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Hans J Bohnert

Publications and source records attributed to Hans J Bohnert.

At least 19 recordsLinked to original sources
PubMed2006

Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase.

Reversible modifications of target proteins by small ubiquitin-like modifier (SUMO) proteins are involved in many cellular processes in yeast and animals. Yet little is known about the function of sumoylation in plants. Here, we show that the SIZ1 gene, which encodes an Arabidopsis SUMO E3 ligase, regulates innate immunity. Mutant siz1 plants exhibit constitutive systemic-acquired resistance (SAR) characterized by elevated accumulation of salicylic acid (SA), increased expression of pathogenesis-related (PR) genes, and increased resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. Transfer of the NahG gene to siz1 plants results in reversal of these phenotypes back to wild-type. Analyses of the double mutants, npr1 siz1, pad4 siz1 and ndr1 siz1 revealed that SIZ1 controls SA signalling. SIZ1 interacts epistatically with PAD4 to regulate PR expression and disease resistance. Consistent with these observations, siz1 plants exhibited enhanced resistance to Pst DC3000 expressing avrRps4, a bacterial avirulence determinant that responds to the EDS1/PAD4-dependent TIR-NBS-type R gene. In contrast, siz1 plants were not resistant to Pst DC3000 expressing avrRpm1, a bacterial avirulence determinant that responds to the NDR1-dependent CC-NBS-type R gene. Jasmonic acid (JA)-induced PDF1.2 expression and susceptibility to Botrytis cinerea were unaltered in siz1 plants. Taken together, these results demonstrate that SIZ1 is required for SA and PAD4-mediated R gene signalling, which in turn confers innate immunity in Arabidopsis.

Arabidopsis↗
PubMed2006

Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis.

A microarray including 1654 cDNAs, mainly derived from dehydration-shocked barley leaf tissues, was utilized to monitor expression changes in leaves of barley plants subjected to slow drying conditions (7 d and 11 d: 7d-WS and 11d-WS) in soil and after rehydration. The results were compared with those obtained under shock-like conditions imposed with a 6 h dehydration treatment. A total number of 173 transcripts (approximately 10% of all transcripts profiled) were declared up- or down-regulated in at least one of the conditions tested. The majority of the transcripts were regulated by only one of the drought treatments, with 57% of the differentially expressed transcripts exclusively affected in the dehydration shock treatment, 6% at 7d-WS, 14% at 11d-WS, and 6% after rehydration. Irrespective of the low percentage of transcripts (10%) with similar expression changes between shock and slow stress treatments, a sizeable portion of these transcripts shared a common expression trend under the different drought treatment conditions, as evidenced by low but significant correlations between the fast occurring and the 7d-WS and 11d-WS treatments (r=0.32 and 0.41, P=0.001, respectively). These results are discussed with respect to the merit of different dehydration treatments in the investigation of the changes in transcript profiling.

Desiccation↗
PubMed2006

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.

Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.uiuc.edu/), a system of open-air rings within which [CO(2)] is elevated to approximately 550 ppm. Data from multiple rings, comparing plants in ambient air and elevated [CO(2)], were analyzed by mixed model ANOVA, linear discriminant analysis (LDA) and data-mining tools. In elevated [CO(2)], decreases in the expression of genes related to chloroplast functions characterized all lines but individual members of distinct multi-gene families were regulated differently between lines. Also, different strategies distinguished the lines with respect to the regulation of genes related to carbohydrate biosynthesis and partitioning, N-allocation and amino acid metabolism, cell wall biosynthesis, and hormone responses, irrespective of the plants' developmental status. Metabolite results paralleled reactions seen at the level of transcript expression. Evolutionary adaptation of species to their habitat and intrinsic genetic plasticity seem to determine the nature of responses to elevated [CO(2)]. Irrespective of their underlying genetic diversity, and evolutionary adaptation to different habitats, a small number of common, predominantly stress-responsive, signature transcripts appear to characterize responses of the Arabidopsis ecotypes in FACE.

