Nutrient interactions and arbuscular mycorrhizas: a meta-analysis of a mycorrhiza-defective mutant and wild-type tomato genotype pair

AbstractThe eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly and man. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at various levels in yeast, and found that Sir3 spreading into Extended Silent Domains (ESD) eventually reached saturation at subtelomeres. We observed that Sir3 spreading into ESDs covered zone associated with specific histone marks in wild-type cells and stopped at zones of histone mark transitions including H3K79 tri-methylation levels. The conserved enzyme Dot1 deposits H3K79 methylation, and we found that it is essential for viability upon overexpression of Sir3, but not of a spreading-defective mutant Sir3A2Q. These data suggest that H3K79 methylation actively blocks Sir3 spreading. Lastly, our meta-analysis uncovers previously uncharacterized discrete subtelomeric domains associated with specific chromatin features offering a new viewpoint on how to separate subtelomeres from the core chromosome.

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Syntaxin-17-Dependent Mitochondrial Dynamics is Essential for Protection Against Oxidative-Stress-Induced Apoptosis

Antioxidants ◽

10.3390/antiox8110522 ◽

2019 ◽

Vol 8 (11) ◽

pp. 522 ◽

Cited By ~ 4

Author(s):

Wang ◽

Xiao ◽

Huang ◽

Liu

Keyword(s):

Oxidative Stress ◽

Mitochondrial Dynamics ◽

Mitochondrial Fission ◽

Autophagic Flux ◽

Wild Type ◽

Dual Roles ◽

Defective Mutant ◽

U2os Cells ◽

Induced Apoptosis

In this study, cell death induced by the oxidant tert-butylhydroperoxide (tBH) was observed in U2OS cells; this phenotype was rescued by Syntaxin 17 (STX17) knockout (KO) but the mechanism is unknown. STX17 plays dual roles in autophagosome–lysosome fusion and mitochondrial fission. However, the contribution of the two functions of STX17 to apoptosis has not been extensively studied. Here, we sought to dissect the dual roles of STX17 in oxidative-stress-induced apoptosis by taking advantage of STX17 knockout cells and an autophagosome–lysosome fusion defective mutant of STX17. We generated STX17 knockout U2OS cells using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system and the STX17 knockout cells were reconstituted with wild-type STX17 and its autophagosome–lysosome fusion defective mutant. Autophagy was assessed by autophagic flux assay, Monomer red fluorescent protein (mRFP)–GFP–LC3 assay and protease protection assay. Golgi, endoplasmic reticulum (ER)/ER–Golgi intermediate compartment (ERGIC) and mitochondrial dynamics were examined by staining the different indicator proteins. Apoptosis was evaluated by caspase cleavage assay. The general reactive oxygen species (ROS) were detected by flow cytometry. In STX17 complete knockout cells, sealed autophagosomes were efficiently formed but their fusion with lysosomes was less defective. The fusion defect was rescued by wild-type STX17 but not the autophagosome–lysosome fusion defective mutant. No obvious defects in Golgi, ERGIC or ER dynamics were observed. Mitochondria were significantly elongated, supporting a role of STX17 in mitochondria fission and the elongation caused by STX17 KO was reversed by the autophagosome–lysosome fusion defective mutant. The clearance of protein aggregation was compromised, correlating with the autophagy defect but not with mitochondrial dynamics. This study revealed a mixed role of STX17 in autophagy, mitochondrial dynamics and oxidative stress response. STX17 knockout cells were highly resistant to oxidative stress, largely due to the function of STX17 in mitochondrial fission rather than autophagy.

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Small deletion in v-src SH3 domain of a transformation defective mutant of rous sarcoma virus restores wild type transforming properties

Virology ◽

10.1016/0042-6822(92)90579-e ◽

1992 ◽

Vol 189 (2) ◽

pp. 556-567 ◽

Cited By ~ 4

Author(s):

Philippe Dezélée ◽

Jean Vianney Barnier ◽

Annie Hampe ◽

Danielle Laugier ◽

Maria Marx ◽

...

