Plant Genetics Research Unit

St. Louis, MO, United States

Plant Genetics Research Unit

St. Louis, MO, United States
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Meihls L.N.,Boyce Thompson Institute for Plant Research | Higdon M.L.,Plant Genetics Research Unit | Ellersieck M.R.,University of Missouri | Tabashnik B.E.,University of Arizona | Hibbard B.E.,Plant Genetics Research Unit
PLoS ONE | Year: 2012

Transgenic corn producing the Bacillus thuringiensis (Bt) toxin Cry3Bb1 has been useful for controlling western corn rootworm, Diabrotica virgifera virgifera LeConte, one of the most economically important crop pests in the United States. However, rapid evolution of resistance by this beetle to Bt corn producing Cry3Bb1 has been reported previously from the laboratory, greenhouse, and field. Here we selected in the greenhouse for resistance to Cry3Bb1 corn in three colonies of WCR derived from Kansas, Minnesota, and Wisconsin, respectively. Three generations of rearing on Cry3Bb1 corn significantly increased larval survival on Cry3Bb1 corn, resulting in similar survival in the greenhouse for selected colonies on Cry3Bb1 corn and isoline corn that does not produce Bt toxin. After four to seven generations of rearing on Cry3Bb1 corn, survival in the field on Cry3Bb1 corn relative to isoline corn more than doubled for selected colonies (72%) compared with control colonies (33%). For both selected and control colonies, survival in the field was significantly lower on Cry3Bb1 corn than on isoline corn. On isoline corn, most fitness components were similar for selected colonies and control colonies. However, fecundity was significantly lower for selected colonies than control colonies, indicating a fitness cost associated with resistance. The rapid evolution of resistance by western corn rootworm to Bt corn reported here and previously underlines the importance of effective resistance management for this pest.

Xiao L.,Capital Normal University | Yang G.,Capital Normal University | Zhang L.,Capital Normal University | Yang X.,CAS Beijing Institute of Genomics | And 21 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

"Drying without dying" is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes. © 2015, National Academy of Sciences. All rights reserved.

Yi H.,Chungnam National University | Dey S.,Presidency University of India | Kumaran S.,Chandigarh Institute of Microbial Technology | Lee S.G.,Washington University in St. Louis | And 2 more authors.
Journal of Biological Chemistry | Year: 2013

Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase. Formation of the cysteine regulatory complex (CRC) is a critical biochemical control feature in plant sulfur metabolism. Here we present the 1.75-3.0 Å resolution x-ray crystal structures of soybean (Glycine max) SAT (GmSAT) in apoenzyme, serine-bound, and CoA-bound forms. The GmSAT-serine and GmSAT-CoA structures provide new details on substrate interactions in the active site. The crystal structures and analysis of site-directed mutants suggest that is169 and Asp154 form a catalytic dyad for general base catalysis and that His189 may stabilize the oxyanion reaction intermediate. Glu177 helps to position Arg 203 and His204 and the β1c-β2c loop for serine binding. A similar role for ionic interactions formed by Lys230 is required for CoA binding. The GmSAT structures also identify Arg253 as important for the enhanced catalytic efficiency of SAT in the CRC and suggest that movement of the residue may stabilize CoA binding in the macromolecular complex. Differences in the effect of cold on GmSAT activity in the isolated enzyme versus the enzyme in the CRC were also observed. A role for CRC formation as a molecular chaperone to maintain SAT activity in response to an environmental stress is proposed for this multienzyme complex in plants.© 2013 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.

Krishnan H.B.,Plant Genetics Research Unit | Krishnan H.B.,University of Missouri | Wang T.T.Y.,U.S. Department of Agriculture
Food Chemistry | Year: 2015

Lunasin is a 5-kDa soybean bioactive peptide with demonstrated anti-cancer and anti-inflammatory properties. Recently, purification methods have been developed to obtain gram quantities of lunasin. However, these methods are cumbersome, time consuming and cost-prohibitive. To overcome these constrains we have developed a novel method which involves extraction of soybean flour with 30% ethanol followed by preferential precipitation of lunasin and protease inhibitors by calcium. The calcium precipitated protein fraction, which we termed as Lunasin Protease Inhibitor Concentrate (LPIC), contains three abundant proteins with molecular weights of 21, 14 and 5 kDa. This simple procedure yields 3.2 g of LPIC from 100 g of soybean flour and the entire isolation procedure can be completed in less than 2 h. Treatment of THP-1 human monocyte cell lines with LPIC resulted in suppression of lipopolysaccharide-stimulated cytokine expression, demonstrating that the LPIC isolated by our simple procedure is biologically active.

Shyama Prasad Rao R.,University of Missouri | Thelen J.J.,University of Missouri | Miernyk J.A.,University of Missouri | Miernyk J.A.,Plant Genetics Research Unit
Frontiers in Plant Science | Year: 2014

Among post-translational modifications, there are some conceptual similarities between Lys-Nε-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins. While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation. Being directly coupled with cellular CoA/acetyl-CoA and NAD/NADH, reversible Lys-Nε-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development. © 2014 Rao, Thelen and Miernyk.

