scholarly journals Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid

2021 ◽  
Vol 17 (3) ◽  
pp. e1009402
Author(s):  
Forrest C. Walker ◽  
Ebrahim Hassan ◽  
Stefan T. Peterson ◽  
Rachel Rodgers ◽  
Lawrence A. Schriefer ◽  
...  
Keyword(s):  
Amino Acid ◽  
Enteric Virus ◽  
Viral Capsid ◽  
Type I ◽  
Murine Norovirus ◽  
Nucleotide Change ◽  
Evolutionary Potential ◽  
Single Nucleotide ◽  
Virus Growth ◽  
Immunodeficient Mice

Interferons (IFNs) are key controllers of viral replication, with intact IFN responses suppressing virus growth and spread. Using the murine norovirus (MNoV) system, we show that IFNs exert selective pressure to limit the pathogenic evolutionary potential of this enteric virus. In animals lacking type I IFN signaling, the nonlethal MNoV strain CR6 rapidly acquired enhanced virulence via conversion of a single nucleotide. This nucleotide change resulted in amino acid substitution F514I in the viral capsid, which led to >10,000-fold higher replication in systemic organs including the brain. Pathogenicity was mediated by enhanced recruitment and infection of intestinal myeloid cells and increased extraintestinal dissemination of virus. Interestingly, the trade-off for this mutation was reduced fitness in an IFN-competent host, in which CR6 bearing F514I exhibited decreased intestinal replication and shedding. In an immunodeficient context, a spontaneous amino acid change can thus convert a relatively avirulent viral strain into a lethal pathogen.

Biochemical mechanism and molecular basis for ALS-inhibiting herbicide resistance in sugarbeet (Beta vulgaris) somatic cell selections

Weed Science ◽  
1998 ◽  
Vol 46 (1) ◽  
pp. 13-23 ◽  
Author(s):  
Terry R. Wright ◽  
Newell F. Bascomb ◽  
Stephen F. Sturner ◽  
Donald Penner
Keyword(s):  
Amino Acid ◽  
Somatic Cell ◽  
Herbicide Resistance ◽  
Double Mutant ◽  
Acetolactate Synthase ◽  
Cross Resistance ◽  
Nucleotide Change ◽  
Wild Type ◽  
Single Nucleotide ◽  
Single Nucleotide Change

Three sugarbeet selections differing in cross-resistance to three classes of acetolactate synthase (ALS)-inhibiting herbicides have been developed using somatic cell selection. Sugarbeet selections resistant to imidazolinone herbicides,Sir-13and93R30B, do not metabolize [14C]-imazethapyr any faster or differently than sensitive, wild-type sugarbeets or a sulfonylurea-resistant/imidazolinone-sensitive selection, Sur. ALS specific activity from the three herbicide-resistant selections ranged from 73 to 93% of the wild-type enzyme extracts in the absence of herbicide, indicating enzyme overexpression was not a factor in resistance. Acetolactate synthase from Sir-13 plants showed a 40-fold resistance to imazethapyr but no resistance to chlorsulfuron or flumetsulam. Polymerase chain reaction amplification and sequencing of two regions of the ALS gene spanning all known sites for ALS-based herbicide resistance in plants indicated a single nucleotide change in theSir-13gene (G337to A337) resulting in a deduced substitution of threonine for alanine at position 113 in the sugarbeet amino acid sequence. Sur ALS was not significantly resistant to imazethapyr, but was 1,000- and 50-fold resistant to chlorsulfuron and flumetsulam, respectively.Surgene sequencing indicated a single nucleotide change(C562to T562) resulting in a serine for proline substitution at position 188 of the ALS primary structure. The93R30Bnucleotide sequence indicated two mutations resulting in two deduced amino acid substitutions: threonine for alanine at position 113 plus serine for proline at position 188. The93R30Bdouble mutant incorporated the changes observed in each of the single mutants above and correlated with higher resistance levels to imazethapyr (> 1,000-fold), chlorsulfuron (4,300-fold), and flumetsulam (200-fold) at the ALS level than observed in either of the single mutants.93R30Brepresents the first double mutant derived by a two-step selection process that incorporates two class-specific ALS-inhibitor resistance mutations to form a single broad cross-resistance trait. The interaction of the two altered amino acids is synergistic with respect to enzyme resistance vs. the resistance afforded by each of the individual mutations.

