The Gibberellic Acid Stimulated-Like gene family in maize and its role in lateral root development

Transcriptomic analysis reveals ethylene as stimulator and auxin as regulator of adventitious root formation in petunia cuttings

Adventitious root (AR) formation in the stem base (SB) of cuttings is the basis for propagation of many plant species and petunia is used as model to study this developmental process. Following AR formation from 2 to 192 hours post-excision (hpe) of cuttings, transcriptome analysis by microarray revealed a change of the character of the rooting zone from SB to root identity. The greatest shift in the number of differentially expressed genes was observed between 24 and 72 hpe, when the categories storage, mineral nutrient acquisition, anti-oxidative and secondary metabolism, and biotic stimuli showed a notable high number of induced genes. Analyses of phytohormone-related genes disclosed multifaceted changes of the auxin transport system, auxin conjugation and the auxin signal perception machinery indicating a reduction in auxin sensitivity and phase-specific responses of particular auxin-regulated genes. Genes involved in ethylene biosynthesis and action showed a more uniform pattern as a high number of respective genes were generally induced during the whole process of AR formation. The important role of ethylene for stimulating AR formation was demonstrated by the application of inhibitors of ethylene biosynthesis and perception as well as of the precursor aminocyclopropane-1-carboxylic acid, all changing the number and length of AR. A model is proposed showing the putative role of polar auxin transport and resulting auxin accumulation in initiation of subsequent changes in auxin homeostasis and signal perception with a particular role of Aux/IAA expression. These changes might in turn guide the entrance into the different phases of AR formation. Ethylene biosynthesis, which is stimulated by wounding and does probably also respond to other stresses and auxin, acts as important stimulator of AR formation probably via the expression of ethylene responsive transcription factor genes, whereas the timing of different phases seems to be controlled by auxin.

Root architecture and root and tuber crop productivity

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.

Post-embryonic root organogenesis in cereals: branching out from model plants

The root architecture of higher plants is amazingly diverse. In this review, we compare the lateral root developmental programme in cereals and Arabidopsis thaliana. In cereals, cells in the endodermis are recruited to form the new root cap and overlying cortical cells divide to facilitate the emergence of the lateral root primordium. The TIR1/ABF2 auxin receptors and the AUX/IAA, ARF, and LBD transcriptional regulatory proteins are conserved in cereals and Arabidopsis. Several elements of this regulatory network are common to lateral and crown roots in cereals. Also, the ground meristem from which crown roots differentiate shows similarities with the root pericycle. Studies in cereals promise to give complementary insights into the mechanisms regulating the development of post-embryonic roots in plants.

Lateral root development in the maize (Zea mays) lateral rootless1 mutant

BACKGROUND AND AIMS

The maize lrt1 (lateral rootless1) mutant is impaired in its development of lateral roots during early post-embryonic development. The aim of this study was to characterize, in detail, the influences that the mutation exerts on lateral root initiation and the subsequent developments, as well as to describe the behaviour of the entire plant under variable environmental conditions.

METHODS

Mutant lrt1 plants were cultivated under different conditions of hydroponics, and in between sheets of moist paper. Cleared whole mounts and anatomical sections were used in combination with both selected staining procedures and histochemical tests to follow root development. Root surface permeability tests and the biochemical quantification of lignin were performed to complement the structural data.

KEY RESULTS

The data presented suggest a redefinition of lrt1 function in lateral roots as a promoter of later development; however, neither the complete absence of lateral roots nor the frequency of their initiation is linked to lrt1 function. The developmental effects of lrt1 are under strong environmental influences. Mutant primordia are affected in structure, growth and emergence; and the majority of primordia terminate their growth during this last step, or shortly thereafter. The lateral roots are impaired in the maintenance of the root apical meristem. The primary root shows disturbances in the organization of both epidermal and subepidermal layers. The lrt1-related cell-wall modifications include: lignification in peripheral layers, the deposition of polyphenolic substances and a higher activity of peroxidase.

