scholarly journals Genetic compensation of triacylglycerol biosynthesis in the green microalga Chlamydomonas reinhardtii

2021 ◽  
Author(s):  
Yi-Ying Lee ◽  
Rudolph Park ◽  
Stephen Miller ◽  
Yantao Li
Keyword(s):  
Abiotic Stress ◽  
Chlamydomonas Reinhardtii ◽  
Insertional Mutagenesis ◽  
Rapid Development ◽  
Redox Homeostasis ◽  
Model Systems ◽  
Knockout Mutant ◽  
Genetic Robustness ◽  
Tag Biosynthesis ◽  
Genetic Compensation

Genetic compensation has been proposed to explain phenotypic differences between gene knockouts and knockdowns in several metazoan and plant model systems. With the rapid development of reverse genetic tools such as CRISPR/Cas9 and RNAi in microalgae, it is increasingly important to assess whether genetic compensation affects the phenotype of engineered algal mutants. While exploring triacylglycerol (TAG) biosynthesis pathways in the model alga Chlamydomonas reinhardtii, it was discovered that knockout of certain genes catalyzing rate-limiting steps of TAG biosynthesis, type-2 diacylglycerol acyltransferase genes (DGTTs), triggered genetic compensation under abiotic stress conditions. Genetic compensation of a DGTT1 null mutation by a related PDAT gene was observed regardless of the strain background or mutagenesis approach, e.g., CRISPR/Cas 9 or insertional mutagenesis. However, no compensation was found in the PDAT knockout mutant. The effect of PDAT knockout was evaluated in a Δvtc1 mutant, in which PDAT was up-regulated under stress, resulting in a 90% increase in TAG content. Knockout of PDAT in the Δvtc1 background induced a 12.8-fold upregulation of DGTT1 and a 272.3% increase in TAG content in Δvtc1/pdat1 cells, while remaining viable. These data suggest that genetic compensation contributes to the genetic robustness of microalgal TAG biosynthetic pathways, maintaining lipid and redox homeostasis in the knockout mutants under abiotic stress. This work demonstrates examples of genetic compensation in microalgae, implies the physiological relevance of genetic compensation in TAG biosynthesis under stress, and provides guidance for future genetic engineering and mutant characterization efforts.

Insertional Mutagenesis of Chlamydomonas reinhardtii

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (24) ◽  
Author(s):  
Chia-Hong Tsai ◽  
Christoph Benning
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Insertional Mutagenesis

scholarly journals Ovarian Tumor Domain-Containing Proteases-Deubiquitylation Enzyme Gene SsCI33130 Involved in the Regulation of Mating/Filamentation and Pathogenicity in Sporisorium scitamineum

2021 ◽  
Vol 12 ◽  
Author(s):  
Huizhong Li ◽  
Yichang Cai ◽  
Quanqing Deng ◽  
Han Bao ◽  
Jianwen Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Small Molecule ◽  
Effective Control ◽  
Economic Losses ◽  
Wild Type ◽  
Knockout Mutant ◽  
Expression Levels ◽  
Sporisorium Scitamineum ◽  
Knockout Mutants ◽  
Sexual Mating

Sugarcane is an important sugar crop. Sugarcane smut, caused by Sporisorium scitamineum, is a worldwide sugarcane disease with serious economic losses and lack of effective control measures. Revealing the molecular pathogenesis of S. scitamineum is very helpful to the development of effective prevention and control technology. Deubiquitinase removes ubiquitin molecules from their binding substrates and participates in a variety of physiological activities in eukaryotes. Based on the transcriptome sequencing data of two isolates (Ss16 and Ss47) of S. scitamineum with different pathogenicities, SsCI33130, a gene encoding an OTU1-deubiquitin enzyme, was identified. The positive knockout mutants and complementary mutants of the SsCI33130 gene were successfully obtained through polyethylene glycol-mediated protoplast transformation technology. In order to study the possible function of this gene in pathogenicity, phenotypic comparison of the growth, morphology, abiotic stress, sexual mating, pathogenicity, and gene expression levels of the knockout mutants, complementary mutants, and their wild type strains were conducted. The results demonstrated that the gene had almost no effect on abiotic stress, cell wall integrity, growth, and morphology, but was related to the sexual mating and pathogenicity of S. scitamineum. The sexual mating ability and pathogenicity between the knockout mutants or between the knockout mutant and wild type were more significantly reduced than between the wild types, the complementary mutants, or the wild types and complementary mutants. The sexual mating between the knockout mutants or between the knockout mutant and wild type could be restored by the exogenous addition of small-molecule signaling substances such as 5 mM cyclic adenosine monophosphate (cAMP) or 0.02 mM tryptophol. In addition, during sexual mating, the expression levels of tryptophol and cAMP synthesis-related genes in the knockout mutant combinations were significantly lower than those in the wild type combinations, while the expression levels in the complementary mutant combinations were restored to the level of the wild type. It is speculated that the SsCI33130 gene may be involved in the development of sexual mating and pathogenicity in S. scitamineum by regulating the synthesis of the small-molecule signaling substances (cAMP or tryptophol) required during the sexual mating of S. scitamineum, thereby providing a molecular basis for the study of the pathogenic mechanisms of S. scitamineum.

