scholarly journals Function of histone H2B monoubiquitination in transcriptional regulation of auxin biosynthesis in Arabidopsis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Li Zhang ◽  
Pan Luo ◽  
Jie Bai ◽  
Lei Wu ◽  
Dong-Wei Di ◽  
...  
Keyword(s):  
Growth And Development ◽  
Large Scale ◽  
Auxin Biosynthesis ◽  
Gene Encoding ◽  
Histone H2b ◽  
Synthetic Genes ◽  
Auxin Homeostasis ◽  
Coding Regions ◽  
Root Waving ◽  
Exogenous Cytokinin

AbstractThe auxin IAA is a vital plant hormone in controlling growth and development, but our knowledge about its complicated biosynthetic pathways and molecular regulation are still limited and fragmentary. cytokinin induced root waving 2 (ckrw2) was isolated as one of the auxin-deficient mutants in a large-scale forward genetic screen aiming to find more genes functioning in auxin homeostasis and/or its regulation. Here we show that CKRW2 is identical to Histone Monoubiquitination 1 (HUB1), a gene encoding an E3 ligase required for histone H2B monoubiquitination (H2Bub1) in Arabidopsis. In addition to pleiotropic defects in growth and development, loss of CKRW2/HUB1 function also led to typical auxin-deficient phenotypes in roots, which was associated with significantly lower expression levels of several functional auxin synthetic genes, namely TRP2/TSB1, WEI7/ASB1, YUC7 and AMI1. Corresponding defects in H2Bub1 were detected in the coding regions of these genes by chromatin immunoprecipitation (ChIP) analysis, indicating the involvement of H2Bub1 in regulating auxin biosynthesis. Importantly, application of exogenous cytokinin (CK) could stimulate CKRW2/HUB1 expression, providing an epigenetic avenue for CK to regulate the auxin homeostasis. Our results reveal a previously unknown mechanism for regulating auxin biosynthesis via HUB1/2-mediated H2Bub1 at the chromatin level.

scholarly journals Multiomics-based dissection of citrus flavonoid metabolism using a Citrus reticulata × Poncirus trifoliata population

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jiaolin Mou ◽  
Zhehui Zhang ◽  
Haiji Qiu ◽  
Yang Lu ◽  
Xiang Zhu ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Large Scale ◽  
Genetic Basis ◽  
Transcriptional Profiling ◽  
Complete Characterization ◽  
Poncirus Trifoliata ◽  
Gene Encoding ◽  
Coding Regions ◽  
Flavonoid Biosynthetic Pathway

AbstractDeciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes. Although citrus plants are among the most important fruit crops worldwide, the genetic basis of secondary metabolism in these plants is largely unknown. Here, we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues (young leaf, old leaf, mature pericarp, and mature pulp) of an F1 pseudo-testcross citrus population. We detected 80 flavonoids in this population and identified 138 quantitative trait loci (QTLs) for 57 flavonoids in these four tissues. Based on transcriptional profiling and functional annotation, twenty-one candidate genes were identified, and one gene encoding flavanone 3-hydroxylase (F3H) was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions. The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.

PROTOTIPE APLIKASI PENYIRAMAN TANAMAN MENGGUNAKAN SENSOR KELEMBABAN TANAH BERBASIS MICRO CONTOLLER ATMEGA 328

2019 ◽  
Vol 5 (1) ◽  
pp. 97-106
Author(s):  
Rudi Budi Agung ◽  
Muhammad Nur ◽  
Didi Sukayadi
Keyword(s):  
Soil Moisture ◽  
Growth And Development ◽  
Large Scale ◽  
Simple Method ◽  
Moisture Sensor ◽  
Sensor Development ◽  
Soil Moisture Sensor ◽  
Application Systems ◽  
Harvesting Systems ◽  
Working Principle

The Indonesian country which is famous for its tropical climate has now experienced a shift in two seasons (dry season and rainy season). This has an impact on cropping and harvesting systems among farmers. In large scale this is very influential considering that farmers in Indonesia are stilldependent on rainfall which results in soil moisture. Some types of plants that are very dependent on soil moisture will greatly require rainfall or water for growth and development. Through this research, researchers tried to make a prototype application for watering plants using ATMEGA328 microcontroller based soil moisture sensor. Development of application systems using the prototype method as a simple method which is the first step and can be developed again for large scale. The working principle of this prototype is simply that when soil moisture reaches a certainthreshold (above 56%) then the system will work by activating the watering system, if it is below 56% the system does not work or in other words soil moisture is considered sufficient for certain plant needs.

