This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.biomedcentral.com/bmcplantbiol/ The latest articles from BMC Plant Biology (ISSN 1471-2229) published by BioMed Central Background: Vitis vinifera is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. Results: The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the Vitis vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. Conclusion: The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data (http://mpss.udel.edu/grape/). http://www.biomedcentral.com/1471-2229/8/53 Alberto Iandolino, Kan Nobuta, Francisco Goes da Silva, Douglas R Cook and Blake C Meyers BMC Plant Biology 2008, 8:53 2008-05-12 doi:10.1186/1471-2229-8-53 BMC Plant Biology 1471-2229 8 53 2008-05-12 Background: Bast fibres from the phloem tissues of flax (Linum usitatissimum) are scientifically interesting and economically useful due in part to a dynamic system of secondary cell wall deposition. To better understand the molecular mechanisms underlying the process of cell wall development in flax, we extracted proteins from individually dissected phloem fibres (i.e. individual cells) at an early stage of secondary cell wall development, and compared these extracts to protein extracts from surrounding, non-fibre cells of the cortex, using fluorescent (DiGE) labels and 2D-gel electrophoresis, with identities assigned to some proteins by mass spectrometry. Results: The abundance of many proteins in fibres was notably different from the surrounding non-fibre cells of the cortex, with approximately 13 % of the 1,850 detectable spots being significantly (>1.5 fold, p[less than or equal to]0.05) enriched in fibres. Following mass spectrometry, we assigned identity to 114 spots, of which 51 were significantly enriched in fibres. We observed that a K+ channel subunit, annexins, porins, secretory pathway components, beta-amylase, beta-galactosidase and pectin and galactan biosynthetic enzymes were among the most highly enriched proteins detected in developing flax fibres, with many of these proteins showing electrophoretic patterns consistent with post-translational modifications. Conclusions: The fibre-enriched proteins we identified are consistent with the dynamic process of secondary wall deposition previously suggested by histological and biochemical analyses, and particularly the importance of galactans and the secretory pathway in this process. The apparent abundance of beta-amylase suggests that starch may be an unappreciated source of materials for cell wall biogenesis in flax bast fibres. Furthermore, our observations confirm previous reports that correlate accumulation proteins such as annexins, and specific heat shock proteins with secondary cell wall deposition. http://www.biomedcentral.com/1471-2229/8/52 Naomi SC Hotte and Michael K Deyholos BMC Plant Biology 2008, 8:52 2008-04-30 doi:10.1186/1471-2229-8-52 BMC Plant Biology 1471-2229 8 52 2008-04-30 Background: Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa. Results: A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT>>AG>AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee. Conclusions: The conventional approach of genomic library was successfully employed although with low efficiency to develop a set of 44 new genomic microsatellite markers of coffee. The characterization/validation of new markers demonstrated them to be highly informative, and useful for genetic studies namely, genetic diversity in coffee germplasm, individualization/bar-coding for germplasm protection, linkage mapping, taxonomic studies, and use as conserved orthologous sets across secondary genepool of coffee. Further, the relative frequency and distribution of different SSR motifs in coffee genome indicated coffee genome to be relatively poor in microsatellites compared to other plant species. http://www.biomedcentral.com/1471-2229/8/51 Prasad SURESH Hendre, Regur Phanindranath, V. Annapurna, Albert Lalremruata and Ramesh K. Aggarwal BMC Plant Biology 2008, 8:51 2008-04-30 doi:10.1186/1471-2229-8-51 BMC Plant Biology 1471-2229 8 51 2008-04-30 Background: NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known. Results: We predict a 3d-structure for the beta-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position. Conclusions: We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the 3d-structure, we are proposing some possible functions for the NLPs. http://www.biomedcentral.com/1471-2229/8/50 Adelmo L. Cechin, Marialva Sinigaglia, Ney Lemke, Sergio Echeverrigaray, Odalys G. Cabrera, Goncalo A. G. Pereira and Jose C. M. Mombach BMC Plant Biology 2008, 8:50 2008-04-30 doi:10.1186/1471-2229-8-50 BMC Plant Biology 1471-2229 8 50 2008-04-30 Background: Plants respond to extracellularly perceived abiotic stresses such as low temperature, drought, and salinity by activation of complex intracellular signaling cascades that regulate acclimatory biochemical and physiological changes. Protein kinases are major signal transduction factors that have a central role in mediating acclimation to environmental changes in eukaryotic