Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding

AbstractDichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.

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Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

PLoS ONE ◽

10.1371/journal.pone.0253741 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253741

Author(s):

Mihai-Silviu Tomescu ◽

Selisha Ann Sooklal ◽

Thuto Ntsowe ◽

Previn Naicker ◽

Barbara Darnhofer ◽

...

Keyword(s):

De Novo ◽

Differential Expression Analysis ◽

Terpene Synthase ◽

Future Research ◽

Terpene Synthases ◽

Illumina Hiseq ◽

Prostate Hyperplasia ◽

Inflammatory Conditions ◽

Urinary Infections ◽

Hypoxis Hemerocallidea

The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.

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Extracellular ATP plays an important role in systemic wound response activation

10.1101/2022.01.06.475278 ◽

2022 ◽

Author(s):

Ronald Myers ◽

Yosef Fichman ◽

Gary Stacey ◽

Ron Mittler

Keyword(s):

Signaling Pathways ◽

Extracellular Atp ◽

Wound Response ◽

Mechanical Wounding ◽

Long Distance ◽

Wound Responses ◽

Systemic Signal ◽

Electric Signals ◽

Multiple Signaling

Mechanical wounding occurs in plants during biotic (e.g., herbivore or pathogen attack) or abiotic (e.g., wind damage or freezing) stresses and is associated with the activation of multiple signaling pathways. These initiate many wound responses at the wounded tissues, as well as trigger long-distance signaling pathways that activate wound responses in tissues that were not affected by the initial wounding event (termed systemic wound response). Among the different systemic signals activated by wounding are electric signals, calcium and reactive oxygen species (ROS) waves, and different plant hormones such as jasmonic acid. The release of glutamate from cells at the wounded tissues was recently proposed to trigger several different systemic signal transduction pathways via glutamate-like receptors (GLRs). However, the role of another important compound released from cells during wounding (i.e., extracellular ATP; eATP) in triggering systemic responses is not clear. Here we show that eATP that accumulates in wounded leaves and is sensed by the purinoreceptor kinase P2K is required for the activation of the ROS wave during wounding. Application of eATP to unwounded leaves triggered the ROS wave, and the activation of the ROS wave by wounding or eATP application was suppressed in mutants deficient in P2K (i.e., p2k1-3, p2k2, and p2k1-3p2k2). In addition, the expression of several systemic wound response transcripts was suppressed in mutants deficient in P2K during wounding. Our findings reveal that in addition to sensing glutamate via GLRs, eATP sensed by P2Ks is playing a key role in the triggering of systemic wound responses in plants.

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Suppressors of Systemin Signaling Identify Genes in the Tomato Wound Response Pathway

Genetics ◽

10.1093/genetics/153.3.1411 ◽

1999 ◽

Vol 153 (3) ◽

pp. 1411-1421

Author(s):

Gregg A Howe ◽

Clarence A Ryan

Keyword(s):

Gene Expression ◽

Proteinase Inhibitors ◽

Constitutive Expression ◽

Wound Response ◽

Mechanical Wounding ◽

Defense Proteins ◽

Amino Acid Peptide ◽

Wound Responses ◽

Extragenic Suppressors

Abstract In tomato plants, systemic induction of defense genes in response to herbivory or mechanical wounding is regulated by an 18-amino-acid peptide signal called systemin. Transgenic plants that overexpress prosystemin, the systemin precursor, from a 35S::prosystemin (35S::prosys) transgene exhibit constitutive expression of wound-inducible defense proteins including proteinase inhibitors and polyphenol oxidase. To study further the role of (pro)systemin in the wound response pathway, we isolated and characterized mutations that suppress 35S::prosys-mediated phenotypes. Ten recessive, extragenic suppressors were identified. Two of these define new alleles of def-1, a previously identified mutation that blocks both wound- and systemin-induced gene expression and renders plants susceptible to herbivory. The remaining mutants defined four loci designated Spr-1, Spr-2, Spr-3, and Spr-4 (for Suppressed in 35S::prosystemin-mediated responses). spr-3 and spr-4 mutants were not significantly affected in their response to either systemin or mechanical wounding. In contrast, spr-1 and spr-2 plants lacked systemic wound responses and were insensitive to systemin. These results confirm the function of (pro)systemin in the transduction of systemic wound signals and further establish that wounding, systemin, and 35S::prosys induce defensive gene expression through a common signaling pathway defined by at least three genes (Def-1, Spr-1, and Spr-2).

