scholarly journals Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress

Open Biology ◽  
2017 ◽  
Vol 7 (6) ◽  
pp. 160330 ◽  
Author(s):  
Erica Acton ◽  
Amy Huei-Yi Lee ◽  
Pei Jun Zhao ◽  
Stephane Flibotte ◽  
Mauricio Neira ◽  
...  
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Gene Annotation ◽  
Wild Type ◽  
Functional Annotations ◽  
Gene Annotations ◽  
Genome Wide ◽  
Bona Fide ◽  
The Impact ◽  
Nutrient Selection

The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, ‘prototrophic’ versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PB prot ) or by backcrossing (Backcrossed, BC prot ) to a wild-type strain. To systematically assess the impact of the auxotrophies, genome-wide fitness profiles of prototrophic and auxotrophic collections were compared across diverse drug and environmental conditions in 250 experiments. Our quantitative profiles uncovered broad impacts of genotype on phenotype for three deletion collections, and revealed genotypic and strain-construction-specific phenotypes. The PB prot collection exhibited fitness defects associated with plasmid maintenance, while BC prot fitness profiles were compromised due to strain loss from nutrient selection steps during strain construction. The repaired prototrophic versions of the YKO collection did not restore wild-type behaviour nor did they clarify gaps in gene annotation resulting from the auxotrophic background. To remove marker bias and expand the experimental scope of deletion libraries, construction of a bona fide prototrophic collection from a wild-type strain will be required.

scholarly journals Impact of Inorganic Carbon Availability on Microcystin Production by Microcystis aeruginosa PCC 7806

2007 ◽  
Vol 73 (21) ◽  
pp. 6994-7002 ◽  
Author(s):  
Sabine J�hnichen ◽  
Tilo Ihle ◽  
Thomas Petzoldt ◽  
J�rgen Benndorf
Keyword(s):  
Microcystis Aeruginosa ◽  
Type Strain ◽  
Inorganic Carbon ◽  
Wild Type Strain ◽  
Light Cycle ◽  
Variable Fluorescence ◽  
Wild Type ◽  
Dark Light ◽  
Sodium Dependent ◽  
The Impact

ABSTRACT Batch culture experiments with the cyanobacterium Microcystis aeruginosa PCC 7806 were performed in order to test the hypothesis that microcystins (MCYSTs) are produced in response to a relative deficiency of intracellular inorganic carbon (Ci,i). In the first experiment, MCYST production was studied under increased Ci,i deficiency conditions, achieved by restricting sodium-dependent bicarbonate uptake through replacement of sodium bicarbonate in the medium with its potassium analog. The same experimental approach was used in a second experiment to compare the response of the wild-type strain M. aeruginosa PCC 7806 with its mcyB mutant, which lacks the ability to produce MCYSTs. In a third experiment, the impact of varying the Ci,i status on MCYST production was examined without suppressing the sodium-dependent bicarbonate transporter; instead, a detailed investigation of a dark-light cycle was performed. In all experiments, a relative Ci,i deficiency was indicated by an elevated variable fluorescence signal and led to enhanced phycocyanin cell quotas. Higher MCYST cell quotas (in the first and third experiments) and increased total (intracellular plus extracellular) MCYST production (in the first experiment) were detected with increased Ci,i deficiency. Furthermore, the MCYST-producing wild-type strain and its mcyB mutant showed basically the same response to restrained inorganic carbon uptake, with elevated variable fluorescence and phycocyanin cell quotas with increased Ci,i deficiency. The response of the wild type, however, was distinctly stronger and also included elevated chlorophyll a cell quotas. These differences indicate the limited ability of the mutant to adapt to low-Ci,i conditions. We concluded that MCYSTs may be involved in enhancing the efficiency of the adaptation of the photosynthetic apparatus to fluctuating inorganic carbon conditions in cyanobacterial cells.

scholarly journals Global Analysis of Cellular Factors and Responses Involved in Pseudomonas aeruginosa Resistance to Arsenite

2005 ◽  
Vol 187 (14) ◽  
pp. 4853-4864 ◽  
Author(s):  
Kislay Parvatiyar ◽  
Eyad M. Alsabbagh ◽  
Urs A. Ochsner ◽  
Michelle A. Stegemeyer ◽  
Alan G. Smulian ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Pseudomonas Aeruginosa ◽  
Glutathione Reductase ◽  
Type Strain ◽  
Wild Type Strain ◽  
Storage Proteins ◽  
Global Analysis ◽  
Wild Type ◽  
Isogenic Mutants ◽  
The Impact

