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Plant gene family

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https://www.readbyqxmd.com/read/30098091/deep-sequencing-identified-potential-mirnas-involved-in-defense-response-stress-and-plant-growth-characteristics-of-wild-genotypes-of-cardamom
#1
F Nadiya, N Anjali, Jinu Thomas, A Gangaprasad, K K Sabu
Cardamom has long been used as a food flavoring agent and in ayurvedic medicines for mouth ulcers, digestive problems, and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reduction in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families including monocot/tissue specific and 14 novel miRNAs in both genotypes...
August 11, 2018: Plant Biology
https://www.readbyqxmd.com/read/30097007/in-silico-insights-on-diverse-interacting-partners-and-phosphorylation-sites-of-respiratory-burst-oxidase-homolog-rbohs-gene-families-from-arabidopsis-and-rice
#2
Gurpreet Kaur, Pratap Kumar Pati
BACKGROUND: NADPH oxidase (Nox) is a critical enzyme involved in the generation of apoplastic superoxide (O2 - ), a type of reactive oxygen species (ROS) and hence regulate a wide range of biological functions in many organisms. Plant Noxes are the homologs of the catalytic subunit from mammalian NADPH oxidases and are known as respiratory burst oxidase homologs (Rbohs). Previous studies have highlighted their versatile roles in tackling different kind of stresses and in plant growth and development...
August 10, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30096455/genome-wide-identification-of-fk506-binding-domain-protein-gene-family-its-characterization-and-expression-analysis-in-tomato-solanum-lycopersicum-l
#3
Muhammad Waseem, Fiaz Ahmad, Sidra Habib, Yanqiag Gao, Zhengguo Li
FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated...
August 7, 2018: Gene
https://www.readbyqxmd.com/read/30094490/response-of-cell-wall-composition-and-rna-seq-transcriptome-to-methyl-jasmonate-in-brachypodium-distachyon-callus
#4
Lucy S Hyde, Till K Pellny, Jackie Freeman, Louise V Michaelson, Rachael Simister, Simon J McQueen-Mason, Rowan A C Mitchell
Methyl-jasmonate induces large increases in p-coumarate linked to arabinoxylan in Brachypodium and in abundance of GT61 and BAHD family transcripts consistent with a role in synthesis of this linkage. Jasmonic acid (JA) signalling is required for many stress responses in plants, inducing large changes in the transcriptome, including up-regulation of transcripts associated with lignification. However, less is known about the response to JA of grass cell walls and the monocot-specific features of arabinoxylan (AX) synthesis and acylation by ferulic acid (FA) and para-coumaric acid (pCA)...
August 9, 2018: Planta
https://www.readbyqxmd.com/read/30094088/the-animal-nuclear-factor-y-an-enigmatic-and-important-heterotrimeric-transcription-factor
#5
REVIEW
Guilin Li, Hang Zhao, Lijun Wang, Ying Wang, Xingqi Guo, Baohua Xu
Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with the ability to bind to CCAAT boxes in nearly all eukaryotes and has long been a topic of interest since it is first identified. In plants, due to each subunit of NF-Y is encoded by multiple gene families, there are a wide variety NF-Y complex combinations that fulfill many pivotal functions. However, the animal NF-Y complex usually has only one type of combination, as each subunit is generally encoded by a single gene. Even though, mounting evidence points to that the animal NF-Y complex is also essential for numerous biological processes involved in proliferation and apoptosis, cancer and tumor, stress responses, growth and development...
