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1. Transposable elements contribute to dynamic genome content in maize

   https://doi.org/10.1111/tpj.14489  

   Anderson, Sarah_N ; Stitzer, Michelle_C ; Brohammer, Alex_B ; Zhou, Peng ; Noshay, Jaclyn_M ; O'Connor, Christine_H ; Hirsch, Cory_D ; Ross‐Ibarra, Jeffrey ; Hirsch, Candice_N ; Springer, Nathan_M ( September 2019 , The Plant Journal)

   Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed ofTEs. We developed an approach to define shared and variableTEinsertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 andPH207) with uniform structural annotations ofTEs. Among these genomes we identified approximately 400 000TEs that are polymorphic, encompassing 1.6 Gb of variableTEsequence. These polymorphicTEs include a combination of recent transposition events as well as deletions of olderTEs. There are examples of polymorphicTEs within each of the superfamilies ofTEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphicTEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variableTEs, providing evidence for the role ofTEs in contributing to the substantial differences in annotated gene content among these genotypes.TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution ofTEs in driving variation in genome organization and gene content.

   This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available athttps://github.com/SNAnderson/maizeTE_variation;https://mcstitzer.github.io/maize_TEs.

    

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2. Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla)

   https://doi.org/10.1002/pld3.415  

   Leong, Bryan J. ; Hurney, Steven ; Fiesel, Paul ; Anthony, Thilani M. ; Moghe, Gaurav ; Jones, Arthur Daniel ; Last, Robert L. ( June 2022 , Plant Direct)

   Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes, and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plantSolanum quitoense(lulo or naranjilla). We characterized three additionalS. quitoensetrichome expressed enzymes and found that virus‐induced gene silencing of each caused changes in acylinositol accumulation. pH was shown to influence the stability and rearrangement of the product of ASAT1H and could potentially play a role in acylinositol biosynthesis. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulatein planta. This suggests that additional enzymes are required in acylinositol biosynthesis. These characterizedS. quitoenseenzymes, nonetheless, provide opportunities to test the biological impact and properties of these triacylinositols in vitro.

    

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3. In vitro plant regeneration and Agrobacterium tumefaciens –mediated transformation of Datura stramonium (Solanaceae)

   https://doi.org/10.1002/aps3.1220  

   Rajewski, Alex C. ; Elkins, Kevan B. ; Henry, Ashley ; Van Eck, Joyce ; Litt, Amy ( February 2019 , Applications in Plant Sciences)

   Datura stramoniumis a pharmacologically and evolutionarily important plant species in the family Solanaceae. Stable transformation methodology of this species would be advantageous for future genetic studies.

   In vitro plant regeneration andAgrobacterium tumefaciens–mediated transformation techniques were developed forD. stramoniumbased on methods reported for tomato. A binary vector containingpAtUBQ10::erGFPwas used for transformation.

   We recovered primary transformants harboring the green fluorescent protein (GFP) transgene that resulted in expression of fluorescence in all tissues analyzed. Transformants were allowed to self‐pollinate, and two of five progeny contained theGFPtransgene and displayed fluorescence identical to the primary transformants.

   We have demonstrated the first stable transformation in the genusDatura. This is a key first step to study the genetic basis of traits in this evolutionarily interesting species.

    

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4. GSK 3‐like kinase BIN 2 phosphorylates RD 26 to potentiate drought signaling in Arabidopsis

   https://doi.org/10.1111/tpj.14484  

   Jiang, Hao ; Tang, Buyun ; Xie, Zhouli ; Nolan, Trevor ; Ye, Huaxun ; Song, Gao‐Yuan ; Walley, Justin ; Yin, Yanhai ( August 2019 , The Plant Journal)

   Plant steroid hormones brassinosteroids (BRs) regulate plant growth and development at many different levels. Recent research has revealed that stress‐responsive NAC (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) transcription factorRD26 is regulated byBRsignaling and antagonizesBES1 in the interaction between growth and drought stress signaling. However, the upstream signaling transduction components that activateRD26 during drought are still unknown. Here, we demonstrate that the function ofRD26 is modulated byGSK3‐like kinaseBIN2 and protein phosphatase 2CABI1. We show thatABI1, a negative regulator inabscisic acid (ABA)signaling, dephosphorylates and destabilizesBIN2 to inhibitBIN2 kinase activity.RD26 protein is stabilized byABAand dehydration in aBIN2‐dependent manner.BIN2 directly interacts and phosphorylatesRD26in vitroandin vivo.BIN2 phosphorylation ofRD26 is required forRD26 transcriptional activation on drought‐responsive genes.RD26 overexpression suppressed the brassinazole (BRZ)  insensitivity ofBIN2 triple mutantbin2 bil1 bil2, andBIN2 function is required for the drought tolerance ofRD26 overexpression plants. Taken together, our data suggest a drought signaling mechanism in which drought stress relievesABI1 inhibition ofBIN2, allowingBIN2 activation. Sequentially,BIN2 phosphorylates and stabilizesRD26 to promote drought stress response.

    

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5. AFAP1‐AS1 : A novel oncogenic long non‐coding RNA in human cancers

   https://doi.org/10.1111/cpr.12397  

   Zhang, Fuyou ; Li, Jianfa ; Xiao, Huizhong ; Zou, Yifan ; Liu, Yuchen ; Huang, Weiren ( October 2017 , Cell Proliferation)

   Long non‐codingRNAs (lncRNAs), a group of non‐protein‐codingRNAs with more than 200 nucleotides in length, are involved in multiple biological processes, such as the proliferation, apoptosis, migration and invasion. Moreover, numerous studies have shown that lncRNAs play important roles as oncogenes or tumour suppressor genes in human cancers. In this paper, we concentrate on actin filament‐associated protein 1‐antisenseRNA1 (AFAP1‐AS1), a well‐known long non‐codingRNAthat is overexpressed in various tumour tissues and cell lines, including oesophageal cancer, pancreatic ductal adenocarcinoma, nasopharyngeal carcinoma, lung cancer, hepatocellular carcinoma, ovarian cancer, colorectal cancer, biliary tract cancer and gastric cancer. Moreover, high expression ofAFAP1‐AS1was associated with the clinicopathological features and cancer progression. In this review, we sum up the current studies on the characteristics ofAFAP1‐AS1in the biological function and mechanism of human cancers.

    

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