ABSTRACT The impact of arsenite [As(III)] on several levels of cellular metabolism and gene regulation was examined in Pseudomonas aeruginosa. P. aeruginosa isogenic mutants devoid of antioxidant enzymes or defective in various metabolic pathways, DNA repair systems, metal storage proteins, global regulators, or quorum sensing circuitry were examined for their sensitivity to As(III). Mutants lacking the As(III) translocator (ArsB), superoxide dismutase (SOD), catabolite repression control protein (Crc), or glutathione reductase (Gor) were more sensitive to As(III) than wild-type bacteria. The MICs of As(III) under aerobic conditions were 0.2, 0.3, 0.8, and 1.9 mM for arsB, sodA sodB, crc, and gor mutants, respectively, and were 1.5- to 13-fold less than the MIC for the wild-type strain. A two-dimensional gel/matrix-assisted laser desorption ionization-time of flight analysis of As(III)-treated wild-type bacteria showed significantly (>40-fold) increased levels of a heat shock protein (IbpA) and a putative allo-threonine aldolase (GlyI). Smaller increases (up to 3.1-fold) in expression were observed for acetyl-coenzyme A acetyltransferase (AtoB), a probable aldehyde dehydrogenase (KauB), ribosomal protein L25 (RplY), and the probable DNA-binding stress protein (PA0962). In contrast, decreased levels of a heme oxygenase (HemO/PigA) were found upon As(III) treatment. Isogenic mutants were successfully constructed for six of the eight genes encoding the aforementioned proteins. When treated with sublethal concentrations of As(III), each mutant revealed a marginal to significant lag period prior to resumption of apparent normal growth compared to that observed in the wild-type strain. Our results suggest that As(III) exposure results in an oxidative stress-like response in P. aeruginosa, although activities of classic oxidative stress enzymes are not increased. Instead, relief from As(III)-based oxidative stress is accomplished from the collective activities of ArsB, glutathione reductase, and the global regulator Crc. SOD appears to be involved, but its function may be in the protection of superoxide-sensitive sulfhydryl groups.

scholarly journals A general framework for modelling the impact of co-infections on pathogen evolution

2019 ◽  
Vol 16 (155) ◽  
pp. 20190165 ◽  
Author(s):  
Mary Bushman ◽  
Rustom Antia
Keyword(s):  
Mutant Strain ◽  
Type Strain ◽  
General Framework ◽  
Wild Type Strain ◽  
Theoretical Models ◽  
Epidemiological Model ◽  
Wild Type ◽  
Pathogen Evolution ◽  
Evolutionary Emergence ◽  
The Impact

Theoretical models suggest that mixed-strain infections, or co-infections, are an important driver of pathogen evolution. However, the within-host dynamics of co-infections vary enormously, which complicates efforts to develop a general understanding of how co-infections affect evolution. Here, we develop a general framework which condenses the within-host dynamics of co-infections into a few key outcomes, the most important of which is the overall R 0 of the co-infection. Similar to how fitness is determined by two different alleles in a heterozygote, the R 0 of a co-infection is a product of the R 0 values of the co-infecting strains, shaped by the interaction of those strains at the within-host level. Extending the analogy, we propose that the overall R 0 reflects the dominance of the co-infecting strains, and that the ability of a mutant strain to invade a population is a function of its dominance in co-infections. To illustrate the utility of these concepts, we use a within-host model to show how dominance arises from the within-host dynamics of a co-infection, and then use an epidemiological model to demonstrate that dominance is a robust predictor of the ability of a mutant strain to save a maladapted wild-type strain from extinction (evolutionary emergence).

Impact of sarA Mutation on Immune System Evasion and Stress Response in Staphylococcus aureus

2020 ◽  
Vol 29 (3) ◽  
pp. 105-112
Author(s):  
Yomna A. Hagag ◽  
Abdelaziz Elgaml ◽  
Ramadan Hassan ◽  
Hany I. Kenawy
Keyword(s):  
Staphylococcus Aureus ◽  
Immune System ◽  
Biofilm Formation ◽  
Type Strain ◽  
Wild Type Strain ◽  
Human Neutrophils ◽  
Bacterial Survival ◽  
Wild Type ◽  
The Impact

