Influence of double-stranded RNAs on growth, sporulation, pathogenicity, and survival of Chalara elegans

1995 ◽  
Vol 73 (7) ◽  
pp. 1001-1009 ◽  
Author(s):  
Zamir K. Punja
Keyword(s):  
Plant Pathogen ◽  
Dry Weight ◽  
Complete Loss ◽  
Thielaviopsis Basicola ◽  
Wild Type ◽  
C Elegans ◽  
Chalara Elegans ◽  
In The Wild ◽  
Rna Fragments ◽  
Type Strains

Three strains of Chalara elegans from diverse geographical areas that contained multiple (4 or 5) double-stranded RNA fragments were compared with spontaneously derived cultures from these strains that were either partially cured or completely free of dsRNA. In the wild-type strains, presence of the dsRNAs was found to significantly enhance phialospore production and pigmentation of colonies, whereas radial growth and mycelial dry weight accumulation were reduced. The rate and overall percentage of phialospore germination on 1% Noble water agar were also significantly reduced by the presence of the dsRNAs. In two partially cured strains (only one 2.8-kb fragment remaining), pathogenicity to various plant tissues was significantly enhanced when compared with the wild-type strains containing multiple dsRNA. However, survival in field soil was enhanced in one strain and reduced in the other. In the completely cured strain, the loss of multiple dsRNA fragments was associated with enhanced growth, reduced phialospore production, and a complete loss of pathogenicity and capability for survival in soil. These results indicate that the effects of dsRNAs in C. elegans vary with the strain. In general, the presence of multiple dsRNAs in this fungus enhanced sporulation, altered colony morphology, and reduced growth and pathogenicity. However, since the complete loss of dsRNA was found to eliminate pathogenicity and reduce survival, it suggests that some dsRNA fragments in C. elegans may confer an advantage to this soil-borne facultative plant pathogen. Key words: black root rot, soil-borne plant pathogen, Thielaviopsis basicola.

Morphological and molecular characterization of Chalara elegans (Thielaviopsis basicola), cause of black root rot on diverse plant species

2000 ◽  
Vol 77 (12) ◽  
pp. 1801-1812 ◽  
Author(s):  
Zamir K Punja ◽  
Li-Juan Sun
Keyword(s):  
British Columbia ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Thielaviopsis Basicola ◽  
Wild Type ◽  
C Elegans ◽  
Chalara Elegans ◽  
Average Similarity ◽  
High Degree ◽  
Diverse Plant Species

The extent of variation in colony morphology and chlamydospore size, septation, and pigmentation was studied in 50 isolates of Chalara elegans Nag Raj et Kendrick (syn. Thielaviopsis basicola (Berk. et Br.) Ferr.) originating from 12 different geographic areas and substrates. In addition, the extent of genetic variation among these isolates was determined using random amplified polymorphic DNA (RAPD) analysis. Five general morphological groups could be distinguished among the isolates, two of which were aberrant phenotypes (albino and mycelial) that were derived upon continuous subculture of some wild-type isolates in the laboratory. The isolates with the most variation in phenotype originated from British Columbia and California. Six primers (10-mers) were used to generate 90 bands in RAPD-PCR, of which 75 were polymorphic. A high degree of diversity was apparent within C. elegans, and some banding patterns generated by specific primers were unique to certain isolates, thereby generating fingerprints. Distinct groups (clusters) were obtained following UPGMA analysis and, generally, these were composed of isolates from similar geographic regions or hosts. However, isolates from some areas, for example, British Columbia, were also found to belong to different clusters. There was generally a good relationship between groups assigned on the basis of morphology and those derived from cluster analysis, that is, isolates within a cluster tended to have similar morphology. In a few isolates, the aberrant phenotypes (albino and mycelial) could be distinguished using RAPDs from the wild type by the absence of 1 or 2 bands, indicating that changes in the nucleotide sequence had occurred, possibly through mutation. The average similarity index among all 50 isolates of C. elegans was 87%. An outgroup species (Chalara thielaviodes) had a similarity value of 40%.

