The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation

Modulation of the Arabidopsis Starch Metabolic Network by the Cytosolic Acetyl-CoA Pathway in the Context of the Diurnal Illumination Cycle

The starch metabolic network was investigated in relation to other metabolic processes by examining a mutant with altered single-gene expression of ATP citrate lyase (ACL), an enzyme responsible for generating cytosolic acetyl-CoA pool from citrate. Previous research has shown that transgenic antisense plants with reduced ACL activity accumulate abnormally enlarged starch granules. In this study, we explored the underlying molecular mechanisms linking cytosolic acetyl-CoA generation and starch metabolism under short-day photoperiods. We performed transcriptome and quantification of starch accumulation in the leaves of wild-type and antisense seedlings with reduced ACL activity. The antisense-ACLA mutant accumulated more starch than the wild type under short-day conditions. Zymogram analyses were conducted to compare the activities of starch-metabolizing enzymes with transcriptomic changes in the seedling. Differential expression between wild-type and antisense-ACLA plants was detected in genes implicated in starch and acetyl-CoA metabolism, and cell wall metabolism. These analyses revealed a strong correlation between the transcript levels of genes responsible for starch synthesis and degradation, reflecting coordinated regulation at the transcriptomic level. Furthermore, our data provide novel insights into the regulatory links between cytosolic acetyl-CoA metabolism and starch metabolic pathways.

Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.)

BACKGROUND

BRASSINAZOLE-RESISTANT (BZR) is a class of specific transcription factor (TFs) involved in brassinosteroid (BR) signal transduction. The regulatory mechanism of target genes mediated by BZR has become one of the key research areas in plant BR signaling networks. However, the functions of the BZR gene family in cucumber have not been well characterized.

RESULTS

In this study, six CsBZR gene family members were identified by analyzing the conserved domain of BES1 N in the cucumber genome. The size of CsBZR proteins ranges from 311 to 698 amino acids and are mostly located in the nucleus. Phylogenetic analysis divided CsBZR genes into three subgroups. The gene structure and conserved domain showed that the BZR genes domain in the same group was conserved. Cis-acting element analysis showed that cucumber BZR genes were mainly involved in hormone response, stress response and growth regulation. The qRT-PCR results also confirmed CsBZR response to hormones and abiotic stress.

CONCLUSION

Collectively, the CsBZR gene is involved in regulating cucumber growth and development, particularly in hormone response and response to abiotic stress. These findings provide valuable information for understanding the structure and expression patterns of BZR genes.

Maize β-amylase7 encodes two proteins using alternative transcriptional start sites: nuclear BAM7 and plastidic BAM2

An unusual β-amylase7 (BAM7) gene in some angiosperms, including grasses such as maize (Zea mays), appears to encode two functionally distinct proteins; a nuclear-localized transcription factor (BAM7) and a plastid-localized starch hydrolase (BAM2). In Arabidopsis (Arabidopsis thaliana), these two proteins are encoded by separate genes on different chromosomes but their physiological functions are not well established. Using the maize BAM7 gene as a model, we detected two populations of transcripts by 5'-RACE that encode the predicted proteins. The two transcripts are apparently synthesized independently using separate core promoters about 1 kb apart, the second of which is located in the first intron of the full-length gene. The N-terminus of the shorter protein, ZmBAM7-S, begins near the 3' end of the first intron of ZmBAM7-L and starts with a predicted chloroplast transit peptide. We previously showed that ZmBAM7-S is catalytically active with properties like those of AtBAM2. Here, we report that ZmBAM7-S targets green fluorescent protein to plastids. The transcript encoding the longer protein, ZmBAM7-L, encodes an additional DNA-binding domain containing a functional nuclear localization signal. This putative dual-function gene originated at least 400 Mya, prior to the emergence of ferns, and has persisted in some angiosperms that lack a separate BAM2 gene. It appears to have been duplicated and subfunctionalized in at least four lineages of land plants, resulting in two genes resembling Arabidopsis BAM2 and BAM7. Targeting of two products from a single gene to different subcellular locations is not uncommon in plants, but it is unusual when they are predicted to serve completely different functions in the two locations.

Genome-wide characterization and expression analysis of α-amylase and β-amylase genes underlying drought tolerance in cassava

BACKGROUND

Starch hydrolysates are energy sources for plant growth and development, regulate osmotic pressure and transmit signals in response to both biological and abiotic stresses. The α-amylase (AMY) and the β-amylase (BAM) are important enzymes that catalyze the hydrolysis of plant starch. Cassava (Manihot esculenta Crantz) is treated as one of the most drought-tolerant crops. However, the mechanisms of how AMY and BAM respond to drought in cassava are still unknown.

