scholarly journals Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

2018 ◽  
Author(s):  
Cong Liu ◽  
Dongying Fan ◽  
Yanfang Li ◽  
Yue Chen ◽  
Lili Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Control Group ◽  
Retinol Dehydrogenase ◽  
Nitrogenous Compounds ◽  
Function And Pathway Analysis ◽  
Valsa Mali

Apple canker is a devastating branch disease caused by Valsa mali (Vm). The endophytic actinomycete Saccharothrix yanglingensis Hhs.015 (Sy Hhs.015) can effectively inhibit the growth of Vm. To reveal the mechanism, by which Vm respond to Sy Hhs.015, the transcriptome of Vm was analyzed using RNA-seq technology. Compared with the control group, 1476 genes were significantly differentially expressed in the treatment group, of which 851 genes were up-regulated and 625 genes were down-regulated. Combined gene function and pathway analysis of differentially expressed genes (DEGs) revealed that Sy Hhs.015 affected the carbohydrate metabolic pathway, which is utilized by Vm for energy production. Approximately 82% of the glycoside hydrolase genes were down-regulated, including three pectinase genes (PGs), which are key pathogenic factors. The cell wall structure of Vm was disrupted by Sy Hhs.015 and cell wall-related genes were found to be down-regulated. Of the peroxisome associated genes, those encoding catalase (CAT) and superoxide dismutase (SOD) which scavenge reactive oxygen species (ROS), as well as those encoding AMACR and ACAA1 which are related to the β-oxidation of fatty acids, were down-regulated. MS and ICL, key genes in glyoxylate cycle, were also down-regulated. In response to the stress of Sy Hhs.015 exposure, Vm increased amino acid metabolism to synthesize the required nitrogenous compounds, while alpha-keto acids, which involved in the TCA cycle, could be used to produce energy by deamination or transamination. Retinol dehydrogenase, associated with cell wall dextran synthesis, and sterol 24-C-methyltransferase, related to cell membrane ergosterol synthesis, were up-regulated. The genes encoding glutathione S-transferase, (GST), which has antioxidant activity and ABC transporters which have an efflux function, were also up-regulated. These results show that the response of Vm to Sy Hhs.015 exposure is a complicated and highly regulated process, and provide a theoretical basis for both clarifying the biocontrol mechanism of Sy Hhs.015 and the response of Vm to stress.

scholarly journals Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

2018 ◽  
Author(s):  
Cong Liu ◽  
Dongying Fan ◽  
Yanfang Li ◽  
Yue Chen ◽  
Lili Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Control Group ◽  
Retinol Dehydrogenase ◽  
Nitrogenous Compounds ◽  
Function And Pathway Analysis ◽  
Valsa Mali

Apple canker is a devastating branch disease caused by Valsa mali (Vm). The endophytic actinomycete Saccharothrix yanglingensis Hhs.015 (Sy Hhs.015) can effectively inhibit the growth of Vm. To reveal the mechanism, by which Vm respond to Sy Hhs.015, the transcriptome of Vm was analyzed using RNA-seq technology. Compared with the control group, 1476 genes were significantly differentially expressed in the treatment group, of which 851 genes were up-regulated and 625 genes were down-regulated. Combined gene function and pathway analysis of differentially expressed genes (DEGs) revealed that Sy Hhs.015 affected the carbohydrate metabolic pathway, which is utilized by Vm for energy production. Approximately 82% of the glycoside hydrolase genes were down-regulated, including three pectinase genes (PGs), which are key pathogenic factors. The cell wall structure of Vm was disrupted by Sy Hhs.015 and cell wall-related genes were found to be down-regulated. Of the peroxisome associated genes, those encoding catalase (CAT) and superoxide dismutase (SOD) which scavenge reactive oxygen species (ROS), as well as those encoding AMACR and ACAA1 which are related to the β-oxidation of fatty acids, were down-regulated. MS and ICL, key genes in glyoxylate cycle, were also down-regulated. In response to the stress of Sy Hhs.015 exposure, Vm increased amino acid metabolism to synthesize the required nitrogenous compounds, while alpha-keto acids, which involved in the TCA cycle, could be used to produce energy by deamination or transamination. Retinol dehydrogenase, associated with cell wall dextran synthesis, and sterol 24-C-methyltransferase, related to cell membrane ergosterol synthesis, were up-regulated. The genes encoding glutathione S-transferase, (GST), which has antioxidant activity and ABC transporters which have an efflux function, were also up-regulated. These results show that the response of Vm to Sy Hhs.015 exposure is a complicated and highly regulated process, and provide a theoretical basis for both clarifying the biocontrol mechanism of Sy Hhs.015 and the response of Vm to stress.