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Characterization and Comparison of Lesions on Ornamental Sweetpotato ‘Blackie’, Tomato ‘Maxifort’, Interspecific Geranium ‘Caliente Coral’, and Bat-faced Cuphea ‘Tiny Mice’

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.5.603 ◽

2014 ◽

Vol 139 (5) ◽

pp. 603-615 ◽

Cited By ~ 5

Author(s):

Joshua K. Craver ◽

Chad T. Miller ◽

Kimberly A. Williams ◽

Daniel L. Boyle

Keyword(s):

Light Microscopy ◽

Ipomoea Batatas ◽

Light Quality ◽

Water Status ◽

Leaf Tissue ◽

Wound Response ◽

Future Research ◽

Specific Cell ◽

Lesion Development ◽

Physiological Disorders

Many plant species are prone to physiological disorders in which lesions develop on the leaf tissue. Nomenclature for such lesions has included intumescences, excrescences, neoplasms, galls, genetic tumors, enations, and oedemata. Interchangeably using these terms causes confusion as to whether these names refer to the same or different disorders. Two of the most commonly used names are oedema and intumescence. The objective of this research was to characterize the development of lesions on ornamental sweetpotato (Ipomoea batatas ‘Blackie’), tomato (Solanum lycopersicum ‘Maxifort’), interspecific hybrid geranium (Pelargonium × ‘Caliente Coral’), and bat-faced cuphea (Cuphea llavea ‘Tiny Mice’) to determine similarities and differences in morphology and nomenclature among these physiological disorders. Light microscopy was used to characterize differences in cross-sectional height, width, and area of lesions on each species. Additionally, leaf tissue samples were embedded in paraffin, and 10-μm cross-sections were stained with Toluidine blue O and observed using light microscopy to identify specific cell layers involved with lesion development. Field emission scanning electron microscopy (SEM) and digital photography were used to observe the microscopic and macroscopic stages of lesion development, respectively, on each species. The lesions observed on ornamental sweetpotato were significantly greater in height and area than on the other three species, whereas tomato lesions were significantly greater in width. Lesions on ornamental sweetpotato and bat-faced cuphea occurred predominantly on the adaxial surface of the leaf, whereas lesions on geranium and tomato occurred predominantly on the abaxial surface. With lesions on tomato, ornamental sweetpotato, and bat-faced cuphea, the epidermis was often subjected to the same hypertrophy apparent in the underlying parenchyma cells, ultimately allowing for greater cell expansion. However, in geranium, the epidermis resisted the expansion of the underlying cells, resulting in the eventual tearing of this tissue layer. Previous research indicates that lesion development on geranium is closely related to water status within the plant and may result in a wound response or provide a means of facilitated gas exchange. On the contrary, development of lesions on ornamental sweetpotato and tomato is believed to involve light quality. Based on these results and observations, two disorders occur across these species. The term “intumescence” should be used when referring to abnormal lesions on ornamental sweetpotato and tomato, and the term “oedema” should be used when referring to lesions on geranium. The term “intumescence” should also be used when referring to bat-faced cuphea lesions resulting from the morphological and anatomical aspects of these lesions closely resembling development on ornamental sweetpotato and tomato. Future research should investigate the role of light quality regarding development on this species.

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Wound Response in Fossil Trees from Antarctica and its Potential as a Paleoenvironmental Indicator

IAWA Journal ◽

10.1163/22941932-90000627 ◽

1996 ◽

Vol 17 (1) ◽

pp. 77-88 ◽

Cited By ~ 7

Author(s):

Michelle K. Putz ◽

Edith L. Taylor

Keyword(s):

Middle Triassic ◽

Secondary Xylem ◽

Wound Response ◽

Mechanical Wounding ◽

Growth Rings ◽

Wound Responses ◽

Show Evidence ◽

Stem Development ◽

Wounded Area ◽

Ice Avalanche

Numerous permineralized axes of Middle Triassic age from Fremouw Peak, Antarctica show evidence of mechanical wounding and wound responses. These consist of both elongate and triangular-shaped scars. Some scars can be detected beneath subsequent secondary xylem, indicating that wounding occurred early in stem development. In other stems, scars remained open suggesting late wounding and the permanent disruption of the cambium. In cross section most stems display little cal1ustissue, but wound periderm can be seen along the margin of the scar. In some stems the wound phellogen has formed phellem and phelloderm within the wounded area oriented perpendicular to the growth rings. Although some scars resemble those produced by fires, we were unable to document the presence of charcoal around scars. In modem ecosystems wounds may be caused by other agents, including debris drifting in floods, flowing ice, avalanche s, and animals . Each of these potential sources is reviewed in relationship to the paleoclimate in the region during the Triassic.