RESULTS

Six MeAMY genes and ten MeBAM genes were identified and characterized in the cassava genome. Both MeAMY and MeBAM gene families contain four genes with alternative splicing. Tandem and fragment replications play important roles in the amplification of MeAMY and MeBAM genes. Both MeBAM5 and MeBAM10 have a BZR1/BES1 domain at the N-terminus, which may have transcription factor functions. The promoter regions of MeAMY and MeBAM genes contain a large number of cis-acting elements related to abiotic stress. MeAMY1, MeAMY2, MeAMY5, and MeBAM3 are proven as critical genes in response to drought stress according to their expression patterns under drought. The starch content, soluble sugar content, and amylase activity were significantly altered in cassava under different levels of drought stress.

CONCLUSIONS

These results provide fundamental knowledge for not only further exploring the starch metabolism functions of cassava under drought stress but also offering new perspectives for understanding the mechanism of how cassava survives and develops under drought.

BES1/BZR1 Family Transcription Factors Regulate Plant Development via Brassinosteroid-Dependent and Independent Pathways

The BES1/BZR1 family is a plant-specific small group of transcription factors possessing a non-canonical bHLH domain. Genetic and biochemical analyses within the last two decades have demonstrated that members of this family are key transcription factors in regulating the expression of brassinosteroid (BR) response genes. Several recent genetic and evolutionary studies, however, have clearly indicated that the BES1/BZR1 family transcription factors also function in regulating several aspects of plant development via BR-independent pathways, suggesting they are not BR specific. In this review, we summarize our current understanding of this family of transcription factors, the mechanisms regulating their activities, DNA binding motifs, and target genes. We selectively discuss a number of their biological functions via BR-dependent and particularly independent pathways, which were recently revealed by loss-of-function genetic analyses. We also highlight a few possible future directions.

Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation

Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α)₈ barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.

Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.)

Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree.

The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2

Starch accumulates in the plastids of green plant tissues during the day to provide carbon for metabolism at night. Starch hydrolysis is catalyzed by members of the β-amylase (BAM) family, which in Arabidopsis thaliana (At) includes nine structurally and functionally diverse members. One of these enzymes, AtBAM2, is a plastid-localized enzyme that is unique among characterized β-amylases since it is tetrameric and exhibits sigmoidal kinetics. Sequence alignments show that the BAM domains of AtBAM7, a catalytically inactive, nuclear-localized transcription factor with an N-terminal DNA-binding domain, and AtBAM2 are more closely related to each other than they are to any other AtBAM. Since the BAM2 gene is found in more ancient lineages, it was hypothesized that the BAM7 gene evolved from BAM2. However, analysis of the genomes of 48 flowering plants revealed 12 species that appear to possess a BAM7 gene but lack a BAM2 gene. Upon closer inspection, these BAM7 proteins have a greater percent identity to AtBAM2 than to AtBAM7, and they share all of the AtBAM2 functional residues that BAM7 proteins normally lack. It is hypothesized that these genes may encode BAM2-like proteins although they are currently annotated as BAM7-like genes. To test this hypothesis, a cDNA for the short form of corn BAM7 (ZmBAM7-S) was designed for expression in Escherichia coli. Small-angle X-ray scattering data indicate that ZmBAM7-S has a tetrameric solution structure that is more similar to that of AtBAM2 than to that of AtBAM1. In addition, partially purified ZmBAM7-S is catalytically active and exhibits sigmoidal kinetics. Together, these data suggest that some BAM7 genes may encode a functional BAM2. Exploring and understanding the β-amylase gene structure could have an impact on the current annotation of genes.