scholarly journals Influences of Histone Stoichiometry on the Target Site Preference of Retrotransposons Ty1 and Ty2 in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 761-776 ◽  
Author(s):  
Lori A Rinckel ◽  
David J Garfinkel
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Promoter Region ◽  
Target Site ◽  
Site Preference ◽  
Wild Type ◽  
Histone Proteins ◽  
Protein Levels ◽  
In The Wild ◽  
Type Strains ◽  
Orientation Bias

Abstract In Saccharomyces cerevisiae, the target site specificity of the retrotransposon Ty1 appears to involve the Ty integration complex recognizing chromatin structures. To determine whether changes in chromatin structure affect Ty1 and Ty2 target site preference, we analyzed Ty transposition at the CAN1 locus in mutants containing altered levels of histone proteins. A Δhta1-htb1 mutant with decreased levels of H2A and H2B histone proteins showed a pattern of Ty1 and Ty2 insertions at CAN1 that was significantly different from that of both the wild-type and a Δhta2-htb2 mutant, which does not have altered histone protein levels. Altered levels of H2A and H2B proteins disrupted a dramatic orientation bias in the CAN1 promoter region. In the wild-type strains, few Ty1 and Ty2 insertions in the promoter region were oriented opposite to the direction of CAN1 transcription. In the Δhta1-htb1 background, however, numerous Ty1 and Ty2 insertions were in the opposite orientation clustered within the TATA region. This altered insertion pattern does not appear to be due to a bias caused by selecting canavanine resistant isolates in the different HTA1-HTB1 backgrounds. Our results suggest that reduced levels of histone proteins alter Ty target site preference and disrupt an asymmetric Ty insertion pattern.

scholarly journals A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1776
Author(s):  
Mourdas Mohamed ◽  
Nguyet Thi-Minh Dang ◽  
Yuki Ogyama ◽  
Nelly Burlet ◽  
Bruno Mugat ◽  
...  
Keyword(s):  
Single Molecule ◽  
Wild Type ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
In The Wild ◽  
Successive Generations ◽  
Type Strains

Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.

scholarly journals Impact of Multiple β-Ketothiolase Deletion Mutations in Ralstonia eutropha H16 on the Composition of 3-Mercaptopropionic Acid-Containing Copolymers

2010 ◽  
Vol 76 (16) ◽  
pp. 5373-5382 ◽  
Author(s):  
Nicole Lindenkamp ◽  
Katja Peplinski ◽  
Elena Volodina ◽  
Armin Ehrenreich ◽  
Alexander Steinbüchel
Keyword(s):  
Ralstonia Eutropha ◽  
Dry Weight ◽  
Deletion Mutants ◽  
Transcriptome Data ◽  
Wild Type ◽  
Acetyl Coenzyme A ◽  
Deletion Mutations ◽  
Knockout Mutants ◽  
In The Wild ◽  
Percentage Ratio

ABSTRACT β-Ketothiolases catalyze the first step of poly(3-hydroxybutyrate) [poly(3HB)] synthesis in bacteria by condensing two molecules of acetyl coenzyme A (acetyl-CoA) to acetoacetyl-CoA. Analyses of the genome sequence of Ralstonia eutropha H16 revealed 15 isoenzymes of PhaA in this bacterium. In this study, we generated knockout mutants of various phaA homologues to investigate their role in and contributions to poly(3HB) metabolism and to suppress biosynthesis of 3HB-CoA for obtaining enhanced molar 3-mercaptopriopionate (3MP) contents in poly(3HB-co-3MP) copolymers when cells were grown on gluconate plus 3-mercaptopropionate or 3,3′-dithiodipropionate. In silico sequence analysis of PhaA homologues, transcriptome data, and other aspects recommended the homologues phaA, bktB, H16_A1713/H16_B1771, H16_A1528, H16_B1369, H16_B0381, and H16_A0170 for further analysis. Single- and multiple-deletion mutants were generated to investigate the influence of these β-ketothiolases on growth and polymer accumulation. The deletion of single genes resulted in no significant differences from the wild type regarding growth and polymer accumulation during cultivation on gluconate or gluconate plus 3MP. Deletion of phaA plus bktB (H16Δ2 mutant) resulted in approximately 30% less polymer accumulation than in the wild type. Deletion of H16_A1713/H16_B1771, H16_A1528, H16_B0381, and H16_B1369 in addition to phaA and bktB gave no differences in comparison to the H16Δ2 mutant. In contrast, deletion of H16_A0170 additionally to phaA and bktB yielded a mutant which accumulated about 30% poly(3HB) (wt/wt of the cell dry weight [CDW]). Although we were not able to suppress poly(3HB) biosynthesis completely, the copolymer compositions could be altered significantly with a lowered percentage ratio of 3HB constituents (from 85 to 52 mol%) and an increased percentage ratio of 3MP constituents (from 15 to 48 mol%), respectively. In this study, we demonstrated that PhaA, BktB, and H16_A0170 are majorly involved in poly(3HB) synthesis in R. eutropha H16. A fourth β-ketothiolase or a combination of several of the other β-ketothiolases contributed to a maximum of only 30% (wt/wt of CDW) of the remaining (co)polymer.