Analysis of Variance↗
PubMed2006

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

BACKGROUND: Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance assessment. This process typically consists of two steps: data normalization and identification of differentially expressed genes through statistical analysis. The Expresso microarray experiment management system implements these steps with a two-stage, log-linear ANOVA mixed model technique, tailored to individual experimental designs. The complement of tools in TM4, on the other hand, is based on a number of preset design choices that limit its flexibility. In the TM4 microarray analysis suite, normalization, filter, and analysis methods form an analysis pipeline. TM4 computes integrated intensity values (IIV) from the average intensities and spot pixel counts returned by the scanner software as input to its normalization steps. By contrast, Expresso can use either IIV data or median intensity values (MIV). Here, we compare Expresso and TM4 analysis of two experiments and assess the results against qRT-PCR data. RESULTS: The Expresso analysis using MIV data consistently identifies more genes as differentially expressed, when compared to Expresso analysis with IIV data. The typical TM4 normalization and filtering pipeline corrects systematic intensity-specific bias on a per microarray basis. Subsequent statistical analysis with Expresso or a TM4 t-test can effectively identify differentially expressed genes. The best agreement with qRT-PCR data is obtained through the use of Expresso analysis and MIV data. CONCLUSION: The results of this research are of practical value to biologists who analyze microarray data sets. The TM4 normalization and filtering pipeline corrects microarray-specific systematic bias and complements the normalization stage in Expresso analysis. The results of Expresso using MIV data have the best agreement with qRT-PCR results. In one experiment, MIV is a better choice than IIV as input to data normalization and statistical analysis methods, as it yields as greater number of statistically significant differentially expressed genes; TM4 does not support the choice of MIV input data. Overall, the more flexible and extensive statistical models of Expresso achieve more accurate analytical results, when judged by the yardstick of qRT-PCR data, in the context of an experimental design of modest complexity.

Algorithms↗
PubMed2006

Dissecting salt stress pathways.

Upon salt-stress treatment, Arabidopsis mobilizes a complex set of pathways that includes alterations in the regulation of gene expression and metabolic adjustments that attempt to establish a new energetic and developmental equilibrium. The responses share common elements with reactions to many other stresses, such as challenges by osmotic fluctuations, pathogens, mechanical interference, or cold stress. Also, hormones, such as ABA, ethylene, and jasmonic acid, play important roles in salt-stress signalling and adaptation. Publicly available and our own transcript profiling data are used here to dissect gene regulation under salt stress in A. thaliana Col-0. Applying the clustering method "fuzzy k-means clustering" on 1500 strongly regulated genes, the salt-stress response could be categorized into distinct segments. Fewer than 25% of the regulated genes are salt stress-specific, while the majority also responded to other stresses and/or hormone treatments. Significantly, roots and shoots showed differences in hormone responsiveness, and early and late responses correlated with different signalling events. A network begins to emerge, revealing the basis of cross-talk between high salinity and other stresses.

Arabidopsis↗
PubMed2006

Unraveling abiotic stress tolerance mechanisms--getting genomics going.

Homeostasis, a set-value for metabolism under optimal conditions, is rarely achieved by plants because of the cost exerted by external stress factors: climatic, biotic, and nutrient imbalances. Among these, stresses caused by abiotic conditions, such as temperature extremes (freezing, cold and heat), water availability (drought and ion excess) and ion toxicity (salinity and heavy metals), have been difficult to dissect because defense responses to abiotic factors require regulatory changes to the activation of multiple genes and pathways. Genomics technologies that have emerged during the past decade have been useful in addressing, in an integrated fashion, the multigenicity of the plant abiotic stress response through genome sequences; cell-, organ-, tissue- and stress-specific transcript collections; transcript, protein and metabolite profiles and their dynamic changes; protein interactions; and mutant screens.

Adaptation, Physiological↗
PubMed2006

Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila.