scholarly journals The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

2020 ◽  
Author(s):  
Lei Wang ◽  
Fangfang Zhou ◽  
Minyi Xu ◽  
Pei Lu ◽  
Ming Lin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Rna Sequencing ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Differentially Expressed ◽  
Control Group ◽  
High Concentration ◽  
Bacteriostatic Effect ◽  
Low Concentration ◽  
Cell Wall Hydrolysis

Abstract Background: To observe the bacteriostatic effect of berberine (BBR) and BBR combined with gentamicin (GEN), levofloxacin (LEV) and amikacin (AMI) on Methicillin resistant Staphylococcus aureus (MRSA), while also exploring the bacteriostatic mechanism of BBR on MRSA. Results: The MICs range of BBR on 26 strains of MRSA was 32-256 µg/mL. BBR combined with GEN, LEV and AMI had obvious bacteriostatic effect on MRSA. After co-culturing MRSA with BBR at 512 µg/mL, 64 µg/mL and 8 µg/mL, respectively, the electrical conductivity increased, compared with the control group, by 8.14%, 13.08% and 12.01%, respectively. Using transmission electron microscopy, we found that low concentration of BBR (8 µg/mL; 1/8 MIC) caused no significant damage to MRSA, and the bacterial structure of MRSA remained intact, while high concentration of BBR (512 µg/mL; 8 MIC) induced the destruction and dissolution of MRSA cell wall structure and the leakage of bacterial contents, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high concentration group compared with the normal control group. Compared with the low concentration group, there were 590 differentially expressed genes in the high concentration group. Compared with the control group, only 19 genes were differentially expressed in the low concentration group. The up-regulated genes are mainly related to the cell wall hydrolysis regulatory genes, while the down-regulated genes are mainly related to the serine protease family. Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with GEN and AMI significantly enhanced the bacteriostatic effect on MRSA, while BBR combined with LEV showed no significant change in the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying and dissolving the structure of MRSA cell wall. RNA-sequencing results further demonstrated that the expression of cell wall hydrolysis genes ssaA, lytM and virulence factor serine protease genes were significantly differentially expressed when high concentration BBR treated on MRSA.

scholarly journals Isolation and Characterization of Differentially Expressed Genes in the Mycelium and Fruit Body of Tuber borchii

2002 ◽  
Vol 68 (9) ◽  
pp. 4574-4582 ◽  
Author(s):  
Isabelle Lacourt ◽  
Sébastien Duplessis ◽  
Simona Abbà ◽  
Paola Bonfante ◽  
Francis Martin
Keyword(s):  
Cell Wall ◽  
Aminolevulinic Acid ◽  
Isocitrate Lyase ◽  
Glyoxylate Cycle ◽  
Fruit Body ◽  
Differentially Expressed ◽  
Vegetative Mycelium ◽  
Tuber Borchii ◽  
Expression Levels ◽  
Isolation And Characterization

ABSTRACT The transition from vegetative mycelium to fruit body in truffles requires differentiation processes which lead to edible fruit bodies (ascomata) consisting of different cell and tissue types. The identification of genes differentially expressed during these developmental processes can contribute greatly to a better understanding of truffle morphogenesis. A cDNA library was constructed from vegetative mycelium RNAs of the white truffle Tuber borchii, and 214 cDNAs were sequenced. Up to 58% of the expressed sequence tags corresponded to known genes. The majority of the identified sequences represented housekeeping proteins, i.e., proteins involved in gene or protein expression, cell wall formation, primary and secondary metabolism, and signaling pathways. We screened 171 arrayed cDNAs by using cDNA probes constructed from mRNAs of vegetative mycelium and ascomata to identify fruit body-regulated genes. Comparisons of signals from vegetative mycelium and fruit bodies bearing 15 or 70% mature spores revealed significant differences in the expression levels for up to 33% of the investigated genes. The expression levels for six highly regulated genes were confirmed by RNA blot analyses. The expression of glutamine synthetase, 5-aminolevulinic acid synthetase, isocitrate lyase, thioredoxin, glucan 1,3-β-glucosidase, and UDP-glucose:sterol glucosyl transferase was highly up-regulated, suggesting that amino acid biosynthesis, the glyoxylate cycle pathway, and cell wall synthesis are strikingly altered during morphogenesis.

