scholarly journals Reinvestigation of grain weight genes TaTGW6 and OsTGW6 casts doubt on their role in auxin regulation in developing grains

2020 ◽  
Author(s):  
Muhammed Rezwan Kabir ◽  
Heather M. Nonhebel
Keyword(s):  
Amino Acid Identity ◽  
Major Effect ◽  
Grain Weight ◽  
Specific Gene ◽  
Large Gene ◽  
Auxin Regulation ◽  
Genes Encoding ◽  
Hydrolysis Of ◽  
Developing Grains ◽  
Maximal Expression

AbstractThe THOUSAND-GRAIN WEIGHT 6 genes (TaTGW6 and OsTGW6) are reported to result in larger grains of wheat and rice by reducing production of indole-3-acetic acid (IAA) in developing grains. However, a critical comparison of data on TaTGW6 and OsTGW6 with other reports on IAA synthesis in cereal grains requires that this hypothesis be reinvestigated. Here, we show that TaTGW6 and OsTGW6 are members of a large gene family that has undergone major, lineage-specific gene expansion. Wheat has nine genes, and rice three genes encoding proteins with more than 80% amino acid identity with TGW6 making it difficult to envisage how a single inactive allele could have a major effect on IAA levels. TGW6 is proposed to affect auxin levels by catalysing the hydrolysis of IAA-glucose (IAA-Glc). However, we show that developing wheat grains contain undetectable levels of ester IAA in comparison to free IAA and do not express an IAA-glucose synthase. Previous work on TGW6, reported maximal expression at 20 days after anthesis (DAA) in wheat and 2 DAA in rice. However, we show that neither gene is expressed in developing grains. Instead, TaTGW6, OsTGW6 and their close homologues are exclusively expressed in pre-emergence inflorescences; TaTGW6 is expressed particularly in microspores prior to mitosis. This combined with evidence for high levels of IAA production from tryptophan in developing grains demonstrates TaTGW6 and OsTGW6 cannot regulate grain size via the hydrolysis of IAA-Glc. Instead, their similarity to rice strictosidine synthase-like (OsSTRL2) suggests they play a key role in pollen development.

scholarly journals ARID2 Chromatin Remodeler in Hepatocellular Carcinoma

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2152
Author(s):  
Robin Loesch ◽  
Linda Chenane ◽  
Sabine Colnot
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Associated Factors ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Chromatin Remodeler ◽  
Chromatin Remodelers ◽  
Genes Encoding ◽  
Gene Alterations

Chromatin remodelers are found highly mutated in cancer including hepatocellular carcinoma. These mutations frequently occur in ARID (AT-rich Interactive Domain) genes, encoding subunits of the ATP-dependent SWI/SNF remodelers. The increasingly prevalent complexity that surrounds the functions and specificities of the highly modular BAF (BG1/BRM-associated factors) and PBAF (polybromo-associated BAF) complexes, including ARID1A/B or ARID2, is baffling. The involvement of the SWI/SNF complexes in diverse tissues and processes, and especially in the regulation of gene expression, multiplies the specific outcomes of specific gene alterations. A better understanding of the molecular consequences of specific mutations impairing chromatin remodelers is needed. In this review, we summarize what we know about the tumor-modulating properties of ARID2 in hepatocellular carcinoma.

Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster

1986 ◽  
Vol 6 (4) ◽  
pp. 1023-1031
Author(s):  
R Terracol ◽  
N Prud'homme
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Copy Number ◽  
Rdna Locus ◽  
Gene Copy ◽  
Specific Gene ◽  
Type I ◽  
28S Rrna ◽  
Wild Type ◽  
Y Chromosomes ◽  
Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

scholarly journals Cantu syndrome-associated SUR2 (ABCC9) mutations in distinct structural domains result in KATP channel gain-of-function by differential mechanisms

2017 ◽  
Author(s):  
Conor McClenaghan ◽  
Alex Hanson ◽  
Monica Sala-Rabanal ◽  
Helen I. Roessler ◽  
Dragana Josifova ◽  
...  
Keyword(s):  
Katp Channel ◽  
Molecular Mechanisms ◽  
Cardiovascular Disorder ◽  
Major Effect ◽  
Channel Activity ◽  
Gain Of Function ◽  
Structural Domains ◽  
Equivalent Position ◽  
Genes Encoding ◽  
Patch Clamp Electrophysiology

