TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis

Unraveling the complexities of ApiAP2 regulation in Plasmodium falciparum

The regulation of gene expression in Plasmodium spp., the causative agents of malaria, relies on precise transcriptional control. Malaria parasites encode a limited repertoire of sequence-specific transcriptional regulators dominated by the apicomplexan APETALA 2 (ApiAP2) protein family. ApiAP2 DNA-binding proteins play critical roles at all stages of the parasite life cycle. Recent studies have provided mechanistic insight into the functional roles of many ApiAP2 proteins. Two major areas that have advanced significantly are the identification of ApiAP2-containing protein complexes and the role of ApiAP2 proteins in malaria parasite sexual development. In this review, we present recent advances on the functional biology of ApiAP2 proteins and their role in regulating gene expression across the blood stages of the parasite life cycle.

DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.

AtSRT1 regulates flowering by regulating flowering integrators and energy signals in Arabidopsis

Epigenetic modifications, such as histone alterations, play crucial roles in regulating the flowering process in Arabidopsis, a typical long-day model plant. Histone modifications are notably involved in the intricate regulation of FLC, a key inhibitor of flowering. Although sirtuin-like protein and NAD+-dependent deacetylases play an important role in regulating energy metabolism, plant stress responses, and hormonal signal transduction, the mechanisms underlying their developmental transitions remain unclear. Thus, this study aimed to reveal how Arabidopsis NAD + -dependent deacetylase AtSRT1 affects flowering by regulating the expression of flowering integrators. Genetic and molecular evidence demonstrated that AtSRT1 mediates histone deacetylation by directly binding near the transcriptional start sites (TSS) of the flowering integrator genes FT and SOC1 and negatively regulating their expression by modulating the expression of the downstream gene LFY to inhibit flowering. Additionally, AtSRT1 directly down-regulates the expression of TOR, a glucose-driven central hub of energy signaling, which controls cell metabolism and growth in response to nutritional and environmental factors. This down-regulation occurs through binding near the TSS of TOR, facilitating the addition of H3K27me3 marks on FLC via the TOR-FIE-PRC2 pathway, further repressing flowering. These results uncover a multi-pathway regulatory network involving deacetylase AtSRT1 during the flowering process, highlighting its interaction with TOR as a hub for the coordinated regulation of energy metabolism and flowering initiation. These findings significantly enhance understanding of the complexity of histone modifications in the regulation of flowering.

High expression of ethylene response factor BcERF98 delays the flowering time of non-heading Chinese cabbage

MAIN CONCLUSION

BcERF98 is induced by ethylene signaling and inhibits the expression of BcFT by interacting with BcNF-YA2 and BcEIP9, thereby inhibiting plant flowering. Several stresses trigger the accumulation of ethylene, which then transmits the signal to ethylene response factors (ERFs) to participate in the regulation of plant development to adapt to the environment. This study clarifies the function of BcERF98, a homolog of AtERF98, in the regulation of plant flowering time mediated by high concentrations of ethylene. Results indicate that BcERF98 is a nuclear and the cell membrane-localized transcription factor and highly responsive to ethylene signaling. BcERF98 inhibits the expression of BcFT by interacting with BcEIP9 and BcNF-YA2, which are related to flowering time regulation, thereby participating in ethylene-mediated plant late flowering regulation. The results have enriched the theoretical knowledge of flowering regulation in non-heading Chinese cabbage (NHCC), providing the scientific basis and gene reserves for cultivating new varieties of NHCC with different flowering times.

Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions

MAIN CONCLUSION

The hop phenological cycle was described in subtropical condition of Brazil showing that flowering can happen at any time of year and this was related to developmental molecular pathways. Hops are traditionally produced in temperate regions, as it was believed that vernalization was necessary for flowering. Nevertheless, recent studies have revealed the potential for hops to flower in tropical and subtropical climates. In this work, we observed that hops in the subtropical climate of Minas Gerais, Brazil grow and flower multiple times throughout the year, independently of the season, contrasting with what happens in temperate regions. This could be due to the photoperiod consistently being inductive, with daylight hours below the described threshold (16.5 h critical). We observed that when the plants reached 7-9 nodes, the leaves began to transition from heart-shaped to trilobed-shaped, which could be indicative of the juvenile to adult transition. This could be related to the fact that the 5th node (in plants with 10 nodes) had the highest expression of miR156, while two miR172s increased in the 20th node (in plants with 25 nodes). Hop flowers appeared later, in the 25th or 28th nodes, and the expression of HlFT3 and HlFT5 was upregulated in plants between 15 and 20 nodes, while the expression of HlTFL3 was upregulated in plants with 20 nodes. These results indicate the role of axillary meristem age in regulating this process and suggest that the florigenic signal should be maintained until the hop plants bloom. In addition, it is possible that the expression of TFL is not sufficient to inhibit flowering in these conditions and promote branching. These findings suggest that the reproductive transition in hop under inductive photoperiodic conditions could occur in plants between 15 and 20 nodes. Our study sheds light on the intricate molecular mechanisms underlying hop floral development, paving the way for potential advancements in hop production on a global scale.