CONCLUSIONS

The present study provides novel insights into the function of the lrt1 gene in root system development. The lrt1 gene participates in the spatial distribution of initiation, but not in its frequency. Later, the development of lateral roots is strongly affected. The effect of the lrt1 mutation is not as obvious in the primary root, with no influences observed on the root apical meristem structure and maintenance; however, development of the epidermis and cortex are impaired.

Mining genes involved in the stratification of Paris polyphylla seeds using high-throughput embryo transcriptome sequencing

Background

Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little genomic or transcriptome data are available for this plant.

Results

In this study, massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform was used to generate a substantial sequence dataset for the P. polyphylla embryo. 369,496 high quality reads were obtained, ranging from 50 to 1146 bp, with a mean of 219 bp. These reads were assembled into 47,768 unigenes, which included 16,069 contigs and 31,699 singletons. Using BLASTX searches of public databases, 15,757 (32.3%) unique transcripts were identified. Gene Ontology and Cluster of Orthologous Groups of proteins annotations revealed that these transcripts were broadly representative of the P. polyphylla embryo transcriptome. The Kyoto Encyclopedia of Genes and Genomes assigned 5961 of the unique sequences to specific metabolic pathways. Relative expression levels analysis showed that eleven phytohormone-related genes and five other genes have different expression patterns in the embryo and endosperm in the seed stratification process.

Conclusions

Gene annotation and quantitative RT-PCR expression analysis identified 464 transcripts that may be involved in phytohormone catabolism and biosynthesis, hormone signal, seed dormancy, seed maturation, cell wall growth and circadian rhythms. In particular, the relative expression analysis of sixteen genes (CYP707A, NCED, GA20ox2, GA20ox3, ABI2, PP2C, ARP3, ARP7, IAAH, IAAS, BRRK, DRM, ELF1, ELF2, SFR6, and SUS) in embryo and endosperm and at two temperatures indicated that these related genes may be candidates for clarifying the molecular basis of seed dormancy in P. polyphlla var. yunnanensis.

Cotton GASL genes encoding putative gibberellin-regulated proteins are involved in response to GA signaling in fiber development

GAST (GA-stimulated transcript)-like genes have been reported as targets of GA regulation in some plant species. In this study, we isolated seven GAST-like cDNAs from cotton (Gossypium hirsutum) cDNA libraries (designated as GhGASL1-GhGASL7). Meanwhile, the genomic DNA clones corresponding to the seven GhGASL genes were isolated by using PCR amplification technique. Analysis of gene structure revealed that four genes (GhGASL1/3/5/6) contain two exons and one intron, while the rest have four exons and three introns. All of the deduced GhGASL proteins contain a putative signal peptide in the N-terminus and a conservative cysteine-rich C-terminal domain. Quantitative RT-PCR analysis indicated that the seven GhGASL genes are differentially expressed in cotton tissues. Among them, GhGASL1/4/7 were predominantly expressed in cotyledons, while the transcripts of GhGASL2/5 were preferentially accumulated at hypocotyls. GhGASL3 mRNA was largely accumulated in fibers, while GhGASL6 transcripts were mainly detected in ovules. Furthermore, GhGASL2/3/5 displayed a relatively high expression levels during early fiber elongation stages, and were regulated by GA. These data suggested that GhGASL genes may be involved in fiber elongation and in response to GA signaling during fiber development.

FaGAST2, a strawberry ripening-related gene, acts together with FaGAST1 to determine cell size of the fruit receptacle

