Dynamic regulation of cortical microtubule organization through prefoldin-DELLA interaction

A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem

Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.

Highlights in gibberellin research: A tale of the dwarf and the slender

It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.

Prefoldin Subunits and Its Associate Partners: Conservations and Specificities in Plants

Prefoldins (PFDs) are ubiquitous co-chaperone proteins that originated in archaea during evolution and are present in all eukaryotes, including yeast, mammals, and plants. Typically, prefoldin subunits form hexameric PFD complex (PFDc) that, together with class II chaperonins, mediate the folding of nascent proteins, such as actin and tubulin. In addition to functioning as a co-chaperone in cytoplasm, prefoldin subunits are also localized in the nucleus, which is essential for transcription and post-transcription regulation. However, the specific and critical roles of prefoldins in plants have not been well summarized. In this review, we present an overview of plant prefoldin and its related proteins, summarize the structure of prefoldin/prefoldin-like complex (PFD/PFDLc), and analyze the versatile landscape by prefoldin subunits, from cytoplasm to nucleus regulation. We also focus the specific role of prefoldin-mediated phytohormone response and global plant development. Finally, we overview the emerging prefoldin-like (PFDL) subunits in plants and the novel roles in related processes, and discuss the next direction in further studies.

Spatial regulation of plant hormone action

Although many plant cell types are capable of producing hormones, and plant hormones can in most cases act in the same cells in which they are produced, they also act as signaling molecules that coordinate physiological responses between different parts of the plant, indicating that their action is subject to spatial regulation. Numerous publications have reported that all levels of plant hormonal pathways, namely metabolism, transport, and perception/signal transduction, can help determine the spatial ranges of hormone action. For example, polar auxin transport or localized auxin biosynthesis contribute to creating a differential hormone accumulation across tissues that is instrumental for specific growth and developmental responses. On the other hand, tissue specificity of cytokinin actions has been proposed to be regulated by mechanisms operating at the signaling stages. Here, we review and discuss current knowledge about the contribution of the three levels mentioned above in providing spatial specificity to plant hormone action. We also explore how new technological developments, such as plant hormone sensors based on FRET (fluorescence resonance energy transfer) or single-cell RNA-seq, can provide an unprecedented level of resolution in defining the spatial domains of plant hormone action and its dynamics.

ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV-B

Reductions in red to far-red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade-sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV-B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer-term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV-B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2-OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF-inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV-B exposure.

The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation

The DELLA genes, also known as 'Green Revolution' genes, encode conserved master growth regulators that control plant development in response to internal and environmental cues. Functioning as nuclear-localized transcription regulators, DELLAs modulate expression of target genes via direct protein-protein interaction of their carboxy-terminal GRAS domain with hundreds of transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here by characterizing new missense alleles of an Arabidopsis DELLA, repressor of ga1-3 (RGA), and co-immunoprecipitation assays, we show that RGA binds histone H2A via the PFYRE subdomain within its GRAS domain to form a TF-RGA-H2A complex at the target chromatin. Chromatin immunoprecipitation followed by sequencing analysis further shows that this activity is essential for RGA association with its target chromatin globally. Our results indicate that, although DELLAs are recruited to target promoters by binding to TFs via the LHR1 subdomain, DELLA-H2A interaction via the PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides insights into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.

GA signaling expands: The plant UBX domain-containing protein 1 is a binding partner for the GA receptor

The plant Ubiquitin Regulatory X (UBX) domain-containing protein 1 (PUX1) functions as a negative regulator of gibberellin (GA) signaling. GAs are plant hormones that stimulate seed germination, the transition to flowering, and cell elongation and division. Loss of Arabidopsis (Arabidopsis thaliana) PUX1 resulted in a "GA-overdose" phenotype including early flowering, increased stem and root elongation, and partial resistance to the GA-biosynthesis inhibitor paclobutrazol during seed germination and root elongation. Furthermore, GA application failed to stimulate further stem elongation or flowering onset suggesting that elongation and flowering response to GA had reached its maximum. GA hormone partially repressed PUX1 protein accumulation, and PUX1 showed a GA-independent interaction with the GA receptor GA-INSENSITIVE DWARF-1 (GID1). This suggests that PUX1 is GA regulated and/or regulates elements of the GA signaling pathway. Consistent with PUX1 function as a negative regulator of GA signaling, the pux1 mutant caused increased GID1 expression and decreased accumulation of the DELLA REPRESSOR OF GA1-3, RGA. PUX1 is a negative regulator of the hexameric AAA+ ATPase CDC48, a protein that functions in diverse cellular processes including unfolding proteins in preparation for proteasomal degradation, cell division, and expansion. PUX1 binding to GID1 required the UBX domain, a binding motif necessary for CDC48 interaction. Moreover, PUX1 overexpression in cell culture not only stimulated the disassembly of CDC48 hexamer but also resulted in co-fractionation of GID1, PUX1, and CDC48 subunits in velocity sedimentation assays. Based on our results, we propose that PUX1 and CDC48 are additional factors that need to be incorporated into our understanding of GA signaling.

MDF is a conserved splicing factor and modulates cell division and stress response in Arabidopsis

The coordination of cell division with stress response is essential for maintaining genome stability in plant meristems. Proteins involved in pre-mRNA splicing are important for these processes in animal and human cells. Based on its homology to the splicing factor SART1, which is implicated in the control of cell division and genome stability in human cells, we analyzed if MDF has similar functions in plants. We found that MDF associates with U4/U6.U5 tri-snRNP proteins and is essential for correct splicing of 2,037 transcripts. Loss of MDF function leads to cell division defects and cell death in meristems and was associated with up-regulation of stress-induced genes and down-regulation of mitotic regulators. In addition, the mdf-1 mutant is hypersensitive to DNA damage treatment supporting its role in coordinating stress response with cell division. Our analysis of a dephosphomutant of MDF suggested how its protein activity might be controlled. Our work uncovers the conserved function of a plant splicing factor and provides novel insight into the interplay of pre-mRNA processing and genome stability in plants.

