Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Laia, Marcelo Luiz de; Moreira, Leandro Márcio; Gonçalves, Janaína Fernandes; Ferro, Maria Inês Tiraboschi; Rodrigues, Any Caroliny Pinto; Santos, Jéssica Naiara dos; Felestrino, Érica Barbosa; Ferro, Jesus Aparecido

doi:10.1016/j.ejbt.2019.10.003

Cited by 3 publications

(7 citation statements)

References 75 publications

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“…Relaxing the binding conditions of the primers as such enables a unique method to probe metagenomic datasets to assess the potential of these primers in complex environments and, with further development, provides a possible means of strengthening the annotations of such datasets where hypothetical and uncharacterized genes can conservatively make up 25-40 % of proteincoding genes [42][43][44][45].…”

Section: Discussion Primer Hits and Gene Annotationsmentioning

confidence: 99%

“…These primers have previously been validated against their intended pure strains [8], but to assess their potential to detect these genes in complex environments with no certainty of the source species, the binding conditions were reduced to a minimum percentage identity of 80 % while maintaining enough stringency to feasibly be able to produce a PCR product. Relaxing the binding conditions of the primers as such enables a unique method to probe metagenomic datasets to assess the potential of these primers in complex environments and, with further development, provides a possible means of strengthening the annotations of such datasets where hypothetical and uncharacterized genes can conservatively make up 25–40 % of protein-coding genes [42–45].…”

Section: Discussionmentioning

confidence: 99%

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Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

2022

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As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.

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Section: Discussion Primer Hits and Gene Annotationsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

2022

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“…The mixture was shaken at 28 °C for 16 h after the addition of DMSO or 100 μM of the inhibitor. Total RNA extraction and cDNA synthesis were performed based on the reported study. , The house-keeping gene DNA gyrase subunit B ( gyrB ) gene was used as the internal control . RNA extraction from plants was performed using the RNA prep Pure Bacteria Kit (Promega), and the gene expression level was measured as described above.…”

Section: Methodsmentioning

confidence: 99%

“…30,45 The house-keeping gene DNA gyrase subunit B (gyrB) gene was used as the internal control. 46 RNA extraction from plants was performed using the RNA prep Pure Bacteria Kit (Promega), and the gene expression level was measured as described above. The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Cs5g06870) was used as an internal control for the analysis of the data.…”

Section: Construction Of Reporter Strains and Screen Of Inhibitorsmentioning

confidence: 99%

Innovative Strategy for the Control of Citrus Canker: Inhibitors Targeting the Type III Secretion System of Xanthomonas citri Subsp. citri

Wang,

He,

Zhang

et al. 2023

J. Agric. Food Chem.

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To find potential type III secretion system (T3SS) inhibitors against citrus canker caused by Xanthomonas citri subsp. citri (Xcc), a new series of 5-phenyl-2-furan carboxylic acid derivatives stitched with 2-mercapto-1,3,4-thiadiazole were designed and synthesized. Among the 30 compounds synthesized, 14 compounds significantly inhibited the promoter activity of a harpin gene hpa1. Eight of the 14 compounds did not affect the growth of Xcc, but significantly reduced the hypersensitive response (HR) of tobacco and decreased the pathogenicity of Xcc on citrus plants. Subsequent studies have demonstrated that these inhibitory molecules effectively suppress the T3SS of Xcc and significantly impair the pathogen’s ability to subvert citrus immunity, resulting in a reduction in the level of disease progression. As a result, our work has identified a series of potentially attractive agents for the control of citrus canker.

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“…53 HrcC and hrcT are two hrc genes, respectively, encoding outer membrane secretory protein and output device proteins. 44 In addition, the mRNA level of hpa1 was also examined to validate the aforementioned findings that the compound F9 had an inhibitory influence on the transcription of hpa1.…”

Section: Hr Inhibition By Compound F9mentioning

confidence: 96%

Design and Synthesis of Mandelic Acid Derivatives for Suppression of Virulence via T3SS against Citrus Canker

Zhang,

Wang,

Shi

et al. 2024

J. Agric. Food Chem.

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Citrus canker, a highly contagious bacterial disease caused by Xanthomonas citri subsp. citri (Xcc), poses a substantial threat to citrus crops, leading to serious reductions in fruit yield and economic losses. Most commonly used bactericides against Xcc lead to the rapid development of resistant subpopulations. Therefore, it is imperative to create novel drugs, such as type III secretion system (T3SS) inhibitors, that specifically target bacterial virulence factors rather than bacterial viability. In our study, we designed and synthesized a series of mandelic acid derivatives including 2-mercapto-1,3,4-thiazole. Seven substances were found to reduce the level of transcription of hpa1 without affecting bacterial viability. In vivo bioassays indicated that compound F9 significantly inhibited hypersensitive response and pathogenicity. RT-qPCR assays showed that compound F9 visibly suppressed the expression of Xcc T3SS-related genes as well as citrus canker susceptibility gene CsLOB1. Furthermore, the combination with compound F9 and quorum-quenching bacteria HN-8 can also obviously alleviate canker symptoms.

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Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Cited by 3 publications

References 75 publications

Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

Innovative Strategy for the Control of Citrus Canker: Inhibitors Targeting the Type III Secretion System of Xanthomonas citri Subsp. citri

Design and Synthesis of Mandelic Acid Derivatives for Suppression of Virulence via T3SS against Citrus Canker

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