scholarly journals Functional Gene Identification and Corresponding Tolerant Mechanism of High Furfural-Tolerant Zymomonas mobilis Strain F211

2021 ◽  
Vol 12 ◽  
Author(s):  
Dongsheng Hu ◽  
Zhiquan Wang ◽  
Mingxiong He ◽  
Yuanyuan Ma
Keyword(s):  
Zymomonas Mobilis ◽  
Functional Complementation ◽  
Gene Identification ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Functional Identification ◽  
Tolerance Mechanism ◽  
Furfural Tolerance ◽  
Lignocellulose Hydrolysate ◽  
Potential Tolerance

Furfural is a major inhibitor in lignocellulose hydrolysate for Zymomonas mobilis. A mutant F211 strain with high furfural tolerance was obtained from our previous study. Thus, its key tolerance mechanism was studied in the present study. The function of mutated genes in F211 was identified by functional complementation experiments, revealing that the improved furfural tolerance was resulted from the C493T mutation of the ZCP4_0270 gene promoting cell flocculation and the mutation (G1075A)/downregulation of ZCP4_0970. Comparative transcriptome analysis revealed 139 differentially expressed genes between F211 and the control, CP4, in response to furfural stress. In addition, the reliability of the RNA-Seq data was also confirmed. The potential tolerance mechanism was further demonstrated by functional identification of tolerance genes as follows: (I) some upregulated or downregulated genes increase the levels of NAD(P)H, which is involved in the reduction of furfural to less toxic furfuryl alcohol, thus accelerating the detoxification of furfural; (II) the mutated ZCP4_0270 and upregulated cellulose synthetase gene (ZCP4_0241 and ZCP4_0242) increased flocculation to resist furfural stress; (III) upregulated molecular chaperone genes promote protein synthesis and repair stress-damaged proteins; and (IV) transporter genes ZCP4_1623–1,625 and ZCP4_1702–1703 were downregulated, saving energy for cell growth. The furfural-tolerant mechanism and corresponding functional genes were revealed, which provides a theoretical basis for developing robust chassis strains for synthetic biology efforts.

Improving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein

2015 ◽  
Vol 99 (12) ◽  
pp. 5363-5371 ◽  
Author(s):  
Fu-Rong Tan ◽  
Li-Chun Dai ◽  
Bo Wu ◽  
Han Qin ◽  
Zong-Xia Shui ◽  
...  
Keyword(s):  
Sigma Factor ◽  
Zymomonas Mobilis ◽  
Furfural Tolerance

scholarly journals Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

2017 ◽  
Vol 109 ◽  
pp. 189-195 ◽  
Author(s):  
Z. Qin ◽  
A. Li ◽  
F. Hou ◽  
Q. Wang ◽  
S. Dong ◽  
...  
Keyword(s):  
Carotenoid Biosynthesis ◽  
Gene Identification ◽  
Rna Seq

scholarly journals Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

2022 ◽  
Vol 23 (2) ◽  
pp. 746
Author(s):  
Bo Li ◽  
Xiangzhan Zhang ◽  
Ruiwei Duan ◽  
Chunhong Han ◽  
Jian Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Developmental Stages ◽  
Genomic Analysis ◽  
Pyrus Communis ◽  
Anthocyanin Content ◽  
Anthocyanin Accumulation ◽  
Rna Seq ◽  
Virus Induced Gene Silencing ◽  
Functional Identification ◽  
Glutathione S Transferase

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

scholarly journals Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

2019 ◽  
Vol 20 (6) ◽  
pp. 1268 ◽  
Author(s):  
Tinashe Zenda ◽  
Songtao Liu ◽  
Xuan Wang ◽  
Guo Liu ◽  
Hongyu Jin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Amino Acid Biosynthesis ◽  
Molecular Networks ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Drought Treatment ◽  
Drought Stress Tolerance

To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R2 = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.

scholarly journals Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0181061 ◽  
Author(s):  
Chunbao Zhang ◽  
Chunjing Lin ◽  
Fuyou Fu ◽  
Xiaofang Zhong ◽  
Bao Peng ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
F1 Hybrids ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Comparative Transcriptome Analysis