scholarly journals Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pests And Diseases ◽  
Fruit Cracking ◽  
Resistant Varieties ◽  
Fruit Decay

Abstract Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

scholarly journals Transcriptomic Analysis Reveals Regulatory Networks for Osmotic Water Stress and Rewatering Response in the Leaves of Ginkgo biloba

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1705
Author(s):  
Wanwen Yu ◽  
Jinfeng Cai ◽  
Huimin Liu ◽  
Zhiguo Lu ◽  
Jingjing Hu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Water Stress ◽  
Water Transport ◽  
Ginkgo Biloba ◽  
Regulatory Networks ◽  
Differentially Expressed ◽  
Control Group ◽  
Gene Coexpression ◽  
Osmotic Water ◽  
Coexpression Networks

To elucidate the transcriptomic regulation mechanisms that underlie the response of Ginkgo biloba to dehydration and rehydration, we used ginkgo saplings exposed to osmotically driven water stress and subsequent rewatering. When compared with a control group, 137, 1453, 1148, and 679 genes were differentially expressed in ginkgo leaves responding to 2, 6, 12, and 24 h of water deficit, and 796 and 1530 genes were differentially expressed responding to 24 and 48 h of rewatering. Upregulated genes participated in the biosynthesis of abscisic acid, eliminating reactive oxygen species (ROS), and biosynthesis of flavonoids and bilobalide, and downregulated genes were involved in water transport and cell wall enlargement in water stress-treated ginkgo leaves. Under rehydration conditions, the genes associated with water transport and cell wall enlargement were upregulated, and the genes that participated in eliminating ROS and the biosynthesis of flavonoids and bilobalide were downregulated in the leaves of G. biloba. Furthermore, the weighted gene coexpression networks were established and correlated with distinct water stress and rewatering time-point samples. Hub genes that act as key players in the networks were identified. Overall, these results indicate that the gene coexpression networks play essential roles in the transcriptional reconfiguration of ginkgo leaves in response to water stress and rewatering.

scholarly journals The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

2020 ◽  
Author(s):  
Lei Wang ◽  
Fangfang Zhou ◽  
Minyi Xu ◽  
Pei Lu ◽  
Ming Lin ◽  
...  
Keyword(s):  
Cell Wall ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Control Group ◽  
High Concentration ◽  
Bacteriostatic Effect ◽  
Low Concentration ◽  
Transmission Electron ◽  
Cell Wall Hydrolysis

Abstract Background: To observe the bacteriostatic effect of berberine (BBR) and BBR combined with gentamicin (GEN), levofloxacin (LEV) and amikacin (AMI) on Methicillin resistant Staphylococcus aureus (MRSA), while also exploring the bacteriostatic mechanism of BBR on MRSA. Methods: The minimal inhibitory concentration (MIC) of BBR, GEN, LEV and AMI on 26 clinical MRSA strains was determined by broth microdilution, while the MICs of BBR combined with GEN, LEV and AMI against MRSA were determined using a microdilution checkerboard. Time-killing curves were used to determine the kinetics of BBR combined with antibiotics for MRSA. We used conductivity tests to assess the changes in membrane permeability in response to BBR on MRSA, while also investigating the changes in MRSA morphology by transmission electron microscopy. RNA-sequencing was used to analyze the expression of differentially expressed genes in reference strain USA300 after its treatment with BBR at different concentrations.Results: The MICs range of BBR on 26 strains of MRSA was 32-256 µg/mL. BBR combined with GEN, LEV and AMI had obvious bacteriostatic effect on MASA. After co-culturing MRSA with BBR at 512 ug/mL, 64 ug/mL and 8 ug/mL, respectively, the electrical conductivity increased, compared with the control group, by 8.14%, 13.08% and 12.01%, respectively. Using transmission electron microscopy, we found that low concentration of BBR (8 ug/mL) had no significant effect on MRSA structure (keeping intact), medium concentration of BBR (64 ug/mL) thinned the cell wall of MRSA, while high concentration of BBR (512 ug/mL) induced the destruction and dissolution of MRSA cell wall structure and the leakage of bacterial contents, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high concentration group compared with the normal control group. Compared with the low concentration group, there were 590 differentially expressed genes in the high concentration group. Compared with the control group, only 19 genes were differentially expressed in the low concentration group. The up-regulated genes are mainly related to the cell wall hydrolysis regulatory genes, while the down-regulated genes are mainly related to the serine protease family.Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with GEN and AMI significantly enhanced the bacteriostatic effect on MRSA, while BBR combined with LEV showed no significant change in the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying and dissolving the structure of MRSA cell wall. RNA-sequencing results further demonstrated that the expression of cell wall hydrolysis genes ssaA, lytM and virulence factor serine protease genes were significantly differentially expressed when high concentration BBR treated on MRSA.

