The Plant Journal

Ivanov, Michail; Buddle, Emily A.; Ankeny, Rachel A.

doi: 10.1111/tpj.70277pmid: 40522595

The development of new gene technologies including gene editing has reinvigorated long‐standing global debates about if and how such technologies should be regulated. Many scientists working in agricultural genomics believe that current regulatory approaches are problematic, often emphasizing that the regulatory system is merely a ‘bottleneck’ that limits research and innovation in crop sciences. The concept of a ‘bottleneck’ is prominent in discussions in this domain, but we contend that what counts as a ‘bottleneck’ depends on point of view and the interests and goals of the party that wishes to describe a particular situation as bottlenecked. In this Focused Review, we provide a short account of recent scholarship on gene editing regulation and argue that regulation is an important part of the research development and innovation process that should not merely be viewed as a ‘bottleneck.’ Regulation permits regulators and diverse publics to engage with research and assess whether the particular application of gene technology is desirable and beneficial beyond the laboratory bench or field. We conclude by providing lessons for scientists working in agricultural genomics, emphasizing the need to move away from visions of ‘bottlenecks’ and embracing regulation's potential to support the promises associated with agricultural genomics.

Shi, Zhenhua; Wang, Lingmin; Zhang, Yingrong; Yu, Zhen

doi: 10.1111/tpj.70303pmid: 40570362

The fact that all cell organisms have electron transport chains and that all cell organisms need to obtain electron donors and electron acceptors from the environment to survive inspired that all cell organisms should have innate bidirectional tropism toward both electron donors and electron acceptors. Here we confirmed this hypothesis in wheat, that is, under a certain voltage condition, the smaller the current in the culture medium, the more roots grew toward the cathode (electron donor). As the current increases, more and more roots grew toward the anode (electron acceptor). More importantly, although the root growth direction was opposite under certain voltage and current conditions, the growth rate of the plant was increased. Moreover, LC–MS/MS‐based metabolomics analysis showed that metabolites involved in energy metabolism (e.g., glucose‐6‐phosphat, fumaric acid, and L‐malic acid) and secondary metabolism (e.g., 4‐methoxycinnamic acid, caffeine, and coumarin) are closely related to this behavior. The relationship between bidirectional electrotropism and energy metabolism was further confirmed by examining the gene expression level of enzymes involved in both the glycolysis pathway and tricarboxylic acid cycle, the activity of antioxidant enzymes, the level of cellular ATP, and the inhibition of malonic acid. This study is the first report of bidirectional electrotropism of living organisms, and as the behavior of bidirectional electrotropism is based on the common of all cellular organisms, the ancestral role of this behavior in the origin and evolution of life is desirable.

Richtmann, Ludwig; Prochetto, Santiago; Thiébaut, Noémie; Sarthou, Manon C. M.; Boutet, Stéphanie; Hanikenne, Marc; Clemens, Stephan; Verbruggen, Nathalie

doi: 10.1111/tpj.70298pmid: 40574703

Cadmium (Cd) is a major environmental pollutant with high toxicity. While Cd exposure reduces root growth, its specific impact on the root meristem and differentiating parts remains poorly understood. This study investigates the spatial and temporal responses of Arabidopsis thaliana roots to Cd stress by dividing roots into root tips (RT) and remaining roots (RR) and employing transcriptomic, ionomic, and metabolomic analyses. Cd exposure altered mineral profiles, with RT accumulating less Cd but showing distinct changes in other elements compared to RR. Metabolomic analysis revealed root part‐specific changes in phytochelatins, flavonoids, and glucosinolates. Transcriptomic data highlighted constitutive differences between RT and RR, reflecting functional specialization. Also, they revealed Cd‐induced root part‐specific and time‐dependent transcriptional responses, including modulation of Fe‐related genes. Phenotypic validation identified ELONGATED HYPOCOTYL 5 as a key regulator limiting Cd accumulation and promoting tolerance, as hy5 mutants exhibited increased Cd sensitivity and accumulation. Additionally, mutants of genes regulated by HY5, such as xyloglucan endotransglucosylase/hydrolase genes (XTH) and MYB12, also showed altered root growth under Cd stress, implicating cell wall remodeling and flavonoid biosynthesis in Cd responses. This study provides a spatially and temporally resolved understanding of Cd's impact on root growth, and highlights HY5's role in Cd tolerance, thereby advancing our knowledge of plant responses to trace metal excess.

Scarfe, Jonathan; Kosmützky, Darius; Nisbet, R. Ellen R.

doi: 10.1111/tpj.70272pmid: 40537033

Recombinant proteins play a crucial role in both fundamental research and biotechnology. In the laboratory, recombinant proteins are used in a myriad of ways, including to label cells, localize proteins and isolate complexes. In the clinic, antibody‐based therapeutics can dramatically increase cancer survival rates, while virus‐like particles (VLPs) are being developed as next‐generation vaccines. These innovations have escalated demands for biopharmaceutical recombinant proteins. However, in traditional systems (e.g. mammalian and microbial) the expression of recombinant proteins can be prohibitively expensive. One sustainable, low‐cost solution is to use a microalgal‐based expression system, such as Chlamydomonas reinhardtii, Phaeodactylum tricornutum, Chlorella sp., Haematococcus pluvialis or Nannochloropsis gaditana. Tools for microalgal protein expression are developing rapidly. Yet our understanding of recombinant protein expression and purification in microalgal systems lags that of traditional systems. Here, we review the impact of commonly used affinity and epitope tags (e.g. Polyhistidine‐tag, Strep‐tag II, HA‐tag and FLAG‐tag) on recombinant protein detection, purification and biofunctionality in microalgae. Additionally, we review fluorescent protein tags (such as GFP, mVenus, DsRed and mCherry) and protease cleavage sites, including ‘self‐cleaving’ 2A peptides. Finally, we provide guidance on experimental design to enhance the likelihood of successfully expressing recombinant proteins in microalgae.

