scholarly journals Discovery of Geranylgeranyl Pyrophosphate Synthase (GGPPS) Paralogs from Haematococcus pluvialis Based on Iso-Seq Analysis and Their Function on Astaxanthin Biosynthesis

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 696
Author(s):  
Danqiong Huang ◽  
Wenfu Liu ◽  
Anguo Li ◽  
Chaogang Wang ◽  
Zhangli Hu
Keyword(s):  
Amino Acids ◽  
Haematococcus Pluvialis ◽  
Enzymatic Reaction ◽  
Biosynthesis Pathway ◽  
Coding Region ◽  
Pantoea Ananatis ◽  
Geranylgeranyl Pyrophosphate ◽  
Geranylgeranyl Pyrophosphate Synthase ◽  
Genome Wide ◽  
The World

Haematococcus pluvialis is widely distributed in the world and well known as the richest natural source of astaxanthin that is a strong antioxidant with excellent commercial value. The pathway of astaxanthin biosynthesis in H. pluvialis has been documented as an enzymatic reaction. Several enzymes have been reported, but their isoforms or homologs have not been investigated genome-wide. To better understand the astaxanthin biosynthesis pathway in H. pluvialis, eight candidates of the geranylgeranyl pyrophosphate synthase gene (HpGGPPS) predicted from Iso-seq data were isolated in this study. The length of coding region of these candidates varied from 960 bp to 1272 bp, composing of 7–9 exons. The putative amino acids of all candidates composed the signature domain of GGPPS gene. However, the motifs in the domain region are varied, indicating different bio-functions. Phylogenetic analysis revealed eight candidates can be clustered into three groups. Only two candidates in Group1 encode the synthase participating in the astaxanthin formation. The yield of astaxanthin from these two candidates, 7.1 mg/g (DW) and 6.5 mg/g (DW) respectively, is significant higher than that from CrtE (2.4 mg/g DW), a GGPPS gene from Pantoea ananatis. This study provides a potential productive pathway for astaxanthin synthesis.

scholarly journals Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Yan Wei ◽  
Wang Jing ◽  
Zhou Youxiang ◽  
Zhao Mingming ◽  
Gong Yan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Camellia Sinensis ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
Tea Plant ◽  
Expression Data ◽  
Marker Assisted Breeding ◽  
Genome Wide ◽  
The World ◽  
Functional Analyses

Tea (Camellia sinensis) is a popular beverage all over the world and a number of studies have focused on the genetic uniqueness of tea and its cultivars. However, molecular mechanisms underlying these phenomena are largely undefined. In this report, based on expression data available from public databases, we performed a series of analyses to identify genes probably relevant to the uniqueness ofC. sinensisand two of its cultivars (LJ43 and ZH2). Evolutionary analyses showed that the evolutionary rates of genes involved in the pathways were not significantly different amongC. sinensis,C. oleifera, andC. azalea. Interestingly, a number of gene families, including genes involved in the pathways synthesizing iconic secondary metabolites of tea plant, were significantly upregulated, expressed inC. sinensis(LJ43) when compared toC. azalea, and this may partially explain its higher content of flavonoid, theanine, and caffeine. Further investigation showed that nonsynonymous mutations may partially contribute to the differences between the two cultivars ofC. sinensis, such as the chlorina and higher contents of amino acids in ZH2. Genes identified as candidates are probably relevant to the uniqueness ofC. sinensisand its cultivars should be good candidates for subsequent functional analyses and marker-assisted breeding.

scholarly journals quemao, a Drosophila Bristle Locus, Encodes Geranylgeranyl Pyrophosphate Synthase

Genetics ◽  
1998 ◽  
Vol 149 (2) ◽  
pp. 1051-1061 ◽  
Author(s):  
Chaoqiang Lai ◽  
Robert McMahon ◽  
Chi Young ◽  
Trudy F C Mackay ◽  
Charles H Langley
Keyword(s):  
Amino Acid ◽  
Larval Instar ◽  
Amino Acid Sequences ◽  
P Element ◽  
Predicted Amino Acid Sequence ◽  
Cdna Clones ◽  
Coding Region ◽  
Geranylgeranyl Pyrophosphate ◽  
Geranylgeranyl Pyrophosphate Synthase ◽  
Rapid Amplification

Abstract The quemao (qm) locus of Drosophila melanogaster is characterized by a P-element-associated mutant lacking most of the large bristles on the thorax and by several EMS-induced recessive lethals. quemao was cloned using a transposon tagging strategy. P-element-mediated transformation demonstrated that the cloned qm DNA sequence (from the 65F cytological region) rescues the mutant phenotype. A 2.3-kb qm transcript was identified by Northern blot analysis by sequencing of the isolated qm cDNA clones and by 5′ rapid amplification cDNA end (RACE). The predicted amino acid sequence (338 residues) of the coding region of the qm transcript shares 42, 31, 13, 20, and 12% identical amino acid sequences with the geranylgeranyl pyrophosphate synthase (GGPPS) of fungi, yeast, plants, archaebacteria, and eubacteria, respectively. It also contains five highly conserved domains common among all known isoprenyl pyrophosphate synthases. The P element associated with the original qm mutant is inserted in the 5′ untranslated region of the transcript. An EMS-induced qm nonsense mutation at the 12th codon leads to recessive lethality at the first larval instar, indicating the essential role of qm in the isoprenoid biosynthesis of insects.

