Isolation and transcription profiling of low-O2 stress-associated cDNA clones from the flooding-stress-tolerant FR13A rice genotype

Understanding the Impacts of Crude Oil and its Induced Abiotic Stresses on Agrifood Production: A Review

In many parts of the world, the agricultural sector is faced with a number of challenges including those arising from abiotic environmental stresses which are the key factors responsible for most reductions in agrifood production. Crude oil contamination, an abiotic stress factor and a common environmental contaminant, at toxic levels has negative impacts on plants. Although various attempts have been made to demonstrate the impact of abiotic stresses on crops, the underlying factors responsible for the effects of crude oil and its induced abiotic stresses on the composition of the stressed plants are poorly understood. Hence, this review provides an in-depth examination of the: (1) effect of petroleum hydrocarbons on plants; (2) impact of abiotic environmental stresses on crop quality; (3) mechanistic link between crude oil stress and its induced abiotic stresses; as well as (4) mode of action/plant response mechanism to these induced stresses. The paper clearly reveals the implications of crude oil-induced abiotic stresses arising from the soil-root-plant route and from direct application on plant leaves.

Identification of GCC-box and TCC-box motifs in the promoters of differentially expressed genes in rice (Oryza sativa L.): Experimental and computational approaches

The transcription factor selectively binds with the cis-regulatory elements of the promoter and regulates the differential expression of genes. In this study, we aimed to identify and validate the presence of GCC-box and TCC-box motifs in the promoters of upregulated differentially expressed genes (UR-DEGs) and downregulated differentially expressed genes (DR-DEGs) under anoxia using molecular beacon probe (MBP) based real-time PCR. The GCC-box motif was detected in UR-DEGs (DnaJ and 60S ribosomal protein L7 genes), whereas, the TCC-box was detected in DR-DEGs (DnaK and CPuORF11 genes). In addition, the mechanism of interaction of AP2/EREBP family transcription factor (LOC_Os03g22170) with GCC-box promoter motif present in DnaJ gene (LOC_Os06g09560) and 60S ribosomal protein L7 gene (LOC_Os08g42920); and TCC-box promoter motif of DnaK gene (LOC_Os02g48110) and CPuORF11 gene (LOC_Os02g01240) were explored using molecular dynamics (MD) simulations analysis including binding free energy calculations, principal component analyses, and free energy landscapes. The binding free energy analysis revealed that AP2/EREBP model residues such as Arg68, Arg72, Arg83, Lys87, and Arg90 were commonly involved in the formation of hydrogen bonds with GCC and TCC-box promoter motifs, suggesting that these residues are critical for strong interaction. The movement of the entire protein bound to DNA was restricted, confirming the stability of the complex. This study provides comprehensive binding information and a more detailed view of the dynamic interaction between proteins and DNA.

The Transcriptome of Brassica napus L. Roots under Waterlogging at the Seedling Stage

Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance by rapeseed is largely unknown. In this study, the transcriptome under 0 h and 12 h of waterlogging was assayed in the roots of ZS9, a tolerant variety, using digital gene expression (DGE). A total of 4432 differentially expressed genes were identified, indicating that the response to waterlogging in rapeseed is complicated. The assignments of the annotated genes based on GO (Gene Ontology) revealed there were more genes induced under waterlogging in “oxidation reduction”, “secondary metabolism”, “transcription regulation”, and “translation regulation”; suggesting these four pathways are enhanced under waterlogging. Analysis of the 200 most highly expressed genes illustrated that 144 under normal conditions were down-regulated by waterlogging, while up to 191 under waterlogging were those induced in response to stress. The expression of genes involved under waterlogging is mediated by multiple levels of transcriptional, post-transcriptional, translational and post-translational regulation, including phosphorylation and protein degradation; in particular, protein degradation might be involved in the negative regulation in response to this stress. Our results provide new insight into the response to waterlogging and will help to identify important candidate genes.

