Publications by authors named "Benildo G de Los Reyes"

28 Publications

  • Page 1 of 1

Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects.

Front Plant Sci 2021 23;12:615277. Epub 2021 Feb 23.

Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.

The phenomenon of transgressive segregation, where a small minority of recombinants are outliers relative to the range of parental phenotypes, is commonly observed in plant breeding populations. While this phenomenon has been attributed to complementation and epistatic effects, the physiological and developmental synergism involved have not been fully illuminated by the QTL mapping approach alone, especially for stress-adaptive traits involving highly complex interactions. By systems-level profiling of the IR29 × Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salinity tolerance phenotypes are created by reconfigured physiological networks due to positive or negative coupling-uncoupling of developmental and physiological attributes of each parent. Real-time growth and hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. Large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The synergism uncovered by the phenomics approach in this study supports the modern views of the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study also supports a breeding paradigm rooted on genomic modeling from multi-dimensional genetic, physiological, and phenotypic profiles to create novel adaptive traits for new crop varieties of the 21st century.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2021.615277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7940525PMC
February 2021

Networks of Physiological Adjustments and Defenses, and Their Synergy With Sodium (Na) Homeostasis Explain the Hidden Variation for Salinity Tolerance Across the Cultivated Germplasm.

Front Plant Sci 2020 8;11:588854. Epub 2020 Dec 8.

Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.

The abilities to mobilize and/or sequester excess ions within and outside the plant cell are important components of salt-tolerance mechanisms. Mobilization and sequestration of Na involves three transport systems facilitated by the plasma membrane H/Na antiporter (SOS1), vacuolar H/Na antiporter (NHX1), and Na/K transporter in vascular tissues (HKT1). Many of these mechanisms are conserved across the plant kingdom. While (upland cotton) is significantly more salt-tolerant relative to other crops, the critical factors contributing to the phenotypic variation hidden across the germplasm have not been fully unraveled. In this study, the spatio-temporal patterns of Na accumulation along with other physiological and biochemical interactions were investigated at different severities of salinity across a meaningful genetic diversity panel across cultivated upland The aim was to define the importance of holistic or integrated effects relative to the direct effects of Na homeostasis mechanisms mediated by , and Multi-dimensional physio-morphometric attributes were investigated in a systems-level context using univariate and multivariate statistics, , and path analysis. Results showed that mobilized or sequestered Na contributes significantly to the baseline tolerance mechanisms. However, the observed variance in overall tolerance potential across a meaningful diversity panel were more significantly attributed to antioxidant capacity, maintenance of stomatal conductance, chlorophyll content, and divalent cation (Mg) contents other than Ca through a complex interaction with Na homeostasis. The multi-tier macro-physiological, biochemical and molecular data generated in this study, and the networks of interactions uncovered strongly suggest that a complex physiological and biochemical synergy beyond the first-line-of defense (Na sequestration and mobilization) accounts for the total phenotypic variance across the primary germplasm of . These findings are consistent with the recently proposed Omnigenic Theory for quantitative traits and should contribute to a modern look at phenotypic selection for salt tolerance in cotton breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.588854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7752944PMC
December 2020

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks.

Front Genet 2020 23;11:594569. Epub 2020 Oct 23.

Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.

Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesis-driven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na exclusion mechanism (-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokinin-regulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory () and biosynthetic () genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors () that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs () were also identified as prominent signatures of FL510, with functional implications to mechanisms that support robust growth, homeostasis, and osmotic stress avoidance. Results of this study demonstrate how genetic recombination creates novel morphology that complements inducible defenses hence transgressive adaptive phenotypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.594569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644915PMC
October 2020

Xenobiotic Effects of Chlorine Dioxide to O157:H7 on Non-host Tomato Environment Revealed by Transcriptional Network Modeling: Implications to Adaptation and Selection.

Front Microbiol 2020 3;11:1122. Epub 2020 Jun 3.

Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States.

serotype O157:H7 is one of the major agents of pathogen outbreaks associated with fresh fruits and vegetables. Gaseous chlorine dioxide (ClO) has been reported to be an effective intervention to eliminate bacterial contamination on fresh produce. Although remarkable positive effects of low doses of ClO have been reported, the genetic regulatory machinery coordinating the mechanisms of xenobiotic effects and the potential bacterial adaptation remained unclear. This study examined the temporal transcriptome profiles of O157:H7 during exposure to different doses of ClO in order to elucidate the genetic mechanisms underlying bacterial survival under such harsh conditions. Dosages of 1 μg, 5 μg, and 10 μg ClO per gram of tomato fruits cause different effects with dose-by-time dynamics. The first hour of exposure to 1 μg and 5 μg ClO caused only partial killing with significant growth reduction starting at the second hour, and without further significant reduction at the third hour. However, 10 μg ClO exposure led to massive bacterial cell death at 1 h with further increase in cell death at 2 and 3 h. The first hour exposure to 1 μg ClO caused activation of primary defense and survival mechanisms. However, the defense response was attenuated during the second and third hours. Upon treatment with 5 μg ClO, the transcriptional networks showed massive downregulation of pathogenesis and stress response genes at the first hour of exposure, with decreasing number of differentially expressed genes at the second and third hours. In contrast, more genes were further downregulated with exposure to 10 μg ClO at the first hour, with the number of both upregulated and downregulated genes significantly decreasing at the second hour. A total of 810 genes were uniquely upregulated at the third hour at 10 μg ClO, suggesting that the potency of xenobiotic effects had led to potential adaptation. This study provides important knowledge on the possible selection of target molecules for eliminating bacterial contamination on fresh produce without overlooking potential risks of adaptation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.01122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286201PMC
June 2020

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran.

Sci Rep 2020 04 20;10(1):6571. Epub 2020 Apr 20.

School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.

Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and 'stale flavor' in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-62649-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170842PMC
April 2020

Novel cis-acting regulatory elements in wild Oryza species impart improved rice bran quality by lowering the expression of phospholipase D alpha1 enzyme (OsPLDα1).

Mol Biol Rep 2020 Jan 22;47(1):401-422. Epub 2019 Oct 22.

School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.

Rice bran oil is good quality edible oil, rich in antioxidants and comprised typically of oleic-linoleic type fatty acids. However, presence of a highly lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) increases free fatty acid content in the oil which further leads to stale flavor and rancidity of the oil, making it unfit for human consumption. In this study, we compared the upstream regions of OsPLDα1 orthologs across 34 accessions representing 5 wild Oryza species and 8 cultivars, to uncover sequence variations and identify cis-elements involved in differential transcription of orthologs. Alignment of the upstream sequences to the Nipponbare OsPLDα1 reference sequence revealed the presence of 39 SNPs. Phylogenetic analysis showed that all the selected cultivars and wild species accessions are closely related to the reference except for three accessions of O. rufipogon (IRGC89224, IRGC104425, and IRGC105902). Furthermore, using exon-specific qRT-PCR, OsPLDα1 expression patterns in immature grains indicated significant differences in transcript abundance between the wild species accessions. In comparison to the control, lowest gene expression was observed in IRGC89224 accession (0.20-fold) followed by IRGC105902 (0.26-fold) and IRGC104425 (0.41-fold) accessions. In-silico analysis of the OsPLDα1 promoter revealed that the copy number variations of CGCGBOXAT, GT1CONSENSUS, IBOXCORE, NODCON2GM, OSE2ROOTNODULE, SURECOREATSULTR11, and SORLIP1AT cis-elements play an important role in the transcriptional activities of orthologous genes. Owing to the presence of ARFAT and SEBF elements only in the IRGC89224 accession, which had the lowest gene expression as well, these putative upstream regulatory sequences have been identified as novel cis-elements which may act as repressors in regulating the OsPLDα1 gene expression. The accessions identified with low OsPLDα1 expressions could be further deployed as potential donors of ideal OsPLDα1 allele for transfer of the desired trait into elite rice cultivars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11033-019-05144-4DOI Listing
January 2020

Genomic and epigenomic bases of transgressive segregation - New breeding paradigm for novel plant phenotypes.

Plant Sci 2019 Nov 7;288:110213. Epub 2019 Aug 7.