scholarly journals Photosynthetic performance in cyanobacteria with increased sulphide tolerance: an analysis comparing wild-type and experimentally derived strains

2021 ◽  
Author(s):  
Elena Martín-Clemente ◽  
Ignacio J. Melero-Jiménez ◽  
Elena Bañares-España ◽  
Antonio Flores-Moya ◽  
María J. García-Sánchez
Keyword(s):  
Resistance Mechanisms ◽  
Photosynthetic Performance ◽  
Oxygenic Photosynthesis ◽  
Wild Type ◽  
Sensitive Species ◽  
Anoxygenic Photosynthesis ◽  
In The Wild ◽  
Photosynthetic Machinery ◽  
Type Strains ◽  
Shed Light

AbstractSulphide is proposed to have influenced the evolution of primary stages of oxygenic photosynthesis in cyanobacteria. However, sulphide is toxic to most of the species of this phylum, except for some sulphide-tolerant species showing various sulphide-resistance mechanisms. In a previous study, we found that this tolerance can be induced by environmental sulphidic conditions, in which two experimentally derived strains with an enhanced tolerance to sulphide were obtained from Microcystis aeruginosa, a sensitive species, and Oscillatoria, a sulphide-tolerant genus. We have now analysed the photosynthetic performance of the wild-type and derived strains in the presence of sulphide to shed light on the characteristics underlying the increased tolerance. We checked whether the sulphide tolerance was a result of higher PSII sulphide resistance and/or the induction of sulphide-dependent anoxygenic photosynthesis. We observed that growth, maximum quantum yield, maximum electron transport rate and photosynthetic efficiency in the presence of sulphide were less affected in the derived strains compared to their wild-type counterparts. Nevertheless, in 14C photoincoporation assays, neither Oscillatoria nor M. aeruginosa exhibited anoxygenic photosynthesis using sulphide as an electron donor. On the other hand, the content of photosynthetic pigments in the derived strains was different to that observed in the wild-type strains. Thus, an enhanced PSII sulphide resistance appears to be behind the increased sulphide tolerance displayed by the experimentally derived strains, as observed in most natural sulphide-tolerant cyanobacterial strains. However, other changes in the photosynthetic machinery cannot be excluded.

scholarly journals Decay of ermC mRNA in a Polynucleotide Phosphorylase Mutant of Bacillus subtilis

1998 ◽  
Vol 180 (22) ◽  
pp. 5968-5977 ◽  
Author(s):  
David H. Bechhofer ◽  
Wei Wang
Keyword(s):  
Bacillus Subtilis ◽  
Rna Structure ◽  
Northern Blot Analysis ◽  
Polynucleotide Phosphorylase ◽  
Wild Type ◽  
Gene Coding ◽  
In The Wild ◽  
Rna Fragments ◽  
Specific Mrna