Contrasting growth and adaptive responses of two oak species to flooding stress: role of non-symbiotic haemoglobin

Soil flooding is an environmental constraint that is increasingly important for forest ecosystems, affecting tree growth and regeneration. As a result, selection pressure will alter forest diversity and distribution by favouring tree species tolerant of soil oxygen deprivation. Sessile and pedunculate oaks are the most abundant oak species and they exhibit a strong differential tolerance to waterlogging. In order to gain some understanding of the mechanisms of tolerance of both species to hypoxia, we undertook the characterization of the physiological, morphological, cellular and molecular responses of both species to flooding stress. Our results indicate that pedunculate oak, the more tolerant species, succeeded in maintaining its growth, water status and photosynthetic activity at a higher level than sessile oak. Furthermore, pedunculate oak developed aerenchyma in its root cortex as well as adventitious roots. The later exhibited a strong accumulation of class1 non-symbiotic haemoglobin localized by in situ hybridization in the protoderm and in some cortical cells. In conclusion, the higher tolerance of pedunculate oak to flooding was associated with an enhanced capacity to maintain photosynthesis and water homeostasis, coupled with the development of adaptive features (aerenchyma, adventitious roots) and with a higher expression of non-symbiotic haemoglobin in the roots.

Identification of transcriptome induced in roots of maize seedlings at the late stage of waterlogging

BACKGROUND

Plants respond to low oxygen stress, particularly that caused by waterlogging, by altering transcription and translation. Previous studies have mostly focused on revealing the mechanism of the response at the early stage, and there is limited information about the transcriptional profile of genes in maize roots at the late stage of waterlogging. The genetic basis of waterlogging tolerance is largely unknown. In this study, the transcriptome at the late stage of waterlogging was assayed in root cells of the tolerant inbred line HZ32, using suppression subtractive hybridization (SSH). A forward SSH library using RNA populations from four time points (12 h, 16 h, 20 h and 24 h) after waterlogging treatment was constructed to reveal up-regulated genes, and transcriptional and linkage data was integrated to identify candidate genes for waterlogging tolerance.

RESULTS

Reverse Northern analysis of a set of 768 cDNA clones from the SSH library revealed a large number of genes were up-regulated by waterlogging. A total of 465 ESTs were assembled into 296 unigenes. Bioinformatic analysis revealed that the genes were involved in complex pathways, such as signal transduction, protein degradation, ion transport, carbon and amino acid metabolism, and transcriptional and translational regulation, and might play important roles at the late stage of the response to waterlogging. A significant number of unigenes were of unknown function. Approximately 67% of the unigenes could be aligned on the maize genome and 63 of them were co-located within reported QTLs.

CONCLUSION

The late response to waterlogging in maize roots involves a broad spectrum of genes, which are mainly associated with two response processes: defense at the early stage and adaption at the late stage. Signal transduction plays a key role in activating genes related to the tolerance mechanism for survival during prolonged waterlogging. The crosstalk between carbon and amino acid metabolism reveals that amino acid metabolism performs two main roles at the late stage: the regulation of cytoplasmic pH and energy supply through breakdown of the carbon skeleton.

MicroRNAs with macro-effects on plant stress responses

Being sessile organisms, plants often have to face challenges posed by environmental stresses. To minimize the cellular damage caused by stress, plants have evolved highly complex but well-coordinated adaptive responses operating at the transcriptional, post-transcriptional, translational and post-translational levels. A thorough understanding of regulation at all levels will provide better tools to improve plant's performance under stress. Dramatic changes in the levels of several hundreds or even thousands of mRNAs/proteins were evident under stress as revealed by high-throughput microarray and proteome analyses and such changes were thought to be dependent on transcriptional (induction or suppression of genes) or post-translational regulation (protein stability and degradation). However, recently discovered 21-24 nt small RNAs (microRNAs [miRNAs] and small-interfering RNAs [siRNAs]), which regulate gene expression at the post-transcriptional level, are also modulated during stress and possibly contribute to the stress-induced changes in profiles of mRNAs or proteins. This review highlights our understanding of the role of small RNAs in plant stress responses.