Background: Staphylococcus aureus is a major human pathogen responsible for a large number of infections. In S. aureus, SarA is an important global locus responsible for the regulation of virulence factors, as well as biofilm formation. Objectives: The aim of this work is to clarify the impact of SarA on biofilm formation, immune system evasion, as well as the survival of S. aureus under stress conditions. Methodology: A comparative study between S. aureus wild type strain, sarA mutant and complemented strains was established addressing the biofilm formation, opsonization, phagocytosis, as well as ability of the bacterium to survive in stressful environments including acidic pH, hyperosmotic and oxidative stress. The in vitro experiments were confirmed by challenging of mice via intraperitoneal injection with the wild type strain, sarA mutant and complemented strains. Results: Mutation of sarA diminished significantly biofilm formation. Moreover, this mutation resulted in a slight decrease in the deposition of the most important opsonin in complement-mediated immunity, named C3 on S. aureus cells. However, this mutation was associated with a significant enhancement of bacterial phagocytosis and killing by human neutrophils. Furthermore, this mutation altered bacterial survival in stressful conditions. It is also noteworthy that sarA mutation resulted in a significant higher survival rates during the challenging of mice. Conclusion: SarA plays a role as a key regulator of biofilm formation, which in turn has a great impact on immune system evasion through affecting opsonization and phagocytosis. In addition, SarA improves the ability of S. aureus to survive in stressful conditions.

scholarly journals Cryptococcus neoformanssecretes small molecules that inhibit IL-1β inflammasome-dependent secretion

2019 ◽  
Author(s):  
Pedro Henrique Bürgel ◽  
Clara Luna Marina ◽  
Pedro H. V. Saavedra ◽  
Patrícia Albuquerque ◽  
Paulo Henrique Holanda ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Cryptococcus Neoformans ◽  
Type Strain ◽  
Wild Type Strain ◽  
Conditioned Media ◽  
Inflammasome Activation ◽  
Wild Type ◽  
Fungal Virulence ◽  
The Impact

AbstractCryptococcus neoformansis an encapsulated yeast that causes disease mainly in immunosuppressed hosts. It is considered a facultative intracellular pathogen because of its capacity to survive and replicate inside phagocytes, especially macrophages. This capacity is heavily dependent on various virulence factors, particularly the glucuronoxylomannan (GXM) component of the polysaccharide capsule, that render the non- or poorly-activated macrophage ineffective against phagocytosed yeast. Strategies utilized by macrophages to prevent this scenario include pyroptosis (a rapid highly inflammatory cell death) and vomocytosis (the expulsion of the pathogen from the intracellular environment without lysis). Inflammasome activation in phagocytes is usually protective against fungal infections, including cryptococcosis. Nevertheless, recognition ofC. neoformansby inflammasome receptors requires specific changes in morphology or the opsonization of the yeast, impairing a proper inflammasome function. In this context, we analyzed the impact of molecules secreted byC. neoformansB3501 strain and its acapsular mutantΔcap67in an inflammasome activationin vitromodel. Our results showed that conditioned media derived from B3501 was capable of inhibiting inflammasome dependent events (i. e. IL-1β secretion and LDH release via pyroptosis) more strongly than conditioned media fromΔcap67, regardless of GXM presence. We also demonstrated that macrophages treated with conditioned media were less responsive against infection with the virulent strain H99, exhibiting lower rates of phagocytosis, increased fungal burdens and enhanced vomocytosis. Moreover, we showed that the aromatic metabolite DL-Indole-3-lactic acid (ILA) was present in B3501’s conditioned media and that this fungal metabolite is involved in the regulation of inflammasome activation byC. neoformans. Overall, the results presented show that conditioned media from a wild-type strain can inhibit an important recognition pathway and subsequent fungicidal functions of macrophages, contributing to fungal survivalin vitroand suggesting that this serves as an important role for secreted molecules during cryptococcal infections.Author’s SummaryCryptococcus neoformansis the agent of cryptococcal meningitis, a disease that can be life-threatening in immunocompromised hosts such as those infected with HIV. The infection thrives in hosts that poorly activate their immune system, mainly because of the yeast’s ability to survive inside macrophages and migrate towards the central nervous system. Emerging data indicate that cryptococci modulate the host immune response, but the underlying mechanisms remain largely uncharacterized. Here we show that secreted molecules from a wild-type strain ofC. neoformansimpair inflammatory responses driven by inflammasome activation, which in turn impact the macrophage antifungal activity. We further show that this inhibition does not involve GXM, the main constituent of the fungal capsule, but rather is partially dependent on DL-Indole-3-lactic acid (ILA), a metabolite not previously implicated in fungal virulence.