ABSTRACT ermC mRNA decay was examined in a mutant ofBacillus subtilis that has a deleted pnpA gene (coding for polynucleotide phosphorylase). 5′-proximal RNA fragments less than 400 nucleotides in length were abundant in thepnpA strain but barely detectable in the wild type. On the other hand, the patterns of 3′-proximal RNA fragments were similar in the wild-type and pnpA strains. Northern blot analysis with different probes showed that the 5′ end of the decay intermediates was the native ermC 5′ end. For one prominent ermCRNA fragment, in particular, it was shown that formation of its 3′ end was directly related to the presence of a stalled ribosome. 5′-proximal decay intermediates were also detected for transcripts encoded by theyybF gene. These results suggest that PNPase activity, which may be less sensitive to structures or sequences that block exonucleolytic decay, is required for efficient decay of specific mRNA fragments. However, it was shown that even PNPase activity could be blocked in vivo at a particular RNA structure.

scholarly journals Supplemental Cellular Protection by a Carotenoid Extends Lifespan via Ins/IGF-1 Signaling inCaenorhabditis elegans

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Koumei Yazaki ◽  
Chinatsu Yoshikoshi ◽  
Satoru Oshiro ◽  
Sumino Yanase
Keyword(s):  
Model Organism ◽  
Lifespan Extension ◽  
Cell Organelle ◽  
Wild Type ◽  
Marine Animals ◽  
Cellular Protection ◽  
C Elegans ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
In The Wild

Astaxanthin (AX), which is produced by some marine animals, is a type of carotenoid that has antioxidative properties. In this study, we initially examined the effects of AX on the aging of a model organismC. elegansthat has the conserved intracellular pathways related to mammalian longevity. The continuous treatments with AX (0.1 to 1 mM) from both the prereproductive and young adult stages extended the mean lifespans by about 16–30% in the wild-type and long-lived mutantage-1ofC. elegans. In contrast, the AX-dependent lifespan extension was not observed even in adaf-16null mutant. Especially, the expression of genes encoding superoxide dismutases and catalases increased in two weeks after hatching, and the DAF-16 protein was translocated to the nucleus in the AX-exposed wild type. These results suggest that AX protects the cell organelle mitochondria and nucleus of the nematode, resulting in a lifespan extension via an Ins/IGF-1 signaling pathway during normal aging, at least in part.

scholarly journals Caenorhabditis elegans triple null mutant lacking UDP-N-acetyl-D-glucosamine:α-3-D-mannoside β1,2-N-acetylglucosaminyltransferase I

2004 ◽  
Vol 382 (3) ◽  
pp. 995-1001 ◽  
Author(s):  
Shaoxian ZHU ◽  
Andrew HANNEMAN ◽  
Vernon N. REINHOLD ◽  
Andrew M. SPENCE ◽  
Harry SCHACHTER
Keyword(s):  
Caenorhabditis Elegans ◽  
Chromosome Number ◽  
Null Mutant ◽  
Wild Type ◽  
Knock Out ◽  
C Elegans ◽  
In The Wild ◽  
Wild Type Worm ◽  
Type C ◽  
Nematode Worm

We have previously reported, from the nematode worm Caenor-habditis elegans, three genes (gly-12, gly-13 and gly-14) encoding enzymically active UDP-N-acetyl-D-glucosamine:α-3-D-mannoside β1,2-N-acetylglucosaminyltransferase I (GnT I), an enzyme essential for hybrid, paucimannose and complex N-glycan synthesis. We now describe a worm with null mutations in all three GnT I genes, gly-14 (III);gly-12 gly-13 (X) (III and X refer to the chromosome number). The triple-knock-out (TKO) worms have a normal phenotype, although they do not express GnT I activity and do not synthesize 31 paucimannose, complex and fucosylated oligomannose N-glycans present in the wild-type worm. The TKO worm has increased amounts of non-fucosylated oligomannose N-glycan structures, a finding consistent with the site of GnT I action. Five fucosylated oligomannose N-glycan structures were observed in TKO, but not wild-type, worms, indicating the presence of unusual GnT I-independent fucosyltransferases. It is concluded that wild-type C. elegans makes a large number of GnT I-dependent N-glycans that are not essential for normal worm development under laboratory conditions. The TKO worm may be more susceptible to mutations in other genes, thereby providing an approach for the identification of genes that interact with GnT I.

