scholarly journals A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing

2020 ◽  
Vol 21 (6) ◽  
pp. 2018 ◽  
Author(s):  
Ting Zou ◽  
Dan Zhou ◽  
Wenjie Li ◽  
Guoqiang Yuan ◽  
Yang Tao ◽  
...  
Keyword(s):  
Pollen Development ◽  
Molecular Mapping ◽  
Higher Plants ◽  
Donor Site ◽  
Splice Junction ◽  
Splice Donor Site ◽  
Terrestrial Plants ◽  
Male Sterile ◽  
Intron Splice ◽  
Rice Mutant

Pollen development plays crucial roles in the life cycle of higher plants. Here we characterized a rice mutant with complete male-sterile phenotype, pollen-less 1 (pl1). pl1 exhibited smaller anthers with arrested pollen development, absent Ubisch bodies, necrosis-like tapetal hypertrophy, and smooth anther cuticular surface. Molecular mapping revealed a synonymous mutation in the fourth exon of PL1 co-segregated with the mutant phenotype. This mutation disrupts the exon-intron splice junction in PL1, generating aberrant mRNA species and truncated proteins. PL1 is highly expressed in the tapetal cells of developing anther, and its protein is co-localized with plasma membrane (PM) and endoplasmic reticulum (ER) signal. PL1 encodes an integrin-α FG-GAP repeat-containing protein, which has seven β-sheets and putative Ca2+-binding motifs and is broadly conserved in terrestrial plants. Our findings therefore provide insights into both the role of integrin-α FG-GAP repeat-containing protein in rice male fertility and the influence of exonic mutation on intronic splice donor site selection.

Phenotypic characterization, genetic analysis, and molecular mapping of a new mutant gene for male sterility in rice

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 303-308 ◽  
Author(s):  
Ling Zuo ◽  
Shuangcheng Li ◽  
Mingguang Chu ◽  
Shiquan Wang ◽  
Qiming Deng ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Molecular Mapping ◽  
Spontaneous Mutation ◽  
Recessive Gene ◽  
Pollen Grains ◽  
Mutant Gene ◽  
Phenotypic Characterization ◽  
Chromosome 4 ◽  
Male Sterile ◽  
Rice Mutant

xs1 is a male-sterile rice mutant derived from a spontaneous mutation. The floret of the mutant, consisting of 6 stamens and 1 pistil, looks the same as that of the wild type except that the filaments are long and thin and the anthers are withered in white transparence. It is confirmed that xs1 is a no-pollen type of male-sterile mutant, for no pollen grains can be stained with I2–KI solution and the anther locules are always hollow. Anther transverse sections indicate that the mutant microspores are abnormally condensed and agglomerated to form a deeply stained cluster at the late microspore stage, which results in cessation of the vacuolation process of microspores, and, therefore, the mutant forms no functional pollens for reproduction. Genetic analysis of 4 F2 populations and 3 BC1F1 populations revealed that the mutation is controlled by a single recessive gene, termed VR1 (Vacuolation retardation 1). Screening of 432 F2 mutant individuals derived from the cross of xs1 × G603 with simple sequence repeat markers revealed that VR1 is located between the molecular markers RM17411 and RM5030, at distances of 0.7 and 1.5 cM, respectively, on chromosome 4. VR1 is a new male fertility controlling gene located on chromosome 4 in rice.

Genetic Analysis and Molecular Mapping of a Male Sterile Mutant in Rice

2009 ◽  
Vol 35 (6) ◽  
pp. 1151-1155
Author(s):  
Ming-Guang CHU ◽  
Shuang-Cheng LI ◽  
Shi-Quan WANG ◽  
Qi-Ming DENG ◽  
Jing ZHANG ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Molecular Mapping ◽  
Male Sterile ◽  
Sterile Mutant

Bioprospecting Cryptogams as Potential Source of Unique Biodynamic Phytochemicals with Diverse Pharmaceutical Applications

2016 ◽  
Vol 1 (1) ◽  
Author(s):  
Brahma N. Singh ◽  
Garima Pandey ◽  
Prateeksha ◽  
J. Kumar
Keyword(s):  
Secondary Metabolites ◽  
Higher Plants ◽  
New Drugs ◽  
Terrestrial Plants ◽  
Pharmacological Activities ◽  
Therapeutic Drugs ◽  
Potential Source ◽  
Therapeutic Value ◽  
Wide Range ◽  
Novel Structures

