Alternative Start Codon Connects eIF5A to Mitochondria

2016 ◽  
Vol 231 (12) ◽  
pp. 2682-2689 ◽  
Author(s):  
Karina Danielle Pereira ◽  
Letícia Tamborlin ◽  
Letícia Meneguello ◽  
André Ricardo Gomes de Proença ◽  
Isadora Cristina de Paula Andrade Almeida ◽  
...  
Keyword(s):  
Start Codon ◽  
Alternative Start Codon

scholarly journals L-DOPA dioxygenase of the fly agaric toadstool: revision of the dodA gene sequence and mechanism of enzymatic pigment production

2020 ◽  
Author(s):  
Douglas M. M. Soares ◽  
Letícia C. P. Gonçalves ◽  
Caroline O. Machado ◽  
Larissa Cerrato Esteves ◽  
Cassius V. Stevani ◽  
...  
Keyword(s):  
Environmental Remediation ◽  
Kinetic Modelling ◽  
Enzymatic Catalysis ◽  
Heme Iron ◽  
Start Codon ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Biotechnological Production ◽  
Pigment Formation ◽  
Alternative Start Codon

ABSTRACTl-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurins pigments. The sequence of the DODAs found in Caryophyllales and Basidiomycetes are not conserved, although betalains are produced both by plants and fungi. Here we revise the coding region of the dodA gene of fly agaric [Amanita muscaria (L.) Lam.] and describe an alternative start codon downstream that enables the heterologous expression of AmDODA, a promiscuous l-DOPA dioxygenase. AmDODA is 43-amino acid residues shorter than the recombinant DODA previously reported but catalyzes the formation of two isomeric seco-DOPAs that are the biosynthetic precursors of betalains and hygroaurins. The putative active site of AmDODA contains two distinct His-His-Glu motifs that can explain the dual cleavage of l-DOPA according to the mechanism proposed for non-heme iron-dependent dioxygenases. Upon addition of excess l-DOPA, both the betaxanthin and hygroaurin adducts of l-DOPA are produced. The kinetic parameters of enzymatic catalysis at pH 8.5 are similar to those reported for other l-DOPA dioxygenases. The rate constants for the conversion of l-DOPA into the betalamic acid and muscaflavin were estimated by kinetic modelling allowing the proposal of a mechanism of pigment formation. These results contribute to understanding the biosynthesis of bacterial, fungal and plant pigments, for the biotechnological production of hygroaurins, and for the development of more promiscuous dioxygenases for environmental remediation.

scholarly journals The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256373
Author(s):  
Raquel Santos da Silva ◽  
Charles Roland Clement ◽  
Eduardo Balsanelli ◽  
Valter Antonio de Baura ◽  
Emanuel Maltempi de Souza ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Start Codon ◽  
Length Variation ◽  
Evolutionary Analysis ◽  
Bactris Gasipaes ◽  
Hypervariable Regions ◽  
Plastid Genomes ◽  
Alternative Start Codon ◽  
The Family ◽  
Generic Relationships

The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.

Translational control of oskar generates short OSK, the isoform that induces pole plasma assembly

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3723-3732 ◽  
Author(s):  
F.H. Markussen ◽  
A.M. Michon ◽  
W. Breitwieser ◽  
A. Ephrussi
Keyword(s):  
Positive Feedback ◽  
Translational Control ◽  
Feedback Mechanism ◽  
Posterior Pole ◽  
Start Codon ◽  
Anterior Pole ◽  
Wild Type ◽  
Alternative Start Codon ◽  
Positive Feedback Mechanism ◽  
Pole Plasm

At the posterior pole of the Drosophila oocyte, oskar induces a tightly localized assembly of pole plasm. This spatial restriction of oskar activity has been thought to be achieved by the localization of oskar mRNA, since mislocalization of the RNA to the anterior induces anterior pole plasm. However, ectopic pole plasm does not form in mutant ovaries where oskar mRNA is not localized, suggesting that the unlocalized mRNA is inactive. As a first step towards understanding how oskar activity is restricted to the posterior pole, we analyzed oskar translation in wild type and mutants. We show that the targeting of oskar activity to the posterior pole involves two steps of spatial restriction, cytoskeleton-dependent localization of the mRNA and localization-dependent translation. Furthermore, our experiments demonstrate that two isoforms of Oskar protein are produced by alternative start codon usage. The short isoform, which is translated from the second in-frame AUG of the mRNA, has full oskar activity. Finally, we show that when oskar RNA is localized, accumulation of Oskar protein requires the functions of vasa and tudor, as well as oskar itself, suggesting a positive feedback mechanism in the induction of pole plasm by oskar.

scholarly journals Expression of the aac(6′)-Ib-cr Gene in Class 1 Integrons

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Sophie Raherison ◽  
Thomas Jove ◽  
Margaux Gaschet ◽  
Emilie Pinault ◽  
Aurore Tabesse ◽  
...  
Keyword(s):  
Amino Acids ◽  
Resistance Gene ◽  
Gene Cassette ◽  
Quinolone Resistance ◽  
Start Codon ◽  
Class 1 Integrons ◽  
Alternative Start Codon ◽  
Class 1

ABSTRACT aac(6′)-Ib-cr is a plasmid-mediated quinolone resistance gene embedded within a gene cassette, most often within an integron. It confers resistance to quinolones and aminoglycosides. We investigated the role of a 101-bp fragment frequently present upstream of the aac(6′)-Ib-cr gene cassette and found that it contributes to the expression of aac(6′)-Ib-cr and provides an alternative start codon, confirming the length of the AAC(6′)-Ib-cr protein to 199 amino acids.