2018: American Journal of Cancer Research
https://www.readbyqxmd.com/read/30093908/genome-wide-analysis-of-cdpk-family-in-foxtail-millet-and-determination-of-sicdpk24-functions-in-drought-stress
#6
Tai-Fei Yu, Wan-Ying Zhao, Jin-Dong Fu, Yong-Wei Liu, Ming Chen, Yong-Bin Zhou, You-Zhi Ma, Zhao-Shi Xu, Ya-Jun Xi
Plant calcium-dependent protein kinases (CDPKs) were reported to play important roles in plant resistance to abiotic stress. Foxtail millet cultivation "H138" was used for RNA-seq analysis. The data from drought-induced de novo transcriptomic sequences of foxtail millet showed that CDPKs were up- or down-regulated by drought to different degrees. In this study, 29 foxtail millet CDPKs were classified into four subgroups. These genes were unevenly distributed on nine foxtail millet chromosomes, and chromosomes 2, 3, and 9 contained the most SiCDPK members...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30092779/genome-wide-identification-of-lipoxygenase-gene-family-in-cotton-and-functional-characterization-in-response-to-abiotic-stresses
#7
Muhammad Shaban, Muhammad Mahmood Ahmed, Heng Sun, Abid Ullah, Longfu Zhu
BACKGROUND: Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited. RESULTS: A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G...
August 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/30092656/characterization-of-gata-gene-family-in-vitis-vinifera-genome-wide-analysis-expression-profiles-and-involvement-in-light-and-phytohormone-response
#8
Zhan Zhang, Chong Ren, Luming Zou, Yi Wang, Shaohua Li, Zhenchang Liang
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 (V. vinifera L.), 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...
August 9, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30092654/genome-wide-characterization-and-expression-profiling-of-diacylglycerol-acyltransferase-genes-from-maize
#9
Bowei Yan, Xiaoxuan Xu, Yingnan Gu, Ying Zhao, Xunchao Zhao, Lin He, Changjiang Zhao, Jingyu Xu, Zuotong Li
Diacylglycerol acyltransferase (DGAT) catalyzes the only rate-limiting step in the pathway of plant oil (TAG) biosynthesis and involves in plant development. In this study, five <i>DGAT</i> family members were identified from maize genome database. Phylogenetic analysis classified the ZmDGATs into type-I, II and III clusters, respectively. The conserved functional domain analysis revealed that the proteins encoded by ZmDGAT1s contained the conserved MBOAT domains, while two ZmDGAT2s encoding proteins harbored the LPLAT domains...
August 9, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/30092047/functional-characterization-of-unique-enzymes-in-xanthomonas-euvesicatoria-related-to-degradation-of-arabinofurano-oligosaccharides-on-hydroxyproline-rich-glycoproteins
#10
Masayuki Nakamura, Yuino Yasukawa, Akira Furusawa, Tamao Fuchiwaki, Takashi Honda, Yuta Okamura, Kiyotaka Fujita, Hisashi Iwai
In this study, we clarified the functions of three uncharacterized enzymes, XCV2724, XCV2728, and XCV2729, in Xanthomonas euvesicatoria, the causal agent of bacterial spot of tomato and pepper. The genes corresponding to the three enzymes are homologs of hypBA1, hypBA2, and hypAA from Bifidobacterium longum and are unique to Xanthomonas spp. among plant pathogenic bacteria. Functional characterization of the recombinant enzymes expressed using microbial systems revealed that they degrade the arabinofurano-oligosaccharides present on hydroxyproline (Hyp)-rich glycoproteins (HRGPs) such as extensin and solanaceous lectins in plant cell walls...
2018: PloS One
https://www.readbyqxmd.com/read/30090111/functional-analysis-of-psavr3c-effector-family-from-phytophthora-provides-probes-to-dissect-skrp-mediated-plant-susceptibility
#11
Ying Zhang, Jie Huang, Sylvans O Ochola, Suomeng Dong
PsAvr3c is an effector identified from oomycete plant pathogen Phytophthora sojae that causes soybean root and stem rot disease. Earlier studies have demonstrated that PsAvr3c binds to a novel soybean spliceosomal complex protein, GmSKRP, to reprogram the splicing of hundreds of pre-mRNAs and consequently subvert host immunity. PsAvr3c family genes are present in some other Phytophthora species, but their function remains unknown. Here, we characterized the functions of PsAvh27b ( PsAvr3c paralog from P. sojae ), ProbiAvh89 and PparvAvh214 (orthologs from P...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30088201/involvement-of-a-coumarin-analog-ad-013-in-the-dna-damage-response-pathways-in-mcf-7-cells
#12
Angelika Długosz, Joanna Drogosz, Dariusz Deredas, Tomasz Janecki, Anna Janecka
Coumarin is a plant-derived compound but as such has no medical uses. Several synthetic coumarin analogs have been shown to possess anti-proliferative activity and to induce apoptosis in cancer cells. Here, we explored DNA damage responses in MCF-7 cells treated with our novel synthetic hybrid compound AD-013, which integrates a coumarin moiety and an α-methylene-δ-lactone motif. The mRNA expression of several genes engaged in DNA-damage-induced responses was assessed by quantitative real-time PCR. The protein levels of a few members of phosphoinositide-3-kinases family (ATM, ATR and DNA-PK) and BRCA1 were assessed by ELISA, while p53 was evaluated by western blot method...