Impact on Arbuscular Mycorrhiza Formation ofPseudomonas Strains Used as Inoculants for Biocontrol of Soil-Borne Fungal Plant Pathogens

1998 ◽  
Vol 64 (6) ◽  
pp. 2304-2307 ◽  
Author(s):  
J. M. Barea ◽  
G. Andrade ◽  
V. Bianciotto ◽  
D. Dowling ◽  
S. Lohrke ◽  
...  
Keyword(s):  
Type Strain ◽  
Plant Pathogens ◽  
Wild Type Strain ◽  
Mycorrhizal Symbiosis ◽  
Antifungal Compound ◽  
Wild Type ◽  
Tomato Root ◽  
Fungal Plant Pathogens ◽  
The Impact ◽  
Mycelial Development

ABSTRACT The arbuscular mycorrhizal symbiosis, a key component of agroecosystems, was assayed as a rhizosphere biosensor for evaluation of the impact of certain antifungal Pseudomonas inoculants used to control soil-borne plant pathogens. The following threePseudomonas strains were tested: wild-type strain F113, which produces the antifungal compound 2,4-diacetylphloroglucinol (DAPG); strain F113G22, a DAPG-negative mutant of F113; and strain F113(pCU203), a DAPG overproducer. Wild-type strain F113 and mutant strain F113G22 stimulated both mycelial development from Glomus mosseae spores germinating in soil and tomato root colonization. Strain F113(pCU203) did not adversely affectG. mosseae performance. Mycelial development, but not spore germination, is sensitive to 10 μM DAPG, a concentration that might be present in the rhizosphere. The results of scanning electron and confocal microscopy demonstrated that strain F113 and its derivatives adhered to G. mosseae spores independent of the ability to produce DAPG.

scholarly journals The Impact of SsPI-1 Deletion on Streptococcus suis Virulence

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 287 ◽  
Author(s):  
Yan Zhao ◽  
Gang Li ◽  
Xin-Yue Yao ◽  
Shu-Guang Lu ◽  
Jing Wang ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Type Strain ◽  
Large Scale ◽  
Wild Type Strain ◽  
Streptococcus Suis ◽  
Wild Type ◽  
Evolution Of Virulence ◽  
Life Threatening ◽  
Systemic Infections ◽  
The Impact

(1) Background: Streptococcus suis is an important zoonotic pathogen that infects pigs and can occasionally cause life-threatening systemic infections in humans. Two large-scale outbreaks of streptococcal toxic shock-like syndrome in China suggest that the pathogenicity of S. suis has been changing in recent years. Genetic analysis revealed the presence of a chromosomal pathogenicity island (PAI) designated SsPI-1 in Chinese epidemic S. suis strains. The purpose of this study is to define the role of SsPI-1 in the virulence of S. suis. (2) Methods: A SsPI-1 deletion mutant was compared to the wild-type strain regarding the ability to attach to epithelial cells, to cause host disease and mortality, and to stimulate host immune response in experimental infection of piglets. (3) Results: Deletion of SsPI-1 significantly reduces adherence of S. suis to epithelial cells and abolishes the lethality of the wild-type strain in piglets. The SsPI-1 mutant causes no significant pathological lesions and exhibits an impaired ability to induce proinflammatory cytokine production. (4) Conclusions: Deletion of the SsPI-1 PAI attenuates the virulence of this pathogen. We conclude that SsPI-1 is a critical contributor to the evolution of virulence in epidemic S. suis.

scholarly journals Transcriptome Analysis of Trichothecene-Induced Gene Expression in Barley

2007 ◽  
Vol 20 (11) ◽  
pp. 1364-1375 ◽  
Author(s):  
Jayanand Boddu ◽  
Seungho Cho ◽  
Gary J. Muehlbauer
Keyword(s):  
Cell Death ◽  
Defense Response ◽  
Type Strain ◽  
Wild Type Strain ◽  
Loss Of Function ◽  
Wild Type ◽  
Genes Encoding ◽  
Basal Defense ◽  
Related Proteins ◽  
The Impact

