scholarly journals Prevalence and Distribution of Listeria monocytogenesinlAAlleles Prone to Phase Variation andinlAAlleles with Premature Stop Codon Mutations among Human, Food, Animal, and Environmental Isolates

2015 ◽  
Vol 81 (24) ◽  
pp. 8339-8345 ◽  
Author(s):  
Clyde S. Manuel ◽  
Anna Van Stelten ◽  
Martin Wiedmann ◽  
Kendra K. Nightingale ◽  
Renato H. Orsi
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
Phase Variation ◽  
Virulence Gene ◽  
Farm Animals ◽  
Nucleotide Substitutions ◽  
Content Type ◽  
Niche Adaptation ◽  
Frameshift Deletion ◽  
Animal Isolates

ABSTRACTInListeria monocytogenes, 18 mutations leading to premature stop codons (PMSCs) in the virulence geneinlAhave been identified to date. While most of these mutations represent nucleotide substitutions, a frameshift deletion in a 5′ seven-adenine homopolymeric tract (HT) ininlAhas also been reported. This HT may play a role in phase variation and was first identified amongL. monocytogeneslineage II ribotype DUP-1039C isolates. In order to better understand the distribution of differentinlAmutations in this ribotype, a newly developed multiplex real-time PCR assay was used to screen 368 DUP-1039C isolates from human, animal, and food-associated sources for three known 5′inlAHT alleles: (i) wild-type (WT) (A7), (ii) frameshift (FS) (A6), and (iii) guanine interruption (A2GA4) alleles. Additionally, 228 DUP-1039C isolates were screened for allinlAPMSCs; data on the presence of allinlAPMSCs for the other 140 isolates were obtained from previous studies. The statistical analysis based on 191 epidemiologically unrelated strains showed that strains withinlAPMSC mutations (n= 41) were overrepresented among food-associated isolates, while strains encoding full-length InlA (n= 150) were overrepresented among isolates from farm animals and their environments. Furthermore, the A6allele was overrepresented and the A7allele was underrepresented among food isolates, while the A6allele was underrepresented among farm and animal isolates. Our results indicate that genetic variation ininlAcontributes to niche adaptation within the lineage II subtype DUP-1039C.

scholarly journals Poor Invasion of Trophoblastic Cells but Normal Plaque Formation in Fibroblastic Cells despite actA Deletion in a Group of Listeria monocytogenes Strains Persisting in Some Food Processing Environments

2010 ◽  
Vol 76 (10) ◽  
pp. 3391-3397 ◽  
Author(s):  
Anne Holch ◽  
Caroline Trebbien Gottlieb ◽  
Marianne Halberg Larsen ◽  
Hanne Ingmer ◽  
Lone Gram
Keyword(s):  
Listeria Monocytogenes ◽  
Molecular Subtype ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Virulence Gene ◽  
Fish Processing ◽  
Trophoblastic Cells ◽  
Processing Plants ◽  
Fibroblastic Cells ◽  
Cell Spread

ABSTRACT We determined mammalian cell invasion and virulence gene (inlA, inlB, and actA) sequences of Listeria monocytogenes strains belonging to a molecular subtype (RAPD 9) that often persists in Danish fish-processing plants. These strains invaded human placental trophoblasts less efficiently than other L. monocytogenes strains, including clinical strains, and they carry a premature stop codon in inlA. Eight of 15 strains, including the RAPD 9 and maternofetal strains, had a 105-nucleotide deletion in actA that did not affect cell-to-cell spread in mouse fibroblasts. The RAPD 9 strains may still be regarded as of low virulence with respect to human listeriosis.

scholarly journals Molecular structure of soybean E-genes and their functional mutations

2020 ◽  
pp. 3-13
Author(s):  
O. Okhrymovych ◽  
◽  
S. Chebotar ◽  
G. Chebotar ◽  
D. Zharikova ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Genetic Network ◽  
Structural Features ◽  
Loss Of Function ◽  
Nucleotide Substitutions ◽  
Early Maturity ◽  
E Gene ◽  
Wide Range

