scholarly journals An update on the maize zein-gene family in the post-genomics era

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Nasr Ullah Khan ◽  
Mohamed Sheteiwy ◽  
Ning Lihua ◽  
Muhammad Mohib Ullah Khan ◽  
Zhao Han
Keyword(s):  
Seed Storage ◽  
Essential Amino Acids ◽  
Regulatory Elements ◽  
Endosperm Development ◽  
Human Consumption ◽  
Widespread Application ◽  
Cis And Trans ◽  
Zein Genes ◽  
Zein Gene

AbstractMaize (Zea mays) is a cereal crop of global food importance. However, the deficiency of essential amino acids, more importantly lysine, methionine and tryptophan, in the major seed storage zein proteins makes corn nutritionally of low value for human consumption. The idea of improving maize nutritional value prompted the search for maize natural mutants harboring low zein contents and higher amount of lysine. These studies resulted in the identification of more than dozens of maize opaque mutants in the previous few decades, o2 mutant being the most extensively studied one. However, the high lysine contents but soft kernel texture and chalky endosperm halted the widespread application and commercial success of maize opaque mutants, which ultimately paved the way for the development of Quality Protein Maize (QPM) by modifying the soft endosperm of o2 mutant into lysine-rich hard endosperm. The previous few decades have witnessed a marked progress in maize zein research. It includes elucidation of molecular mechanism underlying the role of different zein genes in seed endosperm development by cloning different components of zein family, exploring the general organization, function and evolution of zein family members within maize species and among other cereals, and elucidating the cis- and trans-regulatory elements modulating the regulation of different molecular players of maize seed endosperm development. The current advances in high quality reference genomes of maize lines B73 and Mo17 plus the completion of ongoing pan genome sequencing projects of more maize lines with NGS technologies are expected to revolutionize maize zein gene research in near future. This review highlights the recent advances in QPM development and its practical application in the post genomic era, genomic and physical composition and evolution of zein family, and expression, regulation and downstream role of zein genes in endosperm development. Moreover, recent genomic tools and methods developed for functional validation of maize zein genes are also discussed. Graphical abstract

scholarly journals Duplication-Dependent CG Suppression of the Seed Storage Protein Genes of Maize

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 835-848
Author(s):  
Gertrud Lund ◽  
Massimiliano Lauria ◽  
Per Guldberg ◽  
Silvio Zaina
Keyword(s):  
Gene Duplication ◽  
Storage Proteins ◽  
Seed Storage Protein ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Maize Genome ◽  
Ltr Retrotransposons ◽  
Storage Protein Genes ◽  
Zein Genes ◽  
Zein Gene

Abstract This study investigates the prevalence of CG and CNG suppression in single- vs. multicopy DNA regions of the maize genome. The analysis includes the single- and multicopy seed storage proteins (zeins), the miniature inverted-repeat transposable elements (MITEs), and long terminal repeat (LTR) retrotransposons. Zein genes are clustered on specific chromosomal regions, whereas MITEs and LTRs are dispersed in the genome. The multicopy zein genes are CG suppressed and exhibit large variations in CG suppression. The variation observed correlates with the extent of duplication each zein gene has undergone, indicating that gene duplication results in an increased turnover of cytosine residues. Alignment of individual zein genes confirms this observation and demonstrates that CG depletion results primarily from polarized C:T and G:A transition mutations from a less to a more extensively duplicated gene. In addition, transition mutations occur primarily in a CG or CNG context suggesting that CG suppression may result from deamination of methylated cytosine residues. Duplication-dependent CG depletion is likely to occur at other loci as duplicated MITEs and LTR elements, or elements inserted into duplicated gene regions, also exhibit CG depletion.