With the advent of green pharmaceuticals, the secondary metabolites derived from plants have provided numerous leads for the development of a wide range of therapeutic drugs; however the discovery of new drugs with novel structures has declined in the past few years. Cryptogams including lichens, bryophytes, and pteridophytes represent a group of small terrestrial plants that remain relatively untouched in the drug discovery process though some have been used as ethnomedicines by various tribes worldwide. Studies of their secondary metabolites are recent but reveal unique secondary metabolites which are not synthesized by higher plants. These compounds can have the potential to develop more potential herbal drugs for prevention and treatment of diseases The present article . deals with the secondary metabolites and pharmacological activities of cryptogams with an objective to bring them forth as potential source of biodynamic compounds of therapeutic value.

scholarly journals Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
William L. Macken ◽  
Annie Godwin ◽  
Gabrielle Wheway ◽  
Karen Stals ◽  
Liliya Nazlamova ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Donor Site ◽  
Xenopus Tropicalis ◽  
Splice Donor Site ◽  
Homologous Region ◽  
Disease Genes ◽  
Coat Proteins ◽  
Splice Donor ◽  
Severe Intellectual Disability

Abstract Background Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as “coatopathies”. Methods Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1’s splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2’s missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2’s mutation. Results We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β’-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. Conclusions This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.

scholarly journals A 5′ splice site mutation affecting the pre-mRNA splicing of two upstream exons in the collagen COL1A1 gene. Exon 8 skipping and altered definition of exon 7 generates truncated proα1(I) chains with a non-collagenous insertion destabilizing the triple helix

1994 ◽  
Vol 302 (3) ◽  
pp. 729-735 ◽  
Author(s):  
J F Bateman ◽  
D Chan ◽  
I Moeller ◽  
M Hannagan ◽  
W G Cole
Keyword(s):  
Splice Site ◽  
De Novo ◽  
Donor Site ◽  
Mrna Splicing ◽  
Splice Donor Site ◽  
Sequence Motif ◽  
Type I ◽  
Splice Donor ◽  
Site Mutation ◽  
Definition Of

A heterozygous de novo G to A point mutation in intron 8 at the +5 position of the splice donor site of the gene for the pro alpha 1(I) chain of type I procollagen, COL1A1, was defined in a patient with type IV osteogenesis imperfecta. The splice donor site mutation resulted not only in the skipping of the upstream exon 8 but also unexpectedly had the secondary effect of activating a cryptic splice site in the next upstream intron, intron 7, leading to re-definition of the 3′ limit of exon 7. These pre-mRNA splicing aberrations cause the deletion of exon 8 sequences from the mature mRNA and the inclusion of 96 bp of intron 7 sequence. Since the mis-splicing of the mutant allele product resulted in the maintenance of the correct codon reading frame, the resultant pro alpha 1(I) chain contained a short non-collagenous 32-amino-acid sequence insertion within the repetitive Gly-Xaa-Yaa collagen sequence motif. At the protein level, the mutant alpha 1(I) chain was revealed by digestion with pepsin, which cleaved the mutant procollagen within the protease-sensitive non-collagenous insertion, producing a truncated alpha 1(I). This protease sensitivity demonstrated the structural distortion to the helical structure caused by the insertion. In long-term culture with ascorbic acid, which stimulates the formation of a mature crosslinked collagen matrix, and in tissues, there was no evidence of the mutant chain, suggesting that during matrix formation the mutant chain was unable to stably incorporated into the matrix and was degraded proteolytically.

scholarly journals A Novel Splice Donor Site in thegag-polGene Is Required for HIV-1 RNA Stability

2006 ◽  
Vol 281 (27) ◽  
pp. 18644-18651 ◽  
Author(s):  
Martin Lützelberger ◽  
Line S. Reinert ◽  
Atze T. Das ◽  
Ben Berkhout ◽  
Jørgen Kjems
Keyword(s):  
Donor Site ◽  
Rna Stability ◽  
Splice Donor Site ◽  
Splice Donor ◽  
Hiv 1