Plant Development and Crop Yield: The Role of Gibberellins

Gibberellins have been classically related to a few key developmental processes, thus being essential for the accurate unfolding of plant genetic programs. After more than a century of research, over one hundred different gibberellins have been described. There is a continuously increasing interest in gibberellins research because of their relevant role in the so-called "Green Revolution", as well as their current and possible applications in crop improvement. The functions attributed to gibberellins have been traditionally restricted to the regulation of plant stature, seed germination, and flowering. Nonetheless, research in the last years has shown that these functions extend to many other relevant processes. In this review, the current knowledge on gibberellins homeostasis and mode of action is briefly outlined, while specific attention is focused on the many different responses in which gibberellins take part. Thus, those genes and proteins identified as being involved in the regulation of gibberellin responses in model and non-model species are highlighted. The present review aims to provide a comprehensive picture of the state-of-the-art perception of gibberellins molecular biology and its effects on plant development. This picture might be helpful to enhance our current understanding of gibberellins biology and provide the know-how for the development of more accurate research and breeding programs.

The unconventional prefoldin RPB5 interactor mediates the gravitropic response by modulating cytoskeleton organization and auxin transport in Arabidopsis

Gravity-induced root curvature involves the asymmetric distribution of the phytohormone auxin. This response depends on the concerted activities of the auxin transporters such as PIN-FORMED (PIN) proteins for auxin efflux and AUXIN RESISTANT 1 (AUX1) for auxin influx. However, how the auxin gradient is established remains elusive. Here we identified a new mutant with a short root, strong auxin distribution in the lateral root cap and an impaired gravitropic response. The causal gene encoded an Arabidopsis homolog of the human unconventional prefoldin RPB5 interactor (URI). AtURI interacted with prefoldin 2 (PFD2) and PFD6, two β-type PFD members that modulate actin and tubulin patterning in roots. The auxin reporter DR5_rev :GFP showed that asymmetric auxin redistribution after gravistimulation is disordered in aturi-1 root tips. Treatment with the endomembrane protein trafficking inhibitor brefeldin A indicated that recycling of the auxin transporter PIN2 is disrupted in aturi-1 roots as well as in pfd mutants. We propose that AtURI cooperates with PFDs to recycle PIN2 and modulate auxin distribution.

Rapid Quantification Method for Yield, Calorimetric Energy and Chlorophyll a Fluorescence Parameters in Nicotiana tabacum L. Using Vis-NIR-SWIR Hyperspectroscopy

High-throughput and large-scale data are part of a new era of plant remote sensing science. Quantification of the yield, energetic content, and chlorophyll a fluorescence (ChlF) remains laborious and is of great interest to physiologists and photobiologists. We propose a new method that is efficient and applicable for estimating photosynthetic performance and photosystem status using remote sensing hyperspectroscopy with visible, near-infrared and shortwave spectroscopy (Vis-NIR-SWIR) based on rapid multivariate partial least squares regression (PLSR) as a tool to estimate biomass production, calorimetric energy content and chlorophyll a fluorescence parameters. The results showed the presence of typical inflections associated with chemical and structural components present in plants, enabling us to obtain PLSR models with R2P and RPDP values greater than >0.82 and 3.33, respectively. The most important wavelengths were well distributed into 400 (violet), 440 (blue), 550 (green), 670 (red), 700−750 (red edge), 1330 (NIR), 1450 (SWIR), 1940 (SWIR) and 2200 (SWIR) nm operating ranges of the spectrum. Thus, we report a methodology to simultaneously determine fifteen attributes (i.e., yield (biomass), ΔH°area, ΔH°mass, Fv/Fm, Fv’/Fm’, ETR, NPQ, qP, qN, ΦPSII, P, D, SFI, PI(abs), D.F.) with high accuracy and precision and with excellent predictive capacity for most of them. These results are promising for plant physiology studies and will provide a better understanding of photosystem dynamics in tobacco plants when a large number of samples must be evaluated within a short period and with remote acquisition data.

Prefoldin Function in Cellular Protein Homeostasis and Human Diseases

Cellular functions are largely performed by proteins. Defects in the production, folding, or removal of proteins from the cell lead to perturbations in cellular functions that can result in pathological conditions for the organism. In cells, molecular chaperones are part of a network of surveillance mechanisms that maintains a functional proteome. Chaperones are involved in the folding of newly synthesized polypeptides and assist in refolding misfolded proteins and guiding proteins for degradation. The present review focuses on the molecular co-chaperone prefoldin. Its canonical function in eukaryotes involves the transfer of newly synthesized polypeptides of cytoskeletal proteins to the tailless complex polypeptide 1 ring complex (TRiC/CCT) chaperonin which assists folding of the polypeptide chain in an energy-dependent manner. The canonical function of prefoldin is well established, but recent research suggests its broader function in the maintenance of protein homeostasis under physiological and pathological conditions. Interestingly, non-canonical functions were identified for the prefoldin complex and also for its individual subunits. We discuss the latest findings on the prefoldin complex and its subunits in the regulation of transcription and proteasome-dependent protein degradation and its role in neurological diseases, cancer, viral infections and rare anomalies.

Influence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors

BACKGROUND

Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance.

RESULTS

In this study, the disruption of the prefoldin subunit 4 gene (KmPFD4) led to increased concentration of intracellular reactive oxygen species (ROS) and disturbed the assembly of actin and tubulin in the presence of inhibitors, resulting in reduced inhibitor tolerance. Nuclear localization of KmPFD4 indicated that it could regulate gene expression. Transcriptomic analysis showed that upregulated gene expression related to ROS elimination, ATP production, and NAD+ synthesis, which is a response to the presence of inhibitors, disappeared in KmPFD4-disrupted cells. Thus, KmPFD4 impacts inhibitor tolerance by maintaining integration of the cytoskeleton and directly or indirectly affecting the expression of genes in response to inhibitors. Finally, overexpression of KmPFD4 enhanced ethanol fermentation with a 46.27% improvement in productivity in presence of the inhibitors.

CONCLUSION

This study demonstrated that KmPFD4 plays a positive role in the inhibitor tolerance and can be applied for the development of inhibitor-tolerant platform strains.

A comprehensive analysis of prefoldins and their implication in cancer

Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.