scholarly journals Suboptimal Nucleotides in the Infectious, Pathogenic Simian Immunodeficiency Virus Clone SIVmac239

2001 ◽  
Vol 75 (8) ◽  
pp. 4019-4022 ◽  
Author(s):  
Louis Alexander ◽  
Lynn Denekamp ◽  
Susan Czajak ◽  
Ronald C. Desrosiers
Keyword(s):  
Amino Acid ◽  
Simian Immunodeficiency Virus ◽  
High Viral Load ◽  
Virus Genome ◽  
Amino Acid Sequences ◽  
Primer Binding Site ◽  
Nucleotide Change ◽  
Single Nucleotide ◽  
Single Nucleotide Change ◽  
Immunodeficiency Virus

ABSTRACT We analyzed virus sequences in two monkeys infected with SIVmac239 and two monkeys infected with SHIVnef that maintained high, persisting viral loads. Sequence changes were observed consistently at four loci in all four animals: a single nucleotide change in the Lys-tRNA primer binding site in the 5′ long terminal repeat; two nucleotide changes that resulted in two amino acid changes in thepol gene product; and a single nucleotide change in the region of the simian immunodeficiency virus genome where therev and env genes overlap, resulting in changes in the predicted amino acid sequences of both gene products. None of these mutations were seen in short-term cultures of CEM×174 cells infected with SIVmac239 or SHIVnef. At all four positions in all four animals, the new sequences represented consensus sequences for primate lentiviruses, whereas the inoculum sequences at these four loci have either never been or rarely been reported outside of SIVmac239. Thus, although cloned SIVmac239 is consistently pathogenic and consistently induces high viral load set points, it is clearly less than optimal at these four nucleotide positions.

scholarly journals Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Kara B. De León ◽  
Grant M. Zane ◽  
Valentine V. Trotter ◽  
Gregory P. Krantz ◽  
Adam P. Arkin ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Sulfate Reducing Bacteria ◽  
Structural Proteins ◽  
Desulfovibrio Vulgaris ◽  
Type I ◽  
Nucleotide Change ◽  
Single Nucleotide ◽  
Sulfate Reducing ◽  
Single Nucleotide Change ◽  
Reducing Bacteria

ABSTRACT Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered. IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm.

scholarly journals Charged Residues Flanking the Transmembrane Domain of Two Related Toxin–Antitoxin System Toxins Affect Host Response

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 329
Author(s):  
Andrew Holmes ◽  
Jessie Sadlon ◽  
Keith Weaver
Keyword(s):  
Amino Acid ◽  
Enterococcus Faecalis ◽  
Host Response ◽  
Cytoplasmic Membrane ◽  
Transmembrane Domain ◽  
The Other ◽  
Type I ◽  
Transcriptomic Response ◽  
Specific Amino Acid ◽  
Transporter Protein

A majority of toxins produced by type I toxin–antitoxin (TA-1) systems are small membrane-localized proteins that were initially proposed to kill cells by forming non-specific pores in the cytoplasmic membrane. The examination of the effects of numerous TA-1 systems indicates that this is not the mechanism of action of many of these proteins. Enterococcus faecalis produces two toxins of the Fst/Ldr family, one encoded on pheromone-responsive conjugative plasmids (FstpAD1) and the other on the chromosome, FstEF0409. Previous results demonstrated that overexpression of the toxins produced a differential transcriptomic response in E. faecalis cells. In this report, we identify the specific amino acid differences between the two toxins responsible for the differential response of a gene highly induced by FstpAD1 but not FstEF0409. In addition, we demonstrate that a transporter protein that is genetically linked to the chromosomal version of the TA-1 system functions to limit the toxicity of the protein.

scholarly journals Linkage Disequilibrium in Domestic Sheep

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1113-1122
Author(s):  
A F McRae ◽  
J C McEwan ◽  
K G Dodds ◽  
T Wilson ◽  
A M Crawford ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Type I Error ◽  
Statistical Significance ◽  
Domestic Sheep ◽  
Type I ◽  
Single Nucleotide ◽  
Microsatellite Genotype ◽  
Marker Distance ◽  
The Relationship ◽  
Two Populations

