scholarly journals Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin

2020 ◽  
Vol 3 (5) ◽  
pp. e202000670 ◽  
Author(s):  
Jan Borlinghaus ◽  
Anthony Bolger ◽  
Christina Schier ◽  
Alexander Vogel ◽  
Björn Usadel ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Resistance Mechanism ◽  
In Silico Analysis ◽  
Genomic Islands ◽  
Hostile Environment ◽  
Defense Substance ◽  
Individual Candidate ◽  
The Common ◽  
Silico Analysis

The common foodstuff garlic produces the potent antibiotic defense substance allicin after tissue damage. Allicin is a redox toxin that oxidizes glutathione and cellular proteins and makes garlic a highly hostile environment for non-adapted microbes. Genomic clones from a highly allicin-resistant Pseudomonas fluorescens (PfAR-1), which was isolated from garlic, conferred allicin resistance to Pseudomonas syringae and even to Escherichia coli. Resistance-conferring genes had redox-related functions and were on core fragments from three similar genomic islands identified by sequencing and in silico analysis. Transposon mutagenesis and overexpression analyses revealed the contribution of individual candidate genes to allicin resistance. Taken together, our data define a multicomponent resistance mechanism against allicin in PfAR-1, achieved through horizontal gene transfer.

scholarly journals Plant-microbe co-evolution: allicin resistance in a Pseudomonas fluorescens strain (PfAR-1) isolated from garlic

2019 ◽  
Author(s):  
Jan Borlinghaus ◽  
Anthony Bolger ◽  
Christina Schier ◽  
Alexander Vogel ◽  
Martin C. H. Gruhlke ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Allium Sativum ◽  
Bacterial Species ◽  
Resistance Mechanism ◽  
Genomic Islands ◽  
E Coli ◽  
Core Fragment ◽  
Defense Substance ◽  
Individual Candidate ◽  
Increased Susceptibility

The antibiotic defense substance allicin (diallylthiosulfinate) is produced by garlic (Allium sativum L.) after tissue damage, giving garlic its characteristic odor. Allicin is a redox-toxin that oxidizes thiols in glutathione and cellular proteins. A highly allicin-resistant Pseudomonas fluorescens strain (PfAR-1) was isolated from garlic, and genomic clones were shotgun electroporated into an allicin-susceptible P. syringae strain (Ps4612). Recipients showing allicin-resistance had all inherited a group of genes from one of three similar genomic islands (GI), that had been identified in an in silico analysis of the PfAR-1 genome. A core fragment of 8-10 congruent genes with redox-related functions, present in each GI, was shown to confer allicin-specific resistance to P. syringae, and even to an unrelated E. coli strain. Transposon mutagenesis and overexpression analyses revealed the contribution of individual candidate genes to allicin-resistance. Moreover, PfAR-1 was unusual in having 3 glutathione reductase (glr) genes, two copies in two of the GIs, but outside of the core group, and one copy in the PfAR-1 genome. Glr activity was approximately 2-fold higher in PfAR-1 than in related susceptible Pf0-1, with only a single glr gene. Moreover, an E. coli Δglr mutant showed increased susceptibility to allicin, which was complemented by PfAR-1 glr1. Taken together, our data support a multi-component resistance mechanism against allicin, achieved through horizontal gene transfer during coevolution, and allowing exploitation of the garlic ecological niche. GI regions syntenic with PfAR-1 GIs are present in other plant-associated bacterial species, perhaps suggesting a wider role in adaptation to plants per se.

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

In silico analysis of selenoprotein N (Gallus gallus): absence of EF-hand motif and the role of CUGS-helix domain in antioxidant protection

Metallomics ◽  
2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Shi-Yong Zhu ◽  
Li-Li Liu ◽  
Yue-Qiang Huang ◽  
Xiao-Wei Li ◽  
Milton Talukder ◽  
...  
Keyword(s):  
In Silico ◽  
Common Ancestor ◽  
In Silico Analysis ◽  
Antioxidant Protection ◽  
Jnk Pathway ◽  
Downstream Target ◽  
Ef Hand ◽  
Silico Analysis

Abstract Selenoprotein N (SEPN1) is critical to the normal muscular physiology. Mutation of SEPN1 can raise congenital muscular disorder in human. It is also central to maturation and structure of skeletal muscle in chicken. However, human SEPN1 contained an EF-hand motif, which was not found in chicken. And the biochemical and molecular characterization of chicken SEPN1 remains unclear. Hence, protein domains, transcription factors, and interactions of Ca2+ in SEPN1 were analyzed in silico to provide the divergence and homology between chicken and human in this work. The results showed that vertebrates’ SEPN1 evolved from a common ancestor. Human and chicken's SEPN1 shared a conserved CUGS-helix domain with function in antioxidant protection. SEPN1 might be a downstream target of JNK pathway, and it could respond to multiple stresses. Human's SEPN1 might not combine with Ca2+ with a single EF-hand motif in calcium homeostasis, and chicken SEPN1 did not have the EF-hand motif in the prediction, indicating the EF-hand motif malfunctioned in chicken SEPN1.