Numerous GAST-like genes have been reported in higher plants, but only one GAST-like gene (FaGAST1) has been described in strawberry so far. Herein, we have identified a novel strawberry FaGAST gene (FaGAST2) whose expression showed an increase throughout fruit receptacle development and ripening, coinciding with those stages where a decrease in fruit expansion processes (G3-W and R-OR stages) occurs. FaGAST2 only shares 31% and 15.7% amino acid and nucleotide sequence homology, respectively, with the previously reported FaGAST1 gene, but both genes contain a signal peptide and a highly conserved GASA domain (cysteine-rich domain) in the C-terminal region. FaGAST2 expression is mainly confined to the fruit receptacle and is not regulated by auxins, GA(3) or ABA, but is regulated by ethephon, an intracellular generator of ethylene. In addition, the expression of the FaGAST2 gene also increased under oxidative stress conditions (H(2)O(2) or Colletotrichum acutatum infection), suggesting a direct role for FaGAST2 protein in reactive oxygen species scavenging during fruit growth and ripening and during fungal infection. On the other hand, the overexpression of the FaGAST2 gene in different transgenic lines analyzed caused a delay in the growth of strawberry plants and a reduction in the size of the transgenic fruits. The histological studies performed in these fruits showed that their parenchymal cells were smaller than those of the controls, supporting a relationship between FaGAST2 gene expression, strawberry fruit cell elongation and fruit size. However, transitory silencing of FaGAST2 gene expression through RNA interference approaches revealed an increase in FaGAST1 expression, but no changes in fruit cell size were observed. These results support the hypothesis that both genes must act synergistically to determine fruit cell size during fruit development and ripening.

Role of the CPC sequence in the antioxidant activity of GcGAST protein in E.coli

Gibberellic acid stimulated transcriptional protein from Gymnadenia conopsea (GcGAST) is a novel member of GA-induced cysteine-rich protein family, which shared 12 highly conserved cysteine residues with other members in C-terminal domain. In the present paper, the recombinant plasmid, as well as two mutants Serine-Proline-Cysteine (SPC) and Cysteine-Proline-Serine (CPS), were constructed to investigate for the first time the effects of the cysteines in Cysteine-Proline-Cysteine (CPC) sequence on the antioxidant activity of GcGAST protein. It was found that E.coli expressing wt GcGAST exhibited significant resistance against exogenous H(2)O(2). Similar phenomenon was observed for E.coli harboring SPC mutant. In contrast, the host cell overexpressing CPS mutant became more sensitive to H(2)O(2). Some studies on the level of inclusion body revealed that wt GcGAST and SPC mutant embedded in Inclusion bodies (IB) could effectively eliminate H(2)O(2), whereas the mutagenesis to Ser of the second Cys residue in CPC sequence gave rise to the compete loss of H(2)O(2)-eliminating ability. Fourier transform Infrared spectroscopy analysis indicated that the IB of CPS mutant contained more β-sheet secondary structure than wt and SPC mutant. Non-reducing SDS-PAGE combined western-blotting analysis revealed that the disulfide bonds were important for the formation of IBs of wt GcGAST and SPC mutant, whereas non-reducing SDS-PAGE of resolubilized IBs showed that hydrophobic interaction favored the aggregation of IBs in CPS mutant. Taken together, these results suggested that GcGAST possessed antioxidant activity in the level of IB, which made some contribution to cellular resistance to H(2)O(2). More importantly, the second cysteine residue in CPC sequence was more essential for its antioxidant biological function.

Involvement of lignin and hormones in the response of woody poplar taproots to mechanical stress

Mechanical stress is a widespread condition caused by numerous environmental factors that severely affect plant stability. In response to mechanical stress, plants have evolved complex response pathways able to detect mechanical perturbations and inducing a suite of modifications in order to improve anchorage. The response of woody roots to mechanical stresses has been studied mainly at the morphological and biomechanical level, whereas investigations on the factors triggering these important alterations are still at the initial stage. Populus has been widely used to study the response of stem to different mechanical stresses and, since it has the first forest tree genome to be decoded, represents a model woody plant for addressing questions on the mechanisms controlling adaptation of woody roots to changing environments. In this study, a morphological and physiological analysis was used to investigate factors controlling modifications in Populus nigra woody taproots subjected to mechanical stress. An experimental model analyzing spatial and temporal mechanical force distribution along the woody taproot axis enabled us to compare the events occurring in its above-, central- and below-bending sectors. Different morphogenetic responses and local variations of lignin and plant hormones content have been observed, and a relation with the distribution of the mechanical forces along the stressed woody taproots is hypothesized. We investigated the differences of the response to mechanical stress induction during the time; in this regard, we present data referring to the effect of mechanical stress on plant transition from its condition of winter dormancy to that of full vegetative activity.

