in multiple phytochromes, has revealed functional redundancy between phyB, D, and E in controlling flowering time, leaf development, and regulation of the homeobox gene,ATHB-2. In addition, mutant analysis suggests a possible novel role for phyC in suppressing ATHB-2 transcription in the light.
Pollination-, Development-, and Auxin-Specific Regulation of Gibberellin 3β-Hydroxylase Gene Expression in Pea Fruit and Seeds
Authors: Ozga Jocelyn A. , Yu Jody , Reinecke Dennis M. 
Published: March 2003

Abstract
To understand further how pollination, seeds, auxin (4-chloroindole-3-acetic acid [4-Cl-IAA]), and gibberellins (GAs) regulate GA biosynthesis in pea (Pisum sativum) fruit, we studied expression of the gene PsGA3ox1 that codes for the enzyme that converts GA20 to biologically active GA1 using real-time reverse transcription-polymerase chain reaction analysis. PsGA3ox1 mRNA levels were minimally detectable in prepollinated pericarps and ovules (−2 d after anthesis [DAA]), increased dramatically after pollination (0 DAA), then decreased by 1 DAA. Seed PsGA3ox1 mRNA levels increased at 4 DAA and again 8 to 12 DAA, when seed development was rapid. Pericarp PsGA3ox1 mRNA levels peaked coincidentally with rapid pod diameter expansion (6–10 DAA) to accommodate the growing seeds. The effects of seeds and hormones on the expression of pericarpPsGA3ox1 were investigated over a 24-h treatment period. Pericarp PsGA3ox1 mRNA levels gradually increased from 2 to 3 DAA when seeds were present; however, when the seeds were removed, the pericarp transcript levels dramatically declined. When 2-DAA deseeded pericarps were treated with 4-Cl-IAA, PsGA3ox1mRNA levels peaked 4 h after hormone treatment (270-fold increase), then decreased. PsGA3ox1 mRNA levels in deseeded pericarps treated with indole-3-acetic acid or GA3were the same or lower than deseeded controls. These data show thatPsGA3ox1 is expressed and developmentally regulated in pea pericarps and seeds. These data also show that pericarpPsGA3ox1 expression is hormonally regulated and suggest that the conversion of GA20 to GA1 occurs in the pericarp and is regulated by the presence of seeds and 4-Cl-IAA for fruit growth.
Arabidopsis Proteins Containing Similarity to the Universal Stress Protein Domain of Bacteria
Authors: Kerk David , Bulgrien Joshua , Smith Douglas W. , Gribskov Michael 
Published: March 2003

Abstract
We have collected a set of 44 Arabidopsis proteins with similarity to the USPA (universal stress protein A ofEscherichia coli) domain of bacteria. The USPA domain is found either in small proteins, or it makes up the N-terminal portion of a larger protein, usually a protein kinase. Phylogenetic tree analysis based upon a multiple sequence alignment of the USPA domains shows that these domains of protein kinases 1.3.1 and 1.3.2 form distinct groups, as do the protein kinases 1.4.1. This indicates that their USPA domain structures have diverged appreciably and suggests that they may subserve distinct cellular functions. Two USPA fold classes have been proposed: one based on Methanococcus jannaschii MJ0577 (1MJH) that binds ATP, and the other based on the Haemophilus influenzae universal stress protein (1JMV), highly similar to E. coli UspA, which does not bind ATP. A set of common residues involved in ATP binding in 1MJH and conserved in similar bacterial sequences is also found in a distinct cluster of Arabidopsis sequences. Threading analysis, which examines aspects of secondary and tertiary structure, confirms this Arabidopsis sequence cluster as highly similar to 1MJH. This structural approach can distinguish between the characteristic fold differences of 1MJH-like and 1JMV-like bacterial proteins and was used to assign the complete set of candidate Arabidopsis proteins to one of these fold classes. It is clear that all the plant sequences have arisen from a 1MJH-like ancestor.
The Sym35 Gene Required for Root Nodule Development in Pea Is an Ortholog of Nin from Lotus japonicus
Authors: Borisov Alexey Y. , Madsen Lene H. , Tsyganov Viktor E. , Umehara Yosuke , Voroshilova Vera A. , Batagov Arsen O. , Sandal Niels , Mortensen Anita , Schauser Leif , Ellis Noel , Tikhonovich Igor A. , Stougaard Jens 
Published: March 2003