Department of Plant and Soil Science Texas Tech University 215 Experimental Sciences Building, Lubbock, TX 806-834-6421, USA. Electronic address:

For a holistic approach in developing the stress-resilient crops of the 21 century, modern genomic biology will need to re-envision the underappreciated phenomena in classical genetics, and incorporate them into the new plant breeding paradigm. Advances in evolutionary genomics support a theory that genetic recombination under genome shock during hybridization of widely divergent parents is an important driver of adaptive speciation, by virtue of the novelties of rare hybrids and recombinants. The enormous potential of genetic network rewiring to generate developmental or physiological novelties with adaptive advantage to special ecological niches has been appreciated. Developmental and physiological reconfiguration through network rewiring involves intricate molecular synergies controlled both at the genetic and epigenetic levels, as typified by the phenomenon of transgressive segregation, observed in both natural and breeding populations. This paper presents modern views on the possible molecular underpinnings of transgressive phenotypes as they are created in plant breeding, expanded from classical explanations through the Omnigenic Theory for quantitative traits and modern paradigms of epigenetics. Perspectives on how genomic biology can fully exploit this phenomenon to create novel phenotypes beyond what could be achieved through the more reductionist approach of functional genomics are presented in context of genomic modeling.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.plantsci.2019.110213DOI Listing
November 2019

Simultaneous Colorimetric Detection of a Variety of spp. in Food and Environmental Samples by Optical Biosensing Using Oligonucleotide-Gold Nanoparticles.

Front Microbiol 2019 31;10:1138. Epub 2019 May 31.

Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Services, Western Regional Research Center, Albany, CA, United States.

Optical biosensors for rapid detection of significant foodborne pathogens are steadily gaining popularity due to its simplicity and sensitivity. While nanomaterials such as gold nanoparticles (AuNPs) are commonly used as signal amplifiers for optical biosensors, AuNPs can also be utilized as a robust biosensing platform. Many reported optical biosensors were designed for individual pathogen detection in a single assay and have high detection limit (DL). spp. is one of the major causative agents of foodborne sickness, hospitalization and deaths. Unfortunately, there are around 2,000 serotypes of worldwide, and rapid and simultaneous detection of multiple strains in a single assay is lacking. In this study, a comprehensive and highly sensitive simultaneous colorimetric detection of nineteen (19) environmental and outbreak spp. strains was achieved by a novel optical biosensing platform using oligonucleotide-functionalized AuNPs. A pair of newly designed single stranded oligonucleotides (30-mer) was displayed onto the surface of AuNPs (13 nm) as detection probes to hybridize with a conserved genomic region (192-bases) of found on a broad range of spp. strains. The sandwich hybridization (30 min, 55°C) resulted in a structural formation of highly stable oligonucleotide/AuNPs-DNA complexes which remained undisturbed even after subjecting to an increased salt concentration (2 M, final), thus allowing a direct discrimination via color change of target (red color) from non-target (purplish-blue color) reaction mixtures by direct observation using the naked eye. In food matrices (blueberries and chicken meat), nineteen different spp. strains were concentrated using immunomagnetic separation and then simultaneously detected in a 96-well microplate by oligonucleotide-functionalized AuNPs after DNA preparation. Successful oligonucleotide/AuNPs-DNA hybridization was confirmed by gel electrophoresis while AuNPs aggregation in non-target and control reaction mixtures was verified by both spectrophotometric analysis and TEM images. Results showed that the optical AuNP biosensing platform can simultaneously screen nineteen (19) viable spp. strains tested with 100% specificity and a superior detection limit of <10 CFU/mL or g for both pure culture and complex matrices setups. The highly sensitive colorimetric detection system can significantly improve the screening and detection of viable spp. strains present in complex food and environmental matrices, therefore reducing the risks of contamination and incidence of foodborne diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.01138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554661PMC
May 2019

Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation.

Sci Rep 2018 11 5;8(1):16346. Epub 2018 Nov 5.

Department of Plant and Soil Science, 219 Experimental Sciences Building, Texas Tech University, Lubbock, TX, 79409, USA.

Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-34608-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218501PMC
November 2018

Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence.

Rice (N Y) 2016 Dec 29;9(1):51. Epub 2016 Sep 29.

Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.

Background: Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that alcohol dehydrogenase 1 (ADH1)-deficient mutant of rice with reduced alcohol dehydrogenase activity (rad) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and cis-regulatory information content.

Findings: We performed promoter analysis of the publicly available differentially expressed genes in ADH1 mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival.

Conclusions: Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the rad mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040660PMC
http://dx.doi.org/10.1186/s12284-016-0124-3DOI Listing
December 2016

Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.

Plant Sci 2016 Jan 28;242:224-239. Epub 2015 Sep 28.

Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668 Singapore. Electronic address:

In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.plantsci.2015.09.018DOI Listing
January 2016

Implications of miR166 and miR159 induction to the basal response mechanisms of an andigena potato (Solanum tuberosum subsp. andigena) to salinity stress, predicted from network models in Arabidopsis.

