New Insights into the Symbiotic Relationship between Orchids and Fungi

Mycorrhizas play an important role in plant growth and development. In mycorrhizal symbioses, fungi supply soil mineral nutrients, such as nitrogen and phosphorus, to their host plants in exchange for carbon resources. Plants gain as much as 80% of mineral nutrient requirements from mycorrhizal fungi, which form associations with the roots of over 90% of all plant species. Orchid seeds lack endosperms and contain very limited storage reserves. Therefore, the symbiosis with mycorrhizal fungi that form endomycorrhizas is essential for orchid seed germination and protocorm development under natural conditions. The rapid advancement of next-generation sequencing contributes to identifying the orchid and fungal genes involved in the orchid mycorrhizal symbiosis and unraveling the molecular mechanisms regulating the symbiosis. We aim to update and summarize the current understanding of the mechanisms on orchid-fungus symbiosis, and the main focus will be on the nutrient exchange between orchids and their fungal partners.

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Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

10.1101/393637 ◽

2018 ◽

Author(s):

Ivan D. Mateus ◽

Frédéric G. Masclaux ◽

Consolée Aletti ◽

Edward C. Rojas ◽

Romain Savary ◽

...

Keyword(s):

Mycorrhizal Fungi ◽

Large Scale ◽

Molecular Mechanisms ◽

Arbuscular Mycorrhizal ◽

Mycorrhizal Symbiosis ◽

Rna Seq ◽

Plant Host ◽

Transcriptional Responses ◽

Plant Genes ◽

Fungal Genetic

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

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Molecular Basis of Plant-Symbiotic Fungi Interaction: An Overview

Scientific World ◽

10.3126/sw.v5i5.2668 ◽

1970 ◽

Vol 5 (5) ◽

pp. 115-131 ◽

Cited By ~ 6

Author(s):

Anjana Singh

Keyword(s):

Gene Expression ◽

Mycorrhizal Fungi ◽

Molecular Mechanisms ◽

De Novo ◽

Molecular Techniques ◽

Piriformospora Indica ◽

Down Regulation ◽

Symbiotic Fungus ◽

Symbiotic Fungi ◽

Fungal Genes

The intimate symbiotic relationships developed between mycorrhizal fungi and plants, since land colonization by the latter have led to an interdependence between these organisms for many basic processes. The fungi require plants to accomplish their life cycle. Plants depend heavily on mycorrhizal fungi for many different functions, such as mineral nutrition, and abiotic and biotic stress resistance. Substantial evidence has accumulated in recent years about how rational use of this microsymbiont could significantly contribute to decreasing use of fertilizer and pesticide in agriculture, forestry and flori-horticulture, especially, if combined with other beneficial soil microorganism. Symbiotic fungi act as major link between plants and soil, and should, therefore, be considered a central pivot for new strategies in the development of biologically-oriented agricultural practices. To search for functional genes controlling fungal morphogenesis, infection process, metabolism of mycorrhizal roots, down regulation of defense- related genes in plants, are still in infancy, but with the advent of new molecular biology techniques, it is speculated not to be a far cry. And it is hope that it will cover the experimental and technical gap, still existing between the AM and other symbiotic systems which are experimentally more tractable. Plants with constitutively over-expressed defense related genes provide interesting material of determining how fungi contend with plant defense, although, how modification occurs in the expression of other genes in such plant is unclear. Molecular investigation of isogenic myc- mutants from pea and more recently from M. truncatula should also significantly advance our knowledge of plant and fungal gene expression essential to the symbiosis. Polypeptide analysis has already shown those compatible interactions in mycorrhizal pea and tobacco roots are dominated by de novo gene expression. Incompatible interaction in myc- mutant pea roots are mainly characterized by a down regulation of polypeptide synthesis, suggesting that maintenance of the activity of constitutively expressed plant genes may be important in the establishment of symbiotic fungus. The precise signals and molecular mechanism in establishing cellular and functional compatibility in fungal plant symbiosis are unknown. Rapid evolution in molecular techniques is facilitating the possibility of analyzing temporal and spatial gene expression in the two partners. Furthermore, cloning of genomic DNA has been achieved for uncultivable fungi and hybridization with homologous or heterologous probes is opening a vast new area of research for identifying genes essential to the different life stages of these organisms. Moreover, approaches like differential RNA display offers alternative strategies for studying the expression and regulation of those fungal genes underlying molecular mechanisms involved in the establishment, maintenance and functioning of the symbiosis. Mycorrhizal research presents a challenging and exciting period when molecular and genetical tool can be used synergistically. The development of techniques permitting studies of the mycorrhizal fungi, which are at best difficult to culture, will expand our understanding of the value and functioning of below-ground root-fungal symbiosis. The author has screened a novel symbiotic fungus Piriformospora indica. This is a cultivable root colonizing and plant promoting fungus. Another fungi of relevance are species of Sebacina and Geosiphon. Some information on the interaction of P. indica with conventional non-host Arabidopsis thaliana is indicated. The author believes that there are many tools for the analysis of the genetic component of the specific biological question and further hopes that this article shall open vistas and thoughts for further challenging new research. Key Words: Colonization; Microsymbiont; Gene expression; Piriformospora indica. DOI: 10.3126/sw.v5i5.2668 Scientific World, Vol. 5, No. 5, July 2007 115-131