Abstract
Comparative phenotypic analysis of pea (Pisum sativum) sym35 mutants and Lotus japonicus nin mutants suggested a similar function for thePsSym35 and LjNin genes in early stages of root nodule formation. Both the pea and L.japonicus mutants are non-nodulating but normal in their arbuscular mycorrhizal association. Both are characterized by excessive root hair curling in response to the bacterial microsymbiont, lack of infection thread initiation, and absence of cortical cell divisions. To investigate the molecular basis for the similarity, we cloned and sequenced the PsNin gene, taking advantage of sequence information from the previously cloned LjNin gene. An RFLP analysis on recombinant inbred lines mapped PsNinto the same chromosome arm as the PsSym35 locus and direct evidence demonstrating that PsNin is thePsSym35 gene was subsequently obtained by cosegregation analysis and sequencing of three independent Pssym35mutant alleles. L. japonicus and pea root nodules develop through different organogenic pathways, so it was of interest to compare the expression of the two orthologous genes during nodule formation. Overall, a similar developmental regulation of thePsNin and LjNin genes was shown by the transcriptional activation in root nodules of L. japonicus and pea. In the indeterminate pea nodules,PsNin is highly expressed in the meristematic cells of zone I and in the cells of infection zone II, corroborating expression of LjNin in determinate nodule primordia. At the protein level, seven domains, including the putative DNA binding/dimerization RWP-RK motif and the PB1 heterodimerization domain, are conserved between the LjNIN and PsNIN proteins.
A Phylogenomic Investigation of CYCLOIDEA-Like TCP Genes in the Leguminosae
Authors: Citerne Hélène L. , Luo Da , Pennington R. Toby , Coen Enrico , Cronk Quentin C.B. 
Published: March 2003

Abstract
Numerous TCP genes (transcription factors with a TCP domain) occur in legumes. Genes of this class in Arabidopsis (TCP1) and snapdragon (Antirrhinum majus;CYCLOIDEA) have been shown to be asymmetrically expressed in developing floral primordia, and in snapdragon, they are required for floral zygomorphy (bilaterally symmetrical flowers). These genes are therefore particularly interesting in Leguminosae, a family that is thought to have evolved zygomorphy independently from other zygomorphic angiosperm lineages. Using a phylogenomic approach, we show that homologs of TCP1/CYCLOIDEA occur in legumes and may be divided into two main classes (LEGCYCgroup I and II), apparently the result of an early duplication, and each class is characterized by a typical amino acid signature in the TCP domain. Furthermore, group I genes in legumes may be divided into two subclasses (LEGCYC IA and IB), apparently the result of a duplication near the base of the papilionoid legumes or below. Most papilionoid legumes investigated have all three genes present (LEGCYC IA, IB, and II), inviting further work to investigate possible functional difference between the three types. However, within these three major gene groups, the precise relationships of the paralogs between species are difficult to determine probably because of a complex history of duplication and loss with lineage sorting or heterotachy (within-site rate variation) due to functional differentiation. The results illustrate both the potential and the difficulties of orthology determination in variable gene families, on which the phylogenomic approach to formulating hypotheses of function depends.
Syntenic Relationships between Medicago truncatulaand Arabidopsis Reveal Extensive Divergence of Genome Organization,
Authors: Zhu Hongyan , Kim Dong-Jin , Baek Jong-Min , Choi Hong-Kyu , Ellis Leland C. , Küester Helge , McCombie W. Richard , Peng Hui-Mei , Cook Douglas R. 
Published: March 2003

Abstract
Arabidopsis and Medicago truncatula represent sister clades within the dicot subclass Rosidae. We used genetic map-based and bacterial artificial chromosome sequence-based approaches to estimate the level of synteny between the genomes of these model plant species. Mapping of 82 tentative orthologous gene pairs reveals a lack of extended macrosynteny between the two genomes, although marker collinearity is frequently observed over small genetic intervals. Divergence estimates based on non-synonymous nucleotide substitutions suggest that a majority of the genes under analysis have experienced duplication in Arabidopsis subsequent to divergence of the two genomes, potentially confounding synteny analysis. Moreover, in cases of localized synteny, genetically linked loci in M.truncatula often share multiple points of synteny with Arabidopsis; this latter observation is consistent with the large number of segmental duplications that compose the Arabidopsis genome. More detailed analysis, based on complete sequencing and annotation of three M. truncatula bacterial artificial chromosome contigs suggests that the two genomes are related by networks of microsynteny that are often highly degenerate. In some cases, the erosion of microsynteny could be ascribed to the selective gene loss from duplicated loci, whereas in other cases, it is due to the absence of close homologs of M. truncatula genes in Arabidopsis.
Isolation and Properties of Floral Defensins from Ornamental Tobacco and Petunia
Authors: Lay Fung T. , Brugliera Filippa , Anderson Marilyn A. 
Published: March 2003