Genome 2015 Jan 7;58(1):13-24. Epub 2015 Apr 7.

School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA.

MicroRNA (miRNA) mediated changes in gene expression by post-transcriptional modulation of major regulatory transcription factors is a potent mechanism for integrating growth and stress-related responses. Exotic plants including many traditional varieties of Andean potatoes (Solanum tuberosum subsp. andigena) are known for better adaptation to marginal environments. Stress physiological studies confirmed earlier reports on the salinity tolerance potentials of certain andigena cultivars. Guided by the hypothesis that certain miRNAs play important roles in growth modulation under suboptimal conditions, we identified and characterized salinity stress-responsive miRNA-target gene pairs in the andigena cultivar Sullu by parallel analysis of noncoding and coding RNA transcriptomes. Inverse relationships were established by the reverse co-expression between two salinity stress-regulated miRNAs (miR166, miR159) and their target transcriptional regulators HD-ZIP-Phabulosa/Phavulota and Myb101, respectively. Based on heterologous models in Arabidopsis, the miR166-HD-ZIP-Phabulosa/Phavulota network appears to be involved in modulating growth perhaps by mediating vegetative dormancy, with linkages to defense-related pathways. The miR159-Myb101 network may be important for the modulation of vegetative growth while also controlling stress-induced premature transition to reproductive phase. We postulate that the induction of miR166 and miR159 under salinity stress represents important network hubs for balancing gene expression required for basal growth adjustments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1139/gen-2015-0011DOI Listing
January 2015

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.

Rice (N Y) 2015 28;8:14. Epub 2015 Feb 28.

Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576 Singapore.

Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-015-0041-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385054PMC
April 2015

Simultaneous direct detection of Shiga-toxin producing Escherichia coli (STEC) strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles.

Nanoscale 2015 Feb;7(6):2417-26

School of Food and Agriculture, The University of Maine, Orono, ME 04469-5735, USA.

A simultaneous direct detection of Shiga-toxin producing strains of E. coli (STEC; "Big Six" - O26, O45, O103, O111, O121, and O145) as well as O157 strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles (AuNPs) was developed. Initially, conserved regions of stx genes were amplified by asymmetric polymerase chain reaction (asPCR). Pairs of single stranded thiol-modified oligonucleotides (30-mer) were immobilized onto AuNPs and used as probes to capture regions of stx1 (119-bp) and/or stx2 (104-bp) genes from STEC strains. DNA samples from pure cultures and food samples were sandwich hybridized with AuNP-oligo probes at optimal conditions (50 °C, 30 min). A complex was formed from the hybridization of AuNP-probes and target DNA fragments that retained the initial red color of the reaction solutions. For non-target DNA, a color change from red to purplish-blue was observed following an increase in salt concentration, thus providing the basis of simultaneous direct colorimetric detection of target DNA in the samples. Enrichment and pooling systems were incorporated to efficiently process a large number of food samples (ground beef and blueberries) and detection of live targets. The detection limit was <1 log CFU g(-1), requiring less than 1 h to complete after DNA sample preparation with 100% specificity. Gel electrophoresis verified AuNP-DNA hybridization while spectrophotometric data and transmission electron microscope (TEM) images supported color discrimination based on the occurrence of molecular aggregation. In conclusion, the significant features of this approach took advantage of the unique colorimetric properties of AuNPs as a low-cost and simple approach yet with high specificity for simultaneous detection of STEC strains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/c4nr05869kDOI Listing
February 2015

Phenotypic, physiological, and molecular evaluation of rice chilling stress response at the vegetative stage.

Methods Mol Biol 2013 ;956:227-41

School of Biology and Ecology, University of Maine, Orono, ME, USA.

Rice is a chilling-sensitive plant that is particularly prone to injury during the early stages of seedling development and during flowering. Significant variation exists between subspecies with japonica cultivars generally being less sensitive than most indica cultivars. In most temperate and subtropical countries where rice is grown, crop damage often occurs during the early stages of seedling development due to occasional cold snaps coinciding with the first few weeks after direct seeding in late spring to early summer. Irreversible injuries often result in seedling mortality or if the crop survives a stress episode, plant vigor and resistance to pests and diseases are severely compromised. Recent physiological and molecular studies have shown that oxidative stress is the primary cause of early chilling injuries in rice and the differential responses of indica and japonica cultivars are defined to a large extent by gene expression related to oxidative signaling and defenses. In this chapter, we summarize basic phenotypic, physiological, and molecular procedures that can be adopted for routine evaluation of differential responses between cultivars as well as for functional genomics studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-62703-194-3_16DOI Listing
April 2013

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice.