Hepatic T Cell Tolerance Induction in An Inflammatory Environment

2017 ◽  
Vol 36 (2) ◽  
pp. 156-166 ◽  
Author(s):  
Janine Dywicki ◽  
Fatih Noyan ◽  
Ana Clara Misslitz ◽  
Martin Hapke ◽  
Melanie Galla ◽  
...  
Keyword(s):  
T Cells ◽  
Tolerance Induction ◽  
T Cell Tolerance ◽  
Tolerance Mechanism ◽  
Autoreactive T Cells ◽  
Adenoviral Infection ◽  
Precursor Frequency ◽  
Self Antigen ◽  
Very High ◽  
Potential Tolerance

For the development of autoimmune hepatitis (AIH), genetic predisposition and environmental triggers are of major importance. Although experimental AIH can be induced in genetically susceptible mice, the low precursor frequency of autoreactive T cells hampers a deeper analysis of liver-specific T cells. Here, we established a system where the model antigen hemagglutinin (HA) is expressed exclusively in hepatocytes of Rosa26-HA mice following administration of a replication deficient adenovirus expressing Cre recombinase (Ad-Cre). Under these conditions, hepatocytes mimic the generation of altered-self neoantigens. To follow autoreactive T cells during AIH, we adoptively transferred HA-­specific Cl4-TCR and 6.5-TCR T cells into Ad-Cre infected ­Rosa26-HA mice. Alternatively, Rosa26-HA mice have been crossed with TCR transgenic mice that were infected with Ad-Cre to break hepatic tolerance and induce the expression of the HA antigen as a hepatic self-antigen. Surprisingly, neither adoptive transfer nor a very high precursor frequency of autoreactive T cells was able to break tolerance in the context of adenoviral infection. The low proliferation of the antigen experienced autoreactive T cells despite the presence of the autoantigen and inflammation points to anergy as a potential tolerance mechanism. This model underscores the crucial importance of genetic susceptibility to break tolerance against hepatic autoantigens.

scholarly journals RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 571 ◽  
Author(s):  
Junwen Chen ◽  
Kai Hou ◽  
Peng Qin ◽  
Hongchang Liu ◽  
Bin Yi ◽  
...  
Keyword(s):  
Stevia Rebaudiana ◽  
Transcript Profiling ◽  
Gene Identification ◽  
Rna Seq

scholarly journals Transcriptome Analysis Reveals Key Genes and Pathways Associated with Mummify Piglets

Genome ◽  
2021 ◽  
Author(s):  
Shujie Wang ◽  
Pingxian Wu ◽  
Kai Wang ◽  
Xiang Ji ◽  
Dong Chen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Reproductive Capacity ◽  
Signal Pathways ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Promising Candidate ◽  
Pork Consumption ◽  
Differential Genes

China is the country with the largest pork consumption in the world. However, the incidence of high mummify piglets (3-5%) is one of the important factors that cause the slow improvement of pig reproductive capacity, and the genetic mechanism is still unclear. This study aimed to identify candidate genes related to high mummify piglets. RNA-seq technology was used to comparative transcriptome profiling of blood from high piglets mummified and healthy sow at different stages of pregnancy (35d, 56d, 77d and 98d). A total of 137 to 420 DEGs were detected in each stage. Seven differentially expressed genes were significantly differentially expressed at various stages. IL-9R, TLR8, ABLIM3, FSH-α, ASCC1, PRKCZ, and GCK may play an important role in course of mummify piglets. The differential genes we identified between the groups were mainly enriched in immune and inflammation regulation, and others were mainly enriched in reproduction. Considering the function of candidate genes, IL-9R and TLR8 were suggested as the most promising candidate genes involved in mummify piglet traits. We speculate that during pregnancy, it may be the combined effects of the above-mentioned inflammation, immune response, and reproduction-related signal pathways that affect the occurrence of mummifying piglets, and further affect pig reproduction.

Sign in / Sign up

Export Citation Format

Share Document