AbstractThe flowers of the solanaceous plants ornamental tobacco (Nicotiana alata) and petunia (Petunia hybrida) produce high levels of defensins during the early stages of development. In contrast to the well-described seed defensins, these floral defensins are produced as precursors with C-terminal prodomains of 27 to 33 amino acids in addition to a typical secretion signal peptide and central defensin domain of 47 or 49 amino acids. Defensins isolated from N. alata and petunia flowers lack the C-terminal domain, suggesting that it is removed during or after transit through the secretory pathway. Immunogold electron microscopy has been used to demonstrate that the N. alata defensin is deposited in the vacuole. In addition to the eight canonical cysteine residues that define the plant defensin family, the two petunia defensins have an extra pair of cysteines that form a fifth disulfide bond and hence define a new subclass of this family of proteins. Expression of the N. alata defensinNaD1 is predominantly flower specific and is most active during the early stages of flower development. NaD1transcripts accumulate in the outermost cell layers of petals, sepals, anthers, and styles, consistent with a role in protection of the reproductive organs against potential pathogens. The floral defensins inhibit the growth of Botrytis cinerea andFusarium oxysporum in vitro, providing further support for a role in protection of floral tissues against pathogen invasion.
Tobacco Transgenic Lines That Express Fenugreek Galactomannan Galactosyltransferase Constitutively Have Structurally Altered Galactomannans in Their Seed Endosperm Cell Walls
Authors: Reid J.S. Grant , Edwards Mary E. , Dickson Cathryn A. , Scott Catherine , Gidley Michael J. 
Published: March 2003

Abstract
Galactomannans [(1→6)-α-d-galactose (Gal)-substituted (1→4)-β-d-mannans] are major cell wall storage polysaccharides in the endosperms of some seeds, notably the legumes. Their biosynthesis in developing legume seeds involves the functional interaction of two membrane-bound glycosyltransferases, mannan synthase (MS) and galactomannan galactosyltransferase (GMGT). MS catalyzes the elongation of the mannan backbone, whereas GMGT action determines the distribution and amount of Gal substitution. Fenugreek (Trigonella foenum-graecum) forms a galactomannan with a very high degree of Gal substitution (Man/Gal = 1.1), and its GMGT has been characterized. We now report that the endosperm cell walls of the tobacco (Nicotiana tabacum) seed are rich in a galactomannan with a very low degree of Gal substitution (Man/Gal about 20) and that its depositional time course is closely correlated with membrane-bound MS and GMGT activities. Furthermore, we demonstrate that seeds from transgenic tobacco lines that express fenugreek GMGT constitutively in membrane-bound form have endosperm galactomannans with increased average degrees of Gal substitution (Man/Gal about 10 in T1 generation seeds and about 7.5 in T2generation seeds). Membrane-bound enzyme systems from transgenic seed endosperms form galactomannans in vitro that are more highly Gal substituted than those formed by controls under identical conditions. To our knowledge, this is the first report of structural manipulation of a plant cell wall polysaccharide in transgenic plants via a biosynthetic membrane-bound glycosyltransferase.
Nylon Filter Arrays Reveal Differential Gene Expression in Proteoid Roots of White Lupin in Response to Phosphorus Deficiency
Authors: Uhde-Stone Claudia , Zinn Kelly E. , Ramirez-Yáñez Mario , Li Aiguo , Vance Carroll P. , Allan Deborah L. 
Published: March 2003

Abstract
White lupin (Lupinus albus) adapts to phosphorus deficiency (−P) by the development of short, densely clustered lateral roots called proteoid (or cluster) roots. In an effort to better understand the molecular events mediating these adaptive responses, we have isolated and sequenced 2,102 expressed sequence tags (ESTs) from cDNA libraries prepared with RNA isolated at different stages of proteoid root development. Determination of overlapping regions revealed 322 contigs (redundant copy transcripts) and 1,126 singletons (single-copy transcripts) that compile to a total of 1,448 unique genes (unigenes). Nylon filter arrays with these 2,102 ESTs from proteoid roots were performed to evaluate global aspects of gene expression in response to −P stress. ESTs differentially expressed in P-deficient proteoid roots compared with +P and −P normal roots include genes involved in carbon metabolism, secondary metabolism, P scavenging and remobilization, plant hormone metabolism, and signal transduction.
crinkle, a Novel Symbiotic Mutant That Affects the Infection Thread Growth and Alters the Root Hair, Trichome, and Seed Development in Lotus japonicus
Authors: Tansengco Myra L. , Hayashi Makoto , Kawaguchi Masayoshi , Imaizumi-Anraku Haruko , Murooka Yoshikatsu 
Published: March 2003