Gene 2012 Dec 23;511(2):235-42. Epub 2012 Sep 23.

Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore.

Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-1000 to +200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2012.09.048DOI Listing
December 2012

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints.

BMC Genomics 2012 Sep 20;13:497. Epub 2012 Sep 20.

School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA.

Background: The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns.

Results: The most apparent pattern observed was the occurrence of spatially conserved 'core modules' among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as 'regulatory fine-tuners' and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis.

Conclusions: Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-13-497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522565PMC
September 2012

Transcriptome profiling characterizes phosphate deficiency effects on carbohydrate metabolism in rice leaves.

J Plant Physiol 2012 Jan 5;169(2):193-205. Epub 2011 Oct 5.

Institute of Agricultural Science & Technology, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Republic of Korea.

Phosphorus (P) is a structural component of nucleic acids and phospholipids and plays important roles in plant growth and development. P accumulation was significantly reduced (about 35%) in rice leaves from plants grown under low (32 μM) P compared to 320 μM P grown plants. Genome response to low P was examined using the rice 60K oligonucleotide DNA microarrays. At the threshold significance of |log₂| fold>2.0, 21,033 genes (about 33.7% of all genes on the microarray) were affected by P deficiency. Among all genes on the microarray, 4271 genes were sorted into 51 metabolic pathways. Low P affected 1494 (35.0%) genes and the largest category of genes was related to sucrose degradation to ethanol and lactate pathway. To survey the role of P in rice, 25 pathways were selected based on number of affected genes. Among these pathways, cytosolic glycolysis contained the least number of upregulated but most down-regulated genes. Low P decreased glucose, pyruvate and chlorophyll, and genes related to carbon metabolism and chlorophyllide a biosynthesis. However, sucrose and starch levels increased. These results indicate that P nutrition affects diverse metabolic pathways mostly related to glucose, pyruvate, sucrose, starch, and chlorophyll a.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jplph.2011.09.002DOI Listing
January 2012

Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development.

Plant Cell Environ 2010 Dec 28;33(12):2209-30. Epub 2010 Sep 28.

School of Biology and Ecology, University of Maine, Orono, ME 04469, USA.

The R2R3-type OsMyb4 transcription factor of rice has been shown to play a role in the regulation of osmotic adjustment in heterologous overexpression studies. However, the exact composition and organization of its underlying transcriptional network has not been established to be a robust tool for stress tolerance enhancement by regulon engineering. OsMyb4 network was dissected based on commonalities between the global chilling stress transcriptome and the transcriptome configured by OsMyb4 overexpression. OsMyb4 controls a hierarchical network comprised of several regulatory sub-clusters associated with cellular defense and rescue, metabolism and development. It regulates target genes either directly or indirectly through intermediary MYB, ERF, bZIP, NAC, ARF and CCAAT-HAP transcription factors. Regulatory sub-clusters have different combinations of MYB-like, GCC-box-like, ERD1-box-like, ABRE-like, G-box-like, as1/ocs/TGA-like, AuxRE-like, gibberellic acid response element (GARE)-like and JAre-like cis-elements. Cold-dependent network activity enhanced cellular antioxidant capacity through radical scavenging mechanisms and increased activities of phenylpropanoid and isoprenoid metabolic processes involving various abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), ethylene and reactive oxygen species (ROS) responsive genes. OsMyb4 network is independent of drought response element binding protein/C-repeat binding factor (DREB/CBF) and its sub-regulons operate with possible co-regulators including nuclear factor-Y. Because of its upstream position in the network hierarchy, OsMyb4 functions quantitatively and pleiotrophically. Supra-optimal expression causes misexpression of alternative targets with costly trade-offs to panicle development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1365-3040.2010.02221.xDOI Listing
December 2010

Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration.

PLoS One 2010 Apr 21;5(4):e10268. Epub 2010 Apr 21.

Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America.

Background: Precise regulation of the cell cycle is crucial to the growth and development of all organisms. Understanding the regulatory mechanism of the cell cycle is crucial to unraveling many complicated diseases, most notably cancer. Multiple sources of biological data are available to study the dynamic interactions among many genes that are related to the cancer cell cycle. Integrating these informative and complementary data sources can help to infer a mutually consistent gene transcriptional regulatory network with strong similarity to the underlying gene regulatory relationships in cancer cells.