In this review, we discuss features of the molecular structure of known E-loci (early maturity) and their involvement in signaling to plant flowering, depending on the sensitivity of soybean genotypes to the photoperiod. These loci contribute to the adaptation of plants to a wide range of natural conditions due to mutations in genes and QTL that control flowering time. At the molecular level, E-genes are significantly different in structural features, origin and function. The lenghth of the identified genes range from one exon to 525 bp encoding the transcription factor (E1), up to 14 exons and about 20 kb for the GmGIa gene (E2). Among the functional mutations that in most cases lead to partial or complete loss of function, there are single-nucleotide substitutions or deletions, insertions of transposon-like sequences that can lead to amino acid substitutions in the protein, shift of the reading frame, appearance of the premature stop-codon. E-gene products are receptors of signals coming from the environment and they participate in signaling pathways that control the photoperiod. The overall impact and interactions between E-genes have not been fully studied yet, the molecular structure was investigated only for E1-E4, for which a genetic network of interactions was proposed, while at the same time five loci (E6-E9 and E11) were only mapped on soybean chromosomes, and the existence of a separate E5 locus has not yet been established. In eight of the 11 E-loci, the dominant allele causes late flowering. Also there is a pleiotropic effect of E-gene alleles on yield, plant height, stress resistance, and response to low temperatures. Knowledge of the allelic state of only some of the 11 genes is not sufficient. A comprehensive understanding of the functioning of the photoperiodic genetic response network is needed. E-genes are genetic determinants that can be used during selection and creation of new varieties with programmed rates of development.

scholarly journals Deletion of Rv2571c Confers Resistance to Arylamide Compounds in Mycobacterium tuberculosis

2021 ◽  
Vol 65 (5) ◽  
Author(s):  
Catherine D. Shelton ◽  
Matthew B. McNeil ◽  
Julie V. Early ◽  
Thomas R. Ioerger ◽  
Tanya Parish
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Stop Codon ◽  
Fusaric Acid ◽  
Premature Stop Codon ◽  
Acid Resistance ◽  
New Drugs ◽  
Wild Type ◽  
Content Type ◽  
Global Health Problem

ABSTRACT Tuberculosis, caused by Mycobacterium tuberculosis, is an urgent global health problem requiring new drugs, new drug targets, and an increased understanding of antibiotic resistance. We have determined the mode of resistance to be a series of arylamide compounds in M. tuberculosis. We isolated M. tuberculosis resistant mutants to two arylamide compounds which are inhibitory to growth under host-relevant conditions (butyrate as a sole carbon source). Thirteen mutants were characterized, and all had mutations in Rv2571c; mutations included a premature stop codon and frameshifts as well as nonsynonymous polymorphisms. We isolated a further 10 strains with mutations in Rv2571c with resistance. Complementation with a wild-type copy of Rv2571c restored arylamide sensitivity. Overexpression of Rv2571c was toxic in both wild-type and mutant backgrounds. We constructed M. tuberculosis strains with an unmarked deletion of the entire Rv2571c gene by homologous recombination and confirmed that these were resistant to the arylamide series. Rv2571c is a member of the aromatic amino acid transport family and has a fusaric acid resistance domain which is associated with compound transport. Since loss or inactivation of Rv2571c leads to resistance, we propose that Rv2571c is involved in the import of arylamide compounds.

scholarly journals The Distinct Immune-Stimulatory Capacities of Porphyromonas gingivalis Strains 381 and ATCC 33277 Are Determined by the fimB Allele and Gingipain Activity

2019 ◽  
Vol 87 (12) ◽  
Author(s):  
Stephen R. Coats ◽  
Nutthapong Kantrong ◽  
Thao T. To ◽  
Sumita Jain ◽  
Caroline A. Genco ◽  
...  
Keyword(s):  
Cell Surface ◽  
Immune Responses ◽  
Host Cell ◽  
Porphyromonas Gingivalis ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Innate Immune ◽  
Surface Proteins ◽  
Innate Immune Responses ◽  
Content Type