BETA-AMYLASE9 is a plastidial nonenzymatic regulator of leaf starch degradation

β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, a process that buffers the availability of photosynthetically fixed carbon over the diel cycle to maintain energy levels and plant growth at night. However, during vascular plant evolution, the BAM gene family diversified, giving rise to isoforms with different compartmentation and biological activities. Here, we characterized BETA-AMYLASE 9 (BAM9) of Arabidopsis (Arabidopsis thaliana). Among the BAMs, BAM9 is most closely related to BAM4 but is more widely conserved in plants. BAM9 and BAM4 share features including their plastidial localization and lack of measurable α-1,4-glucan hydrolyzing capacity. BAM4 is a regulator of starch degradation, and bam4 mutants display a starch-excess phenotype. Although bam9 single mutants resemble the wild-type (WT), genetic experiments reveal that the loss of BAM9 markedly enhances the starch-excess phenotypes of mutants already impaired in starch degradation. Thus, BAM9 also regulates starch breakdown, but in a different way. Interestingly, BAM9 gene expression is responsive to several environmental changes, while that of BAM4 is not. Furthermore, overexpression of BAM9 in the WT reduced leaf starch content, but overexpression in bam4 failed to complement fully that mutant's starch-excess phenotype, suggesting that BAM9 and BAM4 are not redundant. We propose that BAM9 activates starch degradation, helping to manage carbohydrate availability in response to fluctuations in environmental conditions. As such, BAM9 represents an interesting gene target to explore in crop species.

Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.

Genome-Wide Identification and Expression Analysis of the β-Amylase Gene Family in Chenopodium quinoa

β-Amylase (BAM) is an important starch hydrolase, playing a role in a variety of plant growth and development processes. In this study, 22 BAM gene family members (GFMs) were identified in quinoa (Chenopodium quinoa), an ancient crop gaining modern consumer acceptance because of its nutritional qualities. The genetic structure, phylogenetic and evolutionary relationships, and expression patterns of CqBAM GFMs in different tissues, were analyzed. Phylogenetic analyses assigned the CqBAMs, AtBAMs, and OsBAMs into four clades. The CqBAM gene family had expanded due to segmental duplication. RNA-seq analysis revealed expression of the duplicated pairs to be similar, with the expression of CqBAM GFM pairs showing a degree of tissue specificity that was confirmed by reverse transcription quantitative PCR (RT-qPCR). Several CqBAM GFMs were also responsive to abiotic stresses in shoots and/or roots. In conclusion, the BAM gene family in quinoa was identified and systematically analyzed using bioinformatics and experimental methods. These results will help to elucidate the evolutionary relationship and biological functions of the BAM gene family in quinoa.

Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence

Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding conditions. The phenotypic deviation associated with the tolerance to submergence at the germination stage could be due to natural variation. However, the molecular basis of this variation is still largely unknown. A comprehensive understanding of gene regulation of different genotypes that have diverse rates of coleoptile elongation can provide significant insights into improved rice varieties. To do so, publicly available transcriptome data of five rice genotypes, which have different lengths of coleoptile elongation under submergence tolerance, were analyzed. The aim was to identify the correlation between promoter architecture, associated with transcriptional and hormonal regulation, in diverse genotype groups of rice that have different rates of coleoptile elongation. This was achieved by identifying the putative cis-elements present in the promoter sequences of genes upregulated in each group of genotypes (tolerant, highly tolerant, and extremely tolerant genotypes). Promoter analysis identified transcription factors (TFs) that are common and unique to each group of genotypes. The candidate TFs that are common in all genotypes are MYB, bZIP, AP2/ERF, ARF, WRKY, ZnF, MADS-box, NAC, AS2, DOF, E2F, ARR-B, and HSF. However, the highly tolerant genotypes interestingly possess binding sites associated with HY5 (bZIP), GBF3, GBF4 and GBF5 (bZIP), DPBF-3 (bZIP), ABF2, ABI5, bHLH, and BES/BZR, in addition to the common TFs. Besides, the extremely tolerant genotypes possess binding sites associated with bHLH TFs such as BEE2, BIM1, BIM3, BM8 and BAM8, and ABF1, in addition to the TFs identified in the tolerant and highly tolerant genotypes. The transcriptional regulation of these TFs could be linked to phenotypic variation in coleoptile elongation in response to submergence tolerance. Moreover, the results indicate a cross-talk between the key TFs and phytohormones such as gibberellic acid, abscisic acid, ethylene, auxin, jasmonic acid, and brassinosteroids, for an altered transcriptional regulation leading to differences in germination and coleoptile elongation under submergence. The information derived from the current in silico analysis can potentially assist in developing new rice breeding targets for direct seeding.

Evolutionary innovations in starch metabolism

The traditional view of starch metabolism has focused on the multiplicity of enzymes and enzyme isoforms contributing to the production of the constituent polymers, amylopectin and amylose. However, knowledge of these enzymes has not provided a full insight into many aspects of starch biosynthesis. This enzyme-centered view has recently been augmented by the discovery and characterization of novel proteins with proposed regulatory, scaffolding, and interactive roles. This begins to reveal an unprecedented level of complexity beyond mere glucan biosynthesis, enabling us to envisage how starch granules are initiated and grow into specific forms, allowing it to serve biological roles beyond just carbohydrate storage. This review focuses on very recent findings in this vibrant field, highlighting the evolutionary novelty.

