Genome‐wide screen and functional analysis in <i>Xanthomonas</i> reveal a large number of mRNA‐derived sRNAs, including the novel RsmA‐sequester RsmU

Tang, Dongjie; Chen, Xiaolin; Yu, Jie; Liang, Yuwei; He, Yueqiu; Lu, Tingting; Zhu, Chuanrang; Han, Bin; An, Shi-Qi; Tang, Ji‐Liang

doi:10.1111/mpp.12997

Cited by 10 publications

(9 citation statements)

References 76 publications

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“…The majority of our retrieved sRNAs belonged to intrsRNAs (65.8%), particularly sRNAs overlapped with the 5’- and 3’-ends of mRNAs (Figures 2D and 2E), indicating that mRNA may be the primary origination source of sRNAs in A. dieselolei . This finding is in congruence with recent evidences in different bacteria, such as sRNAs from 3’-UTRs in Salmonella enterica (Chao et al, 2017), 5’UTRs and CDSs in Escherichia coli (Dar and Sorek, 2018; Adams et al, 2021), and CDSs, 5’UTRs as well as 3’-UTRs in Xanthomonas campestris (Tang et al, 2020).…”

Section: Resultssupporting

confidence: 92%

“…Importantly, more and more evidences support that sRNAs can originate from any locations in the genome. In addition to the well-known intergenic and antisense regions, myriad sRNAs are derived from the UTRs (untranslated regions) and CDSs (coding sequences) of mRNAs (Miyakoshi et al, 2015; Dar and Sorek, 2018; Adams and Storz, 2020; Hoyos et al, 2020; Tang et al, 2020; Adams et al, 2021; Krieger et al, 2022; Ponath et al, 2022). Fortunately, with the rapid development of high-throughput sequencing technologies, RNA-seq-based approaches have been created to detect the global sRNA profiling (Hör et al, 2018), especially the differential RNA sequencing (dRNA-seq), which can even capture the sRNAs overlapped with other transcripts (Yu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degraderAlcanivorax dieseloleiB-5

Wei

et al. 2022

Preprint

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Alkanes are widespread in the ocean, and Alcanivorax is one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (~50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model species Alcanivorax dieselolei B-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5'-ends, with 63.4% of transcription start sites (TSSs) and 36.6% of processing sites (PSSs). These sRNAs originated from almost any locations in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes of Alcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with characterized genes of the alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide targets prediction. Overall, the sRNAs landscape lays the ground for uncovering cryptic regulations in the critical marine bacterium, among which both core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.

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Section: Resultssupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degraderAlcanivorax dieseloleiB-5

Wei

et al. 2022

Preprint

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“…mcvR expression was elevated in 8004/pBmcvR, and the mcvR transcript level in the overexpressing strain was more than 4-fold higher compared to the wild-type strain carrying the empty vector pBBad22K grown in NYG, even without addition of arabinose (Figure S3). This is consistent with previous findings that P ara can ensure the overexpression of a target gene in the absence of arabinose in Xcc cells (Tang et al, 2020).…”

Section: Overexpression Of Mcvr Enhances Cell Motility Chemotaxis And...supporting

confidence: 93%

McvR, a single domain response regulator regulates motility and virulence in the plant pathogen Xanthomonas campestris

Ren

Liu

et al. 2022

Molecular Plant Pathology

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Signal transduction pathways mediated by sensor histidine kinases and cognate response regulators control a variety of physiological processes in response to environmental conditions in most bacteria. Comparatively little is known about the mechanism(s) by which single‐domain response regulators (SD‐RRs), which lack a dedicated output domain but harbour a phosphoryl receiver domain, exert their various regulatory effects in bacteria. Here we have examined the role of the SD‐RR proteins encoded by the phytopathogen Xanthomonas campestris pv. campestris (Xcc). We describe the identification and characterization of a SD‐RR protein named McvR (motility, chemotaxis, and virulence‐related response regulator) that is required for virulence and motility regulation in Xcc. Deletion of the mcvR open reading frame caused reduced motility, chemotactic movement, and virulence in Xcc. Global transcriptome analyses revealed the McvR had a broad regulatory role and that most motility and pathogenicity genes were down‐regulated in the mcvR mutant. Bacterial two‐hybrid and protein pull‐down assays revealed that McvR did not physically interact with components of the bacterial flagellum but interacts with other SD‐RR proteins (like CheY) and the subset of DNA‐binding proteins involved in gene regulation. Site‐directed mutagenesis and phosphor‐transfer experiments revealed that the aspartyl residue at position 55 of the receiver domain is important for phosphorylation and the regulatory activity of McvR protein. Taken together, the findings describe a previously unrecognized class of SD‐RR protein that contributes to the regulation of motility and virulence in Xcc.

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“…E. coli RsmA/CsrA is controlled by antagonistic RNA RsmB/CsrB [ 112 ] that does not harbor any known structural homologs in xanthomonads. A potential antagonistic small RNA, RsmU ( Figure 2 ), was recently identified in Xcc [ 113 ], but environmental cues and upstream regulators of Xanthomonas RsmA/CsrA and RsmU have yet to be identified. Intriguingly, flagellar and T4SS assembly genes, which are usually associated with epiphytic fitness, are negatively regulated by Xanthomonas RsmA/CsrA [ 41 , 114 ], suggesting that RsmA/CsrA potentially serves as a molecular switch to distinguish between the epiphytic and endophytic lifestyle of the bacteria.…”

Section: Transcriptional and Post-transcriptional Regulation Of mentioning

confidence: 99%

The HrpG/HrpX Regulon of Xanthomonads—An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria

2021

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Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.

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Genome‐wide screen and functional analysis in Xanthomonas reveal a large number of mRNA‐derived sRNAs, including the novel RsmA‐sequester RsmU

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 10 publications

References 76 publications

High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degraderAlcanivorax dieseloleiB-5

High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degraderAlcanivorax dieseloleiB-5

McvR, a single domain response regulator regulates motility and virulence in the plant pathogen Xanthomonas campestris

The HrpG/HrpX Regulon of Xanthomonads—An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria

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