A genetic approach reveals different modes of action of prefoldins

The prefoldin complex (PFDc) was identified in humans as a co-chaperone of the cytosolic chaperonin T-COMPLEX PROTEIN RING COMPLEX (TRiC)/CHAPERONIN CONTAINING TCP-1 (CCT). PFDc is conserved in eukaryotes and is composed of subunits PFD1-6, and PFDc-TRiC/CCT folds actin and tubulins. PFDs also participate in a wide range of cellular processes, both in the cytoplasm and in the nucleus, and their malfunction causes developmental alterations and disease in animals and altered growth and environmental responses in yeast and plants. Genetic analyses in yeast indicate that not all of their functions require the canonical complex. The lack of systematic genetic analyses in plants and animals, however, makes it difficult to discern whether PFDs participate in a process as the canonical complex or in alternative configurations, which is necessary to understand their mode of action. To tackle this question, and on the premise that the canonical complex cannot be formed if one subunit is missing, we generated an Arabidopsis (Arabidopsis thaliana) mutant deficient in the six PFDs and compared various growth and environmental responses with those of the individual mutants. In this way, we demonstrate that the PFDc is required for seed germination, to delay flowering, or to respond to high salt stress or low temperature, whereas at least two PFDs redundantly attenuate the response to osmotic stress. A coexpression analysis of differentially expressed genes in the sextuple mutant identified several transcription factors, including ABA INSENSITIVE 5 (ABI5) and PHYTOCHROME-INTERACTING FACTOR 4, acting downstream of PFDs. Furthermore, the transcriptomic analysis allowed assigning additional roles for PFDs, for instance, in response to higher temperature.

New insights into gibberellin signaling in regulating plant growth-metabolic coordination

The Green Revolution of the 1960s boosted cereal crop yields in part through widespread adoption of semi-dwarf plant varieties, many of which were later found to have mutations in either gibberellins (GAs) homeostasis or DELLA proteins. GA is essential for plant growth and developmental regulation and plays an important role in improving crop plant architecture for enhanced grain yield under high nitrogen conditions. A complex regulatory network governs the spatially and temporally controlled genes expression through integrative GA signaling in response to multiple endogenous and environmental cues. In this review, we summarize current advances in understanding the molecular mechanisms of DELLA-dependent and DELLA-independent GA signaling pathways and their contributions to plant developmental and metabolic adaptations to changes in nitrogen availability. The progress in molecular understanding of the plant growth-metabolic coordination will facilitate breeding strategies for future sustainable agriculture and a new Green Revolution.

An Anecdote on Prospective Protein Targets for Developing Novel Plant Growth Regulators

Phytohormones are the main regulatory molecules of core signalling networks associated with plant life cycle regulation. Manipulation of hormone signalling cascade enables the control over physiological traits of plant, which has major applications in field of agriculture and food sustainability. Hence, stable analogues of these hormones are long sought after and many of them are currently known, but the quest for more effective, stable and economically viable analogues is still going on. This search has been further strengthened by the identification of the components of signalling cascade such as receptors, downstream cascade members and transcription factors. Furthermore, many proteins of phytohormone cascades are available in crystallized forms. Such crystallized structures can provide the basis for identification of novel interacting compounds using in silico approach. Plenty of computational tools and bioinformatics software are now available that can aid in this process. Here, the metadata of all the major phytohormone signalling cascades are presented along with discussion on major protein-ligand interactions and protein components that may act as a potential target for manipulation of phytohormone signalling cascade. Furthermore, structural aspects of phytohormones and their known analogues are also discussed that can provide the basis for the synthesis of novel analogues.

GR24, A Synthetic Strigolactone Analog, and Light Affect the Organization of Cortical Microtubules in Arabidopsis Hypocotyl Cells

Strigolactones are plant hormones regulating cytoskeleton-mediated developmental events in roots, such as lateral root formation and elongation of root hairs and hypocotyls. The latter process was addressed herein by the exogenous application of a synthetic strigolactone, GR24, and an inhibitor of strigolactone biosynthesis, TIS108, on hypocotyls of wild-type Arabidopsis and a strigolactone signaling mutant max2-1 (more axillary growth 2-1). Owing to the interdependence between light and strigolactone signaling, the present work was extended to seedlings grown under a standard light/dark regime, or under continuous darkness. Given the essential role of the cortical microtubules in cell elongation, their organization and dynamics were characterized under the conditions of altered strigolactone signaling using fluorescence microscopy methods with different spatiotemporal capacities, such as confocal laser scanning microscopy (CLSM) and structured illumination microscopy (SIM). It was found that GR24-dependent inhibition of hypocotyl elongation correlated with changes in cortical microtubule organization and dynamics, observed in living wild-type and max2-1 seedlings stably expressing genetically encoded fluorescent molecular markers for microtubules. Quantitative assessment of microscopic datasets revealed that chemical and/or genetic manipulation of strigolactone signaling affected microtubule remodeling, especially under light conditions. The application of GR24 in dark conditions partially alleviated cytoskeletal rearrangement, suggesting a new mechanistic connection between cytoskeletal behavior and the light-dependence of strigolactone signaling.

Human prefoldin modulates co-transcriptional pre-mRNA splicing

Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

Interaction between the MtDELLA-MtGAF1 Complex and MtARF3 Mediates Transcriptional Control of MtGA3ox1 to Elaborate Leaf Margin Formation in Medicago truncatula

The molecular mechanisms underlying the diversity of leaf shapes have been of great interest to researchers. Leaf shape depends on the pattern of serrations and the degree of indentation of leaf margins. Multiple transcription factors and hormone signaling pathways are involved in this process. In this study, we characterized the developmental roles of SMALL AND SERRATED LEAF (SSL) by analyzing a recessive mutant in the model legume Medicago truncatula. An ortholog of Arabidopsis thaliana GA3-oxidase 1 (GA3ox1), MtGA3ox1/SSL, is required for GA biosynthesis. Loss of function in MtGA3ox1 results in the small plant and lateral organs. The prominent phenotype of the mtga3ox1 mutant is a more pronounced leaf margin, indicating the critical role of GA level in leaf margin formation. Moreover, 35S:MtDELLA2ΔDELLA and 35S:MtARF3 transgenic plants display leaves with a deeply wavy margin, which resembles those of mtga3ox1. Further investigations show that MtGA3ox1 is under the control of MtDELLA1/2/3-MtGAF1 complex-dependent feedback regulation. Further, MtARF3 behaves as a competitive inhibitor of MtDELLA2/3-MtGAF1 complexes to repress the expression of MtGA3ox1 indirectly. These findings suggest that GA feedback regulatory circuits play a fundamental role in leaf margin formation, in which the posttranslational interaction between transcription factors functions as an additional feature.