Abstract The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D′ were also explored. D′ was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D′ may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D′ to determine the true extent of LD.

scholarly journals Lymphocytes are detrimental during the early innate immune response against Listeria monocytogenes

2006 ◽  
Vol 203 (4) ◽  
pp. 933-940 ◽  
Author(s):  
Javier A. Carrero ◽  
Boris Calderon ◽  
Emil R. Unanue
Keyword(s):  
Immune Response ◽  
Listeria Monocytogenes ◽  
Innate Immune Response ◽  
Early Stage ◽  
Bacterial Pathogen ◽  
Interleukin 10 ◽  
Innate Immune ◽  
Type I ◽  
Phagocytic Cells ◽  
Immunodeficient Mice

Mice deficient in lymphocytes are more resistant than normal mice to Listeria monocytogenes infection during the early innate immune response. This paradox remains unresolved: lymphocytes are required for sterilizing immunity, but their presence during the early stage of the infection is not an asset and may even be detrimental. We found that lymphocyte-deficient mice, which showed limited apoptosis in infected organs, were resistant during the first four days of infection but became susceptible when engrafted with lymphocytes. Engraftment with lymphocytes from type I interferon receptor–deficient (IFN-αβR−/−) mice, which had reduced apoptosis, did not confer increased susceptibility to infection, even when the phagocytes were IFN-αβR+/+. The attenuation of innate immunity was due, in part, to the production of the antiinflammatory cytokine interleukin 10 by phagocytic cells after the apoptotic phase of the infection. Thus, immunodeficient mice were more resistant relative to normal mice because the latter went through a stage of lymphocyte apoptosis that was detrimental to the innate immune response. This is an example of a bacterial pathogen creating a cascade of events that leads to a permissive infective niche early during infection.

scholarly journals NCU-G1 is a highly glycosylated integral membrane protein of the lysosome

2009 ◽  
Vol 422 (1) ◽  
pp. 83-90 ◽  
Author(s):  
Oliver Schieweck ◽  
Markus Damme ◽  
Bernd Schröder ◽  
Andrej Hasilik ◽  
Bernhard Schmidt ◽  
...  
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Mouse Liver ◽  
Lysosomal Membrane ◽  
Molecular Forms ◽  
Type I ◽  
Calculated Molecular Mass ◽  
Sorting Motif ◽  
Lysosomal Membrane Proteins

Until recently, a modest number of approx. 40 lysosomal membrane proteins had been identified and even fewer were characterized in their function. In a proteomic study, using lysosomal membranes from human placenta we identified several candidate lysosomal membrane proteins and proved the lysosomal localization of two of them. In the present study, we demonstrate the lysosomal localization of the mouse orthologue of the human C1orf85 protein, which has been termed kidney-predominant protein NCU-G1 (GenBank® accession number: AB027141). NCU-G1 encodes a 404 amino acid protein with a calculated molecular mass of 39 kDa. The bioinformatics analysis of its amino acid sequence suggests it is a type I transmembrane protein containing a single tyrosine-based consensus lysosomal sorting motif at position 400 within the 12-residue C-terminal tail. Its lysosomal localization was confirmed using immunofluorescence with a C-terminally His-tagged NCU-G1 and the lysosomal marker LAMP-1 (lysosome-associated membrane protein-1) as a reference, and by subcellular fractionation of mouse liver after a tyloxapol-induced density shift of the lysosomal fraction using an anti-NCU-G1 antiserum. In transiently transfected HT1080 and HeLa cells, the His-tagged NCU-G1 was detected in two molecular forms with apparent protein sizes of 70 and 80 kDa, and in mouse liver the endogenous wild-type NCU-G1 was detected as a 75 kDa protein. The remarkable difference between the apparent and the calculated molecular masses of NCU-G1 was shown, by digesting the protein with N-glycosidase F, to be due to an extensive glycosylation. The lysosomal localization was impaired by mutational replacement of an alanine residue for the tyrosine residue within the putative sorting motif.

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