Submergence-inducible and circadian rhythmic basic helix-loop-helix protein gene in Nicotiana tabacum

Submergence stress leads to diverse changes in transcription and translation of genes involved in developmental and physiological metabolisms of plants. The basic helix-loop-helix (bHLH) protein family is one of the largest transcriptional factor families in plants, and has been shown to play pivotal roles in diverse biological responses. However, there has been no report on bHLH protein related to submergence stress response. In this study, a novel bHLH gene, NtbHLH, was isolated from tobacco (Nicotiana tabacum) by differential screening of a submergence-stress-induced cDNA library. NtbHLH cDNA is 1027bp in length, with an open reading frame (ORF) of 702 nucleotides encoding 233 amino acid residues that contain the bHLH domain. RNA-blot analyses showed that transcription of NtbHLH was induced by submergence stress, while cold, heat shock, and drought decreased its expression. The gene expression was down-regulated by gibberellins, but ABA and ethylene seemed not to affect it. It was also apparent that NtbHLH expression follows circadian rhythmicity. The electrophoretic mobility shift and chemical cross-linking assays showed that NtbHLH specifically binds to G-box and forms homo-dimers.

Functional analysis of the buckwheat metallothionein promoter: tissue specificity pattern and up-regulation under complex stress stimuli

To shed light on expression regulation of the metallothionein gene from buckwheat (FeMT3), functional promoter analysis was performed with a complete 5' regulatory region and two deletion variants, employing stably transformed tobacco plants. Histochemical GUS assay of transgenic tobacco lines showed the strongest signals in vascular elements of leaves and in pollen grains, while somewhat weaker staining was observed in the roots of mature plants. This tissue specificity pattern implies a possible function of buckwheat MT3 in those tissues. Quantitative GUS assay showed strong up-regulation of all three promoter constructs (proportional to the length of the regulatory region) in leaves submerged in liquid MS medium containing sucrose, after a prolonged time period. This represented a complex stress situation composed of several synergistically related stress stimuli. These findings suggest complex transcriptional regulation of FeMT3, requiring interactions among a number of different factors.

Flooding stress-induced glycine-rich RNA-binding protein from Nicotiana tabacum

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

OsDEG10 encoding a small RNA-binding protein is involved in abiotic stress signaling

Excessive light can be harmful to photosynthetic apparatus since it causes photoinhibition and photooxidation, and plants often encounter hypoxic or anoxic environments when they become submerged by heavy rain or an ensuing flood. In this study, Oryza sativa Differentially Expressed Genes (OsDEGs) from rice under photooxidation and anoxia conditions were isolated using DD-PCR. Among them, OsDEG10 is predicted to encode a small RNA-binding protein (RBP) and the transcript levels of OsDEG10 strongly increased under most of abiotic stress treatments such as high light, anoxia, NaCl, ABA, MV and cold. However, the transcript levels of two rice OsDEG10 homologs were not changed under those treatments. OsDEG10 RNAi transgenic plants were more sensitive to high light and cold stresses compared to wild-type plants. Our results suggest that OsDEG10 is a small RBP involved in the response to various abiotic stresses.

Identification of drought-responsive genes in roots of upland rice (Oryza sativa L)

Background

Rice (Oryza sativa L.) germplasm represents an extraordinary source of genes that control traits of agronomic importance such as drought tolerance. This diversity is the basis for the development of new cultivars better adapted to water restriction conditions, in particular for upland rice, which is grown under rainfall. The analyses of subtractive cDNA libraries and differential protein expression of drought tolerant and susceptible genotypes can contribute to the understanding of the genetic control of water use efficiency in rice.