Fusarium head blight, caused primarily by Fusarium graminearum, is a major disease problem on barley (Hordeum vulgare L.). Trichothecene mycotoxins produced by the fungus during infection increase the aggressiveness of the fungus and promote infection in wheat (Triticum aestivum L.). Loss-of-function mutations in the TRI5 gene in F. graminearum result in the inability to synthesize trichothecenes and in reduced virulence on wheat. We examined the impact of pathogen-derived trichothecenes on virulence and the transcriptional differences in barley spikes infected with a trichothecene-producing wild-type strain and a loss-of-function tri5 trichothecene nonproducing mutant. Disease severity, fungal biomass, and floret necrosis and bleaching were reduced in spikes inoculated with the tri5 mutant strain compared with the wild-type strain, indicating that the inability to synthesize trichothecenes results in reduced virulence in barley. We detected 63 transcripts that were induced during trichothecene accumulation, including genes encoding putative trichothecene detoxification and transport proteins, ubiquitination-related proteins, programmed cell death-related proteins, transcription factors, and cytochrome P450s. We also detected 414 gene transcripts that were designated as basal defense response genes largely independent of trichothecene accumulation. Our results show that barley exhibits a specific response to trichothecene accumulation that can be separated from the basal defense response. We propose that barley responds to trichothecene accumulation by inducing at least two general responses. One response is the induction of genes encoding trichothecene detoxification and transport activities that may reduce the impact of trichothecenes. The other response is to induce genes encoding proteins associated with ubiquitination and cell death which may promote successful establishment of the disease.

scholarly journals Effects of Mutations of RAD50, RAD51, RAD52, and Related Genes on Illegitimate Recombination in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 383-391 ◽  
Author(s):  
Yasumasa Tsukamoto ◽  
Jun-ichi Kato ◽  
Hideo Ikeda
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Quantitative Analysis ◽  
Structural Analysis ◽  
Recombination Rate ◽  
Type Strain ◽  
Negative Selection ◽  
Wild Type Strain ◽  
Illegitimate Recombination ◽  
Wild Type ◽  
In The Wild

Abstract To examine the mechanism of illegitimate recombination in Saccharomyces cerevisiae, we have developed a plasmid system for quantitative analysis of deletion formation. A can1 cyh2 cell carrying two negative selection markers, the CAN1 and CYH2 genes, on a YCp plasmid is sensitive to canavanine and cycloheximide, but the cell becomes resistant to both drugs when the plasmid has a deletion over the CAN1 and CYH2 genes. Structural analysis of the recombinant plasmids obtained from the resistant cells showed that the plasmids had deletions at various sites of the CAN1-CYH2 region and there were only short regions of homology (1-5 bp) at the recombination junctions. The results indicated that the deletion detected in this system were formed by illegitimate recombination. Study on the effect of several rad mutations showed that the recombination rate was reduced by 30-, 10-, 10-, and 10-fold in the rad52, rad50, mre11, and xrs2 mutants, respectively, while in the rud51, 54, 55, and 57 mutants, the rate was comparable to that in the wild-type strain. The rad52 mutation did not affect length of homology at junction sites of illegitimate recombination.

scholarly journals The role of Zur-regulated lipoprotein A in bacterial morphology, antimicrobial susceptibility, and production of outer membrane vesicles in Acinetobacter baumannii

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nayeong Kim ◽  
Hyo Jeong Kim ◽  
Man Hwan Oh ◽  
Se Yeon Kim ◽  
Mi Hyun Kim ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Mutant Strain ◽  
Antimicrobial Susceptibility ◽  
Type Strain ◽  
Wild Type Strain ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Wild Type ◽  
Bacterial Morphology

Abstract Background Zinc uptake-regulator (Zur)-regulated lipoprotein A (ZrlA) plays a role in bacterial fitness and overcoming antimicrobial exposure in Acinetobacter baumannii. This study further characterized the zrlA gene and its encoded protein and investigated the roles of the zrlA gene in bacterial morphology, antimicrobial susceptibility, and production of outer membrane vesicles (OMVs) in A. baumannii ATCC 17978. Results In silico and polymerase chain reaction analyses showed that the zrlA gene was conserved among A. baumannii strains with 97–100% sequence homology. Recombinant ZrlA protein exhibited a specific enzymatic activity of D-alanine-D-alanine carboxypeptidase. Wild-type A. baumannii exhibited more morphological heterogeneity than a ΔzrlA mutant strain during stationary phase. The ΔzrlA mutant strain was more susceptible to gentamicin than the wild-type strain. Sizes and protein profiles of OMVs were similar between the wild-type and ΔzrlA mutant strains, but the ΔzrlA mutant strain produced 9.7 times more OMV particles than the wild-type strain. OMVs from the ΔzrlA mutant were more cytotoxic in cultured epithelial cells than OMVs from the wild-type strain. Conclusions The present study demonstrated that A. baumannii ZrlA contributes to bacterial morphogenesis and antimicrobial resistance, but its deletion increases OMV production and OMV-mediated host cell cytotoxicity.

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