scholarly journals An RNase III processed, antisense RNA pair regulates a Campylobacter jejuni colonization factor

2021 ◽  
Author(s):  
Sarah L Svensson ◽  
Cynthia M. Sharma
Keyword(s):  
Campylobacter Jejuni ◽  
Stress Responses ◽  
Foodborne Pathogen ◽  
Rnase E ◽  
Rnase Iii ◽  
Cis Acting ◽  
Colonization Factor ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Genomic Locations

Small RNAs (sRNAs) are emerging as important and diverse post-transcriptional gene expression regulators in bacterial stress responses and virulence. While originally identified mainly in intergenic regions, genome-wide approaches have revealed sRNAs encoded in diverse contexts, such as processed from parental transcripts by RNase E. Despite its well-known roles in rRNA processing, RNA decay, cleavage of sRNA-mRNA duplexes, the role of RNase III in sRNA biogenesis is less well understood. Here, we show that a pair of cis-encoded sRNAs (CJnc190 and CJnc180) are processed by RNase III in the foodborne pathogen Campylobacter jejuni. While CJnc180 processing requires CJnc190, RNase III cleaves an intramolecular duplex in CJnc190, independent of CJnc180. Moreover, we demonstrate that CJnc190 directly represses translation of the colonization factor PtmG by binding its G-rich ribosome binding site, and show that CJnc180 is a cis-acting antagonist of CJnc190, thereby indirectly affecting ptmG regulation. Our results expand the diversity of known genomic locations of bacterial sRNA sponges and highlight a role for bacterial RNase III that parallels miRNA processing by related eukaryotic Dicer and Drosha.

scholarly journals RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Sarah Lauren Svensson ◽  
Cynthia Mira Sharma
Keyword(s):  
Stress Responses ◽  
Small Rnas ◽  
Foodborne Pathogen ◽  
Transcriptional Regulators ◽  
Rrna Processing ◽  
Rnase E ◽  
Rnase Iii ◽  
Ribosome Binding ◽  
Colonization Factor

Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the foodborne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, In contrast, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that antagonize bacterial sRNAs.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Stefan P. de Vries ◽  
Srishti Gupta ◽  
Abiyad Baig ◽  
Elli Wright ◽  
Amy Wedley ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
In Vivo Models ◽  
Genome Wide

scholarly journals Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Tissue Specificity ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

scholarly journals Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

2014 ◽  
Vol 197 (1) ◽  
pp. 40-50 ◽  
Author(s):  
Chen-Hsun Tsai ◽  
Rick Liao ◽  
Brendan Chou ◽  
Michael Palumbo ◽  
Lydia M. Contreras
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Rapid Identification ◽  
Bacterial Genomes ◽  
Coding Regions ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Genomic Locations ◽  
Regulatory Functions ◽  
Flanking Regions

Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5′ and 3′ untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms.

scholarly journals Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9130
Author(s):  
Jing He ◽  
Xiaohong He ◽  
Pingan Chang ◽  
Huaizhong Jiang ◽  
Daping Gong ◽  
...  
Keyword(s):  
Brassica Juncea ◽  
Gene Structure ◽  
Stress Responses ◽  
Motif Analysis ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
Proliferating Cell ◽  
Tcp Family

Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.

scholarly journals The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicholas M. Negretti ◽  
Christopher R. Gourley ◽  
Prabhat K. Talukdar ◽  
Geremy Clair ◽  
Courtney M. Klappenbach ◽  
...  
Keyword(s):  
Host Cell ◽  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
Small Gtpase ◽  
Host Cells ◽  
Cell Protein ◽  
Host Cell Protein ◽  
Cell Binding ◽  
Actin Reorganization ◽  
Cell Cytosol

AbstractCampylobacter jejuni is a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells by C. jejuni requires cell binding as well as delivery of the Cia proteins (Campylobacter invasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization of C. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate that C. jejuni-stimulated Rac signaling is dependent on IQGAP1.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

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