Monosodium Glutamate Toxicity and the Possible Protective Role of L–Carnitine

2018 ◽  
Vol 6 (1) ◽  
pp. 45-56
Author(s):  
Lalrinzuali Sailo ◽  
◽  
Meesala Krishna Murthy ◽  
Khandayataray Pratima ◽  
Vikas Kumar Roy ◽  
...  
Keyword(s):  
Human Subjects ◽  
Monosodium Glutamate ◽  
Essential Amino Acids ◽  
Protective Role ◽  
Glutamate Toxicity ◽  
Common Salt ◽  
Genotoxic Effects ◽  
Naturally Occurring ◽  
Flavour Enhancer

Monosodium glutamate is naturally available non-essential amino acids, which found in naturally occurring foods and used as flavour enhancer worldwide. Monosodium glutamate is believed to be linked with diverse health problems. The aim of the study was toxic effects of monosodium glutamate (MSG) and the protective role of L-carnitine, light on the available literature from last 25 years about diverse toxicity studies which had been carried out on animal and human models. Google scholar, NCBI, PUBMED, EMBASE, Wangfang databases, and Web of Science databases were used to retrieve the available studies. MSG was linked with deleterious effects particularly in animals including induction of obesity, diabetes, hepatotoxic, neurotoxic and genotoxic effects showed in Literature. Few reports revealed increased hunger, food intake, and obesity in human subjects due to MSG consumption. Hepatotoxic, neurotoxic, and genotoxic effects of monosodium glutamate on humans carried out very limitedly. High consumption of monosodium glutamate may be linked with harmful health effects showed in available literatures. So, it is recommended to use common salt instead of MSG. Furthermore, intensive research is required to explore monosodium glutamate–related molecular and metabolic mechanisms. L-carnitine can protect from Hepatotoxic, neurotoxic, renal impairment and genotoxic effects functionally, biochemically and histopathologically with a corresponding reduction of oxidative stress.

scholarly journals Epigenomic Analysis of RAD51 ChIP-seq Data Reveals cis-regulatory Elements Associated with Autophagy in Cancer Cell Lines

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2547
Author(s):  
Keunsoo Kang ◽  
Yoonjung Choi ◽  
Hyeonjin Moon ◽  
Chaelin You ◽  
Minjin Seo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Homologous Recombination ◽  
Cell Lines ◽  
Regulatory Elements ◽  
Binding Motif ◽  
Genome Wide ◽  
E Box ◽  
Autophagy Pathway ◽  
Mcf 7

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51-bound cis-regulatory elements in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-associated cis-regulatory elements in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway, such as ATG3 and ATG5, were significantly occupied by RAD51 and regulated by RAD51 in HepG2 and MCF-7 cell lines. Taken together, these results unveiled a novel role of RAD51 and provided evidence that RAD51-associated cis-regulatory elements could possibly be involved in regulating autophagy-related genes with E-box binding proteins.

scholarly journals Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hong Wang ◽  
Aiping Duan ◽  
Jing Zhang ◽  
Qi Wang ◽  
Yuexian Xing ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glucocorticoid Receptor ◽  
Protective Effect ◽  
Histone Modification ◽  
Regulatory Networks ◽  
Target Gene ◽  
Regulatory Elements ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractElucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.

scholarly journals A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1007
Author(s):  
Divya Kattupalli ◽  
Asha Sreenivasan ◽  
Eppurathu Vasudevan Soniya
Keyword(s):  
Phytophthora Capsici ◽  
Regulatory Elements ◽  
Piper Nigrum ◽  
Binding Motif ◽  
Altered Expression ◽  
Genome Wide ◽  
A Genome ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

Ecological Synthesis and Its Role in Advancing Knowledge

BioScience ◽  
2020 ◽  
Author(s):  
Benjamin S Halpern ◽  
Eric Berlow ◽  
Rich Williams ◽  
Elizabeth T Borer ◽  
Frank W Davis ◽  
...  
Keyword(s):  
Web Of Science ◽  
Ecological Knowledge ◽  
Ecological Analysis ◽  
Widespread Application ◽  
Ecological Literature ◽  
Research Themes ◽  
Analysis And Synthesis ◽  
Core Questions

Abstract Synthesis has become ubiquitous in ecology. Despite its widespread application to a broad range of research topics, it remains unclear how synthesis has affected the discipline. Using a case study of publications (n = 2304) from the National Center for Ecological Analysis and Synthesis compared with papers with similar keywords from the Web of Science (n = 320,000), we address several questions about the comparative impact of synthesis, the role of synthesis in driving key research themes, and whether synthesis is focused on different topics than is the broader ecological literature. We found much higher citation rates for synthesis papers overall (fivefold more) and within eleven key topic themes (e.g., species richness, biodiversity, climate change, global change). Synthesis papers often played key roles in driving, redirecting, or resolving core questions and exhibited much greater cross-theme connectivity. Together, these results indicate that synthesis in science has played a crucial role in accelerating and advancing ecological knowledge.