Evolution of DELLA function and signaling in land plants

DELLA proteins are master growth regulators that repress responses to a group of plant growth hormones called gibberellins (GAs). Manipulation of DELLA function and signaling was instrumental in the development of high‐yielding crop varieties that saved millions from starvation during the “Green Revolution.” Despite decades of extensive research, it is still unclear how DELLA function and signaling mechanisms evolved within the land plant lineage. Here, we review current knowledge on DELLA protein function with reference to structure, posttranslational modifications, downstream transcriptional targets, and protein–protein interactions. Furthermore, we discuss older and recent findings regarding the evolution of DELLA signaling within the land plant lineage, with an emphasis on bryophytes, and identify future avenues of research that would enable us to shed more light on the evolution of DELLA signaling. Unraveling how DELLA function and signaling mechanisms have evolved could enable us to engineer better crops in an attempt to contribute to mitigating the effects of global warming and achieving global food security.

DELLA genes first appeared in the common ancestor of land plants and underwent two major duplications during land plant evolution.

DELLAs repress gibberellin responses in vascular plants but their function in nonvascular plants remains elusive.

Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum

Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.

Prefoldin subunit 6 of Plasmodium falciparum binds merozoite surface protein-1 (MSP-1)

Malaria is a human disease caused by eukaryotic protozoan parasites of the Plasmodium genus. Plasmodium falciparum (Pf) causes the most lethal form of human malaria and is responsible for widespread mortality worldwide. Prefoldin is a heterohexameric molecular complex that binds and delivers unfolded proteins to chaperonin for correct folding. The prefoldin PFD6 is predicted to interact with merozoite surface protein‐1 (MSP‐1), a protein well known to play a pivotal role in erythrocyte binding and invasion by Plasmodium merozoites. We previously found that the P. falciparum (Pf) genome contains six prefoldin genes and a prefoldin‐like gene whose molecular functions are unidentified. Here, we analyzed the expression of PfPFD‐6 during the asexual blood stages of the parasite and investigated its interacting partners. PfPFD‐6 was found to be significantly expressed at the trophozoite and schizont stages. Pull‐down assays suggest PfPFD‐6 interacts with MSP‐1. In silico analysis suggested critical residues involved in the PfPFD‐6‐MSP‐1 interaction. Our data suggest PfPFD‐6 may play a role in stabilizing or trafficking MSP‐1.

Associations between phytohormones and cellulose biosynthesis in land plants

BACKGROUND

Phytohormones are small molecules that regulate virtually every aspect of plant growth and development, from basic cellular processes, such as cell expansion and division, to whole plant environmental responses. While the phytohormone levels and distribution thus tell the plant how to adjust itself, the corresponding growth alterations are actuated by cell wall modification/synthesis and internal turgor. Plant cell walls are complex polysaccharide-rich extracellular matrixes that surround all plant cells. Among the cell wall components, cellulose is typically the major polysaccharide, and is the load-bearing structure of the walls. Hence, the cell wall distribution of cellulose, which is synthesized by large Cellulose Synthase protein complexes at the cell surface, directs plant growth.

SCOPE

Here, we review the relationships between key phytohormone classes and cellulose deposition in plant systems. We present the core signalling pathways associated with each phytohormone and discuss the current understanding of how these signalling pathways impact cellulose biosynthesis with a particular focus on transcriptional and post-translational regulation. Because cortical microtubules underlying the plasma membrane significantly impact the trajectories of Cellulose Synthase Complexes, we also discuss the current understanding of how phytohormone signalling impacts the cortical microtubule array.

CONCLUSION

Given the importance of cellulose deposition and phytohormone signalling in plant growth and development, one would expect that there is substantial cross-talk between these processes; however, mechanisms for many of these relationships remain unclear and should be considered as the target of future studies.

Unlocking the mechanisms behind the formation of interlocking pavement cells

The leaf epidermal pavement cells with the puzzle-piece shape offer an attractive system for studying the mechanisms underpinning cell morphogenesis in a plant tissue. The formation of the interdigitated lobes and indentations in these interlocking cells relies on the integration of chemical and mechanical signals and cell-to-cell signals to establish interdigitated polar sites defining lobes and indentations. Recent computational and experimental studies have suggested new roles of cell walls, their interplay with mechanical signals, cell polarity signaling regulated by auxin and brassinosteriods, and the cytoskeleton in the regulation of pavement cell morphogenesis. This review summarizes the current state of knowledge on these regulatory mechanisms behind pavement cell morphogenesis in plants and discusses how they could be integrated spatiotemporally to generate the interdigitated polarity patterns and the interlocking shape in pavement cells.

Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8 complex through Hsp90 in Arabidopsis

Although originally identified as the components of the complex aiding the cytosolic chaperonin CCT in the folding of actins and tubulins in the cytosol, prefoldins (PFDs) are emerging as novel regulators influencing gene expression in the nucleus. Work conducted mainly in yeast and animals showed that PFDs act as transcriptional regulators and participate in the nuclear proteostasis. To investigate new functions of PFDs, we performed a co-expression analysis in Arabidopsis thaliana. Results revealed co-expression between PFD and the Sm-like (LSM) genes, which encode the LSM2–8 spliceosome core complex, in this model organism. Here, we show that PFDs interact with and are required to maintain adequate levels of the LSM2–8 complex. Our data indicate that levels of the LSM8 protein, which defines and confers the functional specificity of the complex, are reduced in pfd mutants and in response to the Hsp90 inhibitor geldanamycin. We provide biochemical evidence showing that LSM8 is a client of Hsp90 and that PFD4 mediates the interaction between both proteins. Consistent with our results and with the role of the LSM2–8 complex in splicing through the stabilization of the U6 snRNA, pfd mutants showed reduced levels of this snRNA and altered pre-mRNA splicing patterns.