Arabidopsis thaliana (At) ecotypes Columbia-0 (Col-0), Wassilewskija (WS), Cape Verde Islands (Cvi-0) and a relative, Thellungiella halophila (Th), were exposed to 20-25% over ambient ozone [O3] in a free air concentration enrichment (FACE) experiment (http://www.soyFACE. uiuc.edu), mirroring increases expected in the near future. Col-0 and WS accelerated development and developed lesions within 10 d under increased ozone, while Cvi-0 and Th grew slowly. RNAs were used in microarray hybridizations (Col-0-based 26 000 elements, 70-mer oligonucleotides). A two-step analysis of variance (ANOVA) model, including comparison with values obtained under [O3], was used for analyses. WS showed the greatest number of changes in gene expression in response to ozone. Th showed the least changes, suggesting that its expression state at [O3] was sufficient for resistance at increased ozone. Patterns observed in ambient air controls for Cvi-0 and Col-0 were most similar, while Th showed the greatest number of differences compared with the other controls. Compared with Col-0, however, Cvi-0 showed higher levels of expression of chaperones, receptor kinase-like and photosynthesis-related genes in ambient air. Cvi-0 exhibited ozone-mediated changes in a pathway involving AtSR, a homologue of the mammalian NF kappa B family of redox-sensitive transcription factors, changes in chaperones, WRKY and C2H2 proteins and antioxidants. WS displayed ozone-mediated decreases in the expression of two AtSR/NF kappa B family members, C2-domain proteins and genes associated with cell wall growth and changes in the expression of marker genes for programmed cell death (PCD), among them RCD1, a key regulator in this pathway. Microarray data were verified by reverse transcriptase (RT)-PCR. We relate O3-response diversity across the four lines to different responses among signaling and transcriptional response networks and differences in gene expression at [O3] levels.

Arabidopsis↗
PubMed2005

Chloroplast biogenesis 92: In situ screening for divinyl chlorophyll(ide) a reductase mutants by spectrofluorometry.

Chlorophyll biosynthetic heterogeneity is rooted mainly in parallel divinyl (DV) and monovinyl (MV) biosynthetic routes interconnected by 4-vinyl reductases (4VRs) that convert DV tetrapyrroles to MV tetrapyrroles by conversion of the vinyl group at position 4 of the macrocycle to ethyl. What is not clear at this stage is whether the various 4VR activities are catalyzed by one enzyme of broad specificity or by a family of enzymes encoded by one gene or multiple genes with each enzyme having narrow specificity. Additional research is needed to identify the various regulatory components of 4-vinyl reduction. In this undertaking, Arabidopsis mutants that accumulate DV chlorophyllide a and/or DV chlorophyll [Chl(ide)] a are likely to provide an appropriate resource. Because the Arabidopsis genome has been completely sequenced, the best strategy for identifying 4VR and/or putative regulatory 4VR genes is to screen Arabidopsis Chl mutants for DV Chl(ide) a accumulation. In wild-type Arabidopsis, a DV plant species, only MV chlorophyllide (Chlide) a is detectable. However in Chl mutants lacking 4VR activity, DV Chl(ide) a may accumulate in addition to MV Chl(ide) a. In the current work, an in situ assay of DV Chl(ide) a accumulation, suitable for screening a large number of mutants lacking 4-vinyl Chlide a reductase activity with minimal experimental handling, is described. The assay involves homogenization of the tissues in Tris-HCl:glycerol buffer and the recording of Soret excitation spectra at 77K. DV Chlide a formation is detected by a Soret excitation shoulder at 459 nm over a wide range of DV Chlide a/MV Chl a ratios. The DV Chlide a shoulder became undetectable at DV Chlide a/MV Chl a ratios less than 0.049, that is, at a DV Chlide a content of less than 5%.

Chloroplasts↗
PubMed2005

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes.

