Characterization and analysis of an industrial strain of Streptomyces bingchenggensis by genome sequencing and gene microarray

Genome ◽  
2013 ◽  
Vol 56 (11) ◽  
pp. 677-689 ◽  
Author(s):  
Xiang-Jing Wang ◽  
Bo Zhang ◽  
Yi-Jun Yan ◽  
Jing An ◽  
Ji Zhang ◽  
...  
Keyword(s):  
Natural Products ◽  
Gene Cluster ◽  
Crop Protection ◽  
Gc Content ◽  
Gene Clusters ◽  
High Expression ◽  
Expression Level ◽  
Transcriptional Analysis ◽  
Streptomyces Bingchenggensis ◽  
High Expression Level

Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, a family of macrolide antibiotics that are commercially important in crop protection and veterinary medicine. In addition, S. bingchenggensis produces many other natural products including the polyether nanchangmycin and novel cyclic pentapeptides. To identify the gene clusters involved in the biosynthesis of these compounds, and better clarify the biochemical pathways of these gene clusters, the whole genome of S. bingchenggensis was sequenced, and the transcriptome profile was subsequently investigated by microarray. In comparison with other sequenced genomes in Streptomyces, S. bingchenggensis has the largest linear chromosome consisting of 11 936 683 base pairs (bp), with an average GC content of 70.8%. The 10 023 predicted protein-coding sequences include at least 47 gene clusters correlated with the biosynthesis of known or predicted secondary metabolites. Transcriptional analysis demonstrated an extremely high expression level of the milbemycin gene cluster during the entire growth period and a moderately high expression level of the nanchangmycin gene cluster during the initial hours that subsequently decreased. However, other gene clusters appear to be silent. The genome-wide analysis of the secondary metabolite gene clusters in S. bingchenggensis, coupled with transcriptional analysis, will facilitate the rational development of high milbemycins-producing strains as well as the discovery of new natural products.

scholarly journals High expression level of T-box transcription factor 5 predicts unfavorable survival in stage I and II gastric adenocarcinoma

2015 ◽  
Vol 10 (4) ◽  
pp. 2021-2026 ◽  
Author(s):  
YAN ZHENG ◽  
YUAN-FANG LI ◽  
WEI WANG ◽  
YONG-MING CHEN ◽  
DAN-DAN WANG ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gastric Adenocarcinoma ◽  
Stage I ◽  
High Expression ◽  
Expression Level ◽  
T Box ◽  
High Expression Level

High expression level of geminin predicts a poor clinical outcome in salivary gland carcinomas

2010 ◽  
Vol 56 (7) ◽  
pp. 883-892 ◽  
Author(s):  
Manabu Yamazaki ◽  
Satoshi Fujii ◽  
Yukinori Murata ◽  
Ryuichi Hayashi ◽  
Atsushi Ochiai
Keyword(s):  
Salivary Gland ◽  
Clinical Outcome ◽  
High Expression ◽  
Expression Level ◽  
Poor Clinical Outcome ◽  
Salivary Gland Carcinomas ◽  
High Expression Level

scholarly journals The immune-suppressive landscape in lepromatous leprosy revealed by single-cell RNA sequencing

2022 ◽  
Vol 8 (1) ◽  
Author(s):  
Zihao Mi ◽  
Zhenzhen Wang ◽  
Xiaotong Xue ◽  
Tingting Liu ◽  
Chuan Wang ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Lepromatous Leprosy ◽  
High Expression ◽  
Expression Level ◽  
Intracellular Bacteria ◽  
Monocyte Subset ◽  
Single Cell Rna Sequencing ◽  
High Expression Level

AbstractLepromatous leprosy (L-LEP), caused by the massive proliferation of Mycobacterium leprae primarily in macrophages, is an ideal disease model for investigating the molecular mechanism of intracellular bacteria evading or modulating host immune response. Here, we performed single-cell RNA sequencing of both skin biopsies and peripheral blood mononuclear cells (PBMCs) of L-LEP patients and healthy controls. In L-LEP lesions, we revealed remarkable upregulation of APOE expression that showed a negative correlation with the major histocompatibility complex II gene HLA-DQB2 and MIF, which encodes a pro-inflammatory and anti-microbial cytokine, in the subset of macrophages exhibiting a high expression level of LIPA. The exhaustion of CD8+ T cells featured by the high expression of TIGIT and LAG3 in L-LEP lesions was demonstrated. Moreover, remarkable enhancement of inhibitory immune receptors mediated crosstalk between skin immune cells was observed in L-LEP lesions. For PBMCs, a high expression level of APOE in the HLA-DRhighFBP1high monocyte subset and the expansion of regulatory T cells were found to be associated with L-LEP. These findings revealed the primary suppressive landscape in the L-LEP patients, providing potential targets for the intervention of intracellular bacteria caused persistent infections.

