scholarly journals Phase Variation and Genomic Architecture Changes in Azospirillum

2006 ◽  
Vol 188 (15) ◽  
pp. 5364-5373 ◽  
Author(s):  
Ludovic Vial ◽  
Céline Lavire ◽  
Patrick Mavingui ◽  
Didier Blaha ◽  
Jacqueline Haurat ◽  
...  

ABSTRACT The plant growth-promoting rhizobacterium Azospirillum lipoferum 4B generates in vitro at high frequency a stable nonswimming phase variant designated 4VI, which is distinguishable from the wild type by the differential absorption of dyes. The frequency of variants generated by a recA mutant of A. lipoferum 4B was increased up to 10-fold. The pleiotropic modifications characteristic of the phase variant are well documented, but the molecular processes involved are unknown. Here, the objective was to assess whether genomic rearrangements take place during phase variation of strain 4B. The random amplified polymorphic DNA (RAPD) profiles of strains 4B and 4VI differed. RAPD fragments observed only with the wild type were cloned, and three cosmids carrying the corresponding fragments were isolated. The three cosmids hybridized with a 750-kb plasmid and pulse-field gel electrophoresis analysis revealed that this replicon was missing in the 4VI genome. The same rearrangements took place during phase variation of 4BrecA. Large-scale genomic rearrangements during phase variation were demonstrated for two additional strains. In Azospirillum brasilense WN1, generation of stable variants was correlated with the disappearance of a replicon of 260 kb. For Azospirillum irakense KBC1, the variant was not stable and coincided with the formation of a new replicon, whereas the revertant recovered the parental genomic architecture. This study shows large-scale genomic rearrangements in Azospirillum strains and correlates them with phase variation.

2001 ◽  
Vol 69 (5) ◽  
pp. 3021-3030 ◽  
Author(s):  
Jack S. Ikeda ◽  
Clare K. Schmitt ◽  
Stephen C. Darnell ◽  
Patricia R. Watson ◽  
Jennifer Bispham ◽  
...  

ABSTRACT Although Salmonella enterica serovar Typhimurium can undergo phase variation to alternately express two different types of flagellin subunit proteins, FljB or FliC, no biological function for this phenomenon has been described. In this investigation, we constructed phase-locked derivatives of S. enterica serovar Typhimurium that expressed only FljB (termed locked-ON) or FliC (termed locked-OFF). The role of phase variation in models of enteric and systemic pathogenesis was then evaluated. There were no differences between the wild-type parent strain and the two phase-locked derivatives in adherence and invasion of mouse epithelial cells in vitro, survival in mouse peritoneal macrophages, or in a bovine model of gastroenteritis. By contrast, the locked-OFF mutant was virulent in mice following oral or intravenous (i.v.) inoculation but the locked-ON mutant was attenuated. When these phase-locked mutants were compared in studies of i.v. kinetics in mice, similar numbers of the two strains were isolated from the blood and spleens of infected animals at 6 and 24 h. However, the locked-OFF mutant was recovered from the blood and spleens in significantly greater numbers than the locked-ON strain by day 2 of infection. By 5 days postinfection, a majority of the mice infected with the locked-OFF mutant had died compared with none of the mice infected with the locked-ON mutant. These results suggest that phase variation is not involved in the intestinal stage of infection but that once S. enterica serovar Typhimurium reaches the spleens of susceptible mice those organisms in the FliC phase can grow and/or survive better than those in the FljB phase. Additional experiments with wild-type S. enterica serovar Typhimurium, fully capable of switching flagellin type, supported this hypothesis. We conclude that organisms that have switched to the FliC+phase have a selective advantage in the mouse model of typhoid fever but have no such advantage in invasion of epithelial cells or the induction of enteropathogenesis.


2007 ◽  
Vol 189 (24) ◽  
pp. 8914-8921 ◽  
Author(s):  
Anna Skoglund ◽  
Britta Björkholm ◽  
Christina Nilsson ◽  
Anders F. Andersson ◽  
Cecilia Jernberg ◽  
...  

