Xanthomonas oryzae pv. exoribonuclease R is required for complete virulence in rice, optimal motility, and growth under stress

2021 ◽  
Author(s):  
Sharmila Roy ◽  
Pragya Mittal ◽  
Lavanya Tayi ◽  
Sahitya Bondada ◽  
Malay K Ray ◽  
...  
Keyword(s):  
Bacterial Blight ◽  
Pathogenic Bacteria ◽  
Growth Curves ◽  
In Silico Analysis ◽  
Xanthomonas Oryzae ◽  
Rnase R ◽  
Amino Acid Sequence Alignment ◽  
Suboptimal Temperature ◽  
First Time ◽  
Silico Analysis

Exoribonuclease R (RNase R) is a 3’ hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is required for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various Xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. In order to study its role in virulence, a gene disruption mutant of Xoo RNase R (rnr –) was generated. The Xoo rnr – mutant is moderately virulence deficient and the complementing strain (rnr –/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient deficient minimal and nutrient optimal media. We observed that rnr – mutant has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C, cold stress) indicate that Xoo rnr – mutant grows slower than Xoo wild type (wt) and complementing strain (rnr –/pHM1::rnr). Taken together, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.

scholarly journals The Degenerate EAL-GGDEF Domain Protein Filp Functions as a Cyclic di-GMP Receptor and Specifically Interacts with the PilZ-Domain Protein PXO_02715 to Regulate Virulence in Xanthomonas oryzae pv. oryzae

2014 ◽  
Vol 27 (6) ◽  
pp. 578-589 ◽  
Author(s):  
Fenghuan Yang ◽  
Fang Tian ◽  
Xiaotong Li ◽  
Susu Fan ◽  
Huamin Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Bacterial Virulence ◽  
Xanthomonas Oryzae ◽  
Glutathione S Transferase ◽  
Ggdef Domain ◽  
Domain Protein ◽  
Silico Analysis

Degenerate GGDEF and EAL domain proteins represent major types of cyclic diguanylic acid (c-di-GMP) receptors in pathogenic bacteria. Here, we characterized a FimX-like protein (Filp) which possesses both GGDEF and EAL domains in Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice. Both in silico analysis and enzyme assays indicated that the GGDEF and EAL domains of Filp were degenerate and enzymatically inactive. However, Filp bound to c-di-GMP efficiently within the EAL domain, where Q477, E653, and F654 residues were crucial for the binding. Deletion of the filp gene in X. oryzae pv. oryzae resulted in attenuated virulence in rice and reduced type III secretion system (T3SS) gene expression. Complementation analysis with different truncated proteins indicated that REC, PAS, and EAL domains but not the GGDEF domain were required for the full activity of Filp in vivo. In addition, a PilZ-domain protein (PXO_02715) was identified as a Filp interactor by yeast two-hybrid and glutathione-S-transferase pull-down assays. Deletion of the PXO_02715 gene demonstrated changes in bacterial virulence and T3SS gene expression similar to Δfilp. Moreover, both mutants were impaired in their ability to induce hypersensitive response in nonhost plants. Thus, we concluded that Filp was a novel c-di-GMP receptor of X. oryzae pv. oryzae, and its function to regulate bacterial virulence expression might be via the interaction with PXO_02715.

scholarly journals In Silico Analysis of Genetic VapC Profiles from the Toxin-Antitoxin Type II VapBC Modules among Pathogenic, Intermediate, and Non-Pathogenic Leptospira

2019 ◽  
Vol 7 (2) ◽  
pp. 56
Author(s):  
Alexandre Lopes ◽  
Bruna Azevedo ◽  
Rebeca Emídio ◽  
Deborah Damiano ◽  
Ana Nascimento ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Protein Alignment ◽  
Pathogenic Leptospira ◽  
Leptospira Spp ◽  
Unique Species ◽  
Silico Analysis ◽  
Leptospira Species ◽  
Complex Manner

Pathogenic Leptospira spp. is the etiological agent of leptospirosis. The high diversity among Leptospira species provides an array to look for important mediators involved in pathogenesis. Toxin-antitoxin (TA) systems represent an important survival mechanism on stress conditions. vapBC modules have been found in nearly one thousand genomes corresponding to about 40% of known TAs. In the present study, we investigated TA profiles of some strains of Leptospira using a TA database and compared them through protein alignment of VapC toxin sequences among Leptospira spp. genomes. Our analysis identified significant differences in the number of putative vapBC modules distributed in pathogenic, saprophytic, and intermediate strains: four in L. interrogans, three in L. borgpetersenii, eight in L. biflexa, and 15 in L. licerasiae. The VapC toxins show low identity among amino acid sequences within the species. Some VapC toxins appear to be exclusively conserved in unique species, others appear to be conserved among pathogenic or saprophytic strains, and some appear to be distributed randomly. The data shown here indicate that these modules evolved in a very complex manner, which highlights the strong need to identify and characterize new TAs as well as to understand their regulation networks and the possible roles of TA systems in pathogenic bacteria.