Between 1 and 1.5 billion years ago, eukaryotic organisms acquired the ability to convert light into chemical energy through endosymbiosis with a Cyanobacterium (e.g.,). This event gave rise to "primary" plastids, which are present in green plants, red algae, and glaucophytes ("Plantae" sensu Cavalier-Smith). The widely accepted view that primary plastids arose only once implies two predictions: (1) all plastids form a monophyletic group, as do (2) primary photosynthetic eukaryotes. Nonetheless, unequivocal support for both predictions is lacking (e.g.,). In this report, we present two phylogenomic analyses, with 50 genes from 16 plastid and 15 cyanobacterial genomes and with 143 nuclear genes from 34 eukaryotic species, respectively. The nuclear dataset includes new sequences from glaucophytes, the less-studied group of primary photosynthetic eukaryotes. We find significant support for both predictions. Taken together, our analyses provide the first strong support for a single endosymbiotic event that gave rise to primary photosynthetic eukaryotes, the Plantae. Because our dataset does not cover the entire eukaryotic diversity (but only four of six major groups in), further testing of the monophyly of Plantae should include representatives from eukaryotic lineages for which currently insufficient sequence information is available.

Bayes Theorem↗
PubMed2005

Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress.

One of the best-characterized physiological rhythms in plants is the circadian rhythm of CO(2) metabolism in Crassulacean acid metabolism (CAM) plants, which is the focus here. The central components of the plant circadian clock have been studied in detail only in Arabidopsis (Arabidopsis thaliana). Full-length cDNAs have been obtained encoding orthologs of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), EARLY FLOWERING4 (ELF4), ZEITLUPE (ZTL), FLAVIN-BINDING KELCH REPEAT F-BOX1 (FKF1), EARLY FLOWERING3 (ELF3), and a partial cDNA encoding GIGANTEA in the model stress-inducible CAM plant, Mesembryanthemum crystallinum (Common Ice Plant). TOC1 and LHY/CCA1 are under reciprocal circadian control in a manner similar to their regulation in Arabidopsis. ELF4, FKF1, ZTL, GIGANTEA, and ELF3 are under circadian control in C(3) and CAM leaves. ELF4 transcripts peak in the evening and are unaffected by CAM induction. FKF1 shows an abrupt transcript peak 3 h before subjective dusk. ELF3 transcripts appear in the evening, consistent with their role in gating light input to the circadian clock. Intriguingly, ZTL transcripts do not oscillate in Arabidopsis, but do in M. crystallinum. The transcript abundance of the clock-associated genes in M. crystallinum is largely unaffected by development and salt stress, revealing compensation of the central circadian clock against development and abiotic stress in addition to the well-known temperature compensation. Importantly, the clock in M. crystallinum is very similar to that in Arabidopsis, indicating that such a clock could control CAM without requiring additional components of the central oscillator or a novel CAM oscillator.

Circadian Rhythm↗
PubMed2005

Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana.

In stark contrast to Arabidopsis, a related species, Thellungiella halophila (Thellungiella salsuginea; salt cress), displays extreme tolerance to high salinity, low humidity and freezing. High nucleotide sequence identity permits the use of tools developed for Arabidopsis for Thellungiella transcript profiling, for which a microarray platform with >25,000 DNA elements (70-mer oligonucleotides) was used. Microarray transcript profiling and intensity analysis, quantitative RT-PCR, and metabolite profiles define genes and pathways that showed shared and divergent responses to salinity stress in the two species. Shared responses are exemplified by 40% of the regulated genes functioning in confining ribosomal functions, photosynthesis and cell growth, as well as activating osmolyte production, transport activities and abscisic acid-dependent pathways. An additional 60% of regulated genes distinguished Thellungiella from Arabidopsis. Analysis of the differences showed that Arabidopsis exhibited a global defense strategy that required bulk protein synthesis, while Thellungiella induced genes functioning in protein folding, post-translational modification and protein redistribution. At 150 mm NaCl, Thellungiella maintained unimpeded growth. Transcript intensity analyses and metabolite profiles supported the microarray results, pointing towards a stress-anticipatory preparedness in Thellungiella.

Adaptation, Physiological↗
PubMed2004

Root growth maintenance during water deficits: physiology to functional genomics.

