The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response

Abstract Background Bacterial abortive infection (Abi) systems are type IV toxin–antitoxin (TA) system, which could elicit programmed cell death and constitute a native survival strategy of pathogenic bacteria under various stress conditions. However, no rhizobial AbiE family TA system has been reported so far. Here, a M. huakuii AbiE TA system was identified and characterized. Results A mutation in M. huakuii abiEi gene, encoding an adjacent GntR-type transcriptional regulator, was generated by homologous recombination. The abiEi mutant strain grew less well in rich TY medium, and displayed increased antioxidative capacity and enhanced gentamicin resistance, indicating the abiEi operon was negatively regulated by the antitoxin AbiEi in response to the oxidative stress and a particular antibiotic. The mRNA expression of abiEi gene was significantly up-regulated during Astragalus sinicus nodule development. The abiEi mutant was severely impaired in its competitive ability in rhizosphere colonization, and was defective in nodulation with 97% reduction in nitrogen-fixing capacity. The mutant infected nodule cells contained vacuolation and a small number of abnormal bacteroids with senescence character. RNA-seq experiment revealed it had 5 up-regulated and 111 down-regulated genes relative to wild type. Of these down-regulated genes, 21 are related to symbiosis nitrogen fixation and nitrogen mechanism, 16 are involved in the electron transport chain and antioxidant responses, and 12 belong to type VI secretion system (T6SS). Conclusions M. huakuii AbiEi behaves as a key transcriptional regulator mediating root nodule symbiosis.

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Species boundaries in the Agrobacterium tumefaciens complex and multi-level modular evolution of their antibacterial type VI secretion system and tumor-inducing plasmids

10.1101/2021.05.20.444927 ◽

2021 ◽

Author(s):

Lin Chou ◽

Yu-Chen Lin ◽

Mindia Haryono ◽

Mary Nia M. Santos ◽

Shu-Ting Cho ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Pathogenic Bacteria ◽

Secretion System ◽

Species Boundaries ◽

Type Vi Secretion System ◽

Type Iv ◽

Type Vi Secretion ◽

Modular Evolution ◽

Species Complexes ◽

Genome Phylogeny

Many pathogenic bacteria are recognized as species complexes and uncertainties regarding the organization of their genetic diversity are challenges for research efforts. Within Agrobacterium tumefaciens, multiple genomospecies have been identified; however, the exact species boundaries are unclear, which causes chaos in nomenclature and hampers communication. In this work, we conducted targeted genome sequencing to achieve a comprehensive and balanced taxon sampling within this complex. Our results from genome-wide sequence identity, core genome phylogeny, and gene content not only supported that those recognized genomospecies are distinct biological entities but also identified novel genomospecies. Based on the fully resolved phylogeny, we further investigated the evolution of genes critical in Agrobacterium fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition, multiple losses and one horizontal gene transfer (HGT) event were inferred. For the tumor-inducing plasmids (pTi) and the pTi-encoded type IV secretion system (T4SS) that determine Agrobacterium phytopathogenicity, the evolution of these accessory replicons was decoupled from the chromosomes, thus contributing to another level of complexity. Intriguingly, for both T6SS and T4SS, genes that encode the structural components are highly conserved, whereas extensive diversity exists at multiple levels (i.e., between-species, within-species, intra-genome, and intra-gene) for genes that encode effectors and associated proteins. These findings suggest that opposite modes of selection may act on components conferring different functions within a system. In conclusion, this work provides insights into the genomic diversification of these bacteria and sheds light on the modularity of their molecular evolution.