The functions and mechanisms of prefoldin complex and prefoldin-subunits

The correct folding is a key process for a protein to acquire its functional structure and conformation. Prefoldin is a well-known chaperone protein that regulates the correct folding of proteins. Prefoldin plays a crucial role in the pathogenesis of common neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and Huntington's disease). The important role of prefoldin in emerging fields (such as nanoparticles, biomaterials) and tumors has attracted widespread attention. Also, each of the prefoldin subunits has different and independent functions from the prefoldin complex. It has abnormal expression in different tumors and plays an important role in tumorigenesis and development, especially c-Myc binding protein MM-1. MM-1 can inhibit the activity of c-Myc through various mechanisms to regulate tumor growth. Therefore, an in-depth analysis of the complex functions of prefoldin and their subunits is helpful to understand the mechanisms of protein misfolding and the pathogenesis of diseases caused by misfolded aggregation.

Origin and evolution of gibberellin signaling and metabolism in plants

Gibberellins modulate multiple aspects of plant behavior. The molecular mechanism by which these hormones are perceived and how this information is translated into transcriptional changes has been elucidated in vascular plants: gibberellins are perceived by the nuclear receptor GID1, which then interacts with the DELLA nuclear proteins and promote their degradation, resulting in the modification of the activity of transcription factors with which DELLAs interact physically. However, several important questions are still pending: how does a single molecule perform such a vast array of functions along plant development? What property do gibberellins add to plant behavior? A closer look at gibberellin action from an evolutionary perspective can help answer these questions. DELLA proteins are conserved in all land plants, and predate the emergence of a full gibberellin metabolic pathway and the GID1 receptor in the ancestor of vascular plants. The origin of gibberellin signaling is linked to the exaptation by GID1 of the N-terminal domain in DELLA, which already acted as a transcriptional coactivator domain in the ancestral DELLA proteins. At least the ability to control plant growth seems to be encoded already in the ancestral DELLA protein too, suggesting that gibberellins' functional diversity is the direct consequence of DELLA protein activity. Finally, comparative network analysis suggests that gibberellin signaling increases the coordination of transcriptional responses, providing a theoretical framework for the role of gibberellins in plant adaptation at the evolutionary scale, which further needs experimental testing.

All Roads Lead to Auxin: Post-translational Regulation of Auxin Transport by Multiple Hormonal Pathways

Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.

Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus

Prefoldin (PFD) is a group II chaperonin that is ubiquitously present in the eukaryotic kingdom. Six subunits (PFD1-6) form a jellyfish-like heterohexameric PFD complex and function in protein folding and cytoskeleton organization. However, little is known about its function in plant cell wall-related processes. Here, we report the functional characterization of a PFD gene from Populus deltoides, designated as PdPFD2.2. There are two copies of PFD2 in Populus, and PdPFD2.2 was ubiquitously expressed with high transcript abundance in the cambial region. PdPFD2.2 can physically interact with DELLA protein RGA1_8g, and its subcellular localization is affected by the interaction. In P. deltoides transgenic plants overexpressing PdPFD2.2, the lignin syringyl/guaiacyl ratio was increased, but cellulose content and crystallinity index were unchanged. In addition, the total released sugar (glucose and xylose) amounts were increased by 7.6% and 6.1%, respectively, in two transgenic lines. Transcriptomic and metabolomic analyses revealed that secondary metabolic pathways, including lignin and flavonoid biosynthesis, were affected by overexpressing PdPFD2.2. A total of eight hub transcription factors (TFs) were identified based on TF binding sites of differentially expressed genes in Populus transgenic plants overexpressing PdPFD2.2. In addition, several known cell wall-related TFs, such as MYB3, MYB4, MYB7, TT8 and XND1, were affected by overexpression of PdPFD2.2. These results suggest that overexpression of PdPFD2.2 can reduce biomass recalcitrance and PdPFD2.2 is a promising target for genetic engineering to improve feedstock characteristics to enhance biofuel conversion and reduce the cost of lignocellulosic biofuel production.

AtOFPs regulate cell elongation by modulating microtubule orientation via direct interaction with TONNEAU2

As a group of plant-specific proteins, OVATE family protein (OFP) members have been shown to function as transcriptional repressors and involve in plant growth regulation in Arabidopsis and rice. It has also been shown that OFPs can interact with TONNEAU1 Recruiting Motif (TRM) proteins to regulate tomato fruit shape. In this study, we show that mutant plants with knock-down expression of OFP1, OFP2, OFP3, and OFP5 exhibit longer hypocotyls and cotyledons due to enhanced cell elongation. Overexpression of OFPs disturb the arrangement of cortical microtubule arrays in pavement cells and promote abnormal pavement cell expansion perpendicular to the direction of petiole growth, resulting in the kidney-shaped cotyledons in transgenic plants. OFP2 and OFP5 interact directly with the microtubule regulating protein TONNEAU2 (TON2), and genetic analysis suggests TON2 is required for the function of OFPs. We also show that altering the expression of OFPs affects light and BR regulated microtubule reorientation. BR treatment reduce the protein accumulation of OFP2, suggesting OFP2 mediates BR regulated microtubule reorientation. Taken together, our study provides evidences showing that OFP family proteins negatively regulate cell expansion by modulating microtubule reorganization, which requires the function of TON2.

Gibberellin Enhances the Anisotropy of Cell Expansion in the Growth Zone of the Maize Leaf

Although plant organ shapes are defined by spatio-temporal variations of directional tissue expansion, this is a little characterized aspect of organ growth regulation. Although it is well known that the plant hormone gibberellin increases the leaf length/with ratio, its effects on cell expansion in the growing leaf are largely unknown. To understand how variations in rate and anisotropy of growth establish the typical monocotelydonous leaf shape, we studied the leaf growth zone of maize (Zea mays) with a kinematic analysis of cell expansion in the three directions of growth: proximo-distal, medio-lateral, and dorso-ventral. To determine the effect of gibberellin, we compared a gibberellin-deficient dwarf3 mutant and the overproducing UBI::GA20OX-1 line with their wild types. We found that, as expected, longitudinal growth was dominant throughout the growth zone. The highest degree of anisotropy occurred in the division zone, where relative growth rates in width and thickness were almost zero. Growth anisotropy was smaller in the elongation zone, due to higher lateral and dorso-ventral growth rates. Growth in all directions stopped at the same position. Gibberellin increased the size of the growth zone and the degree of growth anisotropy by stimulating longitudinal growth rates. Inversely, the duration of expansion was negatively affected, so that mature cell length was unaffected, while width and height of cells were reduced. Our study provides a detailed insight in the dynamics of growth anisotropy in the maize leaf and demonstrates that gibberellin specifically stimulates longitudinal growth rates throughout the growth zone.

Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana

Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.

Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana

Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.

Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

The thickening of plant organs is supported by secondary growth, a process by which new vascular tissues (xylem and phloem) are produced. Xylem is composed of several cell types, including xylary fibers, parenchyma and vessel elements. In Arabidopsis, it has been shown that fibers are promoted by the class-I KNOX gene KNAT1 and the plant hormones gibberellins, and are repressed by a small set of receptor-like kinases; however, we lack a mechanistic framework to integrate their relative contributions. Here, we show that DELLAs, negative elements of the gibberellin signaling pathway, physically interact with KNAT1 and impair its binding to KNAT1-binding sites. Our analysis also indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Moreover, the promotion by constitutive overexpression of KNAT1 of fiber formation and the expression of genes required for fiber differentiation were still reverted by DELLA accumulation, in agreement with post-translational regulation of KNAT1 by DELLA proteins. These results suggest that gibberellins enhance fiber development by promoting KNAT1 activity.

NPR1 mediates a novel regulatory pathway in cold acclimation by interacting with HSFA1 factors

NON-EXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1) is a master regulator of plant response to pathogens that confers immunity through a transcriptional cascade mediated by salicylic acid and TGA transcription factors. Little is known, however, about its implication in plant response to abiotic stress. Here, we provide genetic and molecular evidence supporting the fact that Arabidopsis NPR1 plays an essential role in cold acclimation by regulating cold-induced gene expression independently of salicylic acid and TGA factors. Our results demonstrate that, in response to low temperature, cytoplasmic NPR1 oligomers release monomers that translocate to the nucleus where they interact with heat shock transcription factor 1 (HSFA1) to promote the induction of HSFA1-regulated genes and cold acclimation. These findings unveil an unexpected function for NPR1 in plant response to low temperature, reveal a new regulatory pathway for cold acclimation mediated by NPR1 and HSFA1 factors, and place NPR1 as a central hub integrating cold and pathogen signalling for a better adaptation of plants to an ever-changing environment.

Ethylene-induced microtubule reorientation is essential for fast inhibition of root elongation in Arabidopsis

Microtubule reorientation is a long-standing observation that has been implicated in regulating the inhibitory effect of ethylene on axial elongation of plant cells. However, the signaling mechanism underlying ethylene-induced microtubule reorientation has remained elusive. Here, we reveal, by live confocal imaging and kinetic root elongation assays, that the time courses of ethylene-induced microtubule reorientation and root elongation inhibition are highly correlated, and that microtubule reorientation is required for the full responsiveness of root elongation to ethylene treatment. Our genetic analysis demonstrated that the effect of ethylene on microtubule orientation and root elongation is mainly transduced through the canonical linear ethylene signaling pathway. By using pharmacological and genetic analyses, we demonstrate further that the TIR1/AFBs-Aux/IAAs-ARFs auxin signaling pathway, but not the ABP1-ROP6-RIC1 auxin signaling branch, is essential for ethylene-induced microtubule reorientation and root elongation inhibition. Together, these findings offer evidence for the functional significance and elucidate the signaling mechanism for ethylene-induced microtubule reorientation in fast root elongation inhibition in Arabidopsis.

Chloroplast Biogenesis Controlled by DELLA-TOC159 Interaction in Early Plant Development

Chloroplast biogenesis, visible as greening, is the key to photoautotrophic growth in plants. At the organelle level, it requires the development of non-photosynthetic, color-less proplastids to photosynthetically active, green chloroplasts at early stages of plant development, i.e., in germinating seeds. This depends on the import of thousands of different preproteins into the developing organelle by the chloroplast protein import machinery [1]. The preprotein import receptor TOC159 is essential in the process, its mutation blocking chloroplast biogenesis and resulting in albino plants [2]. The molecular mechanisms controlling the onset of chloroplast biogenesis during germination are largely unknown. Germination depends on the plant hormone gibberellic acid (GA) and is repressed by DELLA when GA concentrations are low [3, 4]. Here, we show that DELLA negatively regulates TOC159 protein abundance under low GA. The direct DELLA-TOC159 interaction promotes TOC159 degradation by the ubiquitin/proteasome system (UPS). Moreover, the accumulation of photosynthesis-associated proteins destined for the chloroplast is downregulated posttranscriptionally. Analysis of a model import substrate indicates that it is targeted for removal by the UPS prior to import. Thus, under low GA, the UPS represses chloroplast biogenesis by a dual mechanism comprising the DELLA-dependent destruction of the import receptor TOC159, as well as that of its protein cargo. In conclusion, our data provide a molecular framework for the GA hormonal control of proplastid to chloroplast transition during early plant development.

Brassinosteroids regulate pavement cell growth by mediating BIN2-induced microtubule stabilization

Brassinosteroids (BRs), a group of plant steroid hormones, play important roles in regulating plant development. The cytoskeleton also affects key developmental processes and a deficiency in BR biosynthesis or signaling leads to abnormal phenotypes similar to those of microtubule-defective mutants. However, how BRs regulate microtubule and cell morphology remains unknown. Here, using liquid chromatography-tandem mass spectrometry, we identified tubulin proteins that interact with Arabidopsis BRASSINOSTEROID INSENSITIVE2 (BIN2), a negative regulator of BR responses in plants. In vitro and in vivo pull-down assays confirmed that BIN2 interacts with tubulin proteins. High-speed co-sedimentation assays demonstrated that BIN2 also binds microtubules. The Arabidopsis genome also encodes two BIN2 homologs, BIN2-LIKE 1 (BIL1) and BIL2, which function redundantly with BIN2. In the bin2-3 bil1 bil2 triple mutant, cortical microtubules were more sensitive to treatment with the microtubule-disrupting drug oryzalin than in wild-type, whereas in the BIN2 gain-of-function mutant bin2-1, cortical microtubules were insensitive to oryzalin treatment. These results provide important insight into how BR regulates plant pavement cell and leaf growth by mediating the stabilization of microtubules by BIN2.

Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane

This study identifies and outlines a nontranscriptional branch of the canonical GA signaling pathway that redirects protein traffic from the vacuolar degradation route to the plasma membrane. As a result, the amount of receptors and transporters, such as PIN transporters for the plant hormone auxin, is functionally regulated at the cell surface. The identified branching occurs at the level of DELLA proteins that, besides transcriptional regulation, also target the microtubule (MT) network and protein trafficking. In this work, we provide multiple lines of evidence that DELLA proteins act via their interacting partners Prefoldins and that a downstream MT/CLASP1 module regulates the activity of the retromer complex that directs protein trafficking at the intersection of the vacuolar and recycling pathways.

The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.

Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria

Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.

Functional Contributions of Prefoldin to Gene Expression

Prefoldin is a co-chaperone that evolutionarily originates in archaea, is universally present in all eukaryotes and acts as a co-chaperone by facilitating the supply of unfolded or partially folded substrates to class II chaperonins. Eukaryotic prefoldin is known mainly for its functional relevance in the cytoplasmic folding of actin and tubulin monomers during cytoskeleton assembly. However, the role of prefoldin in chaperonin-mediated folding is not restricted to cytoskeleton components, but extends to both the assembly of other cytoplasmic complexes and the maintenance of functional proteins by avoiding protein aggregation and facilitating proteolytic degradation. Evolution has favoured the diversification of prefoldin subunits, and has allowed the so-called prefoldin-like complex, with specialised functions, to appear. Subunits of both canonical and prefoldin-like complexes have also been found in the nucleus of yeast and metazoan cells, where they have been functionally connected with different gene expression steps. Plant prefoldin has also been detected in the nucleus and is physically associated with a gene regulator. Here we summarise information available on the functional involvement of prefoldin in gene expression, and discuss the implications of these results for the relationship between prefoldin structure and function.

Structure and Function of the Cochaperone Prefoldin

Molecular chaperones are key players in proteostasis, the balance between protein synthesis, folding, assembly and degradation. They are helped by a plethora of cofactors termed cochaperones, which direct chaperones towards any of these different, sometime opposite pathways. One of these is prefoldin (PFD), present in eukaryotes and in archaea, a heterohexamer whose best known role is the assistance to group II chaperonins (the Hsp60 chaperones found in archaea and the eukaryotic cytosolic) in the folding of proteins in the cytosol, in particular cytoskeletal proteins. However, over the last years it has become evident a more complex role for this cochaperone, as it can adopt different oligomeric structures, form complexes with other proteins and be involved in many other processes, both in the cytosol and in the nucleus, different from folding. This review intends to describe the structure and the many functions of this interesting macromolecular complex.

Phenotypic, Hormonal, and Genomic Variation Among Vitis vinifera Clones With Different Cluster Compactness and Reproductive Performance

Previous studies showed that the number of berries is a major component of the compactness level of the grapevine clusters. Variation in number of fruits is regulated by events occurring in the fruitset, but also before during the flower formation and pollination, through factors like the initial number of flowers or the gametic viability. Therefore, the identification of the genetic bases of this variation would provide an invaluable knowledge of the grapevine reproductive development and useful tools for managing yield and cluster compactness. We performed the phenotyping of four clones (two compact and two loose clones) of the Tempranillo cultivar with reproducible different levels of cluster compactness over seasons. Measures of reproductive performance included flower number per inflorescence, berry number per cluster, fruitset, coulure, and millerandage indices. Besides, their levels of several hormones during the inflorescence and flower development were determined, and their transcriptomes were evaluated at critical time points (just before the start and at the end of flowering). For some key reproductive traits, like number of berries per cluster and number of seeds per berry, clones bearing loose clusters showed differences with the compact clones and also differed from each other, indicating that each one follows different paths to produce loose clusters. Variation between clones was observed for abscisic acid and gibberellins levels at particular development stages, and differences in GAs could be related to phenotypic differences. Likewise, various changes between clones were found at the transcriptomic level, mostly just before the start of flowering. Several of the differentially expressed genes between one of the loose clones and the compact clones are known to be over-expressed in pollen, and many of them were related to cell wall modification processes or to the phenylpropanoids metabolism. We also found polymorphisms between clones in candidate genes that could be directly involved in the variation of the compactness level.

Cold-Induced Male Meiotic Restitution in Arabidopsis thaliana Is Not Mediated by GA-DELLA Signaling

Short periods of cold stress induce male meiotic restitution and diploid pollen formation in Arabidopsis thaliana by specifically interfering with male meiotic cytokinesis. Similar alterations in male meiotic cell division and gametophytic ploidy stability occur when gibberellic acid (GA) signaling is perturbed in developing anthers. In this study, we found that exogenous application of GA primarily induces second division restitution (SDR)-type pollen in Arabidopsis, similar to what cold does. Driven by the close similarity in cellular defects, we tested the hypothesis that cold-induced meiotic restitution is mediated by GA-DELLA signaling. Using a combination of chemical, genetic and cytological approaches, however, we found that both exogenously and endogenously altered GA signaling do not affect the cold sensitivity of male meiotic cytokinesis. Moreover, in vivo localization study using a GFP-tagged version of RGA protein revealed that cold does not affect the expression pattern and abundance of DELLA in Arabidopsis anthers at tetrad stage. Expression study found that transcript of RGA appears enhanced in cold-stressed young flower buds. Since our previous work demonstrated that loss of function of DELLA causes irregular male meiotic cytokinesis, we here conclude that cold-induced meiotic restitution is not mediated by DELLA-dependent GA signaling.