AbstractThe complex cardiovascular disorder Cantu Syndrome arises from gain-of-function mutations in either KCNJ8 or ABCC9, the genes encoding the Kir6.1 and SUR2 subunits of ATP-sensitive potassium (KATP) channels. Recent reports indicate that such mutations can increase channel activity by multiple molecular mechanisms. In this study, we determine the mechanism by which KATP function is altered by several mutations in distinct structural domains of SUR2: D207E in the intracellular L0-linker and Y985S, G989E, M1060I, and R1154Q/W in TMD2. Mutations were engineered at their equivalent position in rat SUR2A (D207E, Y981S, G985E, M1056I and R1150Q/W) and functional effects were investigated using macroscopic rubidium (86Rb+) efflux assays and patch clamp electrophysiology. The results show that D207E increases KATP activity by increasing intrinsic stability of the open state, whilst the cluster of Y981S/G985E/M1056I mutations, as well as R1150Q/W, augment Mg-nucleotide activation. The response of mutant channels to inhibition by the sulfonylurea drug glibenclamide, a potential pharmacotherapy for CS, was also tested. There was no major effect on glibenclamide sensitivity for the D207E, Y981S, G985E or M1056I mutations, but glutamine and tryptophan substitution at R1150 resulted in significant decreases in potency.

scholarly journals A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Carolina Ballén-Taborda ◽  
Ye Chu ◽  
Peggy Ozias-Akins ◽  
Patricia Timper ◽  
C. Corley Holbrook ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Array ◽  
Nematode Resistance ◽  
Major Effect ◽  
Root Knot Nematode ◽  
Breeding Programs ◽  
Genes Encoding ◽  
In The Wild ◽  
Arachis Batizocoi ◽  
Lrr Protein

AbstractRoot-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma, [Arachis batizocoi x A. stenosperma]4×. This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma, is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.

Detection of esterase activity in susceptible and organophosphate resistant strains of the cattle tick Boophilus microplus (Acari: Ixodidae)

1997 ◽  
Vol 87 (2) ◽  
pp. 197-202 ◽  
Author(s):  
R. Rosario-Cruz ◽  
E. Miranda-Miranda ◽  
Z. Garcia-Vasquez ◽  
M. Ortiz-Estrada
Keyword(s):  
Esterase Activity ◽  
Boophilus Microplus ◽  
Cattle Tick ◽  
Molecular Weights ◽  
Sds Page ◽  
Genes Encoding ◽  
Resistant Strains ◽  
Hydrolysis Of ◽  
Coomassie Brilliant ◽  
Naphthyl Acetate

AbstractTwo organophosphate (OP) resistant strains of the cattle tick Boophilus microplus (Canestrini) from Mexico and Costa Rica were used to analyse the presence of esterase activity associated with resistance. The concentrations of six major proteins in both resistant strains were increased compared to the susceptible Morelos strain, both when stained with Coomassie Brilliant Blue after SDS-PAGE, and when analysed for esterase activity by the hydrolysis of naphthyl acetate esters. Esterases were named A or B in relation to the substrate preference for alpha or beta naphthyl acetate and numbered according to their position on the SDS—PAGE. The molecular weights of these proteins were: 125, 115, 108, 77, 43 and 67 Kd for Est-Bl, Est-B2, Est-B3, Est-B4, Est-B5 and Est-A respectively. Est-B3 showed cholinesterase (ChE) activity. This study strengthens the hypothesis that the mechanism associated with OP resistance found in many other insects includes an increase of esterase activity, probably as a result of gene amplification. The genes encoding these enzymes could be potentially used as molecular markers to detect resistance in the cattle tick B. microplus using a DNA probe.

scholarly journals A homologue of AMP-activated protein kinase in Drosophila melanogaster is sensitive to AMP and is activated by ATP depletion

2002 ◽  
Vol 367 (1) ◽  
pp. 179-186 ◽  
Author(s):  
David A. PAN ◽  
D. Grahame HARDIE
Keyword(s):  
Drosophila Melanogaster ◽  
Protein Kinase ◽  
Atp Depletion ◽  
Specific Gene ◽  
Specific Substrate ◽  
Intact Cells ◽  
Drosophila Cell ◽  
Α Subunit ◽  
Genes Encoding ◽  
Amp Activated Protein Kinase

We have identified single genes encoding homologues of the α, β and γ subunits of mammalian AMP-activated protein kinase (AMPK) in the genome of Drosophila melanogaster. Kinase activity could be detected in extracts of a Drosophila cell line using the SAMS peptide, which is a relatively specific substrate for the AMPK/SNF1 kinases in mammals and yeast. Expression of double stranded (ds) RNAs targeted at any of the putative α, β or γ subunits ablated this activity, and abolished expression of the α subunit. The Drosophila kinase (DmAMPK) was activated by AMP in cell-free assays (albeit to a smaller extent than mammalian AMPK), and by stresses that deplete ATP (oligomycin and hypoxia), as well as by carbohydrate deprivation, in intact cells. Using a phosphospecific antibody, we showed that activation was associated with phosphorylation of a threonine residue (Thr-184) within the ‘activation loop’ of the α subunit. We also identified a homologue of acetyl-CoA carboxylase (DmACC) in Drosophila and, using a phosphospecific antibody, showed that the site corresponding to the regulatory AMPK site on the mammalian enzyme became phosphorylated in response to oligomycin or hypoxia. By immunofluorescence microscopy of oligomycin-treated Dmel2 cells using the phosphospecific antibody, the phosphorylated DmAMPK α subunit was mainly detected in the nucleus. Our results show that the AMPK system is highly conserved between insects and mammals. Drosophila cells now represent an attractive system to study this pathway, because of the small, well-defined genome and the ability to ablate expression of specific gene products using interfering dsRNAs.