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Predation by Bdellovibrio bacteriovorus HD100 Requires Type IV Pili

Journal of Bacteriology ◽

10.1128/jb.01942-06 ◽

2007 ◽

Vol 189 (13) ◽

pp. 4850-4859 ◽

Cited By ~ 69

Author(s):

Katy J. Evans ◽

Carey Lambert ◽

R. Elizabeth Sockett

Keyword(s):

Life Cycle ◽

Fluorescent Protein ◽

Expression Patterns ◽

Yellow Fluorescent Protein ◽

Critical Role ◽

Type Iv Pili ◽

Gene Encoding ◽

Bdellovibrio Bacteriovorus ◽

Type Iv ◽

Fiber Protein

ABSTRACT Early electron microscopy and more recent studies in our laboratory of Bdellovibrio bacteriovorus cells indicated the presence of narrow fibers at the nonflagellar pole of this unusual predatory bacterium. Analysis of the B. bacteriovorus HD100 genome showed a complete set of genes potentially encoding type IV pili and an incomplete gene set for Flp pili; therefore, the role of type IV pili in the predatory life cycle of B. bacteriovorus HD100 was investigated. Alignment of the predicted PilA protein with known type IV pilins showed the characteristic conserved N terminus common to type IVa pilins. The pilA gene, encoding the type IV pilus fiber protein, was insertionally inactivated in multiple Bdellovibrio replicate cultures, and the effect upon the expression of other pilus genes was monitored by reverse transcriptase PCR. Interruption of pilA in replicate isolates abolished Bdellovibrio predatory capability in liquid prey cultures and on immobilized yellow fluorescent protein-labeled prey, but the mutants could be cultured prey independently. Expression patterns of pil genes involved in the formation of type IV pili were profiled across the predatory life cycle from attack phase predatory Bdellovibrio throughout the intraperiplasmic bdelloplast stages to prey lysis and in prey-independent growth. Taken together, the data show that type IV pili play a critical role in Bdellovibrio predation.

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Mutation in the ntrR Gene, a Member of the vap Gene Family, Increases the Symbiotic Efficiency of Sinorhizobium meliloti

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2001.14.7.887 ◽

2001 ◽

Vol 14 (7) ◽

pp. 887-894 ◽

Cited By ~ 25

Author(s):

Boglárka Oláh ◽

Erno Kiss ◽

Zoltán Györgypál ◽

Judit Borzi ◽

Gyöngyi Cinege ◽

...

Keyword(s):

Nitrogen Fixation ◽

Pathogenic Bacteria ◽

Sinorhizobium Meliloti ◽

Root Nodules ◽

Nifh Gene ◽

Dry Weight ◽

Nodule Occupancy ◽

Gene Encoding ◽

Symbiotic Efficiency ◽

Host Interactions

In specific plant organs, namely the root nodules of alfalfa, fixed nitrogen (ammonia) produced by the symbiotic partner Sinorhizobium meliloti supports the growth of the host plant in nitrogen-depleted environment. Here, we report that a derivative of S. meliloti carrying a mutation in the chromosomal ntrR gene induced nodules with enhanced nitrogen fixation capacity, resulting in an increased dry weight and nitrogen content of alfalfa. The efficient nitrogen fixation is a result of the higher expression level of the nifH gene, encoding one of the subunits of the nitrogenase enzyme, and nifA, the transcriptional regulator of the nif operon. The ntrR gene, controlled negatively by its own product and positively by the symbiotic regulator syrM, is expressed in the same zone of nodules as the nif genes. As a result of the nitrogen-tolerant phenotype of the strain, the beneficial effect of the mutation on efficiency is not abolished in the presence of the exogenous nitrogen source. The ntrR mutant is highly competitive in nodule occupancy compared with the wild-type strain. Sequence analysis of the mutant region revealed a new cluster of genes, termed the “ntrPR operon,” which is highly homologous to a group of vap-related genes of various pathogenic bacteria that are presumably implicated in bacterium-host interactions. On the basis of its favorable properties, the strain is a good candidate for future agricultural utilization.

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Complex transcriptional regulation of the Saccharomyces cerevisiae CYB2 gene encoding cytochrome b2: CYP1(HAP1) activator binds to the CYB2 upstream activation site UAS1-B2.