ChemInform Abstract: THE ROLE OF SOLVENT IN CONJUGATE ADDITIONS LEADING TO CIS- AND TRANS-1-ALKYL-2-ARYL-3-CARBO(AROYL)AZIRIDINES

1977 ◽  
Vol 8 (40) ◽  
pp. no-no
Author(s):  
P. TARBURTON ◽  
P. B. WOLLER ◽  
R. C. BADGER ◽  
E. DOOMES ◽  
N. H. CROMWELL
Keyword(s):  
Conjugate Additions ◽  
Cis And Trans ◽  
Role Of Solvent

scholarly journals Biochemical Aspects of a Serine Protease fromCaesalpinia echinataLam. (Brazilwood) Seeds: A Potential Tool to Access the Mobilization of Seed Storage Proteins

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Priscila Praxedes-Garcia ◽  
Ilana Cruz-Silva ◽  
Andrezza Justino Gozzo ◽  
Viviane Abreu Nunes ◽  
Ricardo José Torquato ◽  
...  
Keyword(s):  
Serine Protease ◽  
Storage Proteins ◽  
Gel Filtration ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Optimum Ph ◽  
Caesalpinia Echinata ◽  
Pepstatin A ◽  
Potential Tool

Several proteins have been isolated from seeds of leguminous, but this is the first report that a protease was obtained from seeds ofCaesalpinia echinataLam., a tree belonging to the Fabaceae family. This enzyme was purified to homogeneity by hydrophobic interaction and anion exchange chromatographies and gel filtration. This 61-kDa serine protease (CeSP) hydrolyses H-D-prolyl-L-phenylalanyl-L-arginine-p-nitroanilide (Km55.7 μM) in an optimum pH of 7.1, and this activity is effectively retained until50∘C. CeSP remained stable in the presence of kosmotropic anions (PO4 3−,SO4 2−, andCH3COO−) or chaotropic cations (K+and Na+). It is strongly inhibited by TLCK, a serine protease inhibitor, but not by E-64, EDTA or pepstatin A. The characteristics of the purified enzyme allowed us to classify it as a serine protease. The role of CeSP in the seeds cannot be assigned yet but is possible to infer that it is involved in the mobilization of seed storage proteins.

The role of mecA and blaZ regulatory elements in mecA expression by regional clones of methicillin-resistant Staphylococcus pseudintermedius

2011 ◽  
Vol 151 (3-4) ◽  
pp. 345-353 ◽  
Author(s):  
C.C. Black ◽  
L.C. Eberlein ◽  
S.M. Solyman ◽  
R.P. Wilkes ◽  
F.A. Hartmann ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Staphylococcus Pseudintermedius ◽  
Methicillin Resistant

Metal Ions on the Membrane Bioreactor in the Slow Progress of Membrane Fouling Studies

2014 ◽  
Vol 926-930 ◽  
pp. 158-161
Author(s):  
Wan You Zhang ◽  
Sheng Chao Ji ◽  
Hai Feng Zhang ◽  
Xi Xin Zhang
Keyword(s):  
Metal Ions ◽  
Membrane Fouling ◽  
Membrane Bioreactor ◽  
Future Research ◽  
Widespread Application ◽  
Slow Progress ◽  
Flocculation Process

Membrane bioreactor (MBR) has developed rapidly in recent years; however, the membrane fouling problems are affecting its further widespread application. This paper discusses the role of metal ions in the mixture in the mechanism; also on the high-priced metal ions coexist in the mixture when the effects of biological flocculation process; finally, the direction of future research in this area are summarized.

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