scholarly journals Genome‐scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae

2020 ◽  
Vol 21 (4) ◽  
pp. 527-540 ◽  
Author(s):  
Lokanand Koduru ◽  
Hyang Yeon Kim ◽  
Meiyappan Lakshmanan ◽  
Bijayalaxmi Mohanty ◽  
Yi Qing Lee ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Leaf Blight ◽  
Xanthomonas Oryzae ◽  
Metabolic Reconstruction ◽  
Rice Leaf ◽  
Genome Scale ◽  
Silico Analysis

Clinical evaluation and mutational analysis of GALK and GALE genes in patients with galactosemia in Greece: one novel mutation and two rare cases

2017 ◽  
Vol 30 (7) ◽  
Author(s):  
Kleopatra H. Schulpis ◽  
Georgia Thodi ◽  
Konstantinos Iakovou ◽  
Maria Chatzidaki ◽  
Yannis Dotsikas ◽  
...  
Keyword(s):  
Clinical Evaluation ◽  
Mutational Analysis ◽  
Screening Program ◽  
Novel Mutation ◽  
In Silico Analysis ◽  
Speech Development ◽  
The Novel ◽  
Speech Delay ◽  
First Time ◽  
Silico Analysis

AbstractBackground:Deficiencies of galactokinase (GALK) and UDP-epimerase (GALE) are implicated with galactose metabolic disorders. The aim of the study was the identification of mutations inMethods:Five patients with GALK and five with GALE deficiency were picked up via the Neonatal Screening Program. Additionally, two females, 4 years old, were referred with late diagnosed galactosemia, as rare cases. Mutational analysis was conducted via Sanger sequencing, while in silico analysis tools were utilized for the novel mutation. Psychomotor and speech development tests were performed, as well.Results:The mutation p.Pro28Thr was identified in both alleles in GALK-deficient patients of Roma (gypsy) origin, whereas the novel p.Asn39Ser was detected in two non-Roma patients. In GALE-deficient patients benign and/or likely benign mutations were found. Psychomotor and speech delay were determined in the Roma GALK patients. In each of the late diagnosed females, four mutations were identified in all galactosemia-related genes.Conclusions:The mutational spectrums of GALE- and GALK-deficient patients in Greece are presented for the first time along with a clinical evaluation. Mutational analysis in all galactosemia-related genes of symptomatic patients is highly recommended for future cases.

scholarly journals In silico analysis of galactinol synthase genes in common bean (Phaseolus vulgaris L.)

2016 ◽  
Vol 19 (4) ◽  
pp. 45-52
Author(s):  
Bang Phi Cao
Keyword(s):  
Common Bean ◽  
In Silico Analysis ◽  
Duplication Event ◽  
Expression Level ◽  
Phylogenic Tree ◽  
Galactinol Synthase ◽  
Reproductive Tissues ◽  
The Common ◽  
First Time ◽  
Silico Analysis

Galactinol synthases (GolS, EC 2.4.1.123) belong to the glycosyltransferase 8 family. These enzymes catalyzes galactosylation of myo-inositol to form galactinol, precursor of raffinose which is solube sucrose playing an important role in stress tolerance in plants. We identified and analyzed a total of three GolS encoded genes in the whole genome of common bean. These genes possessed two or three introns. The predicted proteins contained from 322 to 340 amino acids. The common bean GolS proteins contained all conseved motifs that were characterized for other previously known GolSs. These proteins were acidic and weakly hydrophilic. The phylogenic tree constructed from GolS proteins of Arabidopsis, poplar and common bean showed that only one gene duplication event was detected in the commone bean genome. Common bean GolS genes expressed in all vegetative and reproductive tissues. However, the transcript abundances of each gene varied in different tissues. When comparing the expression levels of these three genes as defined RNAseq, we found that the expression level of PvGolS2 was the lowest, PvGolS1 expressed the strogest leaves and stem, while PvGolS3 expressed in roots and nodules. We discovered that Rhizobium incubation affected on the expression of GolS genes for the first time. In the reproductive tissues, PvGolS1 expressed in most studied tissues. Its expression level correlatively increased with the tissue development.