Molecular and Cellular Biology ◽

10.1128/mcb.11.7.3762 ◽

1991 ◽

Vol 11 (7) ◽

pp. 3762-3772 ◽

Cited By ~ 36

Author(s):

T Lodi ◽

B Guiard

Keyword(s):

Saccharomyces Cerevisiae ◽

Regulatory Region ◽

Transcriptional Regulator ◽

Direct Analysis ◽

Transcriptional Level ◽

Glucose Fermentation ◽

Gene Encoding ◽

Dnase I Footprinting ◽

Mrna Transcripts ◽

Binding Sequence

Expression of the Saccharomyces cerevisiae gene encoding cytochrome b2 (EC 1.2.2.3), CYB2, was investigated by direct analysis of mRNA transcripts and by measurement of the expression of lacZ fused to the CYB2 control regions. These studies indicated that regulation of the CYB2 gene is subject to several metabolic controls at the transcriptional level: inhibition due to glucose fermentation, induction by lactate, and inhibition in anaerobiosis or in absence of heme biosynthesis. Furthermore, we have shown that the CYB2 promoter contains one cis negative regulatory region and two heme-dependent positive regions, one of which is controlled by the transcriptional regulator CYP1 (HAP1) which is involved in the modulation of the expression of several oxygen-regulated genes. The CYP1 (HAP1)-binding sequence was located by gel retardation and DNase I footprinting experiments and compared with the binding sequences previously characterized in detail (UAS1CYC1, UAS'CYP3 (CYC7), and UASCTT1).

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Phosphothreonine Lyase Promotes p65 Degradation in a Mitogen-Activated Protein Kinase/Mitogen- and Stress-Activated Protein Kinase 1-Dependent Manner

Infection and Immunity ◽

10.1128/iai.00508-18 ◽

2018 ◽

Vol 87 (1) ◽

Cited By ~ 1

Author(s):

Mingyu Hou ◽

Wenhui Wang ◽

Feizi Hu ◽

Yuanxing Zhang ◽

Dahai Yang ◽

...

Keyword(s):

Protein Kinase ◽

Pathogenic Bacteria ◽

Critical Role ◽

Nuclear Factor Κb ◽

Mapk Signaling ◽

Mitogen Activated Protein Kinase ◽

Dependent Manner ◽

Content Type ◽

Catalytic Active Site ◽

Mitogen Activated Protein

ABSTRACT Bacterial phosphothreonine lyases have been identified to be type III secretion system (T3SS) effectors that irreversibly dephosphorylate host mitogen-activated protein kinase (MAPK) signaling to promote infection. However, the effects of phosphothreonine lyase on nuclear factor κB (NF-κB) signaling remain largely unknown. In this study, we detected significant phosphothreonine lyase-dependent p65 degradation during Edwardsiella piscicida infection in macrophages, and this degradative effect was blocked by the protease inhibitor MG132. Further analysis revealed that phosphothreonine lyase promotes the dephosphorylation and ubiquitination of p65 by inhibiting the phosphorylation of mitogen- and stress-activated protein kinase-1 (MSK1) and by inhibiting the phosphorylation of extracellular signal-related kinase 1/2 (ERK1/2), p38α, and c-Jun N-terminal kinase (JNK). Moreover, we revealed that the catalytic active site of phosphothreonine lyase plays a critical role in regulating the MAPK-MSK1-p65 signaling axis. Collectively, the mechanism described here expands our understanding of the pathogenic effector in not only regulating MAPK signaling but also regulating p65. These findings uncover a new mechanism by which pathogenic bacteria overcome host innate immunity to promote pathogenesis.