ABSTRACT The Porphyromonas gingivalis strain ATCC 33277 (33277) and 381 genomes are nearly identical. However, strain 33277 displays a significantly diminished capacity to stimulate host cell Toll-like receptor 2 (TLR2)-dependent signaling and interleukin-1β (IL-1β) production relative to 381, suggesting that there are strain-specific differences in one or more bacterial immune-modulatory factors. Genomic sequencing identified a single nucleotide polymorphism in the 33277 fimB allele (A→T), creating a premature stop codon in the 33277 fimB open reading frame relative to the 381 fimB allele. Gene exchange experiments established that the 33277 fimB allele reduces the immune-stimulatory capacity of this strain. Transcriptome comparisons revealed that multiple genes related to carboxy-terminal domain (CTD) family proteins, including the gingipains, were upregulated in 33277 relative to 381. A gingipain substrate degradation assay demonstrated that cell surface gingipain activity is higher in 33277, and an isogenic mutant strain deficient for the gingipains exhibited an increased ability to induce TLR2 signaling and IL-1β production. Furthermore, 33277 and 381 mutant strains lacking CTD cell surface proteins were more immune-stimulatory than the parental wild-type strains, consistent with an immune-suppressive role for the gingipains. Our data show that the combination of an intact fimB allele and limited cell surface gingipain activity in P. gingivalis 381 renders this strain more immune-stimulatory. Conversely, a defective fimB allele and high-level cell surface gingipain activity reduce the capacity of P. gingivalis 33277 to stimulate host cell innate immune responses. In summary, genomic and transcriptomic comparisons identified key virulence characteristics that confer divergent host cell innate immune responses to these highly related P. gingivalis strains.

scholarly journals A P3A-Type ATPase and an R2R3-MYB Transcription Factor Are Involved in Vacuolar Acidification and Flower Coloration in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Jagadeesh Sundaramoorthy ◽  
Gyu Tae Park ◽  
Jeong-Dong Lee ◽  
Jeong Hoe Kim ◽  
Hak Soo Seo ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Anthocyanin Biosynthesis ◽  
Stop Codon ◽  
Binding Capacity ◽  
Premature Stop Codon ◽  
Flower Color ◽  
Myb Transcription Factor ◽  
Nucleotide Substitutions ◽  
Vacuolar Acidification ◽  
Vacuolar Ph

The determination of flower color mainly depends on the anthocyanin biosynthesis pathway and vacuolar pH; however, unlike the former, the mechanism of vacuolar acidification in soybean remains uncharacterized at the molecular level. To investigate this mechanism, we isolated four recessive purple–blue EMS-induced flower mutants from the purple flower soybean cultivar, Pungsannamul. The petals of all the mutants had increased pH compared with those of wild Pungsannamul. One of the mutants had a single nucleotide substitution in GmPH4, a regulator gene encoding an MYB transcription factor, and the substitution resulted in a premature stop codon in its first exon. The other three mutants had nucleotide substitutions in GmPH5, a single new gene that we identified by physical mapping. It corresponds to Glyma.03G262600 in chromosome 3 and encodes a proton pump that belongs to the P3A-ATPase family. The substitutions resulted in a premature stop codon, which may be a defect in the ATP-binding capacity of GmPH5 and possibly a catalytic inefficiency of GmPH5. The result is consistent with their genetic recessiveness as well as the high pH of mutant petals, suggesting that GmPH5 is directly involved in vacuolar acidification. We also found that the expression of GmPH5 and several putative “acidifying” genes in the gmph4 mutant was remarkably reduced, indicating that GmPH4 may regulate the genes involved in determining the vacuolar pH of soybean petals.

scholarly journals Campylobacter jejuniColonization in the Crow Gut Involves Many Deletions within the Cytolethal Distending Toxin Gene Cluster

2018 ◽  
Vol 84 (6) ◽  
Author(s):  
Keya Sen ◽  
Jingrang Lu ◽  
Piyali Mukherjee ◽  
Tanner Berglund ◽  
Eunice Varughese ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Virulence Gene ◽  
Farm Animals ◽  
Toxin Gene ◽  
Broad Host Range ◽  
Cytolethal Distending Toxin ◽  
Gene Markers ◽  
Content Type ◽  
Control Programs ◽  
Geographical Regions

