scholarly journals Genome-Scale Computational Identification and Characterization of UTR Introns in Atalantia buxifolia

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 556
Author(s):  
Chunzhen Cheng ◽  
Xiaobao Shi ◽  
Junwei Wu ◽  
Yongyan Zhang ◽  
Peitao Lü
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Enrichment Analysis ◽  
Cis Acting ◽  
Genes Encoding ◽  
Computational Identification ◽  
Rna Pathways ◽  
Genome Scale ◽  
Identification And Characterization

Accumulated evidence has shown that CDS introns (CIs) play important roles in regulating gene expression. However, research on UTR introns (UIs) is limited. In this study, UIs (including 5′UTR and 3′UTR introns (5UIs and 3UIs)) were identified from the Atalantia buxifolia genome. The length and nucleotide distribution characteristics of both 5UIs and 3UIs and the distributions of cis-acting elements and transcription factor binding sites (TFBSs) in 5UIs were investigated. Moreover, PageMan enrichment analysis was applied to show the possible roles of transcripts containing UIs (UI-Ts). In total, 1077 5UIs and 866 3UIs were identified from 897 5UI-Ts and 670 3UI-Ts, respectively. Among them, 765 (85.28%) 5UI-Ts and 527 (78.66%) 3UI-Ts contained only one UI, and 94 (6.38%) UI-Ts contained both 5UI and 3UI. The UI density was lower than that of CDS introns, but their mean and median intron sizes were ~2 times those of the CDS introns. The A. buxifolia 5UIs were rich in gene-expression-enhancement-related elements and contained many TFBSs for BBR-BPC, MIKC_MADS, AP2 and Dof TFs, indicating that 5UIs play a role in regulating or enhancing the expression of downstream genes. Enrichment analysis revealed that UI-Ts involved in ‘not assigned’ and ‘RNA’ pathways were significantly enriched. Noteworthily, 119 (85.61%) of the 3UI-Ts were genes encoding pentatricopeptide (PPR) repeat-containing proteins. These results will be helpful for the future study of the regulatory roles of UIs in A. buxifolia.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

scholarly journals Identification and characterization of cis-acting elements conferring insulin responsiveness on hamster cholesterol 7α-hydroxylase gene promoter

2000 ◽  
Vol 347 (1) ◽  
pp. 147 ◽  
Author(s):  
Emma DE FABIANI ◽  
Maurizio CRESTANI ◽  
Maria MARRAPODI ◽  
Alessandra PINELLI ◽  
Viviana GOLFIERI ◽  
...  
Keyword(s):  
Gene Promoter ◽  
Cis Acting ◽  
Hydroxylase Gene ◽  
Insulin Responsiveness ◽  
Identification And Characterization

scholarly journals Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

2019 ◽  
Vol 1861 (1) ◽  
pp. 62-74 ◽  
Author(s):  
Alessio Atzori ◽  
Viveka N. Malviya ◽  
Giuliano Malloci ◽  
Jürg Dreier ◽  
Klaas M. Pos ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rnd Transporter ◽  
Identification And Characterization

scholarly journals Identification and Characterization of Quorum-Quenching Activity of N-Acylhomoserine Lactonase from Coagulase-Negative Staphylococci

Antibiotics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 483
Author(s):  
Tomohiro Morohoshi ◽  
Yaoki Kamimura ◽  
Nobutaka Someya
Keyword(s):  
Quorum Sensing ◽  
Opportunistic Pathogen ◽  
Quorum Quenching ◽  
Coagulase Negative Staphylococci ◽  
Sensing Systems ◽  
Genes Encoding ◽  
Acyl Chains ◽  
Gene Homologue ◽  
Identification And Characterization

N-Acylhomoserine lactones (AHLs) are used as quorum-sensing signals in Gram-negative bacteria. Many genes encoding AHL-degrading enzymes have been cloned and characterized in various microorganisms. Coagulase-negative staphylococci (CNS) are present on the skin of animals and are considered low-virulent species. The AHL-lactonase gene homologue, ahlS, was present in the genomes of the CNS strains Staphylococcus carnosus, Staphylococcus haemolyticus, Staphylococcus saprophyticus, and Staphylococcus sciuri. We cloned the candidate ahlS homologue from six CNS strains into the pBBR1MCS5 vector. AhlS from the CNS strains showed a higher degrading activity against AHLs with short acyl chains compared to those with long acyl chains. AhlS from S. sciuri was expressed and purified as a maltose-binding protein (MBP) fusion. Pseudomonas aeruginosa is an opportunistic pathogen that regulates several virulence factors such as elastase and pyocyanin by quorum-sensing systems. When MBP-AhlS was added to the culture of P. aeruginosa PAO1, pyocyanin production and elastase activity were substantially reduced compared to those in untreated PAO1. These results demonstrate that the AHL-degrading activity of AhlS from the CNS strains can inhibit quorum sensing in P. aeruginosa PAO1.

scholarly journals A Novel Triple-Fluorescent HCMV Strain Reveals Gene Expression Dynamics and Anti-Herpesviral Drug Mechanisms

2021 ◽  
Vol 10 ◽  
Author(s):  
Ulfert Rand ◽  
Tobias Kubsch ◽  
Bahram Kasmapour ◽  
Luka Cicin-Sain
Keyword(s):  
Gene Expression ◽  
Hcmv Infection ◽  
Viral Fitness ◽  
High Temporal Resolution ◽  
Detection Techniques ◽  
Drug Candidates ◽  
New Drug ◽  
Gene Expression Dynamics ◽  
Identification And Characterization

Human Cytomegalovirus (HCMV) infection may result in severe outcomes in immunocompromised individuals such as AIDS patients, transplant recipients, and neonates. To date, no vaccines are available and there are only few drugs for anti-HCMV therapy. Adverse effects and the continuous emergence of drug-resistance strains require the identification of new drug candidates in the near future. Identification and characterization of such compounds and biological factors requires sensitive and reliable detection techniques of HCMV infection, gene expression and spread. In this work, we present and validate a novel concept for multi-reporter herpesviruses, identified through iterative testing of minimally invasive mutations. We integrated up to three fluorescence reporter genes into replication-competent HCMV strains, generating reporter HCMVs that allow the visualization of replication cycle stages of HCMV, namely the immediate early (IE), early (E), and late (L) phase. Fluorescent proteins with clearly distinguishable emission spectra were linked by 2A peptides to essential viral genes, allowing bicistronic expression of the viral and the fluorescent protein without major effects on viral fitness. By using this triple color reporter HCMV, we monitored gene expression dynamics of the IE, E, and L genes by measuring the fluorescent signal of the viral gene-associated fluorophores within infected cell populations and at high temporal resolution. We demonstrate distinct inhibitory profiles of foscarnet, fomivirsen, phosphonoacetic acid, ganciclovir, and letermovir reflecting their mode-of-action. In conclusion, our data argues that this experimental approach allows the identification and characterization of new drug candidates in a single step.

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