scholarly journals Functional genomics of autoimmune diseases

2021 ◽  
pp. annrheumdis-2019-216794
Author(s):  
Akari Suzuki ◽  
Matteo Maurizio Guerrini ◽  
Kazuhiko Yamamoto
Keyword(s):  
Autoimmune Diseases ◽  
Association Studies ◽  
Linkage Disequilibrium Block ◽  
Causal Variant ◽  
Genome Wide Association Studies ◽  
Coding Region ◽  
Risk Variants ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Long Non Coding Rna

For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.

scholarly journals Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

Inventions ◽  
2021 ◽  
Vol 6 (2) ◽  
pp. 37
Author(s):  
Aditya Lahiri ◽  
Khushboo Rastogi ◽  
Aniruddha Datta ◽  
Endang M. Septiningsih
Keyword(s):  
Amino Acids ◽  
Reporter Gene ◽  
Nacl Stress ◽  
Stress Conditions ◽  
Lysine Biosynthesis ◽  
Model Parameters ◽  
Saline Stress ◽  
Lysine Content ◽  
Biosynthesis Pathway ◽  
Healthy Functioning

Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for more than half of the global population; thus, increasing the lysine content in rice will help improve global health. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 gene editing strategy has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.

scholarly journals Nucleotide sequence of the two rat cellular rasH genes.

1986 ◽  
Vol 6 (5) ◽  
pp. 1706-1710 ◽  
Author(s):  
M Ruta ◽  
R Wolford ◽  
R Dhar ◽  
D Defeo-Jones ◽  
R W Ellis ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Coding Region ◽  
3T3 Cells ◽  
Ras Gene ◽  
P21 Protein ◽  
Murine Sarcoma Virus ◽  
Sarcoma Virus ◽  
Nih 3T3 ◽  
Murine Sarcoma

We present the nucleotide sequence of the coding region of the rat c-rasH-1 gene and a partial sequence analysis of the rat c-rasH-2 gene. By comparing these sequences with the Harvey murine sarcoma virus ras gene, we predict that the p21 protein encoded by the Harvey virus differs from the cellular c-rasH-1-encoded p21 at only two amino acids; those at positions 12 and 59. Alterations at each of these positions may play a role in activating the viral p21 protein. The c-rasH-2 gene is likely to be a nonfunctional pseudogene because it lacks introns, cannot be activated to transform NIH 3T3 cells, and differs in sequence from both c-rasH-1 and v-rasH at several base pair positions.

scholarly journals Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association

2021 ◽  
Vol 22 (18) ◽  
pp. 9980
Author(s):  
Ganesh R. Koshre ◽  
Feba Shaji ◽  
Neeraja K. Mohanan ◽  
Nimmy Mohan ◽  
Jamshaid Ali ◽  
...  
Keyword(s):  
Rna Binding ◽  
Coding Region ◽  
High Association ◽  
Target Mrnas ◽  
Mrna Metabolism ◽  
Mrna Targets ◽  
Genome Wide ◽  
Global Profile ◽  
Specific Mrna

Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3′-UTR processing, we observed a high association of Star-PAP at the 3′-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3′-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.

scholarly journals Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

2020 ◽  
Author(s):  
Lehai Zhang ◽  
Shifu Wang ◽  
Qian Ren ◽  
Junjie Yang ◽  
Yanqin Lu ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Detection Efficiency ◽  
Evolutionary Relationship ◽  
Clinical Manifestations ◽  
Coding Region ◽  
Gene Coding ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

scholarly journals Genome-wide association studies of yield-related traits in high-latitude japonica rice

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guomin Zhang ◽  
Rongsheng Wang ◽  
Juntao Ma ◽  
Hongru Gao ◽  
Lingwei Deng ◽  
...  
Keyword(s):  
Linear Model ◽  
High Latitude ◽  
Association Studies ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Genome Wide Association Studies ◽  
Heilongjiang Province ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Genome Wide

Abstract Background Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. However, yield is a complex quantitative trait composed of many factors. The purpose of this study was to determine how many genetic loci are associated with yield-related traits. Genome-wide association studies (GWAS) were performed on 450 accessions collected from northeast Asia, including Russia, Korea, Japan and Heilongjiang Province of China. These accessions consist of elite varieties and landraces introduced into Heilongjiang Province decade ago. Results After resequencing of the 450 accessions, 189,019 single nucleotide polymorphisms (SNPs) were used for association studies by two different models, a general linear model (GLM) and a mixed linear model (MLM), examining four traits: days to heading (DH), plant height (PH), panicle weight (PW) and tiller number (TI). Over 25 SNPs were found to be associated with each trait. Among them, 22 SNPs were selected to identify candidate genes, and 2, 8, 1 and 11 SNPs were found to be located in 3′ UTR region, intron region, coding region and intergenic region, respectively. Conclusions All SNPs detected in this research may become candidates for further fine mapping and may be used in the molecular breeding of high-latitude rice.

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