scholarly journals ACTIVITY OF THE SEX-DETERMINING GENE tra-2 IS MODULATED TO ALLOW SPERMATOGENESIS IN THE C. ELEGANS HERMAPHRODITE

Genetics ◽  
1986 ◽  
Vol 114 (1) ◽  
pp. 53-76
Author(s):  
Tabitha Doniach
Keyword(s):  
Sex Determination ◽  
Regulatory Genes ◽  
The State ◽  
The Self ◽  
Wild Type ◽  
Gain Of Function ◽  
C Elegans ◽  
Male Development ◽  
In The Wild ◽  
Mode Of Regulation

ABSTRACT In the nematode C. elegans, there are two sexes, the self-fertilizing hermaphrodite (XX) and the male (XO). The hermaphrodite is essentially a female that makes sperm for a brief period before oogenesis. Sex determination in C. elegans is controlled by a pathway of autosomal regulatory genes, the state of which is determined by the X:A ratio. One of these genes, tra-2, is required for hermaphrodite development, but not for male development, because null mutations in tra-2 masculinize XX animals but have no effect on XO males. Dominant, gain-of-function tra-2 mutations have now been isolated that completely feminize the germline of XX animals so that they make only oocytes and no sperm and, thus, are female. Most of the tra-2(dom) mutations do not correspondingly feminize XO animals, so they do not appear to interfere with control by her-1, a gene thought to negatively regulate tra-2 in XO animals. Thus, these mutations appear to cause gain of tra-2 function in the XX animal only. Dosage studies indicate that 5 of 7 tra-2(dom) alleles are hypomorphic, so they do not simply elevate XX tra-2 activity overall. These properties suggest that in the wild type, tra-2 activity is under two types of control: (1) in males, it is inactivated by her-1 to allow male development to occur, and (2) in hermaphrodites, tra-2 is active but transiently inactivated by another, unknown, regulator to allow hermaphrodite spermatogenesis; this mode of regulation is hindered by the tra-2(dom) mutations, thereby resulting in XX females.

scholarly journals Cloning of the chromosomal determinants encoding hemolysin production and mannose-resistant hemagglutination in Escherichia coli

1982 ◽  
Vol 152 (3) ◽  
pp. 1241-1247
Author(s):  
H Berger ◽  
J Hacker ◽  
A Juarez ◽  
C Hughes ◽  
W Goebel
Keyword(s):  
Escherichia Coli ◽  
High Frequency ◽  
Wild Type ◽  
Chromosomal Dna ◽  
Genetic Determinants ◽  
E Coli ◽  
Gene Banks ◽  
In The Wild ◽  
K 12 ◽  
Type Strains

We have cloned the chromosomal hemolysin determinants from Escherichia coli strains belonging to the four O-serotypes O4, O6, O18, and O75. The hemolysin-producing clones were isolated from gene banks of these strains which were constructed by inserting partial Sau3A fragments of chromosomal DNA into the cosmid pJC74. The hemolytic cosmid clones were relatively stable. The inserts were further subcloned either as SalI fragments in pACYC184 or as BamHI-SalI fragments in a recombinant plasmid (pANN202) containing cistron C (hlyC) of the plasmid-encoded hemolysin determinant. Detailed restriction maps of each of these determinants were constructed, and it was found that, despite sharing overall homology, the determinants exhibited minor specific differences in their structure. These appeared to be restricted to cistron A (hlyA), which is the structural gene for hemolysin. In the gene banks of two of these hemolytic strains, we could also identify clones which carried the genetic determinants for the mannose-resistant hemagglutination antigens Vb and VIc. Both of these fimbrial antigens were expressed in the E. coli K-12 clones to an extent similar to that observed in the wild-type strains. These recombinant cosmids were rather unstable, and, in the absence of selection, segregated at a high frequency.

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