ABSTRACT A large number of genes encoding restriction-modification (R-M) systems are found in the genome of the human pathogen Helicobacter pylori. R-M genes comprise approximately 10% of the strain-specific genes, but the relevance of having such an abundance of these genes is not clear. The type II methyltransferase (MTase) M.HpyAIV, which recognizes GANTC sites, was present in 60% of the H. pylori strains analyzed, whereof 69% were resistant to restriction enzyme digestion, which indicated the presence of an active MTase. H. pylori strains with an inactive M.HpyAIV phenotype contained deletions in regions of homopolymers within the gene, which resulted in premature translational stops, suggesting that M.HpyAIV may be subjected to phase variation by a slipped-strand mechanism. An M.HpyAIV gene mutant was constructed by insertional mutagenesis, and this mutant showed the same viability and ability to induce interleukin-8 in epithelial cells as the wild type in vitro but had, as expected, lost the ability to protect its self-DNA from digestion by a cognate restriction enzyme. The M.HpyAIV from H. pylori strain 26695 was overexpressed in Escherichia coli, and the protein was purified and was able to bind to DNA and protect GANTC sites from digestion in vitro. A bioinformatic analysis of the number of GANTC sites located in predicted regulatory regions of H. pylori strains 26695 and J99 resulted in a number of candidate genes. katA, a selected candidate gene, was further analyzed by quantitative real-time reverse transcription-PCR and shown to be significantly down-regulated in the M.HpyAIV gene mutant compared to the wild-type strain. This demonstrates the influence of M.HpyAIV methylation in gene expression.


2019 ◽  
Author(s):  
Jiaqi Zou ◽  
Zhaobing Tang ◽  
Jia Yan ◽  
Hang Liu ◽  
Yingzhu Chen ◽  
...  

AbstractDespite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid-resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 optrA-carrying E. faecalis clinical isolates with linezolid-resistance. Pulse-field gel electrophoresis and DNA hybridization revealed the presence of optrA in the plasmid in 26 (59%) isolates and in the chromosome in 18 (41%) isolates. Conjugation experiments showed a successful transfer of optrA in 88.5% (23/26) of isolates carrying optrA in plasmids while no transfer occurred in any isolates carrying optrA in the chromosome (0/18). All 23 transconjugants exhibited in vitro resistance to linezolid and several other antibiotics, and were confirmed to contain optrA and other resistance genes. Plasmid typing demonstrated a predominance (18/23 or 78%) of rep9–type plasmids (pCF10 prototype) known to be the best studied sex pheromone responsive plasmids. Full plasmid genome sequencing of one isolate revealed the presence of drug resistance genes (optrA and fexA) and multiple sex pheromone response genes in the same plasmid, which represents the first sex pheromone responsive plasmid carrying optrA from a clinical isolate. PCR-based genotyping revealed the presence of three key sex pheromone response genes (prgA, prgB and prgC) in almost all 23 optrA-carrying isolates tested. Finally, functional studies of these isolates by clumping induction assay detected different degrees of clumping in most of the 23 isolates. Our analysis strongly suggests that optrA-mediated linezolid-resistance can be widely disseminated through sex pheromone plasmid transfer.


2018 ◽  
Vol 54 (No. 4) ◽  
pp. 183-189
Author(s):  
Pranit Kumar Mukherjee ◽  
Raju Mondal ◽  
Sourav Dutta ◽  
Kanti Meena ◽  
Madhumita Roy ◽  
...  

An efficient in vitro micropropagation protocol has been developed using nodal explants of ramie (Boehmeria nivea), with maximum shoots (42) per explant in 5 passages (passage duration: 21 days) on Murashige and Skoog medium supplemented with 2.0 mg/l 6-benzyladenine and 2.0 mg/l AgNO<sub>3</sub>. ½ Murashige and Skoog medium containing 40% sucrose was found to be most effective for the rooting of in vitro developed shoots. Those plantlets were acclimatized and transferred to pots for hardening under glasshouse conditions. About 91% of mericlones survived and showed no ectopic expression in respect of any morphological character in comparison with the parental stock. Furthermore, clonal fidelity of the mericlones was confirmed by using DNA markers (random amplified polymorphic DNA and inter simple sequence repeats) and by polypeptide profiling through SDS-PAGE at a genomic and protein level, respectively, which showed the true-to-type nature of the in vitro micropropagated plants. Thus the protocol developed can be used to generate safe planting material for large-scale cultivation of ramie.  