Kim W.-S.,Plant Genetics Research Unit | Jang S.,University of Missouri | Krishnan H.B.,Plant Genetics Research Unit | Krishnan H.B.,University of Missouri
Crop Science | Year: 2012

Leginsulin, a peptide made up of 37 amino acids, is homologous to pea (Pisum sativum L.) albumin (PA1b) and belongs to the cysteine-knot family. Even though the physiological function and threedimensional structure of leginsulin have been explored, little is known about its expression, accumulation, and distribution among soybean [Glycine max (L.) Merr.] accessions. An antibody generated against leginsulin was used to screen a diverse array of soybean accessions from the USDA Soybean Germplasm Collection to identify soybean accessions that are enriched in leginsulin. Analysis of 50% isopropanol-soluble proteins from 485 soybean lines by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDSPAGE) and western blot analysis enabled the identifi cation of 75 accessions that signifi cantly accumulated leginsulin. Remarkably, all these accessions with the exception of two had their origin from Japan, Korea, or China. Leginsulin was barely detected in most of the commercial North American soybean cultivars used in this study. Western blot analysis revealed low accumulation of leginsulin in the embryonic axis but not in the cotyledons of North American soybean cultivar Williams 82 while in the Chinese PI 458249 leginsulin was abundantly present in both types of tissue. Examination of the soybean cultivar Williams 82 genome sequence revealed the presence of two homologous leginsulin genes (Gm13 g26330 [leginsulin 1] and Gm13 g26340 [leginsulin 2]) on chromosome 13. We have cloned the two leginsulin genes from PI 458249 and found them to be highly similar to that of Williams 82. Northern blot analysis indicated that leginsulin messenger RNA (mRNA) was abundant in Williams 82 embryonic axis but not in the cotyledon. In contrast, leginsulin mRNA was abundantly present in PI 458249, both in the embryonic axis and the cotyledons. © Crop Science Society of America.

Vincent J.A.,University of Missouri | Stacey M.,University of Missouri | Stacey G.,University of Missouri | Bilyeu K.D.,University of Missouri | Bilyeu K.D.,Plant Genetics Research Unit
Plant Genome | Year: 2015

Soybean seeds contain a large amount of P, which is stored as phytic acid (PA). Phytic acid is indigestible by nonruminant livestock and considered an antinutritional factor in soybean meal. Several low PA soybean lines have been discovered, but many of these lines have either minor reductions in PA or inadequate germination and emergence. The reduced PA phenotype of soybean line Gm-lpa-ZC-2 was previously shown to be the result of a mutation in a gene encoding an inositol pentakisphosphate 2-kinase on chromosome 14 (14IPK1). While the 14IPK1 mutation was shown to have no impact on germination and emergence, the reduction in PA was modest (up to 50%). Our objective was to determine the effect on seed P partitioning for a novel mutation of an independent IPK1 gene on chromosome six (06IPK1) on its own and in combination with mutant alleles of the 14IPK1. We developed soybean populations and conducted genotype and phenotype association analyses based on the genotype of the 06IPK1 and 14IPK1 genes and the seed P partitioning profile. The lines with both mutant IPK1 genes had very low PA levels, moderate accumulation of inorganic phosphate (Pi), and accumulation of high amounts of P in lower inositols. The developed lines did not have significant reductions in germination or field emergence. In addition, characterization of the lower inositols produced in the mutant lines suggests that IPK1 is a polyphosphate kinase and provides some insight into the PA biosynthesis pathway in soybean seeds. © Crop Science Society of America.

Becker A.,Donald Danforth Plant Science Center | Chao D.-Y.,Purdue University | Zhang X.,University of Chicago | Salt D.E.,Purdue University | And 2 more authors.
PLoS ONE | Year: 2011

Bulk segregant analysis (BSA) using microarrays, and extreme array mapping (XAM) have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP) between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.

Allen D.K.,Plant Genetics Research Unit | Allen D.K.,Donald Danforth Plant Science Center
Current Opinion in Biotechnology | Year: 2016

Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations and long metabolic steady states such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other metabolically more dynamic tissues such as leaves in greater detail using novel methods in mass spectrometry, isotope labeling strategies, and transient labeling-based flux analyses. Such studies are necessary for a systems level description of plant function that more closely represents biological reality, and provides insights into the genes that will need to be modified as natural resources become ever more limited and environments change. © 2015.

PubMed | Plant Genetics Research Unit
Type: Journal Article | Journal: Plant physiology | Year: 2010

Previous systems analyses in plants have focused on a single developmental stage or time point, although it is often important to additionally consider time-index changes. During seed development a cascade of events occurs within a relatively brief time scale. We have collected protein and transcript expression data from five sequential stages of Arabidopsis (Arabidopsis thaliana) seed development encompassing the period of reserve polymer accumulation. Protein expression profiling employed two-dimensional gel electrophoresis coupled with tandem mass spectrometry, while transcript profiling used oligonucleotide microarrays. Analyses in biological triplicate yielded robust expression information for 523 proteins and 22,746 genes across the five developmental stages, and established 319 protein/transcript pairs for subsequent pattern analysis. General linear modeling was used to evaluate the protein/transcript expression patterns. Overall, application of this statistical assessment technique showed concurrence for a slight majority (56%) of expression pairs. Many specific examples of discordant protein/transcript expression patterns were detected, suggesting that this approach will be useful in revealing examples of posttranscriptional regulation.

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