Maize ZmBES1/BZR1-5 Decreases ABA Sensitivity and Confers Tolerance to Osmotic Stress in Transgenic Arabidopsis

The BRI1-EMS suppressor 1 (BES1)/brassinazole-resistant 1 (BZR1) transcription factors, key components in the brassinosteroid signaling pathway, play pivotal roles in plant growth and development. However, the function of BES1/BZR1 in crops during stress response remains poorly understood. In the present study, we characterized ZmBES1/BZR1-5 from maize, which was localized to the nucleus and was responsive to abscisic acid (ABA), salt and drought stresses. Heterologous expression of ZmBES1/BZR1-5 in transgenic Arabidopsis resulted in decreased ABA sensitivity, facilitated shoot growth and root development, and enhanced salt and drought tolerance with lower malondialdehyde (MDA) content and relative electrolyte leakage (REL) under osmotic stress. The RNA sequencing (RNA-seq) analysis revealed that 84 common differentially expressed genes (DEGs) were regulated by ZmBES1/BZR1-5 in transgenic Arabidopsis. Subsequently, gene ontology and KEGG pathway enrichment analyses showed that the DEGs were enriched in response to stress, secondary metabolism and metabolic pathways. Furthermore, 30 DEGs were assigned to stress response and possessed 2-15 E-box elements in their promoters, which could be potentially recognized and bound by ZmBES1/BZR1-5. Taken together, our results reveal that the ZmBES1/BZR1-5 transcription factor positively regulates salt and drought tolerance by binding to E-box to induce the expression of downstream stress-related genes. Therefore, our study contributes to the better understanding of BES1/BZR1 function in the stress response of plants.

Involvement of five catalytically active Arabidopsis β-amylases in leaf starch metabolism and plant growth

Starch degradation in chloroplasts requires β-amylase (BAM) activity, but in Arabidopsis, there are nine BAM proteins, five of which are thought to be catalytic. Although single-gene knockouts revealed the necessity of BAM3 for starch degradation, contributions of other BAMs are poorly understood. Moreover, it is not possible to detect the contribution of individual BAMs in plants containing multiple active BAMs. Therefore, we constructed a set of five quadruple mutants each expressing only one catalytically active BAM, and a quintuple mutant missing all of these BAMs (B-Null). Using these mutants, we assessed the influence of each individual BAM on plant growth and on leaf starch degradation. Both BAM1 and BAM3 alone support wild-type (WT) levels of growth. BAM3 alone is sufficient to degrade leaf starch completely whereas BAM1 alone can only partially degrade leaf starch. In contrast, BAM2, BAM5, and BAM6 have no detectable effect on starch degradation or plant growth, being comparable with the B-Null plants. B-Null plant extracts contained no measurable amylase activity, whereas BAM3 and BAM1 contributed about 70% and 14% of the WT activity, respectively. BAM2 activity was low but detectable and BAM6 contributed no measurable activity. Interestingly, activity of BAM1 and BAM3 in the mutants varied little developmentally or diurnally, and did not increase appreciably in response to osmotic or cold stress. With these genetic lines, we now have new opportunities to investigate members of this diverse gene family.

Emerging strategies for the identification of protein-metabolite interactions

Interactions between biological molecules enable life. The significance of a cell-wide understanding of molecular complexes is thus obvious. In comparison to protein-protein interactions, protein-metabolite interactions remain under-studied. However, this has been gradually changing due to technological progress. Here, we focus on the interactions between ligands and receptors, the triggers of signalling events. While the number of small molecules with proven or proposed signalling roles is rapidly growing, most of their protein receptors remain unknown. Conversely, there are numerous signalling proteins with predicted ligand-binding domains for which the identities of the metabolite counterparts remain elusive. Here, we discuss the current biochemical strategies for identifying protein-metabolite interactions and how they can be used to characterize known metabolite regulators and identify novel ones.

