Oxford University Press (OUP)
1532-2548
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N enrichment affects the arbuscular mycorrhizal fungi-mediated relationship between a C4 grass and a legume Abstract Arbuscular mycorrhizal fungi (AMF) regulate soil nutrient cycling, directly supplying a host plant with nitrogen (N). AMF can also affect the outcome of interspecific interactions, but a mechanistic understanding of how soil N availability affects AMF-mediated interspecific relationships is currently lacking. We selected one dominant (Bothriochloa ischaemum; C4 grass) and one subordinate (Lespedeza davurica; legume) species in a natural grassland climax community to investigate the mechanism by which AMF influence interspecific interaction (mixed and monoculture) under three levels of N addition (0, low, and high N addition). Under the non-N addition treatment, AMF preferentially supplied N to the roots of B. ischaemum at the expense of N uptake by L. davurica, resulting in inhibited AMF benefits for L. davurica shoot growth. Under the low N addition treatment, interspecific interaction via AMF promoted L. davurica growth. Compared to the non-N addition treatment, N addition largely mitigated the effects, both positive (for B. ischaemum) and negative (for L. davurica), of AMF-mediated interspecific interaction on plant N uptake via AMF. When soil N availability severely limited plant growth, preferential N supply to the C4 grass by AMF was important for maintaining the abundance of the dominant species. When the N limitation for plant growth was alleviated by N addition, the interaction between AMF and soil microorganisms improved nutrient availability for the legume by stimulating activity of the enzyme responsible for soil organic matter mineralization, which is important for maintaining the abundance of the subordinate species. These data could influence strategies for maintaining biodiversity.
Tập 187 Số 3 - Trang 1519-1533 - 2021
Evolutionary Radiation Pattern of Novel Protein Phosphatases Revealed by Analysis of Protein Data from the Completely Sequenced Genomes of Humans, Green Algae, and Higher Plants Abstract In addition to the major serine/threonine-specific phosphoprotein phosphatase, Mg2+-dependent phosphoprotein phosphatase, and protein tyrosine phosphatase families, there are novel protein phosphatases, including enzymes with aspartic acid-based catalysis and subfamilies of protein tyrosine phosphatases, whose evolutionary history and representation in plants is poorly characterized. We have searched the protein data sets encoded by the well-finished nuclear genomes of the higher plants Arabidopsis (Arabidopsis thaliana) and Oryza sativa, and the latest draft data sets from the tree Populus trichocarpa and the green algae Chlamydomonas reinhardtii and Ostreococcus tauri, for homologs to several classes of novel protein phosphatases. The Arabidopsis proteins, in combination with previously published data, provide a complete inventory of known types of protein phosphatases in this organism. Phylogenetic analysis of these proteins reveals a pattern of evolution where a diverse set of protein phosphatases was present early in the history of eukaryotes, and the division of plant and animal evolution resulted in two distinct sets of protein phosphatases. The green algae occupy an intermediate position, and show similarity to both plants and animals, depending on the protein. Of specific interest are the lack of cell division cycle (CDC) phosphatases CDC25 and CDC14, and the seeming adaptation of CDC14 as a protein interaction domain in higher plants. In addition, there is a dramatic increase in proteins containing RNA polymerase C-terminal domain phosphatase-like catalytic domains in the higher plants. Expression analysis of Arabidopsis phosphatase genes differentially amplified in plants (specifically the C-terminal domain phosphatase-like phosphatases) shows patterns of tissue-specific expression with a statistically significant number of correlated genes encoding putative signal transduction proteins.
Tập 146 Số 2 - Trang 323-324 - 2008
The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion Abstract
Identification of regulatory molecules that determine the extent and direction of expansion is necessary to understand how cell morphogenesis is controlled in plants. We recently identifiedCOB (COBRA) as a key regulator of the orientation of cell expansion in the root. Analysis of the Arabidopsis genome sequence indicated that COB belongs to a multigene family consisting of 12 members, all predicted to encode glycosylphosphatidylinositol-anchored proteins. All but two of theCOBL (COB-like) genes are expressed in most organs examined, suggesting possible redundancy. Sequence comparisons, phylogenetic analyses, and exon-intron positions revealed that the COB family is composed of two main subgroups sharing a common architecture, one subgroup being characterized by an additional N-terminal domain. Identification of expressed sequence tags corresponding to potential orthologs in other plant species suggested that COB-related functions are required in all vascular plants. Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface.
Tập 130 Số 2 - Trang 538-548 - 2002
The Institute for Genomic Research Osa1 Rice Genome Annotation Database Abstract
We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.
Tập 138 Số 1 - Trang 18-26 - 2005
Flavonoid Biosynthesis. A Colorful Model for Genetics, Biochemistry, Cell Biology, and Biotechnology
Tập 126 Số 2 - Trang 485-493 - 2001
Identification of the Flavonoid Hydroxylases from Grapevine and Their Regulation during Fruit Development Abstract
Flavonoids are important secondary metabolites in many fruits, and their hydroxylation pattern determines their color, stability, and antioxidant capacity. Hydroxylation of the B-ring of flavonoids is catalyzed by flavonoid 3′-hydroxylase (F3′H) and flavonoid 3′,5′-hydroxylase (F3′5′H), and may also require cytochrome b5. We report the identification of genes encoding F3′H, F3′5′H, and a putative cytochrome b5 from grapevine (Vitis vinifera L. cv Shiraz) and their transcriptional regulation in fruit. Functionality of the genes VvF3′H and VvF3′5′H1 was demonstrated by ectopic expression in petunia (Petunia hybrida), which altered flower color and flavonoid composition as expected. VvF3′H was expressed in grapes before flowering, when 3′-hydroxylated flavonols are made, and all three genes were expressed after flowering, when proanthocyanidins (PAs) are synthesized. In berry skin, expression of all three genes was low at the onset of ripening (véraison) but increased after véraison concomitant with the accumulation of 3′- and 3′,5′-hydroxylated anthocyanins. VvF3′H and VvCytoB5 were expressed in seeds but not VvF3′5′H1, consistent with the accumulation of 3′-hydroxylated PAs in this tissue. VvCytoB5 expression was correlated with expression of both VvF3′H and VvF3′5′H1 in the different grape tissues. In contrast to red grapes, where VvF3′H, VvF3′5′H1, and VvCytoB5 were highly expressed during ripening, the expression of VvF3′5′H1 and VvCytoB5 in white grapes during ripening was extremely low, suggesting a difference in transcriptional regulation. Our results show that temporal and tissue-specific expression of VvF3′H, VvF3′5′H1, and VvCytoB5 in grapes is coordinated with the accumulation of the respective hydroxylated flavonols and PAs, as well as anthocyanins. Understanding the regulation of flavonoid hydroxylases could be used to modify flavonoid composition of fruits.
Tập 140 Số 1 - Trang 279-291 - 2006
Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice Abstract Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.
Tập 140 Số 2 - Trang 411-432 - 2006
Comparison between NO<sub>x</sub> Evolution Mechanisms of Wild-Type and nr<sub>1</sub> Mutant Soybean Leaves
Tập 93 Số 1 - Trang 26-32 - 1990
Nitric Oxide Induces Stomatal Closure and Enhances the Adaptive Plant Responses against Drought Stress
Tập 126 Số 3 - Trang 1196-1204 - 2001