Antioxidative Machinery for Redox Homeostasis During Abiotic Stress

2019 ◽  
pp. 65-90
Author(s):  
Nimisha Amist ◽  
Chanda Bano ◽  
N. B. Singh
Keyword(s):  
Abiotic Stress ◽  
Redox Homeostasis

scholarly journals Mutational analysis of the phototransduction pathway of Chlamydomonas reinhardtii.

1995 ◽  
Vol 131 (2) ◽  
pp. 427-440 ◽  
Author(s):  
G J Pazour ◽  
O A Sineshchekov ◽  
G B Witman
Keyword(s):  
Signal Transduction ◽  
Chlamydomonas Reinhardtii ◽  
Insertional Mutagenesis ◽  
Mutational Analysis ◽  
Signal Transduction Pathway ◽  
Transduction Pathway ◽  
Normal Manner ◽  
Normal Light ◽  
Phototransduction Pathway

Chlamydomonas has two photobehavioral responses, phototaxis and photoshock. Rhodopsin is the photoreceptor for these responses and the signal transduction process involves transmembrane Ca2+ fluxes. This causes transient changes in flagellar beating, ultimately resulting in phototaxis or photoshock. To identify components that make up this signal transduction pathway, we generated nonphototactic strains by insertional mutagenesis. Seven new phototaxis genes were identified (ptx2-ptx8); alleles of six of these are tagged by the transforming DNA and therefore should be easily cloned. To order the mutants in the pathway, we characterized them electrophysiologically, behaviorally, and structurally, ptx5, ptx6, and ptx7 have normal light-induced photoreceptor currents (PRC) and flagellar currents (FC) but their pattern of swimming does not change in the normal manner when the intraflagellar Ca2+ concentration is decreased, suggesting that they have defects in the ability of their axonemes to respond to changes in Ca2+ concentration. ptx2 and ptx8 lack the FC but have normal PRCs, suggesting that they are defective in the flagellar Ca2+ channel or some factor that regulates it. ptx4 mutants have multiple eye-spots. ptx3 mutants are defective in a component essential for phototaxis but bypassed during photoshock; this component appears to be located downstream of the PRC but upstream of the axoneme.

scholarly journals Visualization and Analysis in the Field of Pan-Cancer Studies and Its Application in Breast Cancer Treatment

2021 ◽  
Vol 8 ◽  
Author(s):  
Xianwen Zhang ◽  
Han Lai ◽  
Fan Zhang ◽  
Yixi Wang ◽  
Li Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
International Cooperation ◽  
Cancer Biology ◽  
Rapid Development ◽  
Tumor Biology ◽  
The United States ◽  
Model Systems ◽  
Pan Cancer ◽  
Biology Research ◽  
Cancer Studies