LIKE SEX4 1 Acts as a β-Amylase-Binding Scaffold on Starch Granules during Starch Degradation

In Arabidopsis (Arabidopsis thaliana) leaves, starch is synthesized during the day and degraded at night to fuel growth and metabolism. Starch is degraded primarily by β-amylases, liberating maltose, but this activity is preceded by glucan phosphorylation and is accompanied by dephosphorylation. A glucan phosphatase family member, LIKE SEX4 1 (LSF1), binds starch and is required for normal starch degradation, but its exact role is unclear. Here, we show that LSF1 does not dephosphorylate glucans. The recombinant dual specificity phosphatase (DSP) domain of LSF1 had no detectable phosphatase activity. Furthermore, a variant of LSF1 mutated in the catalytic cysteine of the DSP domain complemented the starch-excess phenotype of the lsf1 mutant. By contrast, a variant of LSF1 with mutations in the carbohydrate binding module did not complement lsf1 Thus, glucan binding, but not phosphatase activity, is required for the function of LSF1 in starch degradation. LSF1 interacts with the β-amylases BAM1 and BAM3, and the BAM1-LSF1 complex shows amylolytic but not glucan phosphatase activity. Nighttime maltose levels are reduced in lsf1, and genetic analysis indicated that the starch-excess phenotype of lsf1 is dependent on bam1 and bam3 We propose that LSF1 binds β-amylases at the starch granule surface, thereby promoting starch degradation.

Expression patterns of alpha-amylase and beta-amylase genes provide insights into the molecular mechanisms underlying the responses of tea plants (Camellia sinensis) to stress and postharvest processing treatments

The alpha-amylase and beta-amylase genes have been identified from tea plants, and their bioinformatic characteristics and expression patterns provide a foundation for further studies to elucidate their biological functions. Alpha-amylase (AMY)- and beta-amylase (BAM)-mediated starch degradation plays central roles in carbohydrate metabolism and participates extensively in the regulation of a wide range of biological processes, including growth, development and stress response. However, the AMY and BAM genes in tea plants (Camellia sinensis) are poorly understood, and the biological functions of these genes remain to be elucidated. In this study, three CsAMY and nine CsBAM genes from tea plants were identified based on genomic and transcriptomic database analyses, and the genes were subjected to comprehensive bioinformatic characterization. Phylogenetic analysis showed that the CsAMY proteins could be clustered into three different subfamilies, and nine CsBAM proteins could be classified into four groups. Putative catalytically active proteins were identified based on multiple sequence alignments, and the tertiary structures of these proteins were analyzed. Cis-element analysis indicated that CsAMY and CsBAM were extensively involved in tea plant growth, development and stress response. In addition, the CsAMY and CsBAM genes were differentially expressed in various tissues and were regulated by stress treatments (e.g., ABA, cold, drought and salt stress), and the expression patterns of these genes were associated with the postharvest withering and rotation processes. Taken together, our results will enhance the understanding of the roles of the CsAMY and CsBAM gene families in the growth, development and stress response of tea plants and of the potential functions of these genes in determining tea quality during the postharvest processing of tea leaves.

The evolution of functional complexity within the β-amylase gene family in land plants

Background

β-Amylases (BAMs) are a multigene family of glucan hydrolytic enzymes playing a key role not only for plant biology but also for many industrial applications, such as the malting process in the brewing and distilling industries. BAMs have been extensively studied in Arabidopsis thaliana where they show a surprising level of complexity in terms of specialization within the different isoforms as well as regulatory functions played by at least three catalytically inactive members. Despite the importance of BAMs and the fact that multiple BAM proteins are also present in other angiosperms, little is known about their phylogenetic history or functional relationship.

Results

Here, we examined 961 β-amylase sequences from 136 different algae and land plant species, including 66 sequenced genomes and many transcriptomes. The extraordinary number and the diversity of organisms examined allowed us to reconstruct the main patterns of β-amylase evolution in land plants. We identified eight distinct clades in angiosperms, which results from extensive gene duplications and sub- or neo-functionalization. We discovered a novel clade of BAM, absent in Arabidopsis, which we called BAM10. BAM10 emerged before the radiation of seed plants and has the feature of an inactive enzyme. Furthermore, we report that BAM4 – an important protein regulating Arabidopsis starch metabolism – is absent in many relevant starch-accumulating crop species, suggesting that starch degradation may be differently regulated between species.

Conclusions

BAM proteins originated sometime more than 400 million years ago and expanded together with the differentiation of plants into organisms of increasing complexity. Our phylogenetic analyses provide essential insights for future functional studies of this important class of storage glucan hydrolases and regulatory proteins.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1395-2) contains supplementary material, which is available to authorized users.