Plant hormones, plant growth regulators

2014 ◽  
Vol 155 (26) ◽  
pp. 1011-1018 ◽  
Author(s):  
György Végvári ◽  
Edina Vidéki
Keyword(s):  
Nervous System ◽  
Growth And Development ◽  
Large Scale ◽  
Essential Role ◽  
Higher Plants ◽  
Structure And Function ◽  
Wide Sense ◽  
Large Scale Integration ◽  
Scale Integration ◽  
And Function

Plants seem to be rather defenceless, they are unable to do motion, have no nervous system or immune system unlike animals. Besides this, plants do have hormones, though these substances are produced not in glands. In view of their complexity they lagged behind animals, however, plant organisms show large scale integration in their structure and function. In higher plants, such as in animals, the intercellular communication is fulfilled through chemical messengers. These specific compounds in plants are called phytohormones, or in a wide sense, bioregulators. Even a small quantity of these endogenous organic compounds are able to regulate the operation, growth and development of higher plants, and keep the connection between cells, tissues and synergy beween organs. Since they do not have nervous and immume systems, phytohormones play essential role in plants’ life. Orv. Hetil., 2014, 155(26), 1011–1018.

Local Auxin Biosynthesis Mediates Plant Growth and Development

2019 ◽  
Vol 24 (1) ◽  
pp. 6-9 ◽  
Author(s):  
Bingsheng Lv ◽  
Zhenwei Yan ◽  
Huiyu Tian ◽  
Xiansheng Zhang ◽  
Zhaojun Ding
Keyword(s):  
Plant Growth ◽  
Growth And Development ◽  
Auxin Biosynthesis ◽  
Plant Growth And Development

scholarly journals EXPLORATION OF BROTH CHICKEN GUT AS GROWTH MEDIA OF Escherichia coli BL21 pET-Endo FOR ENDO-Β-1,4-D-XYLANASE PRODUCTION

2017 ◽  
Vol 13 (2) ◽  
pp. 191
Author(s):  
Anak Agung Istri Ratnadewi ◽  
Moch. Yoris Alidion ◽  
Agung Budi Santoso ◽  
Ika Oktavianawatia
Keyword(s):  
Large Scale ◽  
Incubation Temperature ◽  
Specific Activity ◽  
Hydrolytic Enzyme ◽  
Optimal Growth ◽  
Good Alternative ◽  
Growth Media ◽  
Gene Encoding ◽  
Xylanase Production ◽  
E Coli

<p>Endo-β-1,4-D-xylanase is a hydrolytic enzyme that breakdown the 1.4 chain of xylan polysaccharide. We have succes to transform the plasmid pET-Endo gene encoding endo-1,4-β-D-xylanase from Bacillus sp. originally from termites abdominal to E. coli BL21. The clone was ready for large scale of enzyme production. To reduce production cost, we look for subtitute media for the expensive Luria Berthani broth. Chicken guts broth is good alternative while rich of protein and very cheap. The content of N dissolved chicken guts broth reaches 87 % of LB broth. Growth of E. Coli BL21 in Chicken guts broth and LB broth (as control) was observed by Optical Density (OD) using spectrofotometer. Concentration of glucose added in broth and incubation temperature was varied. The result showed that optimal growth was in addition of 1.5 % glucose and incubated at  37 <sup>o</sup>C for 16 h. This optimal condition was used to grow E. coli BL21 pET-Endo for xylanase production. Enzyme purification was done by Ni-NTA affinity chromatography. Highest protein yield was 0.076 mg/mL obtained in 100 mM imidazole elucidation. The activity and specific activity of xylanase were estimated as 0.042 U/mL and 0.556 U/µg, respectively. The purification factor was 3.16 time and the molecular weight of enzyme was ± 30, 000 Dalton</p>