scholarly journals Theeyeless mouse mutation(ey1) removes an alternative start codon from theRx/rax homeobox gene

genesis ◽  
2001 ◽  
Vol 31 (1) ◽  
pp. 43-53 ◽  
Author(s):  
Priscilla Tucker ◽  
Lois Laemle ◽  
Amanda Munson ◽  
Shami Kanekar ◽  
Edward R. Oliver ◽  
...  
Keyword(s):  
Homeobox Gene ◽  
Start Codon ◽  
Mouse Mutation ◽  
Alternative Start Codon

scholarly journals Alternative start codon is associated to production of human non‐hypusinated EIF5A1 isoform A

2015 ◽  
Vol 29 (S1) ◽  
Author(s):  
Karina Pereira ◽  
Letícia Tamborlin ◽  
Isadora Almeida ◽  
Letícia Meneguello ◽  
Rogério Lourenço ◽  
...  
Keyword(s):  
Start Codon ◽  
Alternative Start Codon

scholarly journals Targeted misexpression of NAC052, acting in H3K4 demethylation, alters leaf morphological and anatomical traits in Arabidopsis thaliana

2019 ◽  
Vol 71 (4) ◽  
pp. 1434-1448
Author(s):  
Roxanne van Rooijen ◽  
Stefanie Schulze ◽  
Patrick Petzsch ◽  
Peter Westhoff
Keyword(s):  
Arabidopsis Thaliana ◽  
Leaf Development ◽  
Bundle Sheath ◽  
Start Codon ◽  
Coding Region ◽  
C4 Species ◽  
Alternative Start Codon ◽  
Chlorotic Leaf ◽  
Flaveria Trinervia ◽  
Genetic Regulator

Abstract In an effort to identify genetic regulators for the cell ontogeny around the veins in Arabidopsis thaliana leaves, an activation-tagged mutant line with altered leaf morphology and altered bundle sheath anatomy was characterized. This mutant had a small rosette area with wrinkled leaves and chlorotic leaf edges, as well as enhanced chloroplast numbers in the (pre-)bundle sheath tissue. It had a bundle-specific promoter from the gene GLYCINE DECARBOXYLASE SUBUNIT-T from the C4 species Flaveria trinervia (GLDTFt promoter) inserted in the coding region of the transcriptional repressor NAC052, functioning in H3K4 demethylation, in front of an alternative start codon in-frame with the natural start codon. Reconstruction of the mutation event of our activation-tagged line by creating a line expressing an N-terminally truncated sequence of NAC052 under control of the GLDTFt promoter confirmed the involvement of NAC052 in leaf development. Our study not only reveals leaf anatomic and transcriptomic effects of an N-terminally truncated NAC052 under control of the GLDTFt promoter, but also identifies NAC052 as a novel genetic regulator of leaf development.

A new start-codon in IFITM5 causes osteogenesis imperfecta type V

2013 ◽  
Author(s):  
Semler Oliver ◽  
Hoyer-Kuhn Heike ◽  
Garbes Lutz ◽  
Netzer Christian ◽  
Schoenau Eckhard
Keyword(s):  
Osteogenesis Imperfecta ◽  
Start Codon ◽  
Osteogenesis Imperfecta Type ◽  
Type V

scholarly journals The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Priya Prasad ◽  
Shantanu Kundu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Gene Arrangement ◽  
Sister Relationship ◽  
Protein Coding ◽  
Relationship Of ◽  
Rna Genes ◽  
Boundary Mapping ◽  
Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

scholarly journals Regulation of Swarming Motility and flhDCSm Expression by RssAB Signaling in Serratia marcescens

2008 ◽  
Vol 190 (7) ◽  
pp. 2496-2504 ◽  
Author(s):  
Po-Chi Soo ◽  
Yu-Tze Horng ◽  
Jun-Rong Wei ◽  
Jwu-Ching Shu ◽  
Chia-Chen Lu ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Binding Site ◽  
Promoter Region ◽  
Transcriptional Start Site ◽  
Direct Interaction ◽  
Underlying Mechanism ◽  
Inhibitory Effect ◽  
Start Codon ◽  
Mobility Shift

ABSTRACT Serratia marcescens cells swarm at 30°C but not at 37°C, and the underlying mechanism is not characterized. Our previous studies had shown that a temperature upshift from 30 to 37°C reduced the expression levels of flhDCSm and hagSm in S. marcescens CH-1. Mutation in rssA or rssB, cognate genes that comprise a two-component system, also resulted in precocious swarming phenotypes at 37°C. To further characterize the underlying mechanism, in the present study, we report that expression of flhDCSm and synthesis of flagella are significantly increased in the rssA mutant strain at 37°C. Primer extension analysis for determination of the transcriptional start site(s) of flhDCSm revealed two transcriptional start sites, P1 and P2, in S. marcescens CH-1. Characterization of the phosphorylated RssB (RssB∼P) binding site by an electrophoretic mobility shift assay showed direct interaction of RssB∼P, but not unphosphorylated RssB [RssB(D51E)], with the P2 promoter region. A DNase I footprinting assay using a capillary electrophoresis approach further determined that the RssB∼P binding site is located between base pair positions −341 and −364 from the translation start codon ATG in the flhDCSm promoter region. The binding site overlaps with the P2 “−35” promoter region. A modified chromatin immunoprecipitation assay was subsequently performed to confirm that RssB∼P binds to the flhDCSm promoter region in vivo. In conclusion, our results indicated that activated RssA-RssB signaling directly inhibits flhDCSm promoter activity at 37°C. This inhibitory effect was comparatively alleviated at 30°C. This finding might explain, at least in part, the phenomenon of inhibition of S. marcescens swarming at 37°C.

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