Results And Principal Findings: We propose an integrative framework that infers gene regulatory modules from the cell cycle of cancer cells by incorporating multiple sources of biological data, including gene expression profiles, gene ontology, and molecular interaction. Among 846 human genes with putative roles in cell cycle regulation, we identified 46 transcription factors and 39 gene ontology groups. We reconstructed regulatory modules to infer the underlying regulatory relationships. Four regulatory network motifs were identified from the interaction network. The relationship between each transcription factor and predicted target gene groups was examined by training a recurrent neural network whose topology mimics the network motif(s) to which the transcription factor was assigned. Inferred network motifs related to eight well-known cell cycle genes were confirmed by gene set enrichment analysis, binding site enrichment analysis, and comparison with previously published experimental results.

Conclusions: We established a robust method that can accurately infer underlying relationships between a given transcription factor and its downstream target genes by integrating different layers of biological data. Our method could also be beneficial to biologists for predicting the components of regulatory modules in which any candidate gene is involved. Such predictions can then be used to design a more streamlined experimental approach for biological validation. Understanding the dynamics of these modules will shed light on the processes that occur in cancer cells resulting from errors in cell cycle regulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010268PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858157PMC
April 2010

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.

BMC Plant Biol 2010 Jan 25;10:16. Epub 2010 Jan 25.

School of Biology and Ecology, University of Maine, Orono, ME 04469, USA.

Background: The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10 degrees C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach.

Results: Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10 degrees C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters.Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2 spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters.

Conclusion: Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2229-10-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826336PMC
January 2010

Reverse engineering module networks by PSO-RNN hybrid modeling.

BMC Genomics 2009 Jul 7;10 Suppl 1:S15. Epub 2009 Jul 7.

Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.

Background: Inferring a gene regulatory network (GRN) from high throughput biological data is often an under-determined problem and is a challenging task due to the following reasons: (1) thousands of genes are involved in one living cell; (2) complex dynamic and nonlinear relationships exist among genes; (3) a substantial amount of noise is involved in the data, and (4) the typical small sample size is very small compared to the number of genes. We hypothesize we can enhance our understanding of gene interactions in important biological processes (differentiation, cell cycle, and development, etc) and improve the inference accuracy of a GRN by (1) incorporating prior biological knowledge into the inference scheme, (2) integrating multiple biological data sources, and (3) decomposing the inference problem into smaller network modules.

Results: This study presents a novel GRN inference method by integrating gene expression data and gene functional category information. The inference is based on module network model that consists of two parts: the module selection part and the network inference part. The former determines the optimal modules through fuzzy c-mean (FCM) clustering and by incorporating gene functional category information, while the latter uses a hybrid of particle swarm optimization and recurrent neural network (PSO-RNN) methods to infer the underlying network between modules. Our method is tested on real data from two studies: the development of rat central nervous system (CNS) and the yeast cell cycle process. The results are evaluated by comparing them to previously published results and gene ontology annotation information.

Conclusion: The reverse engineering of GRNs in time course gene expression data is a major obstacle in system biology due to the limited number of time points. Our experiments demonstrate that the proposed method can address this challenge by: (1) preprocessing gene expression data (e.g. normalization and missing value imputation) to reduce the data noise; (2) clustering genes based on gene expression data and gene functional category information to identify biologically meaningful modules, thereby reducing the dimensionality of the data; (3) modeling GRNs with the PSO-RNN method between the modules to capture their nonlinear and dynamic relationships. The method is shown to lead to biologically meaningful modules and networks among the modules.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-10-S1-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709258PMC
July 2009

Application of cranberry concentrate (Vaccinium macrocarpon) to control Escherichia coli O157:H7 in ground beef and its antimicrobial mechanism related to the downregulated slp, hdeA and cfa.

Food Microbiol 2009 Feb 22;26(1):32-8. Epub 2008 Aug 22.

Department of Food Science and Human Nutrition, The University of Maine, 5735 Hitchner Hall, Orono, ME 04469-5735, USA.