Snakin/GASA proteins: involvement in hormone crosstalk and redox homeostasis

Snakin/GASA proteins are widely distributed among plant species. They are expressed in different plant organs with high tissue and temporal specificity, and their subcellular localization varies among the different members. Interestingly, all of them maintain 12 cysteines of the C-terminus in highly conserved positions of the aminoacid sequences that are essential for their biochemical activity and probably responsible for their protein structure. Despite their common features, their functions are not completely elucidated and little is known about their mode of action. This review focuses on the current knowledge about this intriguing family of peptides and advances comprising gene regulation analyses, expression pattern studies and phenotypic characterization of mutants and transgenic plants. Furthermore, we discuss the roles of Snakin/GASA proteins in several aspects of plant development, plant responses to biotic or abiotic stress and their participation in hormone crosstalk and redox homeostasis.

Tall or short? Slender or thick? A plant strategy for regulating elongation growth of roots by low concentrations of gibberellin

BACKGROUND

Since the plant hormone gibberellin (GA) was discovered as a fungal toxin that caused abnormal elongation of rice shoots, the physiological function of GA has mainly been investigated in relation to the regulation of plant height. However, an indispensable role for GA in root growth has been elucidated by using severely GA-depleted plants, either with a gene mutation in GA biosynthesis or which have been treated by an inhibitor of GA biosynthesis. The molecular sequence of GA signalling has also been studied to understand GA functions in root growth.

SCOPE

This review addresses research progress on the physiological functions of GA in root growth. Concentration-dependent stimulation of elongation growth by GA is important for the regulation of plant height and root length. Thus the endogenous level of GA and/or the GA sensitivity of shoots and roots plays a role in determining the shoot-to-root ratio of the plant body. Since the shoot-to-root ratio is an important parameter for agricultural production, control of GA production and GA sensitivity may provide a strategy for improving agricultural productivity. The sequence of GA signal transduction has recently been unveiled, and some component molecules are suggested as candidate in planta regulatory sites and as points for the artificial manipulation of GA-mediated growth control.

CONCLUSIONS

This paper reviews: (1) the breakthrough dose-response experiments that show that root growth is regulated by GA in a lower concentration range than is required for shoot growth; (2) research on the regulation of GA biosynthesis pathways that are known predominantly to control shoot growth; and (3) recent research on GA signalling pathways, including GA receptors, which have been suggested to participate in GA-mediated growth regulation. This provides useful information to suggest a possible strategy for the selective control of shoot and root growth, and to explain how GA plays a role in rosette and liana plants with tall or short, and slender or thick axial organs.

Potato snakin-1 gene silencing affects cell division, primary metabolism, and cell wall composition

Snakin-1 (SN1) is an antimicrobial cysteine-rich peptide isolated from potato (Solanum tuberosum) that was classified as a member of the Snakin/Gibberellic Acid Stimulated in Arabidopsis protein family. In this work, a transgenic approach was used to study the role of SN1 in planta. Even when overexpressing SN1, potato lines did not show remarkable morphological differences from the wild type; SN1 silencing resulted in reduced height, which was accompanied by an overall reduction in leaf size and severe alterations of leaf shape. Analysis of the adaxial epidermis of mature leaves revealed that silenced lines had 70% to 90% increases in mean cell size with respect to wild-type leaves. Consequently, the number of epidermal cells was significantly reduced in these lines. Confocal microscopy analysis after agroinfiltration of Nicotiana benthamiana leaves showed that SN1-green fluorescent protein fusion protein was localized in plasma membrane, and bimolecular fluorescence complementation assays revealed that SN1 self-interacted in vivo. We further focused our study on leaf metabolism by applying a combination of gas chromatography coupled to mass spectrometry, Fourier transform infrared spectroscopy, and spectrophotometric techniques. These targeted analyses allowed a detailed examination of the changes occurring in 46 intermediate compounds from primary metabolic pathways and in seven cell wall constituents. We demonstrated that SN1 silencing affects cell division, leaf primary metabolism, and cell wall composition in potato plants, suggesting that SN1 has additional roles in growth and development beyond its previously assigned role in plant defense.

Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration

BACKGROUND

The soil represents a reservoir that contains at least twice as much carbon as does the atmosphere, yet (apart from 'root crops') mainly just the above-ground plant biomass is harvested in agriculture, and plant photosynthesis represents the effective origin of the overwhelming bulk of soil carbon. However, present estimates of the carbon sequestration potential of soils are based more on what is happening now than what might be changed by active agricultural intervention, and tend to concentrate only on the first metre of soil depth.

SCOPE

Breeding crop plants with deeper and bushy root ecosystems could simultaneously improve both the soil structure and its steady-state carbon, water and nutrient retention, as well as sustainable plant yields. The carbon that can be sequestered in the steady state by increasing the rooting depths of crop plants and grasses from, say, 1 m to 2 m depends significantly on its lifetime(s) in different molecular forms in the soil, but calculations (http://dbkgroup.org/carbonsequestration/rootsystem.html) suggest that this breeding strategy could have a hugely beneficial effect in stabilizing atmospheric CO(2). This sets an important research agenda, and the breeding of plants with improved and deep rooting habits and architectures is a goal well worth pursuing.

Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration

BACKGROUND

The soil represents a reservoir that contains at least twice as much carbon as does the atmosphere, yet (apart from 'root crops') mainly just the above-ground plant biomass is harvested in agriculture, and plant photosynthesis represents the effective origin of the overwhelming bulk of soil carbon. However, present estimates of the carbon sequestration potential of soils are based more on what is happening now than what might be changed by active agricultural intervention, and tend to concentrate only on the first metre of soil depth.

SCOPE

Breeding crop plants with deeper and bushy root ecosystems could simultaneously improve both the soil structure and its steady-state carbon, water and nutrient retention, as well as sustainable plant yields. The carbon that can be sequestered in the steady state by increasing the rooting depths of crop plants and grasses from, say, 1 m to 2 m depends significantly on its lifetime(s) in different molecular forms in the soil, but calculations (http://dbkgroup.org/carbonsequestration/rootsystem.html) suggest that this breeding strategy could have a hugely beneficial effect in stabilizing atmospheric CO(2). This sets an important research agenda, and the breeding of plants with improved and deep rooting habits and architectures is a goal well worth pursuing.

Transcript profiling during the early development of the maize brace root via Solexa sequencing

Currently, the molecular regulation mechanisms involved in the early development of maize brace root are poorly known. To gain insight into the transcriptome dynamics that are associated with its development, genome-wide gene expression profiling was conducted by Solexa sequencing (Illumina Inc., San Diego, CA, USA). More than five million tags were generated from the stem node tissues without and with just-emerged brace roots, including 149,524 and 178,131 clean tags in the two libraries, respectively. Of these, 82,864 (55.4%) and 91,678 (51.5%) tags were matched to the reference genes. The most differentially expressed tags with a log(2) ratio > 2 or < -2 (P < 0.001) were analyzed further, representing 143 up-regulated and 152 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Many genes or biological pathways were found to be commonly shared between brace root and lateral or adventitious root development, such as genes participating in cell wall degradation and synthesis, auxin transport and signaling, ethylene signaling, etc. Next, the expression patterns of 20 genes were assessed by quantitative real-time PCR, and the results obtained showed general agreement with the Solexa analysis. Furthermore, a comparison of the brace root transcriptome with that of maize primary root revealed substantial differences in the categories and abundances of expressed transcripts. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize brace root and provide a comprehensive set of data that are essential for understanding its molecular regulation.