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1065-1065
Author(s):  
Arnab Ghosh ◽  
Matthias Wolenski ◽  
Christoph Klein ◽  
Karl Welte ◽  
Bruce R. Blazar ◽  
...  

Abstract Background: Adoptive T cell-based immunotherapy holds promise as an additive treatment option for leukemia, but its development has been impeded by the lack of reproducible methods for generating therapeutic numbers of antigen-specific CD8+ cytotoxic T lymphocytes (CTLs). We hypothesized that tumor associated antigens from whole leukemia cell lysates can efficiently pre-expand and activate an antigen-specific T cell precursor population that can be further expanded to obtain large amounts of tumor-specifc CTLs for therapeutic use. Methods: A specific and physiologic T cell activation step using tumor lysate-pulsed bone marrow derived dendritic cells (DC) was combined with a nonspecific large scale expansion system with anti-CD3/anti-CD28-coated microspheres. In order to validate the system we transduced the murine leukemia cell line C1498 with a defined protein (OVA) serving as a surrogate tumor antigen for analyzing anti-tumor CTL responses in vitro and in vivo. Results: Using T cell receptor (TCR)-transgenic OT-I mice, with a TCR specific for H-2Kb and OVA peptide, we could demonstrate, that bone marrow derived DC pulsed with cell lysates from C1498-OVA cells can process and present leukemia cell derived antigens effectively to T cells in vitro in a MHC-I-restricted fashion. Naive T cells within OT-I derived splenocytes could be activated and expanded, generating specific killing against C1498-OVA but not C1498 leukemia cells. Upon adoptive transfer these CTLs mediated potent anti-leukemic effects in tumor bearing animals. Over 80% of mice that received a lethal challenge with C1498-OVA cells by tail vein injection could be rescued after receiving 40 x 106 OT-I CTLs on the following day. In contrast, mice receiving identical treatment after receiving a lethal dose of mock-transfected C1498 cells all died within 47 days as did C1498-OVA challenged mice after PBS treatment only (p &lt; 0.005). In order to simulate the more realistic setting of a naïve T cell population containing a small percentage of antigen-specific T cell precursors only, small amounts of OT-I derived splenocytes were mixed with wild type splenocytes at a ratio of 1:10. Whereas the percentage of C1498-OVA-specific CTLs increased to 5% after priming with C1498-OVA cell lysate-pulsed DC, the frequency dropped to 1.5% after priming with C1498 lysate-pulsed DCs. We then asked the question whether higher yields of leukemia specific CTLs could be generated in our in vitro system by immunizing potential T cell donors with tumor antigen-presenting DC. Syngeneic wild type mice were immunized with C1498-OVA lysate-pulsed DC. Controls received C1498 lysate-pulsed DC. Using the immunized mice as splenocyte donors and the Vα2β5 TCR as a surrogate marker to identify OVA-reactive T cells from wild type mice, the yield of Vα2β5 positive CTLs was in average 3.5 fold higher after only 8 days of repriming and further expansion with anti-CD3/anti-CD28-coated microspheres in vitro. Conclusion: High numbers of CTLs specific against leukemia-associated antigens can be generated and expanded within a relatively short time span of 9–13 days in vitro and mediate robust antigen-specific anti-leukemic effects upon adoptive transfer into leukemia bearing animals. This can be achieved by combining a priming step with tumor cell lysate pulsed DC followed by unspecific large scale expansion using anti-CD3/anti-CD28-coated microspheres.


2021 ◽  
Vol 9 (4) ◽  
pp. 682
Author(s):  
Mohamad Syazwan Ngalimat ◽  
Erneeza Mohd Hata ◽  
Dzarifah Zulperi ◽  
Siti Izera Ismail ◽  
Mohd Razi Ismail ◽  
...  