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling

Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. They are responsible for the context dependent recruitment of Polycomb repressive complexes (PRC) or other repressive proteins to GAGA-motifs, which are contained in Polycomb repressive DNA-elements (PREs). Hallmark of the protein family is the highly conserved BPC domain, which is required for DNA binding. Here we study the evolution and diversification of the BBR/BPC family and its DNA-binding domain. Our analyses supports a further division of the family into four main groups (I-IV) and several subgroups, to resolve a strict monophyletic descent of the BPC domain. We prove a polyphyletic origin for group III proteins, which evolved from group I and II members through extensive loss of domains in the N-terminus. Conserved motif searches lend to the identification of a WAR/KHGTN consensus and a TIR/K motif at the very C-terminus of the BPC-domain. We could show by DPI-ELISA that this signature is required for DNA-binding in AtBPC1. Additional binding studies with AtBPC1, AtBPC6 and mutated oligonucleotides consolidated the binding to GAGA tetramers. To validate these findings, we used previously published ChIP-seq data from GFP-BPC6. We uncovered that many genes of the brassinosteroid signaling pathway are targeted by AtBPC6. Consistently, bpc6, bpc4 bpc6, and lhp1 bpc4 bpc4 mutants display brassinosteroid-dependent root growth phenotypes. Both, a function in brassinosteroid signaling and our phylogenetic data supports a link between BBR/BPC diversification in the land plant lineage and the complexity of flower and seed plant evolution.

Review: The Arabidopsis β-amylase (BAM) gene family: Diversity of form and function

Multi-gene families present a rich research area to study how related proteins evolve to acquire new structures and functions. The β-amylase (BAM) gene family is named for catalytic members' ability to hydrolyze starch into maltose units. However, the family also contains proteins that are catalytically inactive, have additional domains, or are not localized with a starch substrate. Here we review the current knowledge of each of the nine Arabidopsis BAMs, including information on their localization, structural features, expression patterns, regulation and potential functions. We also discuss unique characteristics of studying multi-gene families, such as the consideration of different kinetic parameters when performing assays on leaf extracts, and suggest approaches that may be fruitful in learning more about their unique functions.

Characterization of Brassinazole resistant (BZR) gene family and stress induced expression in Eucalyptus grandis

Brassinosteroids (BRs) are a group of plant hormones which play a pivotal role in modulating cell elongation, stress responses, vascular differentiation and senescence. In response to BRs, BRASSINAZOLE-RESISTANT (BZR) transcription factors (TFs) accumulate in the nucleus, where they modulate thousands of target genes and coordinate many biological processes, especially in regulating defense against biotic and abiotic stresses. In this study, 6 BZR TFs of Eucalyptus grandis (EgrBZR) from a genome-wide survey were characterized by sequence analysis and expression profiling against several abiotic stresses. The results showed that BZR gene family in Eucalyptus was slightly smaller compared to Populus and Arabidopsis, but all phylogenetic groups were represented. Various systematic in silico analysis of these TFs validated the basic properties of BZRs, whereas comparative studies showed a high degree of similarity with recognized BZRs of other plant species. In the organ-specific expression analyses, 4 EgrBZRs were expressed in vascular tissue indicating their possible functions in wood formation. Meanwhile, almost all EgrBZR genes showed differential transcript abundance levels in response to exogenously applied BR, MeJA, and SA, and salt and cold stresses. Besides, protein interaction analysis showed that all EgrBZR genes were associated with BR signaling directly or indirectly. These TFs were proposed as transcriptional activators or repressors of abiotic stress response and growth and development pathways of E. grandis by participating in BR signaling processes. These findings would be helpful in resolving the regulatory mechanism of EgrBZRs in stress resistance conditions but require further functional study of these potential TFs in Eucalyptus.

The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network

Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.

The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network

Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family

The BRASSINAZOLE-RESISTANT (BZR) family of transcription factors (TFs) are positive regulators in the biosynthesis of brassinosteroids. The latter is a class of steroid hormones that affect a variety of developmental and physiological processes in plants. BZR TFs play essential roles in the regulation of plant growth and development, including multiple stress-resistance functions. However, the evolutionary history and individual expression patterns of the legume BZR genes has not been determined. In this study, we performed a genome-wide investigation of the BZR gene family in seven legume species. In total, 52 BZR genes were identified and characterized. By analyzing their phylogeny, we divided these BZR genes into five groups by comparison with orthologs/paralogs in Arabidopsis thaliana. The intron/exon structural patterns and conserved protein motifs of each gene were analyzed and showed high group-specificities. Legume BZR genes were unevenly distributed among their corresponding genomes. Genome and gene sequence comparisons revealed that gene expansion of the BZR TF family in legumes mainly resulted from segmental duplications and that this family has undergone purifying selection. Synteny analysis showed that BZR genes tended to localize within syntenic blocks conserved across legume genomes. The expression patterns of BZR genes among various legume vegetative tissues and in response to different abiotic stresses were analyzed using a combination of public transcriptome data and quantitative PCR. The patterns indicated that many BZR genes regulate legume organ development and differentiation, and significantly respond to drought and salt stresses. This study may provide valuable information for understanding the evolution of BZR gene structure and expression, and lays a foundation for future functional analysis of the legume BZR genes by species and by gene.