ABSTRACTCampylobacterspp. are major causes of gastroenteritis worldwide. The virulence potential ofCampylobactershed in crow feces obtained from a roost area in Bothell, Washington, was studied and compared with that from isolates from other parts of Washington and from a different crow species 7,000 miles away in Kolkata, India.Campylobacterorganisms were isolated from 61% and 69% of the fecal samples obtained from Washington and Kolkata, respectively, and were confirmed to beC. jejuni. The cytolethal distending toxin (CDT) gene cluster from these isolates revealed a truncated sequence of approximately 1,350 bp. Sequencing of the gene cluster revealed two types of mutations: a 668-bp deletion acrosscdtAandcdtBand a 51-bp deletion withincdtB. Some strains had additional 20-bp deletions incdtB. In either case, a functional toxin is not expected; a functional toxin is produced by the expression of three tandem genes,cdtA,cdtB, andcdtC. Reverse transcriptase PCR with total RNA extracted from the isolates showed no expression ofcdtB. A toxin assay performed with these isolates on HeLa cells failed to show cytotoxic effects on the cells. However, the isolates were able to colonize the chicken ceca for a period of at least 4 weeks, similar to that of a clinical isolate. Other virulence gene markers, flagellin A and CadF, were present in 100% of the isolates. Our study suggests that crows carry the bacteriumC. jejunibut with a dysfunctional toxin protein that is expected to drastically reduce its potential to cause diarrhea.IMPORTANCECampylobacters are a major cause of gastroenteritis in humans. Since outbreaks have most often been correlated with poultry or unpasteurized dairy products, contact with farm animals, or contaminated water, historically, the majority of the studies have been with campylobacter isolates from poultry, domestic animals, and human patients. However, the bacterium has a broad host range that includes birds. These reservoirs need to be investigated, because the identification of the source and a determination of the transmission routes for a pathogen are important for the development of evidence-based disease control programs. In this study, two species of the human-commensal crow, from two different geographical regions separated by 7,000 miles of land and water, have been examined for their ability to cause disease by shedding campylobacters. Our results show that the crow may not play a significant role in campylobacteriosis, because the campylobacter organisms they shed produce a nonfunctional toxin.

scholarly journals Spontaneous Loss of Virulence in Natural Populations of Listeria monocytogenes

2017 ◽  
Vol 85 (11) ◽  
Author(s):  
Mylène M. Maury ◽  
Viviane Chenal-Francisque ◽  
Hélène Bracq-Dieye ◽  
Lei Han ◽  
Alexandre Leclercq ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Host Cells ◽  
Single Amino Acid ◽  
Listeriolysin O ◽  
Loss Of Function ◽  
Phenotypic Marker ◽  
Content Type ◽  
Virulence Attenuation

ABSTRACT The pathogenesis of Listeria monocytogenes depends on the ability of this bacterium to escape from the phagosome of the host cells via the action of the pore-forming toxin listeriolysin O (LLO). Expression of the LLO-encoding gene (hly) requires the transcriptional activator PrfA, and both hly and prfA genes are essential for L. monocytogenes virulence. Here, we used the hemolytic activity of LLO as a phenotypic marker to screen for spontaneous virulence-attenuating mutations in L. monocytogenes. Sixty nonhemolytic isolates were identified among a collection of 57,820 confirmed L. monocytogenes strains isolated from a variety of sources (0.1%). In most cases (56/60; 93.3%), the nonhemolytic phenotype resulted from nonsense, missense, or frameshift mutations in prfA. Five strains carried hly mutations leading to a single amino acid substitution (G299V) or a premature stop codon causing strong virulence attenuation in mice. In one strain, both hly and gshF (encoding a glutathione synthase required for full PrfA activity) were missing due to genomic rearrangements likely caused by a transposable element. The PrfA/LLO loss-of-function (PrfA−/LLO−) mutants belonged to phylogenetically diverse clades of L. monocytogenes, and most were identified among nonclinical strains (57/60). Consistent with the rare occurrence of loss-of-virulence mutations, we show that prfA and hly are under purifying selection. Although occurring at a low frequency, PrfA−/LLO− mutational events in L. monocytogenes lead to niche restriction and open an evolutionary path for obligate saprophytism in this facultative intracellular pathogen.

scholarly journals Listeria monocytogenes Associated with New Zealand Seafood Production and Clinical Cases: Unique Sequence Types, Truncated InlA, and Attenuated Invasiveness

2013 ◽  
Vol 80 (4) ◽  
pp. 1489-1497 ◽  
Author(s):  
Cristina D. Cruz ◽  
Andrew R. Pitman ◽  
Sally A. Harrow ◽  
Graham C. Fletcher
Keyword(s):  
New Zealand ◽  
Listeria Monocytogenes ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Potential Health ◽  
Content Type ◽  
Processing Plants ◽  
Seafood Processing ◽  
Sequence Types ◽  
Clinical Cases