The possible use of cranberry concentrate (CC) as a natural food preservative was studied by examining its antimicrobial effect on the growth of Escherichia coli O157:H7 inoculated in ground beef, its organoleptical effect on beef patties, and its antimicrobial mechanism on the gene regulation level. Inoculated ground beef was added with CC and stored at 4 degrees C for 5 days. Bacteria were detected on day 0, 1, 3, and 5. Cranberry concentrate (2.5%, 5%, and 7.5% w/w) reduced total aerobic bacteria 1.5 log, 2.1 log, and 2.7 log CFU/g and E. coli O157:H7 0.4 log, 0.7 log, and 2.4 log CFU/g, respectively, when compared to the control on day 5. Fifty panelists evaluated the burgers supplemented with CC. No differences in appearance, flavor, and taste were found among burgers with 0%, 2.5%, and 5% CC. The expression of E. coli O157:H7 cyclopropane fatty acyl phospholipid synthase (cfa), hypothetical protein (hdeA), outer membrane porin protein C (ompC), hyperosmotically inducible periplasmic protein (osmY), and outer membrane protein induced after carbon starvation (slp) genes with or without CC (2.5% v/v) treatment was investigated by quantitative real-time PCR. Compared to the control, slp, hdeA, and cfa were markedly downregulated, ompC was slightly downregulated, while osmY was slightly affected.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fm.2008.07.014DOI Listing
February 2009

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

BMC Bioinformatics 2008 Apr 21;9:203. Epub 2008 Apr 21.

Lombardi Comprehensive Cancer Center, Georgetown University, 4000 Reservoir Rd, Washington, DC, USA.

Background: Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN) with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM), facilitates the inference. Identifying NMs defined by specific transcription factors (TF) establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO) information.

Results: The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM) classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1) Gene set enrichment analysis (GSEA) to evaluate the clustering results; (2) Leave-one-out cross-validation (LOOCV) to ensure that the SVM classifiers assign TFs to NM categories with high confidence; (3) Binding site enrichment analysis (BSEA) to determine enrichment of the gene clusters for the cognate binding sites of their predicted TFs; (4) Comparison with previously reported results in the literatures to confirm the inferred regulations.

Conclusion: The major contribution of this study is the development of a computational framework to assist the inference of TRN by integrating heterogeneous data from multiple sources and by decomposing a TRN into NM-based modules. The inference capability of the proposed framework is verified statistically (e.g., LOOCV) and biologically (e.g., GSEA, BSEA, and literature validation). The proposed framework is useful for inferring small NM-based modules of TF-target gene relationships that can serve as a basis for generating new testable hypotheses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-9-203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386822PMC
April 2008

An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice.

BMC Genomics 2007 Jun 18;8:175. Epub 2007 Jun 18.

Department of Biological Sciences, University of Maine, Orono, ME 04469, USA.

Background: Plants respond to low temperature through an intricately coordinated transcriptional network. The CBF/DREB-regulated network of genes has been shown to play a prominent role in freeze-tolerance of Arabidopsis through the process of cold acclimation (CA). Recent evidence also showed that the CBF/DREB regulon is not unique to CA but evolutionarily conserved between chilling-insensitive (temperate) and chilling-sensitive (warm-season) plants. In this study, the wide contrast in chilling sensitivity between indica and japonica rice was used as model to identify other regulatory clusters by integrative analysis of promoter architecture (ab initio) and gene expression profiles.

Results: Transcriptome analysis in chilling tolerant japonica rice identified a subset of 121 'early response' genes that were upregulated during the initial 24 hours at 10 degrees C. Among this group were four transcription factors including ROS-bZIP1 and another larger sub-group with a common feature of having as1/ocs-like elements in their promoters. Cold-induction of ROS-bZIP1 preceded the induction of as1/ocs-like element-containing genes and they were also induced by exogenous H2O2 at ambient temperature. Coordinated expression patterns and similar promoter architectures among the 'early response' genes suggest that they belong to a potential regulon (ROS-bZIP-as1/ocs regulatory module) that responds to elevated levels of ROS during chilling stress. Cultivar-specific expression signatures of the candidate genes indicate a positive correlation between the activity of the putative regulon and genotypic variation in chilling tolerance.

Conclusion: A hypothetical model of an ROS-mediated regulon (ROS-bZIP-as1/ocs) triggered by chilling stress was assembled in rice. Based on the current results, it appears that this regulon is independent of ABA and CBF/DREB, and that its activation has an important contribution in configuring the rapid responses of rice seedlings to chilling stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-8-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925099PMC
June 2007

Expression of gamma-tocopherol methyltransferase transgene improves tocopherol composition in lettuce (Latuca sativa L.).

Mol Cells 2005 Feb;19(1):16-22

Division of Biological Resources Sciences, Chonbuk National University, Chonju 561-756, Korea.