Arabidopsis β-Amylase2 Is a K+-Requiring, Catalytic Tetramer with Sigmoidal Kinetics

The Arabidopsis (Arabidopsis thaliana) genome contains nine β-amylase (BAM) genes, some of which play important roles in starch hydrolysis. However, little is known about BAM2, a plastid-localized enzyme reported to have extremely low catalytic activity. Using conservation of intron positions, we determined that the nine Arabidopsis BAM genes fall into two distinct subfamilies. A similar pattern was found in each major lineage of land plants, suggesting that these subfamilies diverged prior to the origin of land plants. Moreover, phylogenetic analysis indicated that BAM2 is the ancestral member of one of these subfamilies. This finding, along with the conservation of amino acids in the active site of BAM2, suggested that it might be catalytically active. We then identified KCl as necessary for BAM2 activity. Unlike BAM1, BAM3, and BAM5, three Arabidopsis BAMs that all exhibited hyperbolic kinetics, BAM2 exhibited sigmoidal kinetics with a Hill coefficient of over 3. Using multi-angle light scattering, we determined that BAM2 was a tetramer, whereas BAM5 was a monomer. Conserved residues from a diverse set of BAM2 orthologs were mapped onto a homology model of the protein, revealing a large, conserved surface away from the active site that we hypothesize is a secondary carbohydrate-binding site. Introduction of bulky methionine for glycine at two points on this surface reduced catalytic activity significantly without disrupting the tetrameric structure. Expression analysis indicated that BAM2 is more closely coexpressed with other starch degradation enzymes than any other BAM, suggesting that BAM2 may play an important role in starch degradation in plants.

Amylases StAmy23, StBAM1 and StBAM9 regulate cold-induced sweetening of potato tubers in distinct ways

Cold-induced sweetening (CIS) in potato is detrimental to the quality of processed products. Conversion of starch to reducing sugars (RS) by amylases is considered one of the main pathways in CIS but is not well studied. The amylase genes StAmy23, StBAM1, and StBAM9 were studied for their functions in potato CIS. StAmy23 is localized in the cytoplasm, whereas StBAM1 and StBAM9 are targeted to the plastid stroma and starch granules, respectively. Genetic transformation of these amylases in potatoes by RNA interference showed that β-amylase activity could be decreased in cold-stored tubers by silencing of StBAM1 and collective silencing of StBAM1 and StBAM9. However, StBAM9 silencing did not decrease β-amylase activity. Silencing StBAM1 and StBAM9 caused starch accumulation and lower RS, which was more evident in simultaneously silenced lines, suggesting functional redundancy. Soluble starch content increased in RNAi-StBAM1 lines but decreased in RNAi-StBAM9 lines, suggesting that StBAM1 may regulate CIS by hydrolysing soluble starch and StBAM9 by directly acting on starch granules. Moreover, StBAM9 interacted with StBAM1 on the starch granules. StAmy23 silencing resulted in higher phytoglycogen and lower RS accumulation in cold-stored tubers, implying that StAmy23 regulates CIS by degrading cytosolic phytoglycogen. Our findings suggest that StAmy23, StBAM1, and StBAM9 function in potato CIS with varying levels of impact.

Dynamic and diverse sugar signaling

Sugars fuel life and exert numerous regulatory actions that are fundamental to all life forms. There are two principal mechanisms underlie sugar 'perception and signal transduction' in biological systems. Direct sensing and signaling is triggered via sugar-binding sensors with a broad range of affinity and specificity, whereas sugar-derived bioenergetic molecules and metabolites modulate signaling proteins and indirectly relay sugar signals. This review discusses the emerging sugar signals and potential sugar sensors discovered in plant systems. The findings leading to informative understanding of physiological regulation by sugars are considered and assessed. Comparative transcriptome analyses highlight the primary and dynamic sugar responses and reveal the convergent and specific regulators of key biological processes in the sugar-signaling network.