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Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes

10.1101/2021.09.02.458788 ◽

2021 ◽

Author(s):

Adam D Steinbrenner ◽

Evan Saldivar ◽

Nile Hodges ◽

Antonio F Chaparro ◽

Eric A Schmelz

Keyword(s):

Plant Defense ◽

Large Scale ◽

Gene Families ◽

Defense Responses ◽

Wound Response ◽

Beet Armyworm ◽

Mechanical Wounding ◽

Terpene Synthases ◽

Wound Responses ◽

Molecular Patterns

Chewing herbivores activate plant defense responses through a combination of mechanical wounding and elicitation by herbivore associated molecular patterns (HAMPs). HAMPs are wound response amplifiers; however, specific defense outputs may also exist that strictly require HAMP-mediated defense signaling. To investigate HAMP-mediated signaling and defense responses, we characterized cowpea transcriptome changes following elicitation by inceptin, a peptide HAMP common in Lepidoptera larvae oral secretions. Following inceptin treatment, we observed large-scale reprogramming of the transcriptome consistent with 3 different response categories: 1) amplification of mechanical wound responses, 2) temporal extension through accelerated or prolonged responses, and 3) examples of inceptin-specific elicitation and suppression. At both early and late timepoints, namely 1 and 6 hours, large sets of transcripts specifically accumulated following inceptin elicitation but not wounding alone. Further inceptin-regulated transcripts were classified as reversing changes induced by wounding alone. Within key signaling and defense related gene families, inceptin-elicited responses commonly targeted select subsets of wound-induced transcripts. Transcripts displaying the largest inceptin-elicited fold-changes included terpene synthases (TPS) and peroxidases (POX) that correspond with induced volatile production and increased peroxidase activity in cowpea. Characterization of inceptin-elicited cowpea defenses via heterologous expression in Nicotiana benthamiana demonstrated that specific cowpea TPS and POX were able to confer terpene emission and the reduced growth of beet armyworm (Spodoptera exigua) herbivores, respectively. Collectively, our present findings in cowpea support a model where HAMP-elicitation both amplifies concurrent wound responses and specifically contributes to the activation of selective outputs associated with direct and indirect anti-herbivore defenses.

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Identification and expression pattern of chemosensory genes in the transcriptome of Propsilocerus akamusi

PeerJ ◽

10.7717/peerj.9584 ◽

2020 ◽

Vol 8 ◽

pp. e9584

Author(s):

Chuncai Yan ◽

Xiaoya Sun ◽

Wei Cao ◽

Ruoqun Li ◽

Cong Zhao ◽

...

Keyword(s):

Differential Expression Analysis ◽

Odorant Receptors ◽

Indicator Organisms ◽

Illumina Hiseq ◽

Chemosensory Genes ◽

Chironomid Species ◽

Gene Level ◽

Illumina Hiseq Platform ◽

Odorant Binding ◽

Simple Sequence

Chironomidae is the most ecologically diverse insects in aquatic and semi-aquatic habitats. Propsilocerus akamusi (Tokunaga) is a dominant and ubiquitous chironomid species in Eastern Asia and its morphologically unique larvae are also considered as indicator organisms to detect water contamination, potential toxicity and waterborne pathogens. Since few studies to date have focused on the olfactory system of P. akamusi, our study aims to elucidate the potential functions of chemosensory genes in P. akamusi. In our study, we found that although signals released from male groups might attract female swarmers, it was a completely male-dominated mating process. Sequencing the transcriptome of P. akamusi on an Illumina HiSeq platform generated 4.42, 4.46 and 4.53 Gb of clean reads for heads, legs, and antennae, respectively. 27,609 unigenes, 20,379 coding sequences (CDSs), and 8,073 simple sequence repeats were finally obtained. The gene-level differential expression analysis demonstrated variants among three different tissues, including 2,019 genes specifically expressed in heads, 1,540 genes in legs, and 2,071 genes in antennae. Additionally, we identified an assortment of putative olfactory genes consisting of 34 odorant binding proteins, 17 odorant receptors, 32 gustatory receptors, 22 ionotropic receptors, six chemosensory proteins as well as 3 sensory neuron membrane proteins; their relative abundances in the above three tissues were also determined by RT-qPCR. Our finding could allow a more plausible understanding of certain olfaction-mediated behaviors in groups of this macroinvertebrate.