Definition and Characterization of a “Trypsinosome” from Specific Peptide Characteristics by Nano-HPLC−MS/MS and in Silico Analysis of Complex Protein Mixtures

2004 ◽  
Vol 3 (6) ◽  
pp. 1138-1148 ◽  
Author(s):  
Thierry Le Bihan ◽  
Mark D. Robinson ◽  
Ian I. Stewart ◽  
Daniel Figeys
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Complex Protein ◽  
Silico Analysis ◽  
Specific Peptide

scholarly journals A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Francesca Caccuri ◽  
Alberto Zani ◽  
Serena Messali ◽  
Marta Giovanetti ◽  
Antonella Bugatti ◽  
...  
Keyword(s):  
Viral Load ◽  
Selection Process ◽  
In Silico Analysis ◽  
High Viral Load ◽  
Current Approach ◽  
The One ◽  
Host Evolution ◽  
Silico Analysis ◽  
Generation Sequencing

Abstract Background Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favouring the appearance of mild SARS-CoV-2 strains are since being accumulating. To better understand the evolution of SARS-CoV-2 pathogenicity and its adaptation to the host, it is therefore crucial to investigate the genetic and phenotypic characteristics of SARS-CoV-2 strains circulating lately in the epidemic. Methods Nasopharyngeal swabs have been analyzed for viral load in the early (March 2020) and late (May 2020) phases of epidemic in Brescia, Italy. Isolation of SARS-CoV-2 from 2 high viral load specimens identified on March 9 (AP66) and on May 8 (GZ69) was performed on Vero E6 cells. Amount of virus released was assessed by quantitative PCR. Genotypic characterization of AP66 and GZ69 was performed by next generation sequencing followed by an in-depth in silico analysis of nucleotide mutations. Results The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect. Vero E6 subculturing, up to passage 4, showed that SARS-CoV-2 GZ69 infection was as productive as the one sustained by the cytopathic strain AP66. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins. Conclusions Identification of the peculiar SARS-CoV-2 GZ69 strain in the late Italian epidemic highlights the need to better characterize viral variants circulating among asymptomatic or paucisymptomatic individuals. The current approach could unravel the ways for future studies aimed at analyzing the selection process which favours viral mutations in the human host.

scholarly journals Cloning and characterization of novel human SLC4A8 gene products encoding Na+-driven Cl−/HCO3− exchanger variants NDCBE-A, -C, and -D

2008 ◽  
Vol 34 (3) ◽  
pp. 265-276 ◽  
Author(s):  
Mark D. Parker ◽  
Patrice Bouyer ◽  
Christopher M. Daly ◽  
Walter F. Boron
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Inhibitory Effect ◽  
Functional Difference ◽  
The Novel ◽  
Equivalent Position ◽  
Rapid Amplification ◽  
Novel Exon ◽  
Silico Analysis

The reported sequences of the human and mouse Na+-driven Cl−/HCO3− exchangers (NDCBEs) differ greatly in their extreme cytosolic COOH termini (Ct). In human NDCBE (NDCBE-B), a 17-amino acid (aa) sequence replaces 66 aa at the equivalent position in mouse NDCBE (NDCBE-A). We performed 5′- and 3′-rapid amplification of cDNA ends (RACE) on human brain cDNA, followed by PCR of full-length cDNAs to determine whether the human SLC4A8 gene was capable of producing the mouselike Ct sequence. Our study confirmed the presence in human cDNA of mouse NDCBE-like transcripts (human NDCBE-A) and also disclosed the existence of three further novel NDCBE transcripts that we have called NDCBE-C, NDCBE-D, and NDCBE-D′. The novel NDCBE-C/D/D′ transcripts initiate at a novel “exon 0” positioned ∼35 kb upstream of the first exon of NDCBE-A/B. NDCBE-C/D/D′ protein products are predicted to be truncated by 54 aa in the cytosolic NH2 terminus (Nt) compared with NDCBE-A/B. Our data, combined with a new in silico analysis of partial transcripts reported by others in the region of the human SLC4A8 gene, increase the known extent of the SLC4A8 gene by 49 kb, to 124 kb. A functional comparison of NDCBE-A/B/C/D expressed in Xenopus oocytes demonstrates that the Nt variation does not affect the basal functional expression of NDCBE, but those with the shorter Ct have a 25–50% reduced functional expression compared with those with the longer Ct. By comparison with an artificially truncated NDCBE that contains neither 17-aa nor 66-aa Ct cassette, we determined that the functional difference is unrelated to the 66-aa cassette of NDCBE-A/C, but is instead due to an inhibitory effect of the 17-aa cassette of NDCBE-B/D.

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

Characterization of Three Key MicroRNAs in Rice Root Architecture under Drought Stress using In silico Analysis and Quantitative Real-time PCR

2014 ◽  
Vol 11 (2) ◽  
pp. 555-565 ◽  
Author(s):  
Behnam Bakhshi ◽  
Ghasem Hosseini Salekdeh ◽  
Mohammad Reza Bihamta ◽  
Masoud Tohidfar
Keyword(s):  
Drought Stress ◽  
Real Time ◽  
Real Time Pcr ◽  
In Silico ◽  
Root Architecture ◽  
In Silico Analysis ◽  
Rice Root ◽  
Quantitative Real Time Pcr ◽  
Silico Analysis

In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis

2007 ◽  
Vol 31 (2) ◽  
pp. 82-91 ◽  
Author(s):  
N.S. Gomathi ◽  
H. Sameer ◽  
Vanaja Kumar ◽  
S. Balaji ◽  
V.N. Azger Dustackeer ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
In Silico Analysis ◽  
Genome Characterization ◽  
Silico Analysis
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