scholarly journals Systematic characterization of gene function in a photosynthetic organism

2020 ◽  
Author(s):  
Josep Vilarrasa-Blasi ◽  
Friedrich Fauser ◽  
Masayuki Onishi ◽  
Silvia Ramundo ◽  
Weronika Patena ◽  
...  
Keyword(s):  
Human Life ◽  
Functional Characterization ◽  
Growth Conditions ◽  
Model Systems ◽  
Mutant Library ◽  
Chemical Treatments ◽  
Photosynthetic Organisms ◽  
Eukaryotic Alga ◽  
Photosynthetic Organism

Photosynthetic organisms are essential for human life, yet most of their genes remain functionally uncharacterized. Single-celled photosynthetic model systems have the potential to accelerate our ability to connect genes to functions. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. 78% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles allow us to place known and previously uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO2-concentrating mechanism, and ciliogenesis. We illustrate the value of this resource by validating novel phenotypes and gene functions, including the discovery of three novel components of a defense pathway that counteracts actin cytoskeleton inhibitors released by other organisms. The data also inform phenotype discovery in land plants: mutants in Arabidopsis thaliana genes exhibit similar phenotypes to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

scholarly journals Identification and Functional Characterization of a Novel Unspliced Transcript Variant of HIC-1 in Human Cancer Cells Exposed to Adverse Growth Conditions

2006 ◽  
Vol 66 (21) ◽  
pp. 10466-10477 ◽  
Author(s):  
Abdul Matin Mondal ◽  
Sivasamy Chinnadurai ◽  
Kamal Datta ◽  
Shyam S. Chauhan ◽  
Subrata Sinha ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Human Cancer ◽  
Functional Characterization ◽  
Growth Conditions ◽  
Transcript Variant ◽  
Human Cancer Cells ◽  
Unspliced Transcript

scholarly journals Discovery and characterization of Hv1-type proton channels in reef-building corals

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gisela Rangel-Yescas ◽  
Cecilia Cervantes ◽  
Miguel A Cervantes-Rocha ◽  
Esteban Suárez-Delgado ◽  
Anastazia T Banaszak ◽  
...  
Keyword(s):  
Ph Regulation ◽  
Functional Characterization ◽  
Model Systems ◽  
Biophysical Properties ◽  
Gene Encoding ◽  
Proton Channels ◽  
Gating Model ◽  
Voltage Dependent ◽  
Insight Into

Voltage-dependent proton-permeable channels are membrane proteins mediating a number of important physiological functions. Here we report the presence of a gene encoding Hv1 voltage-dependent, proton-permeable channels in two species of reef-building corals. We performed a characterization of their biophysical properties and found that these channels are fast-activating and modulated by the pH gradient in a distinct manner. The biophysical properties of these novel channels make them interesting model systems. We have also developed an allosteric gating model that provides mechanistic insight into the modulation of voltage-dependence by protons. This work also represents the first functional characterization of any ion channel in scleractinian corals. We discuss the implications of the presence of these channels in the membranes of coral cells in the calcification and pH-regulation processes and possible consequences of ocean acidification related to the function of these channels.

scholarly journals Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response

Genome ◽  
2018 ◽  
Vol 61 (10) ◽  
pp. 713-723 ◽  
Author(s):  
Zhan Zhang ◽  
Chong Ren ◽  
Luming Zou ◽  
Yi Wang ◽  
Shaohua Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Vitis Vinifera ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Model Systems ◽  
Gata Transcription Factors ◽  
Gata Gene ◽  
Gata Family

The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape, particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress. The potential roles of VvGATA genes in berry development were also investigated. The GATA transcription factors displayed expression diversity among different grape organs and tissues, and some of them showed preferential expression in a specific tissue. Heterotrophic cultured cells were used as model systems for the functional characterization of the VvGATA gene and study of its response to light and phytohormone. Results indicated that some VvGATA genes displayed differential responses to light and phytohormones, suggesting their role in light and hormone signaling pathways. A thorough analysis of GATA transcription factors in grape (V. vinifera L.) presented the characterization and functional prediction of VvGATA genes. The data presented here lay the foundation for further functional studies of grape GATA transcription factors.

scholarly journals A genome-wide algal mutant library reveals a global view of genes required for eukaryotic photosynthesis

2018 ◽  
Author(s):  
Xiaobo Li ◽  
Weronika Patena ◽  
Friedrich Fauser ◽  
Robert E. Jinkerson ◽  
Shai Saroussi ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Protein Coding ◽  
Photosynthetic Organisms ◽  
Protein Coding Genes ◽  
Genome Wide ◽  
A Genome ◽  
Photosynthetic Organism ◽  
Unicellular Organisms ◽  
Life On Earth

Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms that complement the use of multicellular plants by enabling higher-throughput studies. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the flagship unicellular alga Chlamydomonas reinhardtii (Chlamydomonas hereafter). The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We leveraged this feature to perform a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Strikingly, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library is the first genome-wide mapped mutant resource in any unicellular photosynthetic organism, and will accelerate the characterization of thousands of genes in algae, plants and animals.

Functional characterization of human brown adipose tissue metabolism

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin
Keyword(s):  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Functional Characterization ◽  
Human Infants ◽  
Positron Emission ◽  
Brown Adipose ◽  
Treatment Of Obesity ◽  
And Function

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.

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