Progress in understanding the network of mechanisms involved in maize primary root growth maintenance under water deficits is reviewed. These include the adjustment of growth zone dimensions, turgor maintenance by osmotic adjustment, and enhanced cell wall loosening. The role of the hormone abscisic acid (ABA) in maintaining root growth under water deficits is also addressed. The research has taken advantage of kinematic analysis, i.e. characterization of spatial and temporal patterns of cell expansion within the root growth zone. This approach revealed different growth responses to water deficits and ABA deficiency in distinct regions of the root tip. In the apical 3 mm region, elongation is maintained at well-watered rates under severe water deficit, although only in ABA-sufficient roots, whereas the region from 3-7 mm from the apex exhibits maximum elongation in well-watered roots, but progressive inhibition of elongation in roots under water deficit. This knowledge has greatly facilitated discovery of the mechanisms involved in regulating the responses. The spatial resolution with which this system has been characterized and the physiological knowledge gained to date provide a unique and powerful underpinning for functional genomics studies. Characterization of water deficit-induced changes in transcript populations and cell wall protein profiles within the growth zone of the maize primary root is in progress. Initial results from EST and unigene analyses in the tips of well-watered and water-stressed roots highlight the strength of the kinematic approach to transcript profiling.

Adaptation, Physiological↗
PubMed2004

Novel regulation of aquaporins during osmotic stress.

Aquaporin protein regulation and redistribution in response to osmotic stress was investigated. Ice plant (Mesembryanthemum crystallinum) McTIP1;2 (McMIPF) mediated water flux when expressed in Xenopus leavis oocytes. Mannitol-induced water imbalance resulted in increased protein amounts in tonoplast fractions and a shift in protein distribution to other membrane fractions, suggesting aquaporin relocalization. Indirect immunofluorescence labeling also supports a change in membrane distribution for McTIP1;2 and the appearance of a unique compartment where McTIP1;2 is expressed. Mannitol-induced redistribution of McTIP1;2 was arrested by pretreatment with brefeldin A, wortmannin, and cytochalasin D, inhibitors of vesicle trafficking-related processes. Evidence suggests a role for glycosylation and involvement of a cAMP-dependent signaling pathway in McTIP1;2 redistribution. McTIP1;2 redistribution to endosomal compartments may be part of a homeostatic process to restore and maintain cellular osmolarity under osmotic-stress conditions.

Aquaporins↗
PubMed2004

Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles.

Salt cress (Thellungiella halophila) is a small winter annual crucifer with a short life cycle. It has a small genome (about 2 x Arabidopsis) with high sequence identity (average 92%) with Arabidopsis, and can be genetically transformed by the simple floral dip procedure. It is capable of copious seed production. Salt cress is an extremophile native to harsh environments and can reproduce after exposure to extreme salinity (500 mm NaCl) or cold to -15 degrees C. It is a typical halophyte that accumulates NaCl at controlled rates and also dramatic levels of Pro (>150 mm) during exposure to high salinity. Stomata of salt cress are distributed on the leaf surface at higher density, but are less open than the stomata of Arabidopsis and respond to salt stress by closing more tightly. Leaves of salt cress are more succulent-like, have a second layer of palisade mesophyll cells, and are frequently shed during extreme salt stress. Roots of salt cress develop both an extra endodermis and cortex cell layer compared to Arabidopsis. Salt cress, although salt and cold tolerant, is not exceptionally tolerant of soil desiccation. We have isolated several ethyl methanesulfonate mutants of salt cress that have reduced salinity tolerance, which provide evidence that salt tolerance in this halophyte can be significantly affected by individual genetic loci. Analysis of salt cress expressed sequence tags provides evidence for the presence of paralogs, missing in the Arabidopsis genome, and for genes with abiotic stress-relevant functions. Hybridizations of salt cress RNA targets to an Arabidopsis whole-genome oligonucleotide array indicate that commonly stress-associated transcripts are expressed at a noticeably higher level in unstressed salt cress plants and are induced rapidly under stress. Efficient transformation of salt cress allows for simple gene exchange between Arabidopsis and salt cress. In addition, the generation of T-DNA-tagged mutant collections of salt cress, already in progress, will open the door to a new era of forward and reverse genetic studies of extremophile plant biology.