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Involvement of Type IV Pili in Pathogenicity of Plant Pathogenic Bacteria

Genes ◽

10.3390/genes2040706 ◽

2011 ◽

Vol 2 (4) ◽

pp. 706-735 ◽

Cited By ~ 40

Author(s):

Saul Burdman ◽

Ofir Bahar ◽

Jennifer K. Parker ◽

Leonardo De La Fuente

Keyword(s):

Pathogenic Bacteria ◽

Type Iv Pili ◽

Plant Pathogenic Bacteria ◽

Type Iv

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Fresh extension of Vibrio cholerae competence type IV pili predisposes them for motor-independent retraction

10.1101/2021.03.09.434644 ◽

2021 ◽

Author(s):

Jennifer L. Chlebek ◽

Triana N. Dalia ◽

Nicolas Biais ◽

Ankur B. Dalia

Keyword(s):

Cell Surface ◽

Vibrio Cholerae ◽

Conformational Changes ◽

Pathogenic Bacteria ◽

Ectopic Expression ◽

Type Iv Pili ◽

Therapeutic Interventions ◽

Dynamic Activity ◽

Type Iv ◽

Additional Support

ABSTRACTBacteria utilize dynamic appendages called type IV pili (T4P) to interact with their environment and mediate a wide variety of functions. Pilus extension is mediated by an extension ATPase motor, commonly called PilB, in all T4P. Pilus retraction, however, can either occur with the aid of an ATPase motor, or in the absence of a retraction motor. While much effort has been devoted to studying motor-dependent retraction, the mechanism and regulation of motor-independent retraction remains poorly characterized. We have previously demonstrated that Vibrio cholerae competence T4P undergo motor-independent retraction in the absence of the dedicated retraction ATPases PilT and PilU. Here, we utilize this model system to characterize the factors that influence motor-independent retraction. We find that freshly extended pili frequently undergo motor-independent retraction, but if these pili fail to retract immediately, they remain statically extended on the cell surface. Importantly, we show that these static pili can still undergo motor-dependent retraction via tightly regulated ectopic expression of PilT, suggesting that these T4P are not broken, but simply cannot undergo motor-independent retraction. Through additional genetic and biophysical characterization of pili, we suggest that pilus filaments undergo conformational changes during dynamic extension and retraction. We propose that only some conformations, like those adopted by freshly extended pili, are capable of undergoing motor-independent retraction. Together, these data highlight the versatile mechanisms that regulate T4P dynamic activity and provide additional support for the long-standing hypothesis that motor-independent retraction occurs via spontaneous depolymerization.SIGNIFICANCEExtracellular pilus fibers are critical to the virulence and persistence of many pathogenic bacteria. A crucial function for most pili is the dynamic ability to extend and retract from the cell surface. Inhibiting this dynamic pilus activity represents an attractive approach for therapeutic interventions, however, a detailed mechanistic understanding of this process is currently lacking. Here, we use the competence pilus of Vibrio cholerae to study how pili retract in the absence of dedicated retraction motors. Our results reveal a novel regulatory mechanism of pilus retraction that is an inherent property of the external pilus filament. Thus, understanding the conformational changes that pili adopt under different conditions may be critical for the development of novel therapeutics that aim to target the dynamic activity of these structures.

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The 3’UTR of the orb2 gene encoding the Drosophila CPEB translation factor plays a critical role in spermatogenesis

10.1101/2020.08.24.264762 ◽

2020 ◽

Author(s):

Rudolf A. Gilmutdinov ◽

Eugene N. Kozlov ◽

Ludmila V. Olenina ◽

Alexei A. Kotov ◽

Justinn Barr ◽

...

Keyword(s):