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Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts

Emerging Topics in Life Sciences ◽

10.1042/etls20190069 ◽

2019 ◽

Vol 4 (1) ◽

pp. 59-76 ◽

Cited By ~ 2

Author(s):

Alison E. Fowler ◽

Rebecca E. Irwin ◽

Lynn S. Adler

Keyword(s):

Defense Mechanisms ◽

Poor Quality ◽

Future Research ◽

Immune Priming ◽

Social Bees ◽

Bee Health ◽

Landscape Scales ◽

And Function ◽

Solitary Species

Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.

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Insect Behavioral Change and the Potential Contributions of Neuroinflammation—A Call for Future Research

Genes ◽

10.3390/genes12040465 ◽

2021 ◽

Vol 12 (4) ◽

pp. 465

Author(s):

Colleen A. Mangold ◽

David P. Hughes

Keyword(s):

Behavioral Change ◽

Potential Role ◽

Insect Behavior ◽

Future Research ◽

Cell Physiology ◽

Behavioral Manipulation ◽

Neuroimmune Communication ◽

And Function ◽

Neuron Function ◽

Insect Innate Immunity

Many organisms are able to elicit behavioral change in other organisms. Examples include different microbes (e.g., viruses and fungi), parasites (e.g., hairworms and trematodes), and parasitoid wasps. In most cases, the mechanisms underlying host behavioral change remain relatively unclear. There is a growing body of literature linking alterations in immune signaling with neuron health, communication, and function; however, there is a paucity of data detailing the effects of altered neuroimmune signaling on insect neuron function and how glial cells may contribute toward neuron dysregulation. It is important to consider the potential impacts of altered neuroimmune communication on host behavior and reflect on its potential role as an important tool in the “neuro-engineer” toolkit. In this review, we examine what is known about the relationships between the insect immune and nervous systems. We highlight organisms that are able to influence insect behavior and discuss possible mechanisms of behavioral manipulation, including potentially dysregulated neuroimmune communication. We close by identifying opportunities for integrating research in insect innate immunity, glial cell physiology, and neurobiology in the investigation of behavioral manipulation.

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Abstract P625: Non-coding Rna Regulation Of Gene Expression In Angiotensin Ii-induced Vascular Damage

Hypertension ◽

10.1161/hyp.66.suppl_1.p625 ◽

2015 ◽

Vol 66 (suppl_1) ◽

Author(s):

Kugeng Huo ◽

Tlili Barhoumi ◽

Júlio C Fraulob-Aquino ◽

Chantal Richer ◽

Mathieu Lajoie ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression Analysis ◽

Regulation Of Gene Expression ◽

Vascular Damage ◽

Mesenteric Arteries ◽

Functional Enrichment ◽

Molecular Networks ◽

Mirna Cluster ◽

Ang Ii ◽

Illumina Hiseq

Introduction: Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRs), account for ~98% of the transcribed RNAs. They have been shown to play a role in cardiovascular disease. Vascular damage is an early manifestation and a cause of end-organ damage in hypertension. However, it is unknown whether ncRNAs are involved in the development of vascular injury in hypertension. We hypothesize that ncRNA regulation participates in mechanisms of vascular remodeling and plays an important role in the pathophysiology of hypertension. Methods and Results: Ten-week old male C57BL/6 mice were infused or not with angiotensin (Ang) II for 14 days. Systolic blood pressure (BP) determined by telemetry was increased by Ang II infusion compared to control (146±8 vs 113±5 mmHg, P<0.001). Total RNA was extracted from mesenteric arteries for total and small RNA deep sequencing using Illumina HiSeq-2500. Sequences were aligned to the mm10 genome with STAR, annotated and counted using HTSeq-count or miRDeep2. Differential expression analysis was done in R. Differentially expressed (DE) mRNAs (550 up & 266 down), lncRNAs (7 up & 42 down), miRs (23 up & 12 down) were identified in the Ang II-treated group (1.5 fold change, q<0.05). Targetscan was used to predict interactions between DE miRs and the inversely correlated DE mRNAs or DE lncRNAs. MEME Suite was used to predict DE transcription factor binding sites in the promoter region of genes encoding DE mRNAs, lncRNAs and miRs. Cytoscape was used to construct molecular networks integrating the above interactions and the gene expression profile and to perform functional enrichment analysis, which revealed enrichment of extracellular matrix and developmental processes in DE miR-targeting DE mRNAs (q<1E-20). Ten DE miRNAs whose expression levels correlated (P<0.05) with BP were identified, 9 of which are located in a single miRNA cluster that is conserved in humans. Conclusions: We have identified a conserved miRNA cluster that may play a pivotal role in the regulation of vascular damage in hypertension. A sub-network of genes that participates in the interaction between the miRNA cluster and other BP-correlated RNAs was selected for future investigation to identify therapeutic targets.

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