Abscisic Acid↗
PubMed2004

Virtual-SAGE: a new approach to EST data analysis.

We present a computer program, termed V-SAGE (Virtual-SAGE), designed to facilitate the analysis of gene expression profiles by combining elements of SAGE (Serial Analysis of Gene Expression) with high-throughput EST analysis. The program re-iteratively correlates sequence tags adjacent to poly(A) tail sequence strings with a second or several tags located within the cDNA adjacent to the recognition sequences of frequently-cutting endonucleases. By recording tags and their distance, the program generates an expression profile from large numbers of sequences, groups sequences according to tags, and identifies alternatively spliced transcripts as well as transcripts that are characterized by 3'-UTR sequences of different length. We discuss the application of V-SAGE to a collection of corn root segment transcripts.

Algorithms↗
PubMed2004

Loss of TIP1;1 aquaporin in Arabidopsis leads to cell and plant death.

Arabidopsis TIP1;1 (gammaTIP) is a member of the tonoplast family of aquaporins (AQP). Using RNA interference (RNAi) we reduced TIP1;1 to different extent in various lines. When most severely affected, miniature plants died, a phenotype partially complemented by the TIP1;1 homolog McMIP-F. Less severely affected lines produced small plants, early senescence, and showed lesion formation. The relative water content in TIP1;1 RNAi plants was not significantly affected. Global expression profiling suggested a disturbance in carbon metabolism in RNAi lines with upregulated transcripts for functions in carbon acquisition and respiration, vesicle transport, signaling and transcription, and radical oxygen stress. Metabolite profiles showed low glucose, fructose, inositol, and threonic, succinic, fumaric, and malic acids, but sucrose levels were similar to WT. Increased amounts were found for raffinose and several unknown compounds. TIP1;1 RNAi plants also contained high starch and apoplastic carbohydrate increased. A GFP-TIP1;1 fusion protein indicated tonoplast location in spongy mesophyll cells, and high signal intensity in palisade mesophyll associated with vesicles near plastids. Signals in vascular tissues were strongest not only in vesicle-like structures but also outlined large vacuoles. Compromised routing of carbohydrate and lack of sucrose provision for cell-autonomous functions seems to characterize this RNAi phenotype. We suggest a function for TIP1;1 in vesicle-based metabolite routing through or between pre-vacuolar compartments and the central vacuole. Phenotype and expression characteristics support a view of TIP1;1 functioning as a marker for vesicles that are targeted to the central vacuole.

Aquaporins↗
PubMed2003

Salinity stress-tolerant and -sensitive rice (Oryza sativa L.) regulate AKT1-type potassium channel transcripts differently.

In the indica rice (Oryza sativa L.) a cDNA was characterized that encoded OsAKT1 homologous to inward-rectifying potassium channels of the AKT/KAT subfamily. Transcript analysis located OsAKT1 predominantly in roots with low abundance in leaves. Cell-specificity of OsAKT expression was analyzed by in situ hybridizations. In roots, strongest signals were localized to the epidermis and the endodermis, whereas lower transcript levels were detected in cells of the vasculature and the cortex. In leaves, expression was detected in xylem parenchyma, phloem, and mesophyll cells. Transcriptional regulation and cell specificity of OsAKT1 during salt stress was compared in rice lines showing different salinity tolerance. In the salt-tolerant, sodium-excluding varieties Pokkali and BK, OsAKT1 transcripts disappeared from the exodermis in plants treated with 150 mM NaCl for 48 h but OsAKT1 transcription was not repressed in these cells in the salt-sensitive, sodium-accumulating variety IR29. Significantly, all lines were able to maintain potassium levels under sodium stress conditions, while sodium concentrations in the leaves of IR29 increased 5-10-fold relative to the sodium concentration in BK or Pokkali. The divergent, line-dependent and salt-dependent, regulation of this channel does not significantly affect potassium homeostasis under salinity stress. Rather, repression in Pokkali/BK and lack of repression in IR29 correlate with the overall tolerance character of these lines.

Amino Acid Sequence↗