Abstract
To elucidate the mechanisms involved inRhizobium-legume symbiosis, we examined a novel symbiotic mutant, crinkle (Ljsym79), from the model legume Lotus japonicus. On nitrogen-starved medium, crinkle mutants inoculated with the symbiont bacterium Mesorhizobium loti MAFF 303099 showed severe nitrogen deficiency symptoms. This mutant was characterized by the production of many bumps and small, white, uninfected nodule-like structures. Few nodules were pale-pink and irregularly shaped with nitrogen-fixing bacteroids and expressing leghemoglobin mRNA. Morphological analysis of infected roots showed that nodulation incrinkle mutants is blocked at the stage of the infection process. Confocal microscopy and histological examination ofcrinkle nodules revealed that infection threads were arrested upon penetrating the epidermal cells. Starch accumulation in uninfected cells and undeveloped vascular bundles were also noted incrinkle nodules. Results suggest that theCrinkle gene controls the infection process that is crucial during the early stage of nodule organogenesis. Aside from the symbiotic phenotypes, crinkle mutants also developed morphological alterations, such as crinkly or wavy trichomes, short seedpods with aborted embryos, and swollen root hairs.crinkle is therefore required for symbiotic nodule development and for other aspects of plant development.
Transgenic Studies on the Involvement of Cytokinin and Gibberellin in Male Development
Authors: Huang Shihshieh , Cerny R. Eric , Qi Youlin , Bhat Deepti , Aydt Carrie M. , Hanson Doris D. , Malloy Kathleen P. , Ness Linda A. 
Published: March 2003

AbstractNumerous plant hormones interact during plant growth and development. Elucidating the role of these various hormones on particular tissue types or developmental stages has been difficult with exogenous applications or constitutive expression studies. Therefore, we used tissue-specific promoters expressing CKX1 andgai, genes involved in oxidative cytokinin degradation and gibberellin (GA) signal transduction, respectively, to study the roles of cytokinin and GA in male organ development. Accumulation of CKX1 in reproductive tissues of transgenic maize (Zea mays) resulted in male-sterile plants. The male development of these plants was restored by applications of kinetin and thidiazuron. Similarly, expression of gai specifically in anthers and pollen of tobacco (Nicotiana tabacum) and Arabidopsis resulted in the abortion of these respective tissues. Thegai-induced male-sterile phenotype exhibited by the transgenic plants was reversible by exogenous applications of kinetin. Our results provide molecular evidence of the involvement of cytokinin and GA in male development and support the hypothesis that the male development is controlled in concert by multiple hormones. These studies also suggest a potential method for generating maintainable male sterility in plants by using existing agrochemicals that would reduce the expense of seed production for existing hybrid crops and provide a method to produce hybrid varieties of traditionally non-hybrid crops.
Mapping the Proteome of Barrel Medic (Medicago truncatula),
Authors: Watson Bonnie S. , Asirvatham Victor S. , Wang Liangjiang , Sumner Lloyd W. 
Published: March 2003

Abstract
A survey of six organ-/tissue-specific proteomes of the model legume barrel medic (Medicago truncatula) was performed. Two-dimensional polyacrylamide gel electrophoresis reference maps of protein extracts from leaves, stems, roots, flowers, seed pods, and cell suspension cultures were obtained. Five hundred fifty-one proteins were excised and 304 proteins identified using peptide mass fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Nanoscale high-performance liquid chromatography coupled with tandem quadrupole time-of-flight mass spectrometry was used to validate marginal matrix-assisted laser desorption ionization time-of-flight mass spectrometry protein identifications. This dataset represents one of the most comprehensive plant proteome projects to date and provides a basis for future proteome comparison of genetic mutants, biotically and abiotically challenged plants, and/or environmentally challenged plants. Technical details concerning peptide mass fingerprinting, database queries, and protein identification success rates in the absence of a sequenced genome are reported and discussed. A summary of the identified proteins and their putative functions are presented. The tissue-specific expression of proteins and the levels of identified proteins are compared with their related transcript abundance as quantified through EST counting. It is estimated that approximately 50% of the proteins appear to be correlated with their corresponding mRNA levels.