MO039IDENTIFICATION OF A RECURRENT SYNONYMOUS GENETIC VARIANT IN NPHP3 LEADING TO NEPHRONOPHTHISIS AND CONGENITAL HEPATIC FIBROSIS

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Eric Olinger ◽  
Intisar Al Alawi ◽  
Elisa Molinari ◽  
Eissa Ali Faqeih ◽  
Mohamed Al Hamed ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Splicing ◽  
Donor Site ◽  
Saudi Arabian ◽  
Bioinformatic Analysis ◽  
Initial Assessment ◽  
Splice Donor Site ◽  
Uk Biobank ◽  
Pathogenic Variants ◽  
Exon 20

Abstract Background and Aims Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice and has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. Filtering of variants and scoring variants in terms of pathogenicity still represents a major challenge and may explain why ∼50% of patients remain without diagnosis after initial assessment. Method In this study, we performed WES to determine the genetic cause of a hepato-renal ciliopathy syndrome in a genetically unsolved consanguineous family from Oman with 2 affected children. For variants filtering and annotation Qiagen Clinical Insight tool was used. Database searches for identical alleles in patients with similar phenotypes were performed using Genomics England, UK Biobank and a Saudi Arabian cohort. RNA studies were used to confirm a splicing defect. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project and from UK Biobank, a major biomedical database. Results Initial bioinformatic analysis of WES data from 2 affected sibs excluded obvious pathogenic variants in known genes associated with primary ciliopathy syndromes with liver and kidney phenotypes. However, by manual curation of variants in candidate genes, a rare homozygous synonymous allele in NPHP3 was identified (c.2805C>T; p.(Gly935Gly)), mid-exon 20 and within a region of shared homozygosity on chromosome 3. Correct segregation was confirmed via Sanger sequencing in the parents and the 2 affected sibs. The variant was rare in gnomAD (2/251374 alleles) and was found heterozygously in just one individual within the UK Biobank cohort of 200,000 exomes. Using various in silico tools, the allele was shown to activate a cryptic splice donor site in the middle of exon 20. RT-PCR with sequencing of parental whole blood RNA confirmed alternative splicing leading to frameshift p.Gly935GlyfsTer47. The identical homozygous allele was identified in 2 additional unsolved families within the Genomics England 100,000 Genomes Project and in 1 Saudi Arabian family with similar hepato-renal phenotypes. Conclusion This study shows that automated filtering of WES data may exclude synonymous variants which are pathogenic, especially if they are mid-exon. Here we identified a recurrent synonymous NPHP3 variant leading to a splice defect as the cause of a hepato-renal ciliopathy phenotype in four families. In unsolved cases, rare synonymous alleles in candidate genes need to be reassessed for impact on RNA splicing and possible pathogenicity.

Genetic Diversity Analysis of Salvadora Oleoides Decne: An Evergreen Dry Land Fruit Tree of Rajasthan, India

2021 ◽  
Author(s):  
Juleri M Upendra ◽  
Shari Nair ◽  
Satyawada R Rao ◽  
Harchand R Dagla
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Splice Junction ◽  
Genetic Distances ◽  
Climatic Conditions ◽  
Fruit Tree ◽  
Group Method ◽  
Dry Land ◽  
Intron Splice ◽  
Semi Arid

Abstract Genetic diversity of Salvadora oleoides Decne is analyzed by cumulative data of 10 Random Amplified Polymorphic DNA (RAPD), 10 Inter Simple Sequence Repeats (ISSR) and 7 Intron Splice Junction (ISJ) markers. The plant is an evergreen fruit tree and well distributed in semi-arid and sub-humid climatic conditions of Rajasthan, India. RAPD, ISSR and ISJ primers accounted for 84.4%, 85.3%, 85.9% polymorphism. Average 0.23 PIC is accounted for RAPD, ISSR and ISJ primers. The genetic similarity ranged between 0.42-0.89. Analysis of molecular variance (AMOVA) revealed higher variation (73%) at intra-population than inter-population (27%) level. Genetic distances based on Un-weighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) is correlated with physical distances or climatic conditions of Salvadora oleoides Decne in a semi-arid and sub-humid environment of Rajasthan. The present investigation may help in the understanding of gene flow systems between physical distances and environmental heterogeneity of the populations for better management of Salvadora oleoides Decne in the region.

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