scholarly journals GABA-Producing Lactococcus lactis Strains Isolated from Camel’s Milk as Starters for the Production of GABA-Enriched Cheese

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 633
Author(s):  
Begoña Redruello ◽  
Yasmine Saidi ◽  
Lorena Sampedro ◽  
Victor Ladero ◽  
Beatriz del Rio ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Health Benefits ◽  
In Silico Analysis ◽  
Bioactive Compound ◽  
Starter Cultures ◽  
Safety Properties ◽  
Camel's Milk ◽  
First Time ◽  
Multiple Health ◽  
Silico Analysis

The multiple health benefits attributed to the bioactive compound γ-aminobutyric acid (GABA) have prompted the food industry to investigate the development of functional GABA-rich foods via the use of GABA-producing microorganisms. This study reports the isolation of six GABA-producing Lactococcus lactis strains from camel’s milk; this is the first time that such microorganisms have been isolated from milk. The sequencing and in silico analysis of their genomes, and the characterisation of their technological and safety properties, confirmed their potential as starters. Experimental cheeses made with all six strains (individually) accumulated GABA at concentrations of up to 457 mg/kg. These GABA-producing L. lactis strains could be used as starter cultures for the manufacture of functional GABA-enriched cheeses that provide health benefits to consumers.

Detection and in silico Analysis of rmpA Gene from Soilborne Pathogenic Bacteria

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Laith AbdulHassan Mohamed-Jawad
Keyword(s):  
Klebsiella Pneumoniae ◽  
Staphylococcus Epidermidis ◽  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Multiple Sequence ◽  
Bacterial Gene ◽  
New Approach ◽  
Geological Processes ◽  
Bacillus Spp ◽  
Silico Analysis

Soil serves as an ecosystem for diverse microbes that perform various roles and that range from useful organisms in biological and geological processes to dangerous transmitters of diseases. Most type of soilborne bacteria are harmful to humans and causing severe problems. Klebsiella pneumoniae consider a serious nosocomial pathogen that cause pneumonia, UTIs, wound and liver abscesses. One hundred fifty (150) soil samples isolated randomly during the period November 2014- February 2015. Bacterium Klebsiella pneumoniae was the commonest pathogen (36.70%) followed by Staphylococcus aureus (22.78%), Staphylococcus epidermidis (12.65%), Bacillus spp. (10.12%), Pseudomonas aeruginosa (5.06%), Enterobacter cloacae (5.06%), Streptococcus spp.(2.53%), Citrobacter spp.(1.26%) and Pantoea spp.(1.26%) respectively. All K. pneumoniae isolates detected and confirmed by conventional PCR using rmpA gene size 530bp. The positive isolates were sequenced and search for homology. The multiple sequence alignment showed that our bacterial gene have differences in NAD-dependent epimerase and NAD (p)- binding domain sequence at different sites. The differences in the nucleotides at gene sequence for the isolated strain which may give new approach for developing higher sensitive K. pneumoniae strains and for better understanding of the rmpA gene structure that should provide new tools for disease management. Keywords:

scholarly journals First method for dissolving zinc thiazole and re-evaluation of its antibacterial properties against rice bacterial blight disease

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Xian Chen ◽  
Lan Zhou ◽  
Pedro Laborda ◽  
Yancun Zhao ◽  
Kaihuai Li ◽  
...  
Keyword(s):  
Cell Wall ◽  
Bacterial Blight ◽  
Antibacterial Properties ◽  
Xanthomonas Oryzae ◽  
Antibacterial Mechanism ◽  
Control Efficacy ◽  
Rice Bacterial Blight ◽  
Bacterial Blight Disease ◽  
Blight Disease ◽  
First Time

Abstract Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most destructive diseases in rice-growing regions worldwide. Zinc thiazole is a novel bactericide and has been applied for BB control for 10 years. However, zinc thiazole is highly insoluble in water and in most organic solvents. In this work, we found for the first time that zinc thiazole can be dissolved in dimethyl sulfoxide (DMSO), and the solubility of zinc thiazole in DMSO is more than 20 mg/mL. Dissolved zinc thiazole at 25 μg/mL significantly inhibited the growth of Xoo by 58.81%. Interestingly, zinc thiazole at 25 μg/mL enhanced the cell division and altered the cell wall integrity of Xoo. The application of dissolved zinc thiazole at 100 μg/mL reduced the incidence of rice bacterial blight (BB) by providing 64.71% control efficacy, while zinc thiazole as suspension concentrate (SC) at 100 μg/mL only provided 43.42% control efficacy. Taken together, this study provides for the first time a method for dissolving zinc thiazole, and may help to better understand the antibacterial mechanism of zinc thiazole.