As a major food crop, rice (Oryza sativa) is produced and consumed by nearly 90% of the population in Asia with less than 9% produced outside Asia. Hence, reports on large scale grain losses were alarming and resulted in a heightened awareness on the importance of rice plants’ health and increased interest against phytopathogens in rice. To serve this interest, this review will provide a summary on bacterial rice pathogens, which can potentially be controlled by plant growth-promoting bacteria (PGPB). Additionally, this review highlights PGPB-mediated functional traits, including biocontrol of bacterial rice pathogens and enhancement of rice plant’s growth. Currently, a plethora of recent studies address the use of PGPB to combat bacterial rice pathogens in an attempt to replace existing methods of chemical fertilizers and pesticides that often lead to environmental pollutions. As a tool to combat bacterial rice pathogens, PGPB presented itself as a promising alternative in improving rice plants’ health and simultaneously controlling bacterial rice pathogens in vitro and in the field/greenhouse studies. PGPB, such as Bacillus, Pseudomonas, Enterobacter, Streptomyces, are now very well-known. Applications of PGPB as bioformulations are found to be effective in improving rice productivity and provide an eco-friendly alternative to agroecosystems.


1998 ◽  
Vol 180 (5) ◽  
pp. 1224-1231 ◽  
Author(s):  
Linda Kaltenbach ◽  
Bruce Braaten ◽  
Julie Tucker ◽  
Margareta Krabbe ◽  
David Low

ABSTRACT The global regulator Lrp plays a central role as both a repressor and an activator in Pap phase variation. Unlike most other members of the Lrp regulon such as ilvIH, activation ofpapBA transcription requires the coregulator PapI and is methylation dependent. We developed a two-color genetic screen to identify Lrp mutations that inhibit Pap phase variation but still activate ilvIH transcription, reasoning that such mutations might identify PapI binding or methylation-responsive domains. Amino acid substitutions in Lrp at position 126, 133, or 134 greatly reduced the rate of Pap switching from phase off to phase on but had much smaller effects on ilvIH transcription. In vitro analyses indicated that the T134A and E133G Lrp variants maintained affinities for pap and ilvIH DNAs similar to those of wild-type Lrp. In addition, both mutant Lrp’s were as responsive to PapI as wild-type Lrp, evidenced by an increase in affinity forpap Lrp binding sites 4, 5, and 6. Thus, in vitro analyses did not reveal the step(s) in Pap phase variation where these Lrp mutants were inhibited. In vivo analyses showed that both the T134A and E133G Lrp mutants activated transcription of a phase-on-lockedpap derivative containing a mutation in Lrp binding site 3. Further studies indicated that the T134A Lrp mutant was blocked in a step in Pap phase variation that does not involve PapI. Our data suggest that these mutant Lrp’s are defective in a previously unidentified interaction required for the switch from the phase-off to the phase-on pap transcription state.


2007 ◽  
Vol 408 (1) ◽  
pp. 131-138 ◽  
Author(s):  
Isabel Cardoso ◽  
Maria Rosário Almeida ◽  
Nelson Ferreira ◽  
Gemma Arsequell ◽  
Gregorio Valencia ◽  
...  

Destabilization of the tetrameric fold of TTR (transthyretin) is important for aggregation of the protein which culminates in amyloid fibril formation. Many TTR mutations interfere with tetramer stability, increasing the amyloidogenic potential of the protein. The vast majority of proposed TTR fibrillogenesis inhibitors are based on in vitro assays with isolated protein, limiting their future use in clinical assays. In the present study we investigated TTR fibrillogenesis inhibitors using a cellular system that produces TTR intermediates/aggregates in the medium. Plasmids carrying wild-type TTR, V30M or L55P cDNA were transfected into a rat Schwannoma cell line and TTR aggregates were investigated in the medium using a dot-blot filter assay followed by immunodetection. Results showed that, in 24 h, TTR L55P forms aggregates in the medium, whereas, up to 72 h, wild-type TTR and V30M do not. A series of 12 different compounds, described in the literature as in vitro TTR fibrillogenesis inhibitors, were tested for their ability to inhibit L55P aggregate formation; in this system, 2-[(3,5-dichlorophenyl) amino] benzoic acid, benzoxazole, 4-(3,5-difluorophenyl) benzoic acid and tri-iodophenol were the most effective inhibitors, as compared with the reference iododiflunisal, previously shown by ex vivo and in vitro procedures to stabilize TTR and inhibit fibrillogenesis. Among these drugs, 2-[(3,5-dichlorophenyl) amino] benzoic acid and tri-iodophenol stabilized TTR from heterozygotic carriers of V30M in the same ex vivo conditions as those used previously for iododiflunisal. The novel cellular-based test herein proposed for TTR fibrillogenesis inhibitor screens avoids not only lengthy and cumbersome large-scale protein isolation steps but also artefacts associated with most current in vitro first-line screening methods, such as those associated with acidic conditions and the absence of serum proteins.