A cDNA encoding gamma-tocopherol methyltransferase (gamma-TMT) from Arabidopsis thaliana was overexpressed in lettuce (Latuca sativa L.) to improve the tocopherol composition. Seven lines of lettuce (T0) containing the gamma-TMT transgene were produced by Agrobacterium-mediated transformation. The inheritance and expression of the transgene were confirmed by DNA and RNA gel blot analyses as well as quantification of tocopherols and gamma-TMT activities. The ratio of alpha-/gamma-tocopherol content (TR) varied from 0.6 to 1.2 in non-transformed plants, while the T0 plants had ratios of 0.8 to 320. The ratio ranged from 0.4 to 544 in 41 T1 progenies of the T0 transgenic line gTM3, and the phenotypic segregation indicated monogenic inheritance of the transgene (i.e., 3:1 = dominant:wild-type classes). There was a tight relationship between the TR phenotype and gamma-TMT activity, and enzyme activities were affected by the copy number and transcript levels of the transgene. The TR phenotype was stably expressed in T2 progenies of T1 plants. The results from this study indicated that a stable inheritance and expression of Arabidopsis gamma-TMT transgene in lettuce results in a higher enzyme activity and the conversion of the gamma-tocopherol pool to alpha-tocopherol in transgenic lettuce.
View Article and Find Full Text PDF

Download full-text PDF

Source
February 2005

The OsLti6 genes encoding low-molecular-weight membrane proteins are differentially expressed in rice cultivars with contrasting sensitivity to low temperature.

Gene 2005 Jan;344:171-80

Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA.

Rice (Oryza sativa L.) is sensitive to chilling particularly at early stages of seedling establishment. Two closely related genes (OsLti6a, OsLti6b), which are induced by low temperature during seedling emergence were isolated from a cold tolerant temperate japonica rice cultivar. These genes are closely related to the Arabidopsis rare cold-inducible (RCI2) and barley low-temperature-inducible (BLT101) genes. Based on direct biochemical and indirect physiological evidence and similarity with a conserved protein domain in the Cluster of Orthologous Groups (COG) database (e.g., yeast PMP3), the rice genes belong to a class of low-molecular-weight hydrophobic proteins involved in maintaining the integrity of the plasma membrane during cold, dehydration and salt stress conditions. Both genes exhibit a genotype-specific expression signature characterized by early and late stress-inducible expression in tolerant and intolerant genotypes, respectively. The differences in temporal expression profiles are consistent with cultivar differences in cold-induced membrane leakiness and seedling vigor. The presence of CRT/DRE promoter cis-elements is consistent with the synchronized expression of OsLti6 genes with the C-repeat binding factor/drought responsive element-binding protein (CBF/DREB) transcriptional activator. The present results indicate that the Oslti6 genes are part of a battery of cold stress defense-related genes regulated by a common switch.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2004.09.033DOI Listing
January 2005

Cultivar-specific seedling vigor and expression of a putative oxalate oxidase germin-like protein in sugar beet (Beta vulgaris L.).

Theor Appl Genet 2003 Jun 21;107(1):54-61. Epub 2003 Mar 21.

USDA-ARS, Sugar Beet and Bean Research Unit, 494 PSSB, Michigan State University, East Lansing, MI 48824-1325, USA.

For genetic screening and breeding purposes, an in vitro germination system that reflects relative field emergence potential was used to screen for germination-enhancing and stress-induced genes from germinating seedlings from two varieties of sugar beet. Three full-length germin-like protein (GLP) gene classes were recovered from stress-germinated seedlings of a superior emerging variety. GLP gene expression, oxalate oxidase protein activity, the H(2)O(2) content of stressed seedlings, but not catalase activity, were induced by stress germination conditions (e.g. excess water, NaCl, mannitol, or oxalate) in a good emerging hybrid and were not induced in a poor emerging variety. Only one of the three germin-like protein genes ( BvGer165) was differentially regulated, and was induced only in the good emerger. Hydrogen peroxide promoted germination and partially compensated solute-depressed germination percentages. Unlike other solute recovery by hydrogen peroxide regimes, recovery in oxalic acid plus H(2)O(2) was cultivar-independent. A block in oxalate metabolism is postulated to contribute to lower germination under stress in the lower emerging variety. Selection for stress-induced germin expression, or for down-stream targets, presents the first direct target to enable breeding for improved field emergence of sugar beet.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-003-1229-9DOI Listing
June 2003