scholarly journals The Xanthomonas oryzae pv. oryzae PilZ Domain Proteins Function Differentially in Cyclic di-GMP Binding and Regulation of Virulence and Motility

2015 ◽  
Vol 81 (13) ◽  
pp. 4358-4367 ◽  
Author(s):  
Fenghuan Yang ◽  
Fang Tian ◽  
Huamin Chen ◽  
William Hutchins ◽  
Ching-Hong Yang ◽  
...  
Keyword(s):  
Type Iii Secretion ◽  
Bacterial Blight ◽  
Pathogenic Bacteria ◽  
Xanthomonas Oryzae ◽  
Wild Type ◽  
Binding Motifs ◽  
Content Type ◽  
Reading Frame ◽  
Bacterial Blight Pathogen

ABSTRACTThe PilZ domain proteins have been demonstrated to be one of the major types of receptors mediating cyclic di-GMP (c-di-GMP) signaling pathways in several pathogenic bacteria. However, little is known about the function of PilZ domain proteins in c-di-GMP regulation of virulence in the bacterial blight pathogen of riceXanthomonas oryzaepv. oryzae. Here, the roles of PilZ domain proteins PXO_00049 and PXO_02374 in c-di-GMP binding, regulation of virulence and motility, and subcellular localization were characterized in comparison with PXO_02715, identified previously as an interactor with the c-di-GMP receptor Filp to regulate virulence. The c-di-GMP binding motifs in the PilZ domains were conserved in PXO_00049 and PXO_02374 but were less well conserved in PXO_02715. PXO_00049 and PXO_02374 but not PXO_02715 proteins bound to c-di-GMP with high affinityin vitro, and the R141and R10residues in the PilZ domains of PXO_00049 and PXO_02374, respectively, were crucial for c-di-GMP binding. Gene deletion of PXO_00049 and PXO_02374 resulted in significant increases in virulence andhrpgene transcription, indicating their negative regulation of virulence via type III secretion system expression. All mutants showed significant changes in sliding motility but not exopolysaccharide production and biofilm formation. Intransexpression of the full-length open reading frame (ORF) of each gene in the relevant mutants led to restoration of the phenotype to wild-type levels. Moreover, PXO_00049 and PXO_02374 displayed mainly multisite subcellular localizations, whereas PXO_02715 showed nonpolar distributions in theX. oryzaepv. oryzae cells. Therefore, this study demonstrated the different functions of the PilZ domain proteins in mediation of c-di-GMP regulation of virulence and motility inX. oryzaepv. oryzae.

Evaluation of resistance of rice genotypes (derived from the cross between HKR-127 and IRBB-60) against bacterial blight caused by Xanthomonas oryzae pv. oryzae

2019 ◽  
Vol 9 (4) ◽  
pp. 142-147
Author(s):  
Kirti Mehta ◽  
Nikita Baliyan ◽  
Rahul Kumar Meena ◽  
Shikha Yashveer
Keyword(s):  
Resistance Genes ◽  
Evaluation System ◽  
Bacterial Blight ◽  
Pathogenic Bacteria ◽  
Rice Variety ◽  
Xanthomonas Oryzae ◽  
Lesion Length ◽  
Bacterial Diseases ◽  
Agricultural Produce ◽  
Rice Genotypes

Rice crop is susceptible to various bacterial diseases and one such commonly known disease is Bacterial Blight (BB) caused by the pathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo). Rice variety HKR-127 is widely accepted by rice farmers, users and buyers in Haryana (India) owing to its high agricultural produce, medium lanky grains, and outstanding cooking characteristics, however, HKR-127 exhibits less endurance to BB. The aim of the study conducted at CCS Haryana Agricultural University was to investigate the genetic potential of BC3F2 and BC3F3 pyramided rice genotypes (cross HKR-127 x IRBB -60) having resistance genes (Xa21, xa13, and xa5). These genotypes were tested for virulence against BB under artificial conditions using Clip method of artificial inoculation. On average, five leaves per plant were inoculated and visually scored after 14 days. Disease reaction rating was done on a 0-9 scale of the standard evaluation system (SES) for rice. Rice genotypes with all the three genes exhibited relatively low mean lesion length compared to single or double combinations thus establishing higher resistance of threegene genotypes to BB. The lines obtained in our study can be used as genetic resources for BB resistance in breeding programs that will be paving the way for an environmentally-friendly means to achieve a better disease management. Moreover, the success will facilitate future efforts to transfer combinations of BB resistance genes into other preferred rice cultivars. 

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