Increased Gibberellins and Light Levels Promotes Cell Wall Thickness and Enhance Lignin Deposition in Xylem Fibers

Light intensity and hormones (gibberellins; GAs) alter plant growth and development. A fine regulation triggered by light and GAs induces changes in stem cell walls (CW). Cross-talk between light-stimulated and GAs-induced processes as well as the phenolic compounds metabolism leads to modifications in lignin formation and deposition on cell walls. How these factors (light and GAs) promote changes in lignin content and composition. In addition, structural changes were evaluated in the stem anatomy of tobacco plants. GA₃ was sprayed onto the leaves and paclobutrazol (PAC), a GA biosynthesis inhibitor, via soil, at different irradiance levels. Fluorescence microscopy techniques were applied to detect lignin, and electron microscopy (SEM and TEM) was used to obtain details on cell wall structure. Furthermore, determination of total lignin and monomer contents were analyzed. Both light and GAs induces increased lignin content and CW thickening as well as greater number of fiber-like cells but not tracheary elements. The assays demonstrate that light exerts a role in lignification under GA₃ supplementation. In addition, the existence of an exclusive response mechanism to light was detected, that GAs are not able to replace.

Exploiting DELLA Signaling in Cereals

The spectacular yield increases in rice and wheat during the green revolution were partly realized by reduced gibberellin (GA) synthesis or sensitivity, both causing the accumulation of DELLA proteins. Although insights into the regulation of plant growth and development by DELLA proteins advanced rapidly in arabidopsis (Arabidopsis thaliana), DELLA-mediated regulation of downstream responses in cereals has received little attention to date. Furthermore, translating this research from arabidopsis to cereals is challenging given their different growth patterns and our phylogenetic analysis which reveals that DELLA-related DGLLA proteins exist in cereals but not in arabidopsis. Therefore, understanding the molecular basis of DELLA function in cereals holds great potential to improve yield. In this review, we propose to extend the focus of DELLA functional research to cereals, and highlight the appropriate tools that are now available to achieve this.

Prefoldins Negatively Regulate Cold Acclimation in Arabidopsis thaliana by Promoting Nuclear Proteasome-Mediated HY5 Degradation

The process of cold acclimation is an important adaptive response whereby many plants from temperate regions increase their freezing tolerance after being exposed to low non-freezing temperatures. The correct development of this response relies on proper accumulation of a number of transcription factors that regulate expression patterns of cold-responsive genes. Multiple studies have revealed a variety of molecular mechanisms involved in promoting the accumulation of these transcription factors. Interestingly, however, the mechanisms implicated in controlling such accumulation to ensure their adequate levels remain largely unknown. In this work, we demonstrate that prefoldins (PFDs) control the levels of HY5, an Arabidopsis transcription factor with a key role in cold acclimation by activating anthocyanin biosynthesis, in response to low temperature. Our results show that, under cold conditions, PFDs accumulate into the nucleus through a DELLA-dependent mechanism, where they interact with HY5, triggering its ubiquitination and subsequent degradation. The degradation of HY5 would result, in turn, in anthocyanin biosynthesis attenuation, ensuring the accurate development of cold acclimation. These findings uncover an unanticipated nuclear function for PFDs in plant responses to abiotic stresses.

Overgrowth (Della) mutants of wheat: development, growth and yield of intragenic suppressors of the Rht-B1c dwarfing gene

A suppressor screen using the dwarf Rht-B1c Della mutant of wheat (Triticum aestivum L.) led to the isolation of overgrowth mutants, which retained the original dwarfing gene but grew at a faster rate because of a new mutation elsewhere in that gene. Forty-six alleles were identified, which included amino acid substitutions, premature stop codons, and splice site alterations. The sites of amino acid substitution were primarily localised around conserved motifs in the DELLA protein, and these mutants showed a wide range in their extent of growth recovery (dwarf, semidwarf, tall). Detailed growth comparisons were made on a wide height range of backcrossed overgrowth alleles, comparing stem and spike growth, leaf size, tillering, phenological development, coleoptile length, grain dormancy and grain yield. There were large and reproducible differences between alleles for some traits, whereas others were largely unaffected or varied with growth conditions. Some of the overgrowth alleles offer promise as alternatives to the Rht-B1b and Rht-D1b dwarfing genes, allowing a wider range of height control, improved grain dormancy and equivalent grain yield. The collection of mutants will also be valuable as a resource to study the effect of height on different physiological or agronomic traits, and in elucidating DELLA protein function.

Agronomic performance of Populus deltoides trees engineered for biofuel production

BACKGROUND

One of the major barriers to the development of lignocellulosic feedstocks is the recalcitrance of plant cell walls to deconstruction and saccharification. Recalcitrance can be reduced by targeting genes involved in cell wall biosynthesis, but this can have unintended consequences that compromise the agronomic performance of the trees under field conditions. Here we report the results of a field trial of fourteen distinct transgenic Populus deltoides lines that had previously demonstrated reduced recalcitrance without yield penalties under greenhouse conditions.

RESULTS

Survival and productivity of the trial were excellent in the first year, and there was little evidence for reduced performance of the transgenic lines with modified target gene expression. Surprisingly, the most striking phenotypic effects in this trial were for two empty-vector control lines that had modified bud set and bud flush. This is most likely due to somaclonal variation or insertional mutagenesis. Traits related to yield, crown architecture, herbivory, pathogen response, and frost damage showed few significant differences between target gene transgenics and empty vector controls. However, there were a few interesting exceptions. Lines overexpressing the DUF231 gene, a putative O-acetyltransferase, showed early bud flush and marginally increased height growth. Lines overexpressing the DUF266 gene, a putative glycosyltransferase, had significantly decreased stem internode length and slightly higher volume index. Finally, lines overexpressing the PFD2 gene, a putative member of the prefoldin complex, had a slightly reduced volume index.

CONCLUSIONS

This field trial demonstrates that these cell wall modifications, which decreased cell wall recalcitrance under laboratory conditions, did not seriously compromise first-year performance in the field, despite substantial challenges, including an outbreak of a stem boring insect (Gypsonoma haimbachiana), attack by a leaf rust pathogen (Melampsora spp.), and a late frost event. This bodes well for the potential utility of these lines as advanced biofuels feedstocks.