Review: Post-translational cross-talk between brassinosteroid and sucrose signaling

A direct link has been elucidated between brassinosteroid function and perception, and sucrose partitioning and transport. Sucrose regulation and brassinosteroid signaling cross-talk at various levels, including the well-described regulation of transcriptional gene expression: BZR-like transcription factors link the signaling pathways. Since brassinosteroid responses depend on light quality and quantity, a light-dependent alternative pathway was postulated. Here, the focus is on post-translational events. Recent identification of sucrose transporter-interacting partners raises the question whether brassinosteroid and sugars jointly affect plant innate immunity and plant symbiotic interactions. Membrane permeability and sensitivity depends on the number of cell surface receptors and transporters. More than one endocytic route has been assigned to specific components, including brassinosteroid-receptors. The number of such proteins at the plasma membrane relies on endocytic recycling, internalization and/or degradation. Therefore, vesicular membrane trafficking is gaining considerable attention with regard to plant immunity. The organization of pattern recognition receptors (PRRs), other receptors or transporters in membrane microdomains participate in endocytosis and the formation of specific intracellular compartments, potentially impacting biotic interactions. This minireview focuses on post-translational events affecting the subcellular compartmentation of membrane proteins involved in signaling, transport, and defense, and on the cross-talk between brassinosteroid signals and sugar availability.

Quantitative Analysis of Protein-DNA Interaction by qDPI-ELISA

The specific binding of DNA-binding proteins to their cognate DNA motifs is a crucial step for gene expression control and chromatin organization in vivo. The development of methods for the identification of in vivo binding regions by, e.g. chromatin immunoprecipitation (ChIP) or DNA adenine methyltransferase identification (Dam-ID) added an additional level of qualitative information for data mining in systems biology or applications in synthetic biology. In this respect, the in vivo techniques outpaced methods for thorough characterization of protein-DNA interaction and, especially, of the binding motifs at single base-pair resolution. The elucidation of DNA-binding capacities of proteins is frequently done with methods such as yeast one-hybrid, electrophoretic mobility shift assay (EMSA) or systematic evolution of ligands by exponential enrichment (SELEX) that provide only qualitative binding information and are not suited for automation or high-throughput screening of several DNA motifs. Here, we describe the quantitative DNA-protein-Interaction-ELISA (qDPI-ELISA) protocol, which makes use of fluorescent fusion proteins and, hence, is faster and easier to handle than the classical DPI-ELISA. Although every DPI-ELISA experiment delivers quantitative information, the qDPI-ELISA has an increased consistency, as it does not depend on immunological detection. We demonstrate the high comparability between probes and different protein extracts in qDPI-ELISA experiments.

New mechanistic links between sugar and hormone signalling networks

Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks.

β-Amylase1 and β-amylase3 are plastidic starch hydrolases in Arabidopsis That Seem to Be Adapted for Different Thermal, pH, and stress conditions

Starch degradation in chloroplasts requires β-amylase (BAM) activity, which is encoded by a multigene family. Of nine Arabidopsis (Arabidopsis thaliana) BAM genes, six encode plastidic enzymes, but only four of these are catalytically active. In vegetative plants, BAM1 acts during the day in guard cells, whereas BAM3 is the dominant activity in mesophyll cells at night. Plastidic BAMs have been difficult to assay in leaf extracts, in part because of a cytosolic activity encoded by BAM5. We generated a series of double mutants lacking BAM5 and each of the active plastidic enzymes (BAM1, BAM2, BAM3, and BAM6) and found that most of the plastidic activity in 5-week-old plants was encoded by BAM1 and BAM3. Both of these activities were relatively constant during the day and the night. Analysis of leaf extracts from double mutants and purified BAM1 and BAM3 proteins revealed that these proteins have distinct properties. Using soluble starch as the substrate, BAM1 and BAM3 had optimum activity at pH 6.0 to 6.5, but at high pH, BAM1 was more active than BAM3, consistent with its known daytime role in the guard cell stroma. The optimum temperature for BAM1, which is transcriptionally induced by heat stress, was about 10°C higher than that of BAM3, which is transcriptionally induced by cold stress. The amino acid composition of BAM1 and BAM3 orthologs reflected differences that are consistent with known adaptations of proteins from heat- and cold-adapted organisms, suggesting that these day- and night-active enzymes have undergone thermal adaptation.