Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity

Knowledge of cellular compartmentation is critical to an understanding of many aspects of biological function in plant cells but it remains an under-emphasised concept in the use of and investment in plant functional genomic tools. The emerging effort in plant subcellular proteomics is discussed, and the current datasets that are available for a series of organelles and cellular membranes isolated from a range of plant species are noted. The benefit of knowing subcellular location in determining the role of proteins of unknown function is considered alongside the challenges faced in this endeavour. These include clear problems in dealing with contamination during the isolation of subcellular compartments, the meaningful integration of these datasets once completed to assemble a jigsaw of the cellular proteome as a whole, and the use of the wider literature in supplementing this proteomic discovery effort.

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Agrobacterium tumefaciens Gene Transfer: How a Plant Pathogen Hacks the Nuclei of Plant and Nonplant Organisms

Phytopathology ◽

10.1094/phyto-12-14-0380-rvw ◽

2015 ◽

Vol 105 (10) ◽

pp. 1288-1301 ◽

Cited By ~ 38

Author(s):

Salim Bourras ◽

Thierry Rouxel ◽

Michel Meyer

Keyword(s):

Genetic Transformation ◽

Host Cell ◽

Dna Integration ◽

Genome Wide ◽

Genomic Tools ◽

Genome Features ◽

Integration Mechanisms ◽

Dna Fragment ◽

Eukaryotic Genomes

Agrobacterium species are soilborne gram-negative bacteria exhibiting predominantly a saprophytic lifestyle. Only a few of these species are capable of parasitic growth on plants, causing either hairy root or crown gall diseases. The core of the infection strategy of pathogenic Agrobacteria is a genetic transformation of the host cell, via stable integration into the host genome of a DNA fragment called T-DNA. This genetic transformation results in oncogenic reprogramming of the host to the benefit of the pathogen. This unique ability of interkingdom DNA transfer was largely used as a tool for genetic engineering. Thus, the artificial host range of Agrobacterium is continuously expanding and includes plant and nonplant organisms. The increasing availability of genomic tools encouraged genome-wide surveys of T-DNA tagged libraries, and the pattern of T-DNA integration in eukaryotic genomes was studied. Therefore, data have been collected in numerous laboratories to attain a better understanding of T-DNA integration mechanisms and potential biases. This review focuses on the intranuclear mechanisms necessary for proper targeting and stable expression of Agrobacterium oncogenic T-DNA in the host cell. More specifically, the role of genome features and the putative involvement of host’s transcriptional machinery in relation to the T-DNA integration and effects on gene expression are discussed. Also, the mechanisms underlying T-DNA integration into specific genome compartments is reviewed, and a theoretical model for T-DNA intranuclear targeting is presented.

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Gut bacteria are essential for normal cuticle development in herbivorous turtle ants

Nature Communications ◽

10.1038/s41467-021-21065-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Christophe Duplais ◽

Vincent Sarou-Kanian ◽

Dominique Massiot ◽

Alia Hassan ◽

Barbara Perrone ◽

...

Keyword(s):

Evolutionary History ◽

Nitrogen Assimilation ◽

Isotope Ratio Mass Spectrometry ◽

Gut Bacteria ◽

Resonance Spectroscopy ◽

Nitrogen Flow ◽

Isotopic Enrichment ◽

History Of ◽

Cuticle Development

AbstractAcross the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.

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Dawn and photoperiod sensing by phytochrome A

10.1101/253989 ◽

2018 ◽

Author(s):

Daniel D Seaton ◽

Gabriela Toledo-Ortiz ◽

Akane Kubota ◽

Ashwin Ganpudi ◽

Takato Imaizumi ◽

...

Keyword(s):

Meta Analysis ◽

Transcriptional Regulator ◽

Functional Genomic ◽

Sensitive Detector ◽

Phytochrome A ◽

Direct Control ◽

Complex Regulation ◽

Subsequent Activation ◽

Seasonal Responses

AbstractIn plants, light receptors play a pivotal role in photoperiod sensing, enabling them to track seasonal progression. Photoperiod sensing arises from an interaction between the plant’s endogenous circadian oscillator and external light cues. Here, we characterise the role of phytochrome A (phyA) in photoperiod sensing. Our meta-analysis of functional genomic datasets identified phyA as a principal transcriptional regulator of morning-activated genes, specifically in short photoperiods. We demonstrate that PHYA expression is under the direct control of the PHYTOCHROME INTERACTING FACTOR transcription factors, PIF4 and PIF5. As a result, phyA protein accumulates during the night, especially in short photoperiods. At dawn phyA activation by light results in a burst of gene expression, with consequences for anthocyanin accumulation. The combination of complex regulation of PHYA transcript and the unique molecular properties of phyA protein make this pathway a sensitive detector of both dawn and photoperiod.Significance statementThe changing seasons subject plants to a variety of challenging environments. In order to deal with this, many plants have mechanisms for inferring the season by measuring the duration of daylight in a day. A number of well-known seasonal responses such as flowering are responsive to daylength or photoperiod. Here, we describe how the photoreceptor protein phytochrome A senses short photoperiods. This arises from its accumulation during long nights, as happens during winter, and subsequent activation by light at dawn. As a result of this response, the abundance of red anthocyanin pigments is increased in short photoperiods. Thus, we describe a mechanism underlying a novel seasonal phenotype in an important model plant species.

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