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Physiological and transcriptomic response of Medicago truncatula to high and low benefit mycorrhizal fungi

10.1101/2020.12.11.421693 ◽

2020 ◽

Author(s):

Kevin R. Cope ◽

Arjun Kafle ◽

Jaya Krishna Yakha ◽

Philip E. Pfeffer ◽

Gary D. Strahan ◽

...

Keyword(s):

Medicago Truncatula ◽

Mycorrhizal Fungi ◽

Host Plants ◽

Molecular Mechanisms ◽

Plant Biomass ◽

Arbuscular Mycorrhizal ◽

Defense Responses ◽

Ammonium Transporter ◽

Nitrogen And Phosphorus ◽

Transcriptomic Response

Arbuscular mycorrhizal (AM) fungi provide their host plants with greater access to limited mineral nutrients, but the amount they provide can be variable. Here, we evaluated the capacity of the high-benefit fungus Rhizophagus irregularis 09 and the low-benefit fungus Glomus aggregatum 165 to transfer nitrogen and phosphorus to the host plant Medicago truncatula, and identified putative molecular mechanisms regulating the physiological response of the host to these fungi. R. irregularis led to an increase in plant biomass and transferred more nitrogen and phosphate to the host than G. aggregatum. This increase was linked to elevated expression of known mycorrhiza-induced phosphate (PT8), ammonium (AMT2;3), and nitrate (NPF4.12) transporters in the roots, as well as the putative ammonium transporter NIP1;5. R. irregularis also stimulated the expression of photosynthesis related genes in the shoot and the upregulation of the mycorrhiza-induced sugar transporter SWEET1.2 and the lipid biosynthesis gene RAM2 in the roots, which is indicative of increased carbon flux to this fungus. In contrast, G. aggregatum induced biotic stress defense response genes (e.g., Medtr4g120760 and Medtr8g096900) in the shoots, and several genes associated with the GO term "response to water deprivation" in the roots of M. truncatula. This could indicate that the host perceives colonization by the low-benefit fungus as pathogen attack, or that G. aggregatum is more effective than R. irregularis at priming host defense responses. Our findings reveal novel insights into the molecular mechanisms by which host plants reward high- but sanction low-benefit arbuscular mycorrhizal symbionts.

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Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review

Antibiotics ◽

10.3390/antibiotics10040437 ◽

2021 ◽

Vol 10 (4) ◽

pp. 437

Author(s):

Ilaria Maria Saracino ◽

Matteo Pavoni ◽

Angelo Zullo ◽

Giulia Fiorini ◽

Tiziana Lazzarotto ◽

...

Keyword(s):

Antibiotic Resistance ◽

Next Generation Sequencing ◽

Literature Review ◽

Molecular Mechanisms ◽

World Health ◽

Next Generation ◽

Culture Methods ◽

Phenotypic Resistance ◽

H Pylori ◽

Generation Sequencing

Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a “high-priority” bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a “fastidious” microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.