Keyword(s):

Rous Sarcoma Virus ◽

Sh3 Domain ◽

Wild Type ◽

Small Deletion ◽

Rous Sarcoma ◽

Defective Mutant ◽

Sarcoma Virus

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Functional asymmetry of the regions juxtaposed to the membrane-binding sequence of polyomavirus middle T antigen

Molecular and Cellular Biology ◽

10.1128/mcb.12.11.5050-5058.1992 ◽

1992 ◽

Vol 12 (11) ◽

pp. 5050-5058

Author(s):

J Dahl ◽

U Thathamangalam ◽

R Freund ◽

T L Benjamin

Keyword(s):

Complete Removal ◽

T Antigen ◽

Site Directed Mutagenesis ◽

Wild Type ◽

Hydrophobic Membrane ◽

Amino Terminal ◽

Charged Amino Acids ◽

Defective Mutant ◽

Polyomavirus Middle T Antigen ◽

Membrane Anchoring

The functional importance of the two clusters of positively charged amino acids which flank the hydrophobic membrane-anchoring sequence of polyomavirus middle T (mT) protein has been investigated by using site-directed mutagenesis. A clear asymmetry was apparent. No effect on transformation was seen following multiple alterations or complete removal of the cluster at the carboxyl end of the protein. In contrast, a single substitution replacing the first arginine amino terminal to the hydrophobic stretch with glutamic acid, but not with lysine, histidine, or methionine, produced a partially transformation-defective mutant with a novel phenotype. This mutant failed to confer anchorage-independent growth on F111 established rat embryo fibroblasts but induced foci with altered morphology compared with wild-type mT. Biochemical studies on this mutant revealed that F111 clones expressing levels of mutant mT equivalent to those of wild-type controls showed a 65% reduction in pp60c-src activation and an 87% reduction in mT-associated phosphatidylinositol 3-kinase activity. However, F111 clones expressing seven times more mutant mT than did wild-type controls showed equal or greater levels of kinase activities yet remained incompletely transformed. Possible mechanisms involving this transformation-sensitive region of mT are discussed.

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A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

PeerJ ◽

10.7717/peerj.5382 ◽

2018 ◽

Vol 6 ◽

pp. e5382 ◽

Cited By ~ 33

Author(s):

Fernanda Cornejo-Granados ◽

Luigui Gallardo-Becerra ◽

Miriam Leonardo-Reza ◽

Juan Pablo Ochoa-Romo ◽

Adrian Ochoa-Leyva

Keyword(s):

Developmental Stage ◽

High Throughput Sequencing ◽

Meta Analysis ◽

Biological Factor ◽

Rrna Gene ◽

Wild Type ◽

Biological Factors ◽

Sequencing Data ◽

Freshwater Environment ◽

The Impact

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.

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Pharmacogenetic association between NAT2 gene polymorphisms and isoniazid induced hepatotoxicity: trial sequence meta-analysis as evidence

Bioscience Reports ◽

10.1042/bsr20180845 ◽

2019 ◽

Vol 39 (1) ◽

Cited By ~ 7

Author(s):

Saif Khan ◽

Raju K. Mandal ◽

Abdulbaset Mohamed Elasbali ◽

Sajad A. Dar ◽

Arshad Jawed ◽

...

Keyword(s):