scholarly journals The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

2019 ◽  
Author(s):  
Lei Wang ◽  
Fangfang Zhou ◽  
Minyi Xu ◽  
Wei Gong ◽  
Shuiying Ji
Keyword(s):  
Cell Wall ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Control Group ◽  
High Concentration ◽  
Bacteriostatic Effect ◽  
Low Concentration ◽  
Kinetics Of

Abstract Background: To observe the bacteriostatic effect of berberine on MRSA, while also exploring the bacteriostatic mechanism of BBR on MRSA. Methods: The MIC of BBR, gentamicin, levofloxacin，amikacin was determined by broth microdilution, while the MICs of BBR combined with gentamicin, levofloxacin，amikacin against MRSA were determined using microdilution checkerboard. Time-killing test were used to determine the kinetics of BBR combined with antibiotics for MRSA. We used conductivity to assess the changes in membrane permeability in response to BBR on MRSA, while also investigating the changes in MRSA morphology by TEM. RNA-sequencing was used to analyze the expression of differentially expressed genes in USA300 after its treatment with BBR. Results: The MICs range of BBR on MRSA was 32-256 µg/mL. The range of FICIs of BBR combined with gentamicin, levofloxacin，amikacin were 0.53-1.06, 0.62-1.5, 0.16-1.25. After co-culturing MRSA with BBR at 512 ug/mL, 64 ug/mL,8 ug/mL, respectively, the conductivity of these group increased by 8.14%,13.08% and 12.01%, respectively. Using TEM, we found that low-concentration of BBR had no significant effect on MRSA structure, medium-concentration of BBR thinned the cell wall of MRSA, while high-concentration of BBR destroyed cell wall, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high-concentration group compared with the control group, of which 561 genes were up-regulated and 193 genes were down-regulated. Compared with the low-concentration group, there were 590 differentially expressed genes, of which 402 genes were up-regulated and 188 genes were down-regulated. Compared with the control group, 19 genes were differentially expressed in the low-concentration group, of which 11 genes were up-regulated,8 genes were down-regulated. Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with antibiotics significantly enhanced the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying the structure of cell wall. RNA-sequencing results demonstrated that the expression of cell wall hydrolysis genes and virulence factor were significantly differentially expressed on MRSA.

Bacterial Peptidoglycan Stapling with Functionalized D-Amino Acids

2019 ◽  
Author(s):  
Sylvia L. Rivera ◽  
Akbar Espaillat ◽  
Arjun K. Aditham ◽  
Peyton Shieh ◽  
Chris Muriel-Mundo ◽  
...  
Keyword(s):  
Cell Wall ◽  
Clinical Success ◽  
Bacterial Species ◽  
Enzymatic Reaction ◽  
Amino Acid Derivative ◽  
Wall Structure ◽  
Live Bacteria ◽  
Cross Links ◽  
Osmotic Lysis ◽  
Bacterial Peptidoglycan

Transpeptidation reinforces the structure of cell wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many bacterial species makes it challenging to determine cross-link function precisely. Here we present a technique to covalently link peptide strands by chemical rather than enzymatic reaction. We employ bio-compatible click chemistry to induce triazole formation between azido- and alkynyl-D-alanine residues that are metabolically installed in the cell walls of Gram-positive and Gram-negative bacteria. Synthetic triazole cross-links can be visualized by substituting azido-D-alanine with azidocoumarin-D-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell wall stapling protects the model bacterium Escherichia coli from β-lactam treatment. Chemical control of cell wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.<br>

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