Results

Two subtractive libraries were constructed using cDNA of drought susceptible and tolerant genotypes submitted to stress against cDNA of well-watered plants. In silico analysis revealed 463 reads, which were grouped into 282 clusters. Several genes expressed exclusively in the tolerant or susceptible genotypes were identified. Additionally, proteome analysis of roots from stressed plants was performed and 22 proteins putatively associated to drought tolerance were identified by mass spectrometry.

Conclusion

Several genes and proteins involved in drought-response, as well as genes with no described homologs were identified. Genes exclusively expressed in the tolerant genotype were, in general, related to maintenance of turgor and cell integrity. In contrast, in the susceptible genotype, expression of genes involved in protection against cell damage was not detected. Several protein families identified in the proteomic analysis were not detected in the cDNA analysis. There is an indication that the mechanisms of susceptibility to drought in upland rice are similar to those of lowland varieties.

A novel nonsymbiotic hemoglobin from oak: cellular and tissue specificity of gene expression

This study presents the isolation and characterization of a novel nonsymbiotic Hb gene from sessile oak (Quercus petraea) seedlings, herein designated QpHb1. The cellular and tissue expression of QpHb1 was analysed by Northern blotting and in situ hybridization. The encoded protein was predicted to consist of 161 amino acid residues, and shares 71 and 51% amino acid sequence identity with the Arabidopsis class 1 and 2 nonsymbiotic Hb, respectively. Northern blot analysis revealed that QpHb1 was strongly expressed in roots. Spatial expression analysis of QpHb1 in the root apical region of sessile oak by in situ hybridization indicated that transcripts were mostly abundant in protoxylem cell initials, some cortical cells and the protoderm. In addition, when comparing the expression profile of QpHb1 in sessile and pedunculate oak (Quercus robur), two species with contrasted hypoxia tolerance, the transcript level of QpHb1 rose early in the most flood-tolerant species, pedunculate oak, during root submergence. The spatial-temporal expression of QpHb1 suggests that this gene could participate in perception and signalling during hypoxia.

Anoxia-enhanced expression of genes isolated by suppression subtractive hybridization from pondweed (Potamogeton distinctus A. Benn.) turions

Pondweed (Potamogeton distinctus A. Benn.), a monocot aquatic plant species, has turions, which are overwintering buds forming underground as an asexual reproductive organ. Turions not only survive for more than one month but also elongate under strict anoxia, maintaining high-energy charge by activation of fermentation. We cloned 82 cDNA fragments of genes, that are up-regulated during anoxic growth of pondweed turions, by suppression subtractive hybridization. The transcript levels of 44 genes were confirmed to be higher under anoxia than those in air by both Northern blot analysis and a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) method. A homology search for their nucleotide sequences revealed that some of them are highly homologous to known sequences of genes from other plants. They included alcohol dehydrogenase, pyruvate decarboxylase (PDC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), vacuolar H(+)-translocating pyrophosphatase and a plasma membrane intrinsic protein. Time courses of transcript accumulation of some genes under anoxia were different from those in air. The activity of PDC increased under anoxic conditions but the activities of GAPDH and pyrophosphatase remained constant after anoxic treatment. Anoxically up-regulated genes are possibly involved in physiological events to control energy production, pH regulation and cell growth under anoxia. These results suggest that transcriptional regulation of these genes serves as an essential part of survival and growth of pondweed turions under anoxia.

Salt stress response in rice: genetics, molecular biology, and comparative genomics

Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers. Salt-tolerant transgenic rice plants have been produced using a host of different genes and transcript profiling by micro- and macroarray-based methods has opened the gates for the discovery of novel salt stress mechanisms in rice, and comparative genomics is turning out to be a critical input in this respect. In this paper, we present a comprehensive review of the genetic, molecular biology, and comparative genomics effort towards the generation of salt-tolerant rice. From the data on comprehensive transcript expression profiling of clones representing salt-stress-associated genes of rice, it is shown that transcriptional and translational machineries are important determinants in controlling salt stress response, and gene expression response in tolerant and susceptible rice plants differs mainly in quantitative terms.