August 7, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/30088087/marker-trait-association-for-low-light-intensity-tolerance-in-rice-genotypes-from-eastern-india
#13
Suvendhu S Dutta, Wricha Tyagi, Gratify Pale, Judith Pohlong, C Aochen, Avinash Pandey, Arunava Pattanayak, Mayank Rai
Light intensity is a crucial environmental factor that affects photosynthesis and ultimately, grain yield in rice. However, no gene or marker directly associated with improved performance under low-light intensity under field conditions has been identified till date. With an aim of identifying genes and markers associated with improved performance (measured in terms of better yields) under low-light intensity, an integrated field screening, in silico and wet lab validation analysis was performed. Field-based screening of a diverse set of 110 genotypes led to the identification of two physiological and three morphological parameters critical for low-light tolerance in rice...
August 7, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30087396/acr11-modulates-levels-of-reactive-oxygen-species-and-salicylic-acid-associated-defense-response-in-arabidopsis
#14
Shashi Kant Singh, Tzu-Ying Sung, Tsui-Yun Chung, Shao-Yu Lin, Sang-Chu Lin, Jo-Chien Liao, Wei-Yu Hsieh, Ming-Hsiun Hsieh
The ACT domain (aspartate kinase, chorismate mutase and TyrA), an allosteric effector binding domain, is commonly found in amino acid metabolic enzymes. In addition to ACT domain-containing enzymes, plants have a novel family of ACT domain repeat (ACR) proteins, which do not contain any recognizable catalytic domain. Arabidopsis has 12 ACR proteins, whose functions are largely unknown. To study the functions of Arabidopsis ACR11, we have characterized two independent T-DNA insertion mutants, acr11-2 and acr11-3...
August 7, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30085848/development-of-a-screening-platform-to-identify-small-molecules-that-modify-elp1-pre-mrna-splicing-in-familial-dysautonomia
#15
Monica Salani, Fabio Urbina, Anthony Brenner, Elisabetta Morini, Ranjit Shetty, C Scott Gallagher, Emily A Law, Sara Sunshine, Dylan J Finneran, Graham Johnson, Lisa Minor, Susan A Slaugenhaupt
Familial dysautonomia (FD) is an autonomic and sensory neuropathy caused by a mutation in the splice donor site of intron 20 of the ELP1 gene. Variable skipping of exon 20 leads to a tissue-specific reduction in the level of ELP1 protein. We have shown that the plant cytokinin kinetin is able to increase cellular ELP1 protein levels in vivo and in vitro through correction of ELP1 splicing. Studies in FD patients determined that kinetin is not a practical therapy due to low potency and rapid elimination. To identify molecules with improved potency and efficacy, we developed a cell-based luciferase splicing assay by inserting renilla (Rluc) and firefly (Fluc) luciferase reporters into our previously well-characterized ELP1 minigene construct...
August 7, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/30084143/evolutionary-and-ecological-links-between-plant-and-fungal-viruses
#16
REVIEW
Marilyn J Roossinck
I. II. III. IV. References SUMMARY: Plants and microorganisms have been interacting in both positive and negative ways for millions of years. They are also frequently infected with viruses that can have positive or negative impacts. A majority of virus families with members that infect fungi have counterparts that infect plants, and in some cases the phylogenetic analyses of these virus families indicate transmission between the plant and fungal kingdoms. These similarities reflect the host relationships; fungi are evolutionarily more closely related to animals than to plants but share very few viral signatures with animal viruses...