High Expression Level of SP1, CSF1R, and PAK1 Correlates with Sensitivity of Leukemia Cells to the Antibiotic Mithramycin

2020 ◽  
Vol 54 (3) ◽  
pp. 458-463
Author(s):  
E. R. Vagapova ◽  
T. D. Lebedev ◽  
A. D. Tikhonova ◽  
B. V. Goikhman ◽  
K. A. Ivanenko ◽  
...  
Keyword(s):  
High Expression ◽  
Expression Level ◽  
Leukemia Cells ◽  
High Expression Level

High expression level of levansucrase from Bacillus licheniformis RN-01 and synthesis of levan nanoparticles

2013 ◽  
Vol 54 ◽  
pp. 30-36 ◽  
Author(s):  
Santhana Nakapong ◽  
Rath Pichyangkura ◽  
Kazuo Ito ◽  
Masaru Iizuka ◽  
Piamsook Pongsawasdi
Keyword(s):  
Bacillus Licheniformis ◽  
High Expression ◽  
Expression Level ◽  
High Expression Level

Mo1775 High Expression Level of PPARγ in CD24 Knockout Mice and Gender Specific Metabolic Changes: A Model of Insulin-Sensitive Obesity

2014 ◽  
Vol 146 (5) ◽  
pp. S-656-S-657
Author(s):  
Shiran Shapira ◽  
Nataly Shemesh ◽  
Rachel Dankner ◽  
Diana Kazanov ◽  
Ilan Aroch ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Metabolic Changes ◽  
High Expression ◽  
Expression Level ◽  
And Gender ◽  
Gender Specific ◽  
High Expression Level

scholarly journals Evolution and Functional Analysis of orf1 Within nif Gene Cluster from Paenibacillus graminis RSA19

2019 ◽  
Vol 20 (5) ◽  
pp. 1145 ◽  
Author(s):  
Qin Li ◽  
Xiaomeng Liu ◽  
Haowei Zhang ◽  
Sanfeng Chen
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Transcriptional Analysis ◽  
Facultative Anaerobic ◽  
Orf1 Gene ◽  
Nif Gene ◽  
Nif Gene Cluster ◽  
Paenibacillus Species

Paenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. Genomic sequence analysis has revealed that a compact nif (nitrogen fixation) gene cluster comprising 9–10 genes nifBHDKENX(orf1)hesAnifV is conserved in diazotrophic Paenibacillus species. The evolution and function of the orf1 gene within the nif gene cluster of Paenibacillus species is unknown. In this study, a careful comparison analysis of the compositions of the nif gene clusters from various diazotrophs revealed that orf1 located downstream of nifENX was identified in anaerobic Clostridium ultunense, the facultative anaerobic Paenibacillus species and aerobic diazotrophs (e.g., Azotobacter vinelandii and Azospirillum brasilense). The predicted amino acid sequences encoded by the orf1 gene, part of the nif gene cluster nifBHDKENXorf1hesAnifV in Paenibacillus graminis RSA19, showed 60–90% identity with those of the orf1 genes located downstream of nifENX from different diazotrophic Paenibacillus species, but shared no significant identity with those of the orf1 genes from different taxa of diazotrophic organisms. Transcriptional analysis showed that the orf1 gene was expressed under nitrogen fixation conditions from the promoter located upstream from nifB. Mutational analysis suggested that the orf1 gene functions in nitrogen fixation in the presence of a high concentration of O2.

scholarly journals Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization

Marine Drugs ◽  
2019 ◽  
Vol 17 (7) ◽  
pp. 388 ◽  
Author(s):  
Li Liao ◽  
Shiyuan Su ◽  
Bin Zhao ◽  
Chengqi Fan ◽  
Jin Zhang ◽  
...  
Keyword(s):  
Data Mining ◽  
Natural Products ◽  
Gene Cluster ◽  
Genomic Data ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Biosynthetic Gene ◽  
Base Pairs ◽  
Peptide Synthetase

Rare actinobacterial species are considered as potential resources of new natural products. Marisediminicola antarctica ZS314T is the only type strain of the novel actinobacterial genus Marisediminicola isolated from intertidal sediments in East Antarctica. The strain ZS314T was able to produce reddish orange pigments at low temperatures, showing characteristics of carotenoids. To understand the biosynthetic potential of this strain, the genome was completely sequenced for data mining. The complete genome had 3,352,609 base pairs (bp), much smaller than most genomes of actinomycetes. Five biosynthetic gene clusters (BGCs) were predicted in the genome, including a gene cluster responsible for the biosynthesis of C50 carotenoid, and four additional BGCs of unknown oligosaccharide, salinixanthin, alkylresorcinol derivatives, and NRPS (non-ribosomal peptide synthetase) or amino acid-derived compounds. Further experimental characterization indicated that the strain may produce C.p.450-like carotenoids, supporting the genomic data analysis. A new xanthorhodopsin gene was discovered along with the analysis of the salinixanthin biosynthetic gene cluster. Since little is known about this genus, this work improves our understanding of its biosynthetic potential and provides opportunities for further investigation of natural products and strategies for adaptation to the extreme Antarctic environment.

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