ABSTRACTListeriosis is caused by the food-borne pathogenListeria monocytogenes, which can be found in seafood and processing plants. To evaluate the risk to human health associated with seafood production in New Zealand, multi-virulence-locus sequence typing (MVLST) was used to define the sequence types (STs) of 31L. monocytogenesisolates collected from seafood-processing plants, 15 from processed foods, and 6 from human listeriosis cases. The STs of these isolates were then compared with those from a collection of seafood isolates and epidemic strains from overseas. A total of 17 STs from New Zealand clustered into two lineages: seafood-related isolates in lineages I and II and all human isolates in lineage II. None of the New Zealand STs matched previously described STs from other countries. Isolates (belonging to ST01-N and ST03-N) from mussels and their processing environments, however, were identical to those of sporadic listeriosis cases in New Zealand. ST03-N isolates (16 from mussel-processing environments, 2 from humans, and 1 from a mussel) contained aninlApremature stop codon (PMSC) mutation. Therefore, the levels of invasiveness of 22 isolates from ST03-N and the three other common STs were compared using human intestinal epithelial Caco-2 cell lines. STs carryinginlAPMSCs, including ST03-N isolates associated with clinical cases, had a low invasion phenotype. The close relatedness of some clinical and environmental strains, as revealed by identical MVLST profiles, suggests that local and persistent environmental strains in seafood-processing environments pose a potential health risk. Furthermore, a PMSC ininlAdoes not appear to giveL. monocytogenesa noninvasive profile.

scholarly journals Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States

2013 ◽  
Vol 21 (2) ◽  
pp. 119-125 ◽  
Author(s):  
L. C. Pawloski ◽  
A. M. Queenan ◽  
P. K. Cassiday ◽  
A. S. Lynch ◽  
M. J. Harrison ◽  
...  
Keyword(s):  
United States ◽  
Bordetella Pertussis ◽  
Stop Codon ◽  
The United States ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Content Type ◽  
Routine Surveillance ◽  
Nucleotide Insertion ◽  
Positive Isolate

ABSTRACTPertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s.Bordetella pertussisisolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting thatB. pertussisis losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting andprnsequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481in theprngene (prnIS481positive). The firstprnIS481-positive isolate was found in 1994, and the nextprnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in theprngene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found inprn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficientB. pertussisisolates throughout the United States.

scholarly journals Natural Variant of Collagen-Like Protein A in Serotype M3 Group A Streptococcus Increases Adherence and Decreases Invasive Potential

2015 ◽  
Vol 83 (3) ◽  
pp. 1122-1129 ◽  
Author(s):  
Anthony R. Flores ◽  
Brittany E. Jewell ◽  
Erika M. Versalovic ◽  
Randall J. Olsen ◽  
Beth A. Bachert ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Group A Streptococcus ◽  
Stop Codon ◽  
Protein A ◽  
Premature Stop Codon ◽  
Invasive Disease ◽  
Content Type ◽  
Invasive Strain ◽  
Group A ◽  
Epithelial Barriers

Group AStreptococcus(GAS) predominantly exists as a colonizer of the human oropharynx that occasionally breaches epithelial barriers to cause invasive diseases. Despite the frequency of GAS carriage, few investigations into the contributory molecular mechanisms exist. To this end, we identified a naturally occurring polymorphism in the gene encoding the streptococcal collagen-like protein A (SclA) in GAS carrier strains. All previously sequenced invasive serotype M3 GAS possess a premature stop codon in thesclAgene truncating the protein. The carrier polymorphism is predicted to restore SclA function and was infrequently identified by targeted DNA sequencing in invasive strains of the same serotype. We demonstrate that a strain with the carriersclAallele expressed a full-length SclA protein, while the strain with the invasivesclAallele expressed a truncated variant. An isoallelic mutant invasive strain with the carriersclAallele exhibited decreased virulence in a mouse model of invasive disease and decreased multiplication in human blood. Further, the isoallelic invasive strain with the carriersclAallele persisted in the mouse nasopharynx and had increased adherence to cultured epithelial cells. Repair of the premature stop codon in the invasivesclAallele restored the ability to bind the extracellular matrix proteins laminin and cellular fibronectin. These data demonstrate that a mutation in GAS carrier strains increases adherence and decreases virulence and suggest selection against increased adherence in GAS invasive isolates.

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