August 7, 2018: New Phytologist
https://www.readbyqxmd.com/read/30083437/genome-wide-analysis-reveals-four-key-transcription-factors-associated-with-cadmium-stress-in-creeping-bentgrass-agrostis-stolonifera-l
#17
Jianbo Yuan, Yuqing Bai, Yuehui Chao, Xinbo Sun, Chunyan He, Xiaohong Liang, Lijuan Xie, Liebao Han
Cadmium (Cd) toxicity seriously affects the growth and development of plants, so studies on uptake, translocation, and accumulation of Cd in plants are crucial for phytoremediation. However, the molecular mechanism of the plant response to Cd stress remains poorly understood. The main objective of this study was to reveal differentially expressed genes (DEGs) under lower (BT2_5) and higher (BT43) Cd concentration treatments in creeping bentgrass. A total of 463,184 unigenes were obtained from creeping bentgrass leaves using RNA sequencing technology...
2018: PeerJ
https://www.readbyqxmd.com/read/30083357/loss-or-duplication-of-key-regulatory-genes-coincides-with-environmental-adaptation-of-the-stomatal-complex-in-nymphaea-colorata-and-kalanchoe-laxiflora
#18
Meizhi Xu, Fei Chen, Shilian Qi, Liangsheng Zhang, Shuang Wu
The stomatal complex is critical for gas and water exchange between plants and the atmosphere. Originating over 400 million years ago, the structure of the stomata has evolved to facilitate the adaptation of plants to various environments. Although the molecular mechanism of stomatal development in Arabidopsis has been widely studied, the evolution of stomatal structure and its molecular regulators in different species remains to be answered. In this study, we examined stomatal development and the orthologues of Arabidopsis stomatal genes in a basal angiosperm plant, Nymphaea colorata , and a member of the eudicot CAM family, Kalanchoe laxiflora , which represent the adaptation to aquatic and drought environments, respectively...
2018: Horticulture Research
https://www.readbyqxmd.com/read/30083172/genome-wide-identification-and-functional-analysis-of-nadph-oxidase-family-genes-in-wheat-during-development-and-environmental-stress-responses
#19
Chun-Hong Hu, Xiao-Yong Wei, Bo Yuan, Lin-Bo Yao, Tian-Tian Ma, Peng-Peng Zhang, Xiang Wang, Peng-Qi Wang, Wen-Ting Liu, Wen-Qiang Li, Lai-Sheng Meng, Kun-Ming Chen
As the key producers of reactive oxygen species (ROS), NADPH oxidases (NOXs), also known as respiratory burst oxidase homologs (RBOHs), play crucial roles in various biological processes in plants with considerable evolutionary selection and functional diversity in the entire terrestrial plant kingdom. However, only limited resources are available on the phylogenesis and functions of this gene family in wheat. Here, a total of 46 NOX family genes were identified in the wheat genome, and these NOXs could be classified into three subgroups: typical TaNOXs, TaNOX-likes, and ferric reduction oxidases (TaFROs)...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30083084/the-genetic-locus-underlying-red-foliage-and-fruit-skin-traits-is-mapped-to-the-same-location-in-the-two-pear-bud-mutants-red-zaosu-and-max-red-bartlett
#20
Huabai Xue, Suke Wang, Jia-Long Yao, Xiaoli Zhang, Jian Yang, Long Wang, Yanli Su, Lei Chen, Huirong Zhang, Xiugen Li
Background: Red-skinned pears are attractive to consumers because of their aesthetic appeal and the antioxidant-associated health benefits provided by the anthocyanins in their red skin. In China, the 'Red Zaosu' (RZS) red bud mutation of the Zaosu (ZS) pear has been used as a parent in Asian pear breeding to generate new cultivars with crispy red fruit and red tender shoots resembling those of the 'Max Red Bartlett' (MRB) pears. Results: In this study, a segregation ratio of 1:1 was observed between plants with red or green shoots in four families with RZS as the only red shoot gene donor parent, suggesting that the red shoot trait of RZS is associated with a dominant gene...
2018: Hereditas
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