Gene Polymorphisms ◽

Meta Analysis ◽

Term Treatment ◽

Wild Type ◽

Severe Problem ◽

Trial Sequence ◽

Increased Risk ◽

Long Term Treatment ◽

Nat2 Gene

Abstract Hepatotoxicity is a severe problem generally faced by tuberculosis (TB) patients. It is a well-known adverse reaction due to anti-TB drugs in TB patients undergoing long-term treatment. The studies published previously have explored the connection of N-acetyltransferase 2 (NAT2) gene polymorphisms with isoniazid-induced hepatotoxicity, but the results obtained were inconsistent and inconclusive. A comprehensive trial sequence meta-analysis was conducted employing 12 studies comprising 3613 controls and 933 confirmed TB cases using the databases namely, EMBASE, PubMed (Medline) and Google Scholar till December 2017. A significant association was observed with individuals carrying variant allele at position 481C>T (T vs. C: P = 0.001; OR = 1.278, 95% CI = 1.1100–1.484), at position 590G>A (A vs. G: P = 0.002; OR = 1.421, 95% CI = 1.137–1.776) and at position 857G>A (A vs. G: P = 0.0022; OR = 1.411, 95% CI = 1.052–1.894) to higher risk of hepatotoxicity vis-à-vis wild-type allele. Likewise, the other genetic models of NAT2 gene polymorphisms have also shown increased risk of hepatotoxicity. No evidence of publication bias was observed. These results suggest that genetic variants of NAT2 gene have significant role in isoniazid induced hepatotoxicity. Thus, NAT2 genotyping has the potential to improve the understanding of the drug–enzyme metabolic capacity and help in early predisposition of isoniazid-induced hepatotoxicity.

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Transformation-deficient mutants of Bacillus subtilis impaired in competence-specific nuclease activities

Journal of Bacteriology ◽

10.1128/jb.152.1.166-174.1982 ◽

1982 ◽

Vol 152 (1) ◽

pp. 166-174

Author(s):

J A Mulder ◽

G Venema

Keyword(s):

Molecular Weight ◽

Bacillus Subtilis ◽

Sodium Dodecyl Sulfate ◽

Sodium Dodecyl ◽

Magnesium Ions ◽

Polyacrylamide Gels ◽

Wild Type ◽

Molecular Weights ◽

Defective Mutant ◽

Mutant Strains

A comparison of the nucleolytic activities in competent and physiologically low-competent wild-type cultures of Bacillus subtilis in DNA-containing sodium dodecyl sulfate-polyacrylamide gels revealed the existence of three competence-associated nuclease activities with apparent molecular weights of 13,000, 15,000, and 26,000. The three activities, which were dependent on manganese or magnesium ions, were specifically present in the competent fraction of a competent culture. The competence-associated nucleolytic activities of eight transformation-defective mutant strains were assayed, resulting in the following three classes of mutants: (i) four strains which, according to this assay, were not impaired in any of the nucleolytic activities mentioned above; (ii) one strain which was strongly impaired in the 13,000- and 26,000-molecular-weight activities, but showed a considerable level of the 15,000-molecular-weight activity; and (iii) three strains which were severely impaired in all three activities. The results indicated that the 26,000-molecular-weight activity was a dimer of the 13,000-molecular-weight activity and that this nuclease was involved in the entry of DNA.

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Does the lack of root hairs alter root system architecture of Zea mays?

10.5194/egusphere-egu21-9710 ◽

2021 ◽

Author(s):

Steffen Schlüter ◽

Eva Lippold ◽

Maxime Phalempin ◽

Doris Vetterlein

Keyword(s):

Zea Mays ◽

Root System ◽

Root Hair ◽

System Architecture ◽

Volume Fraction ◽

Root Hairs ◽

Root System Architecture ◽

Root Diameter ◽

Wild Type ◽

Defective Mutant

Root hairs are one root trait among many which enables plants to adapt to environmental conditions. How different traits are coordinated and whether some are mutually exclusive is currently poorly understood. Comparing a root hair defective mutant with its corresponding wild-type we explored if and how the mutant exhibited root growth adaption strategies and as to how far this depended on the substrate.Zea mays root hair defective mutant (rth3) and the corresponding wild-type siblings were grown on two substrates with contrasting texture and hence nutrient mobility. Root system architecture was investigated over time using repeated X-ray computed tomography.There was no plastic adaption of root system architecture to the lack of root hairs, which resulted in lower uptake in particular in the substrate with low P mobility. The function of the root hairs for anchoring did not result in different depth profiles of the root length density between genotypes. Both maize genotypes showed a marked response to substrate. This was well reflected in the spatiotemporal development of rhizosphere volume fraction but especially in the strong response of root diameter to substrate, irrespective of genotype.The most salient root plasticity trait was root diameter in response to substrate, whereas coping mechanisms for missing root hairs were less evident. Further experiments are required to elucidate whether observed differences can be explained by mechanical properties beyond mechanical impedance, root or microbiome ethylene production or differences in diffusion processes within the root or the rhizosphere.

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