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MicroRNAs from Snellenius manilae bracovirus regulate innate and cellular immune responses of its host Spodoptera litura

Communications Biology ◽

10.1038/s42003-020-01563-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Cheng-Kang Tang ◽

Chih-Hsuan Tsai ◽

Carol-P. Wu ◽

Yu-Hsien Lin ◽

Sung-Chan Wei ◽

...

Keyword(s):

Immune Responses ◽

Spodoptera Litura ◽

Molecular Mechanisms ◽

Innate Immune ◽

Sequencing Analysis ◽

Innate Immune Responses ◽

Cellular Immune Responses ◽

Next Generation Sequencing Analysis ◽

Cellular Immune ◽

Generation Sequencing

AbstractTo avoid inducing immune and physiological responses in insect hosts, parasitoid wasps have developed several mechanisms to inhibit them during parasitism, including the production of venom, specialized wasp cells, and symbioses with polydnaviruses (PDVs). These mechanisms alter the host physiology to give the wasp offspring a greater chance of survival. However, the molecular mechanisms for most of these alterations remain unclear. In the present study, we applied next-generation sequencing analysis and identified several miRNAs that were encoded in the genome of Snellenius manilae bracovirus (SmBV), and expressed in the host larvae, Spodoptera litura, during parasitism. Among these miRNAs, SmBV-miR-199b-5p and SmBV-miR-2989 were found to target domeless and toll-7 in the host, which are involved in the host innate immune responses. Microinjecting the inhibitors of these two miRNAs into parasitized S. litura larvae not only severely decreased the pupation rate of Snellenius manilae, but also restored the phagocytosis and encapsulation activity of the hemocytes. The results demonstrate that these two SmBV-encoded miRNAs play an important role in suppressing the immune responses of parasitized hosts. Overall, our study uncovers the functions of two SmBV-encoded miRNAs in regulating the host innate immune responses upon wasp parasitism.

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Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

Scientific Reports ◽

10.1038/s41598-021-87886-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Sebastiana ◽

A. Gargallo-Garriga ◽

J. Sardans ◽

M. Pérez-Trujillo ◽

F. Monteiro ◽

...

Keyword(s):

Molecular Mechanisms ◽

Positive Impact ◽

Ectomycorrhizal Fungus ◽

Cork Oak ◽

Mycorrhizal Symbiosis ◽

Gamma Aminobutyric Acid ◽

Ectomycorrhizal Symbiosis ◽

Ectomycorrhizal Roots ◽

Oak Tree ◽

Mycorrhizal Roots

AbstractMycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

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Genomics of ageing in twins

Proceedings of The Nutrition Society ◽

10.1017/s0029665114000640 ◽

2014 ◽

Vol 73 (4) ◽

pp. 526-531 ◽

Cited By ~ 3

Author(s):

Massimo Mangino

Keyword(s):

Molecular Mechanisms ◽

Twin Studies ◽

Later Life ◽

Twin Design ◽

The Past ◽

Human Ageing ◽

Classical Twin Design ◽

Environmental Component ◽

Early Life Events ◽

Generation Sequencing

Ageing is a complex multifactorial process, reflecting the progression of all degenerative pathways within an organism. Due to the increase of life expectancy, in recent years, there is a pressing need to identify early-life events and risk factors that determine health outcomes in later life. So far, genetic variation only explains ~20–25 % of the variability of human survival to age 80+. This clearly implies that other factors (environmental, epigenetic and lifestyle) contribute to lifespan and the rate of healthy ageing within an individual. Twin studies in the past two decades proved to be a very powerful tool to discriminate the genetic from the environmental component. The aim of this review is to describe the basic concepts of the twin study design and to report some of the latest studies in which high-throughput technologies (e.g. genome/epigenome-wide assay, next generation sequencing, MS metabolic profiling) combined with the classical twin design have been applied to the analysis of novel ‘omics’ to further understand the molecular mechanisms of human ageing.

