SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments

The outer integument of Arabidopsis ovules exhibits marked polarity in its development, growing extensively from the abaxial side, but only to a very limited extent from the adaxial side of the ovule. Mutations in two genes affect this asymmetric growth. In strong inner no outer (ino) mutants outer integument growth is eliminated, whereas in superman (sup) mutants integument growth on the adaxial side is nearly equal to wild-type growth on the abaxial side. Through complementation and reporter gene analysis, a region of INO 5′-flanking sequences was identified that contains sufficient information for appropriate expression of INO. Using this INO promoter (P-INO) we show that INO acts as a positive regulator of transcription from P-INO, but is not sufficient for de novo initiation of transcription in other plant parts. Protein fusions demonstrate nuclear localization of INO, consistent with a proposed role as a transcription factor for this member of the YABBY protein family. Through its ability to inhibit expression of the endogenous INO gene and transgenes driven by P-INO, SUP is shown to be a negative regulator of INO transcription. Substitution of another YABBY protein coding region (CRABS CLAW) for INO overcomes this negative regulation, indicating that SUP suppresses INO transcription through attenuation of the INO positive autoregulatory loop.

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Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1805437115 ◽

2018 ◽

Vol 115 (34) ◽

pp. E8007-E8016 ◽

Cited By ~ 17

Author(s):

Alexandre Bolze ◽

Bertrand Boisson ◽

Barbara Bosch ◽

Alexander Antipenko ◽

Matthieu Bouaziz ◽

...

Keyword(s):

De Novo ◽

Lymphoid Organ ◽

Untranslated Regions ◽

Incomplete Penetrance ◽

Developmental Defect ◽

Coding Region ◽

Protein Coding ◽

Complete Penetrance ◽

Sporadic Disease ◽

Isolated Congenital Asplenia

Isolated congenital asplenia (ICA) is the only known human developmental defect exclusively affecting a lymphoid organ. In 2013, we showed that private deleterious mutations in the protein-coding region of RPSA, encoding ribosomal protein SA, caused ICA by haploinsufficiency with complete penetrance. We reported seven heterozygous protein-coding mutations in 8 of the 23 kindreds studied, including 6 of the 8 multiplex kindreds. We have since enrolled 33 new kindreds, 5 of which are multiplex. We describe here 11 new heterozygous ICA-causing RPSA protein-coding mutations, and the first two mutations in the 5′-UTR of this gene, which disrupt mRNA splicing. Overall, 40 of the 73 ICA patients (55%) and 23 of the 56 kindreds (41%) carry mutations located in translated or untranslated exons of RPSA. Eleven of the 43 kindreds affected by sporadic disease (26%) carry RPSA mutations, whereas 12 of the 13 multiplex kindreds (92%) carry RPSA mutations. We also report that 6 of 18 (33%) protein-coding mutations and the two (100%) 5′-UTR mutations display incomplete penetrance. Three mutations were identified in two independent kindreds, due to a hotspot or a founder effect. Finally, RPSA ICA-causing mutations were demonstrated to be de novo in 7 of the 23 probands. Mutations in RPSA exons can affect the translated or untranslated regions and can underlie ICA with complete or incomplete penetrance.

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Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons

10.1101/356832 ◽

2018 ◽

Author(s):

Alexandre Bolze ◽

Bertrand Boisson ◽

Barbara Bosch ◽

Alexander Antipenko ◽

Matthieu Bouaziz ◽

...

Keyword(s):

De Novo ◽

Lymphoid Organ ◽

Untranslated Regions ◽

Incomplete Penetrance ◽

Developmental Defect ◽

Coding Region ◽

Protein Coding ◽

Complete Penetrance ◽

Sporadic Disease ◽

Isolated Congenital Asplenia

AbstractIsolated congenital asplenia (ICA) is the only known human developmental defect exclusively affecting a lymphoid organ. In 2013, we showed that private deleterious mutations in the protein-coding region of RPSA, encoding ribosomal protein SA, caused ICA by haploinsufficiency with complete penetrance. We reported seven heterozygous protein-coding mutations in 8 of the 23 kindreds studied, including 6 of the 8 multiplex kindreds. We have since enrolled 33 new kindreds, 5 of which are multiplex. We describe here eleven new heterozygous ICA-causing RPSA protein-coding mutations, and the first two mutations in the 5’-UTR of this gene, which disrupt mRNA splicing. Overall, 40 of the 73 ICA patients (55%) and 23 of the 56 kindreds (41%) carry mutations located in translated or untranslated exons of RPSA. Eleven of the 43 kindreds affected by sporadic disease (26%) carry RPSA mutations, whereas 12 of the 13 multiplex kindreds (92%) carry RPSA mutations. We also report that six of eighteen (33%) protein-coding mutations and the two (100%) 5’-UTR mutations display incomplete penetrance. Three mutations were identified in 2 independent kindreds, due to a hotspot or a founder effect. Lastly, RPSA ICA-causing mutations were demonstrated to be de novo in 7 of the 23 probands. Mutations in RPSA exons can affect the translated or untranslated regions and can underlie ICA with complete or incomplete penetrance.