2021 ◽  
Vol 8 ◽  
Author(s):  
Zhongke Sun ◽  
Zonghao Yue ◽  
Hongzhan Liu ◽  
Keshi Ma ◽  
Chengwei Li

Microbial-assisted biofortification attracted much attention recently due to its sustainable and eco-friendly nature for improving nutrient content in wheat. An endophytic strain Bacillus altitudinis WR10, which showed sophistical regulation of iron (Fe) homeostasis in wheat seedlings, inspired us to test its potential for enhancing Fe biofortification in wheat grain. In this study, assays in vitro indicated that WR10 has versatile plant growth-promoting (PGP) traits and bioinformatic analysis predicted its non-pathogenicity. Two inoculation methods, namely, seed soaking and soil spraying, with 107 cfu/ml WR10 cells were applied once before sowing of wheat (Triticum aestivum L. cv. Zhoumai 36) in the field. After wheat maturation, evaluation of yield and nutrients showed a significant increase in the mean number of kernels per spike (KPS) and the content of total nitrogen (N), potassium (K), and Fe in grains. At the grain filling stage, the abundance of Bacillus spp. and the content of N, K, and Fe in the root, the stem, and the leaf were also increased in nearly all tissues, except Fe in the stem and the leaf. Further correlation analysis revealed a positive relationship between the total abundance of Bacillus spp. and the content of N, K, and Fe in grains. Seed staining confirmed the enhanced accumulation of Fe, especially in the embryo and the endosperm. Finally, using a hydroponic coculture model, qPCR quantification indicated effective colonization, internalization, translocation, and replication of strain WR10 in wheat within 48 h. Collectively, strain WR10 assisted successful Fe biofortification in wheat in the field, laying a foundation for further large-scale investigation of its applicability and effectiveness.


2001 ◽  
Vol 183 (5) ◽  
pp. 1540-1551 ◽  
Author(s):  
Eric R. Lafontaine ◽  
Nikki J. Wagner ◽  
Eric J. Hansen

ABSTRACT The UspA1 protein of Moraxella catarrhalis has been shown to function as an adhesin that mediates adherence to human epithelial cell lines in vitro (E. R. Lafontaine, L. D. Cope, C. Aebi, J. L. Latimer, G. H. McCracken, Jr., and E. J. Hansen, J. Bacteriol. 182:1364–1373, 2000). In the present study, cell lysates prepared from individual colonies of several M. catarrhalis wild-type strains were analyzed by Western blot analysis using monoclonal antibodies (MAbs) specific for the UspA1 protein. Expression of UspA1 was shown to exhibit phase variation that was correlated with both adherence ability in vitro and the number of guanine (G) residues contained within a homopolymeric [poly(G)]tract located upstream of the uspA1 open reading frame (ORF). Nucleotide sequence analysis revealed that isolates expressing relatively high levels of UspA1 had 10 G residues in theiruspA1 poly(G)tracts, whereas isolates that expressed much lower levels of UspA1 had 9 G residues. This poly(G) tract was located 30 nucleotides (nt) upstream of the uspA1 ORF and 168 nt downstream of the uspA1 transcriptional start site. Primer extension experiments, RNA slot blot analysis, and catreporter constructs were used to demonstrate that M. catarrhalis isolates with 10 G residues in theiruspA1 poly(G) tracts expressed two-to threefold moreuspA1 mRNA than did isolates which had 9 G residues in their poly(G)tracts. Northern hybridization analysis revealed that an intact uspA1 mRNA was readily detectable in RNA fromM. catarrhalis isolates that had 10 G residues in theiruspA1 poly(G) tracts, whereas no full-lengthuspA1 mRNA was observed in isolates whose poly(G)tracts contained 9 G residues. M. catarrhalis strain O35EuspA1 genes that contained wild-type and mutated poly(G) tracts were expressed in Haemophilus influenzae to demonstrate that the length and composition of the poly(G)tract affected expression of UspA1.


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