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

Abstract 2722: Large Scale Mutation Discovery Screen Identifies Functionally Variant UGDH Alleles in Patients with Atrioventricular Valve Defects

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Jeroen Bakkers ◽  
Sonja Chocron ◽  
Victor Gouriev ◽  
Kelly Smith ◽  
Ronald Lekanne dit Deprez ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Congenital Heart Defects ◽  
Congenital Heart ◽  
Large Scale ◽  
Heart Defects ◽  
Glucose Dehydrogenase ◽  
Model Organisms ◽  
Missense Mutations ◽  
Coding Regions

Background: Congenital heart defects are the most common birth defects. Although genetic dispositions are believed to cause CHDs, only few genes have been identified that harbour mutations causing such defects. Studies in model organisms have identified many essential genes for cardiac development. UDP-glucose dehydrogenase (UGDH) enzymatic activity is required for the signal transduction of FGF and Wnt ligands and zebrafish jekyll/ugdh mutations lack AV valves. Methods and Results: From literature candidate genes were selected that are essential for AV canal-, septum-, and valve formation. By large scale sequencing we analysed the coding regions of 36 candidate genes in 192 patients with reported AVSDs. As a result we identified 457 genetic variations of which 207 variants are in flanking non-coding regions, 156 variants are in coding regions but silent and 94 variants are non-synonymous variants that alter the protein sequence. Comparison with the available databases such as HapMap and screening 350 control individuals resulted in the validation of 49 non-synonomous missense mutations in 23 genes only present in the patient group. These included novel GATA4 missense mutations (R285C and M224V) located in the highly conserved DNA binding domains, which by in vitro analysis significantly reduce transcriptional activity of the protein. Three patients with mitral valvar prolapse and mitral regurgitation were identified with novel missense mutations in the UDP-glucose dehydrogenase (UGDH) gene (R141C and E416D). In vitro experiments demonstrated a negative affect on enzyme activity and stability by a change in protein conformation. Furthermore, experiments in zebrafish jekyll/ugdh mutants showed that UGDH R141C and UGDH E416D couldn’t rescue the defects in AV formation demonstrating an inactivating effect of these missense mutations in vivo. Conclusions: A model organism based candidate gene screen in CHD patients resulted in the identification of novel functional missense mutations in the UGDH gene not previously implicated in congenital heart defects.

N6-methyladenosine modification modulate in the heat stress of sheep (Ovis aries)

2019 ◽  
Author(s):  
Zengkui Lu ◽  
Huihua Wang ◽  
Youji Ma ◽  
Mingxing Chu ◽  
Kai Quan ◽  
...  
Keyword(s):  
Heat Stress ◽  
Signaling Pathways ◽  
Stress Responses ◽  
Large Scale ◽  
Ovis Aries ◽  
Stop Codons ◽  
Coding Regions ◽  
Mrna Methylation ◽  
Response To Stress ◽  
And Control

Abstract Background: Intensive and large-scale development of the sheep industry and increases in global temperature are increasingly exposing sheep to heat stress. N6-methyladenosine (m6A) mRNA methylation varies in response to stress, and can link external stress with complex transcriptional and post-transcriptional processes. However, no m6A mRNA methylation map has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Results: A total of 8,306 and 12,958 m6A peaks were detected in heat stress and control groups, respectively, with 2,697 and 5,494 genes associated with each. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO revealed that differential m6A-containing genes were mainly enriched in the nucleus and were involved in several stress responses and substance metabolism processes. KEGG pathway analysis found that differential m6A-containing genes were significantly enriched in Rap1, FoxO, MAPK, and other signaling pathways of the stress response, and TGF-beta, AMPK, Wnt, and other signaling pathways involved in fat metabolism. These m6A-modified genes were moderately expressed in both heat stress and control sheep, and the enrichment of m6A modification was significantly negatively correlated with gene expression. Conclusions: Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep, and it also provided a new way for the study of animal response to heat stress.

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