Loss of function of OsL1 gene cause early flowering in rice under short-day conditions

Heading date is one of the important agronomic traits that affects rice yield. In this study, we cloned a new rice B3 family gene, OsL1, which regulates rice heading date. Importantly, osl1-1 and osl1-2, two different types of mutants of OsL1 were created using the gene editing technology CRISPR/Cas9 system and exhibited 4 days earlier heading date than that of the wild type under short-day conditions. Subsequently, the plants overexpressing OsL1, OE-OsL1, showed a 2-day later heading date than the wild type in Changsha and a 5-day later heading date in Lingshui, but there was no significant difference in other yield traits. Moreover, the results of subcellular localization study indicated that OsL1 protein was located in the nucleus and the expression pattern analysis showed that OsL1 gene was expressed in rice roots, stems, leaves, and panicles, and the expression level was higher at the root and weak green panicle. In addition, the OsL1 gene was mainly expressed at night time under short-light conditions. The transcriptomic analysis indicated that OsL1 might be involved in the Hd1-Hd3a pathway function. Together, our results revealed that the cloning and functional analysis of OsL1 can provide new strategy for molecular design breeding of rice with suitable fertility period.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01444-1.

Epigenetic insight into floral transition and seed development in plants

Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.

Plant-TFClass: a structural classification for plant transcription factors

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.

Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]

Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].

The RAV transcription factor TEMPRANILLO1 involved in ethylene-mediated delay of chrysanthemum flowering

TEMPRANILLO1 (TEM1) is a transcription factor belonging to related to ABI3 and VP1 family, which is also known as ethylene response DNA-binding factor 1 and functions as a repressor of flowering in Arabidopsis. Here, a putative homolog of AtTEM1 was isolated and characterized from chrysanthemum, designated as CmTEM1. Exogenous application of ethephon leads to an upregulation in the expression of CmTEM1. Knockdown of CmTEM1 promotes floral initiation, while overexpression of CmTEM1 retards floral transition. Further phenotypic observations suggested that CmTEM1 involves in the ethylene-mediated inhibition of flowering. Transcriptomic analysis established that expression of the flowering integrator CmAFL1, a member of the APETALA1/FRUITFULL subfamily, was downregulated significantly in CmTEM1-overexpressing transgenic plants compared with wild-type plants but was verified to be upregulated in amiR-CmTEM1 lines by quantitative RT-PCR. In addition, CmTEM1 is capable of binding to the promoter of the CmAFL1 gene to inhibit its transcription. Moreover, the genetic evidence supported the notion that CmTEM1 partially inhibits floral transition by targeting CmAFL1. In conclusion, these findings demonstrate that CmTEM1 acts as a regulator of ethylene-mediated delayed flowering in chrysanthemum, partly through its interaction with CmAFL1.

Transcriptome Analysis Reveals Key Genes and Pathways Associated with the Regulation of Flowering Time in Cabbage (Brassica oleracea L. var. capitata)

Flowering time is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the molecular regulatory mechanism underlying flowering time regulation in cabbage remains unclear. In this study, transcriptome analysis was performed using two sets of cabbage materials: (1) the early-flowering inbred line C491 (P1) and late-flowering inbred line B602 (P2), (2) the early-flowering individuals F2-B and late-flowering individuals F2-NB from the F2 population. The analysis revealed 9508 differentially expressed genes (DEGs) common to both C491_VS_ B602 and F2-B_VS_F2-NB. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed that plant hormone signal transduction and the MAPK signaling pathway were mainly enriched in up-regulated genes, and ribosome and DNA replication were mainly enriched in down-regulated genes. We identified 321 homologues of Arabidopsis flowering time genes (Ft) in cabbage. Among them, 25 DEGs (11 up-regulated and 14 down-regulated genes) were detected in the two comparison groups, and 12 gene expression patterns closely corresponded with the different flowering times in the two sets of materials. Two genes encoding MADS-box proteins, Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), showed significantly reduced expression in the late-flowering parent B602 compared with the early-flowering parent C491 via qRT-PCR analysis, which was consistent with the RNA-seq data. Next, the expression levels of Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2) were analyzed in two other groups of early-flowering and late-flowering inbred lines, which showed that their expression patterns were consistent with those in the parents. Sequence analysis revealed that three and one SNPs between B602 and C491 were identified in Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), respectively. Therefore, BoSEP2-1 and BoSEP2-2 were designated as candidates for flowering time regulation through a potential new regulatory pathway. These results provide new insights into the molecular mechanisms underlying flowering time regulation in cabbage.