Peppino Margutti, Micaela Y.; Cislaghi, Ana P.; Herrera‐Vásquez, Ariel; Palomeque, Julieta R.; Bellino Tabera, Francisco R.; Alvarez, María E.; Blanco‐Herrera, Francisca; Cecchini, Nicolás M.

doi: 10.1111/tpj.70295pmid: 40552656

Xi, Zengde; Wang, Mengyao; Wang, Fei; Wang, Jianbo

doi: 10.1111/tpj.70297pmid: 40552675

Heterosis has been widely applied in crop breeding and has significantly improved grain yield worldwide. Many studies have attempted to elucidate heterosis from various perspectives; however, its genetic basis—especially at the translational level—remains elusive. In this study, we performed RNA‐seq and ribosome profiling on the inter‐subspecific hybrid rice ZY19 (Oryza sativa L. subsp. indica Kato × O. sativa L. subsp. japonica Kato) and its parental lines to examine genome‐wide translational dynamics. Differential gene expression between the hybrid and its parents revealed a strong discordance between transcriptional and translational levels, and translational regulation appeared to buffer the transcriptional differences. Although additive and non‐additive gene expression patterns shifted during translation, additive expression remained the predominant pattern at the translational level in the hybrid. Moreover, a high proportion of single‐parent expression genes also exhibited additive expression. In the hybrid, allele‐specific expression (ASE) was differentially regulated in transcription and translation. Notably, cis and trans‐regulation tended to function independently in transcription, whereas they were more likely to act together in translation. Finally, we investigated the effects of various regulatory mechanisms and elements on translation and found that genes with more alternative splicing (AS) events had a lower translational efficiency (TE) than genes with fewer AS events. In addition, translation was repressed by the upstream open reading frames (uORFs), downstream open reading frames (dORFs), N6‐methyladenosines (m6As) and microRNAs (miRNAs). Overall, our study provides new insights into the molecular mechanisms of heterosis in inter‐subspecific hybrid rice.

McConnachie, Matthew; Nguyen, Tuan‐Anh Minh; Kim, Truc; Nguyen, Trinh‐Don; Dang, Thu‐Thuy T.

doi: 10.1111/tpj.70288pmid: 40545552

Plant natural products or specialized metabolites play a vital role in drug discovery and development, with many clinically important derivatives such as the anticancer drugs topotecan (derived from the natural alkaloid camptothecin) and etoposide (derived from the natural polyphenol podophyllotoxin). Remarkable advances in understanding plant natural product metabolism have been achieved at an unprecedented pace over the past 15 years. The integration of high‐throughput technologies in genomics, transcriptomics, and metabolomics has generated vast datasets that provide a more comprehensive understanding of plant metabolism. Additionally, advances in computational tools, machine learning, and data analytics have played a crucial role in processing and interpreting the massive amounts of newly available data, enabling researchers to uncover intricate regulatory networks and identify key components of biosynthetic pathways. This review navigates the evolving landscape of plant biosynthetic pathway elucidation accelerated by innovative multidisciplinary strategies that capitalize on big data. We highlight recent advances in plant‐specialized biosynthesis that illustrate how big data are increasingly leveraged to unravel the complexities of plant metabolism.

doi: 10.1111/tpj.70286pmid: 40554853

Akter, Nargis; Tezuka, Takumi; Rattanawong, Kasidit; Satoh, Aya; Kinoshita, Atsuko; Sato, Yutaka; Okamoto, Takashi

doi: 10.1111/tpj.70305pmid: 40570546

Oryza sativa BABY BOOM 1 (OsBBM1), a member of the AP2/ERF family of transcription factors, is expressed from paternal allele in rice zygote and plays a crucial role in initiating zygotic development. However, the mechanism how the paternal OsBBM1 drives this development remains unclear. Rice zygotes with four different gamete combinations with or without functional paternal OsBBMs were produced by electrofusion, using gametes isolated from bbms triple mutants and wild‐type rice plants. Developmental and gene expression profiles of these types of zygotes were intensively analyzed and compared. Mutations in OsBBM1, OsBBM2, and OsBBM3 on the paternal alleles caused developmental arrest or delay in the zygotes, while defects in OsBBMs on the maternal allele had minimal effects on zygotic development. Paternal allele of OsBBMs significantly influenced gene expression profiles related to regulation of basic cellular processes, such as chromosome/chromatin organization/assembly and cell cycle/division compared to the maternal allele of OsBBMs. Majority of these genes were upregulated in zygotes from paternal/parental alleles via paternal OsBBMs. Paternal OsBBMs initiate early development of rice zygotes through the regulation of expression profiles of genes controlling status of chromosome/chromatin and cell cycle/division.

doi: 10.1111/tpj.70280pmid: 40526900