Deletion Mutant ◽

Critical Role ◽

Self Regulation ◽

Biological Processes ◽

Apparent Effect ◽

Gene Encoding ◽

Cytoplasmic Polyadenylation ◽

Polarized Cells ◽

Biological Context

AbstractCPEB proteins are conserved translation regulators involved in multiple biological processes. One of these proteins in Drosophila, Orb2, is a principal player in spermatogenesis. It is required for meiosis and spermatid differentiation. During the later process orb2 mRNAs and proteins are localized within the developing spermatid. To evaluate the role of orb2 mRNA 3’UTR in spermatogenesis, we used the CRISPR/Cas9 system to generate a deletion of the orb2 3’UTR, orb2R. This deletion disrupts the process of spermatid differentiation, but has no apparent effect on meiosis. While this deletion appears to destabilize the orb2 mRNA and reduce the levels of Orb2 protein, this is not the primary cause of the differentiation defects. Instead, differentiation appears to be disrupted because orb2 mRNAs and proteins are not properly localized within the differentiating spermatids. Other transcripts and proteins involved in spermatogenesis are also mislocalized in orb2R spermatids.Author summaryThe conserved family of cytoplasmic polyadenylation element binding (CPEB) proteins can activate or repress translation of target mRNAs, depending on the specific biological context, through interaction with special cytoplasmic polyadenylation element (CPE) sequences. These proteins function mainly in highly polarized cells. Orb2, one of the two Drosophila melanogaster CPEB proteins, is predominantly expressed in the testes and is crucial for spermatogenesis. The 3’UTR of orb2 transcript contains multiple CPE-like motifs, which is indicative of orb2 self-regulation. We have generated a deletion that removes the greater portion of 3’UTR. While this deletion causes a reduction in the levels of orb2 mRNA and the protein, this does not appear to be responsible for the defects in spermatogenesis observed in the deletion mutant. Instead, it is the mislocalization of the mRNA and protein in the developing spermatids.

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Identification and Regulation of a Novel Citrobacter rodentium Gut Colonization Fimbria (Gcf)

Journal of Bacteriology ◽

10.1128/jb.02486-14 ◽

2015 ◽

Vol 197 (8) ◽

pp. 1478-1491 ◽

Cited By ~ 2

Author(s):

Gustavo G. Caballero-Flores ◽

Matthew A. Croxen ◽

Verónica I. Martínez-Santos ◽

B. Brett Finlay ◽

José L. Puente

Keyword(s):

Escherichia Coli ◽

Intestinal Epithelium ◽

Pathogenic Bacteria ◽

Critical Role ◽

Growth Conditions ◽

Citrobacter Rodentium ◽

Content Type ◽

Gut Colonization ◽

Successful Infection

ABSTRACTThe Gram-negative enteric bacteriumCitrobacter rodentiumis a natural mouse pathogen that has been extensively used as a surrogate model for studying the human pathogens enteropathogenic and enterohemorrhagicEscherichia coli. All three pathogens produce similar attaching and effacing (A/E) lesions in the intestinal epithelium. During infection, these bacteria employ surface structures called fimbriae to adhere and colonize the host intestinal epithelium. ForC. rodentium, the roles of only a small number of its genome-carried fimbrial operons have been evaluated. Here, we report the identification of a novelC. rodentiumcolonization factor, calledgutcolonizationfimbria (Gcf), which is encoded by a chaperone-usher fimbrial operon. AgcfAmutant shows a severe colonization defect within the first 10 days of infection. Thegcfpromoter is not active inC. rodentiumunder severalin vitrogrowth conditions; however, it is readily expressed in aC. rodentiumΔhns1mutant lacking the closest ortholog of theEscherichia colihistone-like nucleoid structuring protein (H-NS) but not in mutants with deletion of the other four genes encoding H-NS homologs. H-NS binds to the regulatory region ofgcf, further supporting its direct role as a repressor of thegcfpromoter that starts transcription 158 bp upstream of the start codon of its first open reading frame. Thegcfoperon possesses interesting novel traits that open future opportunities to expand our knowledge of the structure, regulation, and function during infection of these important bacterial structures.IMPORTANCEFimbriae are surface bacterial structures implicated in a variety of biological processes. Some have been shown to play a critical role during host colonization and thus in disease. Pathogenic bacteria possess the genetic information for an assortment of fimbriae, but their function and regulation and the interplay between them have not been studied in detail. This work provides new insights into the function and regulation of a novel fimbria called Gcf that is important for early establishment of a successful infection byC. rodentiumin mice, despite being poorly expressed underin vitrogrowth conditions. This discovery offers an opportunity to better understand the individual role and the regulatory mechanisms controlling the expression of specific fimbrial operons that are critical during infection.

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