Reproductive competence is regulated independently of vegetative phase change in Arabidopsis thaliana

A long-standing question in plant biology is how the acquisition of reproductive competence is related to the juvenile-to-adult vegetative transition. We addressed this question by examining the expression pattern and mutant phenotypes of two families of miRNAs-miR156/miR157 and miR172-that operate in the same pathway and play important roles in these processes. The phenotype of mutants deficient for miR156/miR157, miR172, and all three miRNAs demonstrated that miR156/miR157 regulate the timing of vegetative phase change but have only a minor effect on reproductive competence, whereas miR172 has a minor role in vegetative phase change but has a major effect on reproductive competence. MIR172B is directly downstream of the miR156/SPL module, but temporal variation in the level of miR156 in the shoot apex and leaf-to-leaf variation in miR156 expression in young primordia was not associated with a change in the level of miR172 in these tissues. Additionally, although miR172 levels increase from leaf to leaf later in leaf development, this variation is largely insensitive to changes in the abundance of miR156. Our results indicate that the acquisition of reproductive competence in Arabidopsis is regulated by miR172 through a mechanism that is independent of the vegetative phase change pathway.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

Transcriptional signatures of wheat inflorescence development

In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.

Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis

Vegetable oils are not only major components of human diet but also vital for industrial applications. WRINKLED1 (WRI1) is a pivotal transcription factor governing plant oil biosynthesis, but the underlying DNA-binding mechanism remains incompletely understood. Here, we resolved the structure of Arabidopsis WRI1 (AtWRI1) with its cognate double-stranded DNA (dsDNA), revealing two antiparallel β sheets in the tandem AP2 domains that intercalate into the adjacent major grooves of dsDNA to determine the sequence recognition specificity. We showed that AtWRI1 represented a previously unidentified structural fold and DNA-binding mode. Mutations of the key residues interacting with DNA element affected its binding affinity and oil biosynthesis when these variants were transiently expressed in tobacco leaves. Seed oil content was enhanced in stable transgenic wri1-1 expressing an AtWRI1 variant (W74R). Together, our findings offer a structural basis explaining WRI1 recognition and binding of DNA and suggest an alternative strategy to increase oil yield in crops through WRI1 bioengineering.

Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean

The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.

Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction

Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.

Characterization of Squamosa-Promoter Binding Protein-Box Family Genes Reveals the Critical Role of MsSPL20 in Alfalfa Flowering Time Regulation

SQUAMOSA Promoter-binding protein-Like (SPL) genes affect a broad range of plant biological processes and show potential application in crop improvement by genetic modification. As the most widely planted forage crop in the world, biomass and abiotic stresses tolerance are important breeding targets for alfalfa (Medicago sativa L.). Nevertheless, the systematic analysis of SPL genes in alfalfa genome remains lacking. In the present study, we characterized 22 putative non-redundant SPL genes in alfalfa genome and uncovered the abundant structural variation among MsSPL genes. The phylogenetic analysis of plant SPL proteins separated them into 10 clades and clade J was an alfalfa-specific clade, suggesting SPL genes in alfalfa might have experienced gene duplication and functional differentiation within the genome. Meanwhile, 11 MsSPL genes with perfect matches to miRNA response elements (MREs) could be degraded by miR156, and the cleavage sites were gene specific. In addition, we investigated the temporal and spatial expression patterns of MsSPL genes and their expression patterns in response to multiple treatments, characterizing candidate SPL genes in alfalfa development and abiotic stress tolerant regulation. More importantly, overexpression of the alfalfa-specific SPL gene (MsSPL20) showed stable delayed flowering time, as well as increased biomass. Further studies indicated that MsSPL20 delayed flowering time by regulating the expression of genes involved in floret development, including HD3A, FTIP1, TEM1, and HST1. Together, our findings provide valuable information for future research and utilization of SPL genes in alfalfa and elucidate a possibly alfalfa-specific flowering time regulation, thereby supplying candidate genes for alfalfa molecular-assisted breeding.