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Leakage of K, Mg, Cl, Ca and Mn from imbibing seeds, grains and isolated seed parts

Seed Science Research ◽

10.1017/s0960258500000945 ◽

1991 ◽

Vol 1 (4) ◽

pp. 229-233 ◽

Cited By ~ 16

Author(s):

John N. A. Lott ◽

Vandy Cavdek ◽

Joanne Carson

Keyword(s):

Neutron Activation Analysis ◽

Instrumental Neutron Activation Analysis ◽

Activation Analysis ◽

The Other ◽

Mineral Nutrient ◽

Species Comparisons ◽

Five Elements ◽

Nutrient Reserves ◽

Seed Coats ◽

Storage Reserves

AbstractInstrumental neutron activation analysis (NAA) was used to quantify the amounts of K, Mg, Cl, Ca and Mn leaked into water from imbibing dry seeds, dry fruits and isolated seed parts. A number of intact monocot and dicot dry seeds or fruits were studied as were some isolated parts such as testa, endosperm and embryo. All samples studied leaked detectable amounts of the five elements measured but the amounts leaked varied greatly. In most cases K was leaked in greater amounts than the other elements while Mn was leaked least. The leakage of Ca was highest from isolated seed coats and from mericarps of three umbelliferous species. Comparisons of the amount of element leaked with the total amount of that element present in the starting material showed that leakage, especially of K, represents a substantial loss of mineral nutrient reserves. The degree of leakage of elements did not appear to be closely related to the types of organic storage reserves present.

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Deciphering the Chitin Code in Plant Symbiosis, Defense, and Microbial Networks

Annual Review of Microbiology ◽

10.1146/annurev-micro-051921-114809 ◽

2021 ◽

Vol 75 (1) ◽

pp. 583-607

Author(s):

Devanshi Khokhani ◽

Cristobal Carrera Carriel ◽

Shivangi Vayla ◽

Thomas B. Irving ◽

Christina Stonoha-Arther ◽

...

Keyword(s):

Mycorrhizal Fungi ◽

Growth And Development ◽

Fungal Growth ◽

Mycorrhizal Symbiosis ◽

Signal Molecules ◽

Symbiotic Relationship ◽

Beneficial Microbes ◽

Symbiotic Interactions ◽

Microbe Interactions ◽

Structural Polymer

Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.

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Lateralized and Segmental Overgrowth in Children

Cancers ◽

10.3390/cancers13246166 ◽

2021 ◽

Vol 13 (24) ◽

pp. 6166

Author(s):

Alessandro Mussa ◽

Diana Carli ◽

Simona Cardaropoli ◽

Giovanni Battista Ferrero ◽

Nicoletta Resta

Keyword(s):

Molecular Mechanisms ◽

Management Strategies ◽

Tissue Growth ◽

Body Region ◽

Molecular Defects ◽

Embryonic Tissues ◽

Cellular Signaling Pathway ◽

Segmental Overgrowth ◽

Generation Sequencing ◽

Specific Management

Congenital disorders of lateralized or segmental overgrowth (LO) are heterogeneous conditions with increased tissue growth in a body region. LO can affect every region, be localized or extensive, involve one or several embryonic tissues, showing variable severity, from mild forms with minor body asymmetry to severe ones with progressive tissue growth and related relevant complications. Recently, next-generation sequencing approaches have increased the knowledge on the molecular defects in LO, allowing classifying them based on the deranged cellular signaling pathway. LO is caused by either genetic or epigenetic somatic anomalies affecting cell proliferation. Most LOs are classifiable in the Beckwith–Wiedemann spectrum (BWSp), PI3KCA/AKT-related overgrowth spectrum (PROS/AROS), mosaic RASopathies, PTEN Hamartoma Tumor Syndrome, mosaic activating variants in angiogenesis pathways, and isolated LO (ILO). These disorders overlap over common phenotypes, making their appraisal and distinction challenging. The latter is crucial, as specific management strategies are key: some LO is associated with increased cancer risk making imperative tumor screening since childhood. Interestingly, some LO shares molecular mechanisms with cancer: recent advances in tumor biological pathway druggability and growth downregulation offer new avenues for the treatment of the most severe and complicated LO.

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