scholarly journals A switch toward demethylation is associated with the expression of myeloperoxidase in acute myeloblastic and promyelocytic leukemias

Blood ◽  
1992 ◽  
Vol 80 (8) ◽  
pp. 2066-2073 ◽  
Author(s):  
M Lubbert ◽  
W Oster ◽  
WD Ludwig ◽  
A Ganser ◽  
R Mertelsmann ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Myeloid Cell ◽  
Leukemic Cells ◽  
Myeloid Differentiation ◽  
Specific Gene ◽  
Methylation Analysis ◽  
Myeloid Leukemias ◽  
Different Types ◽  
Genes Encoding ◽  
Specific Proteins

Abstract Expression of numerous genes encoding myeloid-specific proteins is tightly regulated during normal myeloid differentiation. This heterogeneous group of genes thus offers a tool for dissection of different maturational steps of myelopoiesis. We have previously shown that the human myeloperoxidase (MPO) gene is modified at numerous CpG residues in normal myeloid cells and in myeloid cell lines in a development-specific and expression-associated manner. In the present work, we have applied this type of methylation analysis to primary leukemia myeloid cell samples. We found that expression of MPO messenger RNA (mRNA) is grossly limited to leukemias of late myeloblastic and promyelocytic stages; expression is thus associated with progressive demethylation in the 5′ region of the MPO gene. This modification was not global. Low-level induction of MPO mRNA expression in very immature leukemic cells using phorbol ester was not accompanied by progressive demethylation. This type of methylation analysis of a myeloid-specific gene may yield a molecular indicator for different types of myeloid leukemias.

scholarly journals NDT80 and the Meiotic Recombination Checkpoint Regulate Expression of Middle Sporulation-Specific Genes in Saccharomyces cerevisiae

1998 ◽  
Vol 18 (10) ◽  
pp. 5750-5761 ◽  
Author(s):  
Shelley R. Hepworth ◽  
Helena Friesen ◽  
Jacqueline Segall
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Meiotic Recombination ◽  
Active Form ◽  
Specific Gene ◽  
Subsequent Generation ◽  
Genes Encoding ◽  
Recombination Checkpoint ◽  
Sporulation Genes ◽  
Meiosis I

ABSTRACT Distinct classes of sporulation-specific genes are sequentially expressed during the process of spore formation in Saccharomyces cerevisiae. The transition from expression of early meiotic genes to expression of middle sporulation-specific genes occurs at about the time that cells exit from pachytene and form the meiosis I spindle. To identify genes encoding potential regulators of middle sporulation-specific gene expression, we screened for mutants that expressed early meiotic genes but failed to express middle sporulation-specific genes. We identified mutant alleles ofRPD3, SIN3, and NDT80 in this screen. Rpd3p, a histone deacetylase, and Sin3p are global modulators of gene expression. Ndt80p promotes entry into the meiotic divisions. We found that entry into the meiotic divisions was not required for activation of middle sporulation genes; these genes were efficiently expressed in a clb1 clb3 clb4 strain, which fails to enter the meiotic divisions due to reduced Clb-dependent activation of Cdc28p kinase. In contrast, middle sporulation genes were not expressed in a dmc1 strain, which fails to enter the meiotic divisions because a defect in meiotic recombination leads to aRAD17-dependent checkpoint arrest. Expression of middle sporulation genes, as well as entry into the meiotic divisions, was restored to a dmc1 strain by mutation of RAD17. Our studies also revealed that NDT80 was a temporally distinct, pre-middle sporulation gene and that its expression was reduced, but not abolished, on mutation of DMC1,RPD3, SIN3, or NDT80 itself. In summary, our data indicate that Ndt80p is required for expression of middle sporulation genes and that the activity of Ndt80p is controlled by the meiotic recombination checkpoint. Thus, middle genes are expressed only on completion of meiotic recombination and subsequent generation of an active form of Ndt80p.

scholarly journals Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster.

1986 ◽  
Vol 6 (4) ◽  
pp. 1023-1031 ◽  
Author(s):  
R Terracol ◽  
N Prud'homme
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Copy Number ◽  
Rdna Locus ◽  
Gene Copy ◽  
Specific Gene ◽  
Type I ◽  
28S Rrna ◽  
Wild Type ◽  
Y Chromosomes ◽  
Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

Sign in / Sign up

Export Citation Format

Share Document