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A dynamic representation-based, de novo method for protein-coding region prediction and biological information detection

Digital Signal Processing ◽

10.1016/j.dsp.2015.08.007 ◽

2015 ◽

Vol 46 ◽

pp. 10-18 ◽

Cited By ~ 4

Author(s):

Sajid A. Marhon ◽

Stefan C. Kremer

Keyword(s):

De Novo ◽

Biological Information ◽

Coding Region ◽

Protein Coding ◽

Dynamic Representation ◽

Information Detection

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nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽

10.1186/s12864-020-07182-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Surajit Bhattacharya ◽

Hayk Barseghyan ◽

Emmanuèle C. Délot ◽

Eric Vilain

Keyword(s):

De Novo ◽

Genome Mapping ◽

Gene List ◽

Sufficient Information ◽

Rna Seq ◽

Structural Variants ◽

De Novo Genome Assembly ◽

Pathogenic Variants ◽

Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

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The identification, cloning, and sequence analysis of the coat protein coding region of a birch isolate (I2) of cherry leaf roll nepovirus

Archives of Virology ◽

10.1007/bf01379093 ◽

1993 ◽

Vol 131 (1-2) ◽

pp. 209-215 ◽

Cited By ~ 10

Author(s):

N. W. Scott ◽

J. I. Cooper ◽

M. L. Edwards

Keyword(s):

Sequence Analysis ◽

Coat Protein ◽

Leaf Roll ◽

Coding Region ◽

Protein Coding

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Selection on Rapidly Evolving Proteins in the Arabidopsis Genome

Genetics ◽

10.1093/genetics/163.2.723 ◽

2003 ◽

Vol 163 (2) ◽

pp. 723-733 ◽

Cited By ~ 1

Author(s):

Marianne Barrier ◽

Carlos D Bustamante ◽

Jiaye Yu ◽

Michael D Purugganan

Keyword(s):

Expressed Sequence Tag ◽

Amino Acid Replacement ◽

Adaptive Divergence ◽

Coding Region ◽

Protein Coding ◽

Hierarchical Bayesian Analysis ◽

Brassicaceae Species ◽

Replacement Site ◽

Orthologous Loci ◽

Selection Intensities

Abstract Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (ω = Ka/Ks). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of ω among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (∼5%) have an estimated ω > 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci.

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Surface and Internalized Escherichia coli O157:H7 on Field-Grown Spinach and Lettuce Treated with Spray-Contaminated Irrigation Water

Journal of Food Protection ◽

10.4315/0362-028x-73.6.1023 ◽

2010 ◽

Vol 73 (6) ◽

pp. 1023-1029 ◽

Cited By ~ 122

Author(s):

MARILYN C. ERICKSON ◽

CATHY C. WEBB ◽

JUAN CARLOS DIAZ-PEREZ ◽

SHARAD C. PHATAK ◽

JOHN J. SILVOY ◽

...

Keyword(s):

Escherichia Coli ◽

Irrigation Water ◽

Enrichment Culture ◽

Field Studies ◽

Plate Count ◽

Escherichia Coli O157 ◽

Adaxial Side ◽

Abaxial Side ◽

E Coli ◽

Contaminated Irrigation Water

Numerous field studies have revealed that irrigation water can contaminate the surface of plants; however, the occurrence of pathogen internalization is unclear. This study was conducted to determine the sites of Escherichia coli O157:H7 contamination and its survival when the bacteria were applied through spray irrigation water to either field-grown spinach or lettuce. To differentiate internalized and surface populations, leaves were treated with a surface disinfectant wash before the tissue was ground for analysis of E. coli O157:H7 by direct plate count or enrichment culture. Irrigation water containing E. coli O157:H7 at 102, 104, or 106 CFU/ml was applied to spinach 48 and 69 days after transplantation of seedlings into fields. E. coli O157:H7 was initially detected after application on the surface of plants dosed at 104 CFU/ml (4 of 20 samples) and both on the surface (17 of 20 samples) and internally (5 of 20 samples) of plants dosed at 106 CFU/ml. Seven days postspraying, all spinach leaves tested negative for surface or internal contamination. In a subsequent study, irrigation water containing E. coli O157:H7 at 108 CFU/ml was sprayed onto either the abaxial (lower) or adaxial (upper) side of leaves of field-grown lettuce under sunny or shaded conditions. E. coli O157:H7 was detectable on the leaf surface 27 days postspraying, but survival was higher on leaves sprayed on the abaxial side than on leaves sprayed on the adaxial side. Internalization of E. coli O157:H7 into lettuce leaves also occurred with greater persistence in leaves sprayed on the abaxial side (up to 14 days) than in leaves sprayed on the adaxial side (2 days).

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Insights into the Genome Sequence ofChromobacterium amazonenseIsolated from a Tropical Freshwater Lake

International Journal of Genomics ◽

10.1155/2018/1062716 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

Alexandre Bueno Santos ◽

Patrícia Silva Costa ◽

Anderson Oliveira do Carmo ◽

Gabriel da Rocha Fernandes ◽

Larissa Lopes Silva Scholte ◽

...

Keyword(s):

De Novo ◽

Genomic Diversity ◽

Protein Coding ◽

Biotechnological Potential ◽

Draft Assembly ◽

Functional Studies ◽

Alpha Hemolysin ◽

Type Iv ◽

Nudix Hydrolases ◽

Colicin V

Members of the genusChromobacteriumhave been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis ofChromobacterium amazonensestrain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike otherChromobacteriumspecies, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of theC. amazonensestrain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involvingChromobacterium-related isolates and improves our understanding of the global genomic diversity ofChromobacteriumspecies.

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Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication

Journal of General Virology ◽

10.1099/vir.0.052126-0 ◽

2013 ◽

Vol 94 (7) ◽

pp. 1486-1495 ◽

Cited By ~ 17

Author(s):

Graham J. Belsham

Keyword(s):

Disease Virus ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

Initiation Codon ◽

Coding Region ◽

Protein Coding ◽

Coding Sequence ◽

Bhk Cells ◽

Leader Protein ◽

Mouth Disease Virus

The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the ‘spacer’ region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence resulted in a previously undetected accumulation of frameshift mutations within the ‘spacer’ region. These mutations block the inappropriate fusion of amino acid sequences to the amino-terminus of the capsid protein precursor. Modification, by site-directed mutagenesis, of the Lab initiation codon, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production.

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