To survive and thrive in a dynamic environment, plants must continuously monitor their surroundings and adjust their development and physiology accordingly. Changes in gene expression underlie these developmental and physiological adjustments and are traditionally attributed to widespread transcriptional reprogramming. Growing evidence, however, suggests that post-transcriptional mechanisms also play a vital role in tailoring gene expression to a plant's environment. Untranslated regions (UTRs) act as regulatory hubs for post-transcriptional control, harbouring cis elements that affect an mRNA's processing, localisation, translation and stability and thereby tune the abundance of the encoded protein. Here, we review recent advances made in understanding the critical function UTRs exert in the post-transcriptional control of gene expression in the context of a plant's abiotic environment. We summarise the molecular mechanisms at play, present examples of UTR-controlled signalling cascades and discuss the potential that resides within UTRs to render plants more resilient to a changing climate.

Untranslated yet indispensable - UTRs act as key regulators in the environmental control of gene expression.

Since allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes are coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3' UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and down-regulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal APA's significant role in drought stress response but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.16150

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response.

Summary Spartina alterniflora is an exo‐recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high‐quality, chromosome‐level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high‐throughput chromosome conformation capture (Hi‐C) technology and Illumina‐based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole‐genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’. RNA‐seq analysis identified several ion transporter genes including the high‐affinity K + transporters ( HKTs ), SaHKT1;2 , SaHKT1;3 and SaHKT1;8 , and high copy number of Salt Overly Sensitive ( SOS ) up‐regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ‐ECS , GSH‐S , GPX , GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte. 

The Spartina alterniflora genome sequence provides insights into the salt‐tolerance mechanisms of exo‐recretohalophytes

Dwarfed stature is a desired agronomic trait for pomegranate (Punica granatum L.), with its advantages such as lower cost and increased yield. A comprehensive understanding of regulatory mechanisms underlying the growth repression would provide a genetic foundation to molecular-assisted dwarfing cultivation of pomegranate. Our previous study induced dwarfed pomegranate seedlings via exogenous application of plant growth retardants (PGRs) and highlighted the important roles of differential expression of plant growth-related genes in eliciting the dwarfed phenotype of pomegranate. Alternative polyadenylation (APA) is an important post-transcriptional mechanism and has been demonstrated to act as a key regulator in plant growth and development. However, no attention has been paid to the role of APA in PGR-induced dwarfing in pomegranate. In this study, we characterized and compared APA-mediated regulation events underlying PGR-induced treatments and normal growth condition. Genome-wide alterations in the usage of poly(A) sites were elicited by PGR treatments, and these changes were involved in modulating the growth and development of pomegranate seedlings. Importantly, ample specificities were observed in APA dynamics among the different PGR treatments, which mirrors their distinct nature. Despite the asynchrony between APA events and differential gene expression, APA was found to regulate transcriptome via influencing microRNA (miRNA)-mediated mRNA cleavage or translation inhibition. A global preference for lengthening of 3’ untranslated regions (3’ UTRs) was observed under PGR treatments, which was likely to host more miRNA target sites in 3’ UTRs and thus suppress the expression of the corresponding genes, especially those associated with developmental growth, lateral root branching, and maintenance of shoot apical meristem. Together, these results highlighted the key role of APA-mediated regulations in fine-tuning the PGR-induced dwarfed stature of pomegranate, which provides new insights into the genetic basis underlying the growth and development of pomegranate.

/pdf/genome-wide-alternative-polyadenylation-dynamics-underlying-krul7jp3.pdf

Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate

Phosphorus (P), a critical macronutrient for plant growth and reproduction, is primarily acquired and translocated in the form of inorganic phosphate (Pi) by roots. Pi deficiency is widespread in many natural ecosystems, including forest plantations, due to its slow movement and easy fixation in soils. Plants have evolved complex and delicate regulation mechanisms on molecular and physiological levels to cope with Pi deficiency. Over the past two decades, extensive research has been performed to decipher the underlying molecular mechanisms that regulate the Pi starvation responses (PSR) in plants. This review highlights the prospects of Pi uptake, transport, and signaling in woody plants based on the backbone of model and crop plants. In addition, this review also highlights the interactions between phosphorus and other mineral nutrients such as Nitrogen (N) and Iron (Fe). Finally, this review discusses the challenges and potential future directions of Pi research in woody plants, including characterizing the woody-specific regulatory mechanisms of Pi signaling and evaluating the regulatory roles of Pi on woody-specific traits such as wood formation and ultimately generating high Phosphorus Use Efficiency (PUE) woody plants. 

Phosphorus uptake, transport, and signaling in woody and model plants

High salt stress continues to challenge the growth and survival of many plants. Alternative polyadenylation (APA) produces mRNAs with different 3'-untranslated regions (3' UTRs) to regulate gene expression at the post-transcriptional level. However, the roles of alternative 3' UTRs in response to salt stress remain elusive. Here, we report the function of alternative 3' UTRs in response to high salt stress in S. alterniflora (Spartina alterniflora), a monocotyledonous halophyte tolerant of high salt environments. We found that high salt stress induced global APA dynamics, and ∼42% of APA genes responded to salt stress. High salt stress led to 3' UTR lengthening of 207 transcripts through increasing the usage of distal poly(A) sites. Transcripts with alternative 3' UTRs were mainly enriched in salt stress-related ion transporters. Alternative 3' UTRs of HIGH-AFFINITY K+ TRANSPORTER 1 (SaHKT1) increased RNA stability and protein synthesis in vivo. Regulatory AU-rich elements were identified in alternative 3' UTRs, boosting the protein level of SaHKT1. RNAi-knock-down experiments revealed that the biogenesis of 3' UTR lengthening in SaHKT1 was controlled by the poly(A) factor CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 30 (SaCPSF30). Over-expression of SaHKT1 with an alternative 3' UTR in rice (Oryza sativa) protoplasts increased mRNA accumulation of salt-tolerance genes in an AU-rich element-dependent manner. These results suggest that mRNA 3' UTR lengthening is a potential mechanism in response to high salt stress. These results also reveal complex regulatory roles of alternative 3' UTRs coupling APA and regulatory elements at the post-transcriptional level in plants.

Alternative 3'-untranslated regions regulate high salt tolerance of Spartina alterniflora.

Cryptochrome 1 Ubiquitously Regulates Hypocotyl Elongation from Arabidopsis to Sacred Lotus (Nelumbo nucifera)

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Alternative 3'-untranslated regions regulate high salt tolerance of Spartina alterniflora.

Cryptochrome 1 Ubiquitously Regulates Hypocotyl Elongation from Arabidopsis to Sacred Lotus (Nelumbo nucifera)