Although all cancers are molecularly distinct, many share common driver mutations. Pan-cancer analysis, utilizes next-generation sequencing (NGS), pan-cancer model systems, and pan-cancer projects such as The Cancer Genome Atlas (TCGA), to assess frequently mutated genes and other genomic abnormalities that are common among many cancer types, regardless of the tumor origin, providing new directions for tumor biology research. However, there is currently no study that has objectively analyzed the results of pan-cancer studies on cancer biology. For this study, 999 articles on pan-cancer published from 2006 to 2020 were obtained from the Scopus database, and bibliometric methods were used to analyze citations, international cooperation, co-authorship and keyword co-occurrence clusters. Furthermore, we also focused on and summarized the application of pan-cancer in breast cancer. Our result shows that the pan-cancer studies were first published in 2006 and entered a period of rapid development after 2013. So far, 86 countries have carried out international cooperation in sharing research. Researchers form the United States and Canada have published the most articles and have made the most extensive contribution to this field, respectively. Through author keyword analysis of the 999 articles, TCGA, biomarkers, NGS, immunotherapy, DNA methylation, prognosis, and several other keywords appear frequently, and these terms are hot spots in pan-cancer studies. There are four subtypes of breast cancer (luminalA, luminalB, HER2, and basal-like) according to pan-cancer analysis of breast cancer. Meanwhile, it was found that breast cancer has genetic similarity to pan-gynecological cancers, such as ovarian cancer, which indicates related etiology and possibly similar treatments. Collectively, with the emergence of new detection methods, new cancer databases, and the involvement of more researchers, pan-cancer analyses will play a greater role in cancer biology research.

scholarly journals Arbuscular Mycorrhiza-Mediated Regulation of Polyamines and Aquaporins During Abiotic Stress: Deep Insights on the Recondite Players

2021 ◽  
Vol 12 ◽  
Author(s):  
Karuna Sharma ◽  
Samta Gupta ◽  
Sarda Devi Thokchom ◽  
Pooja Jangir ◽  
Rupam Kapoor
Keyword(s):  
Abiotic Stress ◽  
Mycorrhizal Fungi ◽  
Defense Mechanisms ◽  
Redox Homeostasis ◽  
Arbuscular Mycorrhizal ◽  
Antioxidant Defense System ◽  
Current State ◽  
Stress Signals ◽  
Different Origins ◽  
Molecular Bases

Environmental stresses of (a)biotic origin induce the production of multitudinous compounds (metabolites and proteins) as protective defense mechanisms in plants. On account of the regulation of some of these compounds, arbuscular mycorrhizal fungi (AMF) reinforce the inherent tolerance of plants toward the stress of different origins and kind. This article reviews two specific fundamental mechanisms that are categorically associated with mycorrhiza in alleviating major abiotic stresses, salt, drought, and heavy metal (HM) toxicity. It puts emphasis on aquaporins (AQPs), the conduits of water and stress signals; and polyamines (PAs), the primordial stress molecules, which are regulated by AMF to assure water, nutrient, ion, and redox homeostasis. Under stressful conditions, AMF-mediated host AQP responses register distinct patterns: an upregulation to encourage water and nutrient uptake; a downregulation to restrict water loss and HM uptake; or no alterations. The patterns thereof are apparently an integrative outcome of the duration, intensity, and type of stress, AMF species, the interaction of fungal AQPs with that of plants, and the host type. However, the cellular and molecular bases of mycorrhizal influence on host AQPs are largely unexplored. The roles of PAs in augmenting the antioxidant defense system and improving the tolerance against oxidative stress are well-evident. However, the precise mechanism by which mycorrhiza accords stress tolerance by influencing the PA metabolism per se is abstruse and broadly variable under different stresses and plant species. This review comprehensively analyzes the current state-of-art of the involvement of AMF in “PA and AQP modulation” under abiotic stress and identifies the lesser-explored landscapes, gaps in understanding, and the accompanying challenges. Finally, this review outlines the prospects of AMF in realizing sustainable agriculture and provides insights into potential thrust areas of research on AMF and abiotic stress.

scholarly journals GeneHummus: A pipeline to define gene families and their expression in legumes and beyond

2018 ◽  
Author(s):  
Jose V. Die ◽  
Moamen Mahmoud Elmassry ◽  
Kimberly Hathaway LeBlanc ◽  
Olaitan I. Awe ◽  
Allissa Dillman ◽  
...  
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
High Specificity ◽  
Gene Families ◽  
Model Systems ◽  
Auxin Receptor ◽  
Plant Gene ◽  
Sequencing Technologies ◽  
Specificity And Sensitivity ◽  
The Impact

AbstractDuring the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called ‘orphan crops’) is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. Analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. Here, we present the GeneHummus pipeline, a step-by-step R-based pipeline for the identification, characterization and expression analysis of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. We anticipate that our pipeline should be suitable for any plant gene family, and likely other gene families, vastly improving the speed and ease of genomic data processing.

Sign in / Sign up

Export Citation Format

Share Document