organisms. In this study, we characterized the function of the sucrose nonfermenting 1-related protein kinase2 (SnRK2) SAPK4 in the salt stress response of rice. Results: Translational fusion of SAPK4 with the green fluorescent protein (GFP) showed subcellular localization in cytoplasm and nucleus. To examine the role of SAPK4 in salt tolerance we generated transgenic rice plants with over-expression of rice SAPK4 under control of the CaMV-35S promoter. The SAPK4 transcript level was not significantly modified in transgenic plants grown under control conditions, however, salt treatment resulted in increased transcript accumulation compared with wild-type rice indicating posttranscriptional regulation of SAPK4. Induced expression of SAPK4 resulted in improved germination and growth and development under salt stress both in seedlings and mature plants. In response to salt stress, the SAPK4-overexpressing rice accumulated less Na+ and Cl- and showed improved photosynthesis. SAPK4-regulated genes with functions in ion homeostasis and oxidative stress response were identified: the vacuolar H+-ATPase, the Na+/H+ antiporter NHX1, the Cl- channel OsCLC1 and a catalase. Conclusions: Our results show that SAPK4 regulates ion homeostasis and growth and development under salinity and suggest function of SAPK4 as a regulatory factor in plant salt stress acclimation. Identification of signaling elements involved in stress adaptation in plants presents a powerful approach to identify transcriptional activators of adaptive mechanisms to environmental changes that have the potential to improve tolerance in crop plants. http://www.biomedcentral.com/1471-2229/8/49 Calliste J. Diedhiou, Olga V. Popova, Karl-Josef Dietz and Dortje Golldack BMC Plant Biology 2008, 8:49 2008-04-28 doi:10.1186/1471-2229-8-49 BMC Plant Biology 1471-2229 8 49 2008-04-28 Background: The regulation of the chloroplast antioxidant capacity depends on nuclear gene expression. For the 2-Cys peroxiredoxin-A gene (2CPA) a cis-regulatory element was recently characterized, which responds to photosynthetic redox signals. Results: In a yeast-one-hybrid screen for cis-regulatory binding proteins, the transcription factor Rap2.4a was isolated. Rap2.4a controls the transcript abundance of the prominent chloroplast antioxidant enzyme through binding to the CGCG core of a CE3-like element. Rap2.4a activity is regulated by dithiol/disulfide transition of regulatory cysteinyl residues and subsequent changes in the quaternary structure. The mid-point redox potential of Rap2.4a activation is -269 mV (pH 7.0). Conclusion: The redox sensitivity of Rap2.4a establishes an efficient switch mechanism for redox control of nuclear gene activity of chloroplast antioxidants, in which Rap2.4 is a redox-sensor and a transducer of redox information. http://www.biomedcentral.com/1471-2229/8/48 Jehad Shaikhali, Isabelle Heiber, Thorsten Seidel, Elke Stroeher, Heiko Hiltscher, Stefan Birkmann, Karl-Josef Dietz and Margarete Baier BMC Plant Biology 2008, 8:48 2008-04-26 doi:10.1186/1471-2229-8-48 BMC Plant Biology 1471-2229 8 48 2008-04-26 Background: Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. Results: We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. Conclusions: The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling. http://www.biomedcentral.com/1471-2229/8/47 Juergen Ehlting, Vincent Sauveplane, Alexandre Olry, Jean-Francois Ginglinger, Nicholas J Provart and Daniele Werck-Reichhart BMC Plant Biology 2008, 8:47 2008-04-23 doi:10.1186/1471-2229-8-47 BMC Plant Biology 1471-2229 8 47 2008-04-23 Background: Tropospheric ozone, the most abundant air pollutant is detrimental to plant and animal health including humans. In sensitive plant species even a few hours of exposure to this potent oxidant leads to severe oxidative stress that manifests as visible cell death. In resistant plants usually no visible symptoms are observed. Naturally occurring variability to acute ozone in plants provides a valuable resource for examining molecular basis of the differences in responses to ozone. From our earlier study in Medicago truncatula, we have identified cultivar Jemalong is ozone sensitive and PI 464815 (JE154) is an ozone-resistant accession. Analyses of transcriptome changes in ozone-sensitive and resistant accession will provide important clues for understanding the molecular changes governing the plant responses to ozone. Results: Acute ozone treatment (300 nL L-1 for six hours) led to a reactive oxygen species (ROS) burst in sensitive Jemalong six hours post-fumigation. In resistant JE154 increase in ROS levels was much reduced compared to Jemalong. Based on the results of ROS profiling, timepoints for microarray analysis were one hour into the ozone treatment, end of treatment and onset of an ozone-induced ROS burst at 12 hours. Replicated temporal transcriptome analysis in these two accessions were conducted using 17K oligonucleotide arrays. More than 2000 genes were differentially expressed in the two accessions. Significantly enriched gene ontologies (GOs) were identified using the Cluster Enrichment analysis software. Real-time PCR analysis was used to confirm the differential expression patterns of a subset of these genes. Conclusions: This study provided a cogent view of the unique and shared transcriptional responses in an ozone-resistant and sensitive accession that exemplifies the complexity of oxidative signaling in plants. A striking finding was the alacrity of JE154 in altering its gene expression patterns in response to ozone, in stark contrast to delayed transcriptional response of Jemalong. GOs involved in signalling, hormonal pathways, antioxidants and secondary metabolism are altered in both accessions. However, the repertoire of genes responding in each of these categories was different between the two accessions. This study has identified unique genes and processes that will aid in dissecting the molecular mechanisms governing ozone resistance or sensitivity in plants. http://www.biomedcentral.com/1471-2229/8/46 Michael C Puckette, Yuhong Tang and Ramamurthy Mahalingam BMC Plant Biology 2008, 8:46 2008-04-23 doi:10.1186/1471-2229-8-46 BMC Plant Biology 1471-2229 8 46 2008-04-23 Background: Aquaporins, also called major intrinsic proteins (MIPs), constitute an ancient superfamily of channel proteins that facilitate the transport of water and small solutes across cell membranes. MIPs are found in almost all living organisms and are particularly abundant in plants where they form a divergent group of proteins able to transport a wide selection of substrates. Results: Analyses of the whole genome of Physcomitrella patens resulted in the identification of 23 MIPs, belonging to seven different subfamilies, of which only five have been previously described. Of the newly discovered subfamilies one was only identified in P. patens (Hybrid Intrinsic Protein, HIP) whereas the other was found to be present in a wide variety of dicotyledonous plants and forms a major previously unrecognized MIP subfamily (X Intrinsic Proteins, XIPs). Surprisingly also some specific groups within subfamilies present in Arabidopsis thaliana and Zea mays could be identified in P. patens. Conclusions: Our results suggest an early diversification of MIPs resulting in a large number of subfamilies already in primitive terrestrial plants. During the evolution of higher plants some of these subfamilies were subsequently lost while the remaining subfamilies expanded and in some cases diversified, resulting in the formation of more specialized groups within these subfamilies. http://www.biomedcentral.com/1471-2229/8/45 Jonas A H Danielson and Urban Johanson BMC Plant Biology 2008, 8:45 2008-04-22 doi:10.1186/1471-2229-8-45 BMC Plant Biology 1471-2229 8 45 2008-04-22 Background: In bacteria, such as Salmonella typhimurium, tryptophan is synthesized from indole-3-glycerole phosphate (IGP) by a tryptophan synthase alpha beta beta alpha heterotetramer. Plants have evolved multiple alpha (TSA) and beta (TSB) homologs, which have probably diverged in biological function and their ability of subunit interaction. There is some evidence for a tryptophan synthase (TS) complex in Arabidopsis. On the other hand maize (Zea mays) expresses the TSA-homologs BX1 and IGL that efficiently cleave IGP, independent of interaction with TSB. Results: In order to clarify, how tryptophan is synthesized in maize, two TSA homologs, hitherto uncharacterized ZmTSA and ZmTSAlike, were functionally analyzed. ZmTSA is localized in plastids, the major site of tryptophan biosynthesis in plants. It catalyzes the tryptophan synthase alpha-reaction (cleavage of IGP), and forms a tryptophan synthase complex with ZmTSB1 in vitro. The catalytic efficiency of the alpha-reaction is strongly enhanced upon complex formation. A 160 kD tryptophan synthase complex was partially purified from maize leaves and ZmTSA was identified as native alpha-subunit of this complex by mass spectrometry. ZmTSAlike, for which no in vitro activity was detected, is localized in the cytosol. ZmTSAlike, BX1, and IGL were not detectable in the native tryptophan synthase complex in leaves. Conclusions: It was demonstrated in vivo and in vitro that maize forms a tryptophan synthase complex and ZmTSA functions as alpha-subunit in this complex. http://www.biomedcentral.com/1471-2229/8/44 Verena Kriechbaumer, Linda Weigang, Andreas Fiesselmann, Thomas Letzel, Monika Frey, Alfons Gierl and Erich Glawischnig BMC Plant Biology 2008, 8:44 2008-04-22 doi:10.1186/1471-2229-8-44 BMC Plant Biology 1471-2229 8 44 2008-04-22 Background: We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens. Results: By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns. Conclusion: This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development. http://www.biomedcentral.com/1471-2229/8/43 Jason A Peiffer, Shail Kaushik, Hajime Sakai, Mario Arteaga-Vazquez, Nidia Sanchez-Leon, Hassan Ghazal, Jean-Philippe Vielle-Calzada and Blake C Meyers BMC Plant Biology 2008, 8:43 2008-04-21 doi:10.1186/1471-2229-8-43 BMC Plant Biology 1471-2229 8 43 2008-04-21