scholarly journals Identification of small open reading frames (sORFs) associated with heat tolerance in nitrogen-fixing root nodules of Phaseolus vulgaris wild-type and cv BAT93

2021 ◽  
pp. 28-37
Author(s):  
Alejandra Zayas-del Moral ◽  
Damián Martínez- Reyes ◽  
Carmen Quinto ◽  
Federico Sanchez ◽  
Claudia Díaz- Camino
Keyword(s):  
Heat Stress ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Low Income ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Nitrogen Fixing ◽  
Next Generation Sequencing Technology ◽  
Reading Frames ◽  
Small Open Reading Frames

Common bean is an important legume crop and a major source of protein for low-income groups around the world. Legumes have the ability to engage symbiotic interactions with nitrogen-fixing soil bacteria. In this study, next-generation sequencing technology was used to perform transcriptome analyses of a yet unexplored group of peptides encoded by small open reading frames (sORFs; < 150 codons) in nitrogen-fixing symbiotic nodules of two heat-tolerant genotypes of common bean (Phaseolus vulgaris L): the cultivar BAT93 and a wild genotype (named P. vulgaris 7) from the south of Mexico. After heat stress, total RNA was isolated and used for transcriptome analysis. Sixty differentially expressed sORFs were identified between control and heat stress treatments. The expression profiles of these sORFs suggest that, regardless the evolutionary closeness between P. vulgaris BAT93 and P. vulgaris 7, each genotype has independently adapted their molecular signaling pathways to survive heat stress. The dataset developed may provide a useful resource for future genetic and genomic studies in these species

scholarly journals Two neuronal peptides encoded from a single transcript regulate mitochondrial function in Drosophila

2020 ◽  
Author(s):  
Justin A. Bosch ◽  
Berrak Ugur ◽  
Israel Pichardo-Casas ◽  
Jorden Rabasco ◽  
Felipe Escobedo ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Double Mutant ◽  
Open Reading Frames ◽  
Biological Functions ◽  
Neuronal Function ◽  
Phenotypic Analysis ◽  
Single Transcript ◽  
Sequence Similarities ◽  
Reading Frames ◽  
Small Open Reading Frames

SummaryNaturally produced peptides (<100 amino acids) are important regulators of physiology, development, and metabolism. Recent studies have predicted that thousands of peptides may be translated from transcripts containing small open reading frames (smORFs). Here, we describe two previously uncharacterized peptides in Drosophila encoded by conserved smORFs, Sloth1 and Sloth2. These peptides are translated from the same bicistronic transcript and share sequence similarities, suggesting that they encode paralogs. We provide evidence that Sloth1/2 are highly expressed in neurons, localize to mitochondria, and form a complex. Double mutant analysis in animals and cell culture revealed that sloth1 and sloth2 are not functionally redundant, and their loss causes animal lethality, reduced neuronal function, impaired mitochondrial function, and neurodegeneration. These results suggest that phenotypic analysis of smORF genes in Drosophila can provide a wealth of information on the biological functions of this poorly characterized class of genes.

scholarly journals Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13

2020 ◽  
Vol 8 (6) ◽  
pp. 888
Author(s):  
Justas Vaitekūnas ◽  
Renata Gasparavičiūtė ◽  
Jonita Stankevičiūtė ◽  
Gintaras Urbelis ◽  
Rolandas Meškys
Keyword(s):  
Recombinant Expression ◽  
Expression Profiles ◽  
Peptide Mass Fingerprinting ◽  
Sole Source ◽  
Open Reading Frames ◽  
Expression Of Genes ◽  
Peptide Mass ◽  
Genes Encoding ◽  
Protein Expression Profiles ◽  
Reading Frames

N-Heterocyclic compounds are widely spread in the biosphere, being constituents of alkaloids, cofactors, allelochemicals, and artificial substances. However, the fate of such compounds including a catabolism of hydroxylated pyridines is not yet fully understood. Arthrobacter sp. IN13 is capable of using 4-hydroxypyridine as a sole source of carbon and energy. Three substrate-inducible proteins were detected by comparing protein expression profiles, and peptide mass fingerprinting was performed using MS/MS. After partial sequencing of the genome, we were able to locate genes encoding 4-hydroxypyridine-inducible proteins and identify the kpi gene cluster consisting of 16 open reading frames. The recombinant expression of genes from this locus in Escherichia coli and Rhodococcus erytropolis SQ1 allowed an elucidation of the biochemical functions of the proteins. We report that in Arthrobacter sp. IN13, the initial hydroxylation of 4-hydroxypyridine is catalyzed by a flavin-dependent monooxygenase (KpiA). A product of the monooxygenase reaction is identified as 3,4-dihydroxypyridine, and a subsequent oxidative opening of the ring is performed by a hypothetical amidohydrolase (KpiC). The 3-(N-formyl)-formiminopyruvate formed in this reaction is further converted by KpiB hydrolase to 3-formylpyruvate. Thus, the degradation of 4-hydroxypyridine in Arthrobacter sp. IN13 was analyzed at genetic and biochemical levels, elucidating this catabolic pathway.

scholarly journals Hundreds of putatively functional small open reading frames in Drosophila

2011 ◽  
Vol 12 (11) ◽  
pp. R118 ◽  
Author(s):  
Emmanuel Ladoukakis ◽  
Vini Pereira ◽  
Emile G Magny ◽  
Adam Eyre-Walker ◽  
Juan Couso
Keyword(s):  
Open Reading Frames ◽  
Reading Frames ◽  
Small Open Reading Frames

scholarly journals Effect of inoculation associated to leaf sprayed Co+Mo on the yield and grain nutrients in common bean (Phaseolus vulgaris L)

2008 ◽  
Vol 51 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
João Francisco Berton Junior ◽  
Julio Cesar Pires Santos ◽  
Cileide Maria Medeiros Coelho ◽  
Osmar Klauberg Filho
Keyword(s):  
Phaseolus Vulgaris ◽  
Grain Yield ◽  
Common Bean ◽  
Protein Content ◽  
Nitrogen Source ◽  
Mineral Nitrogen ◽  
Nitrogen Fixing ◽  
Phaseolus Vulgaris L ◽  
Rhizobium Tropici ◽  
The Common

The objective of this work was to evaluate the efficiency of nitrogen fixing inoculum associated with Co + Mo leaf spray on the common bean grain yield and grain nutrients, cv. FT Nobre. Three dosages of the inoculant (0, 200 and 400 g/50 kg seeds), combined with four Co + Mo leaf spray levels (T0=0,0; T1=4.9,49; T2=7.3,73; and T3=9.7,97 g ha-1 of Co and Mo, respectively) were tested. The grain yield with the use of the inoculant (400 g / 5O kg seed-1) associated with the higher level of Co+Mo (T2 and T3) was very similar to the mineral nitrogen condition fertilizer recommended for the bean (70 kg ha-1 of N). With the increased inoculant dosage, an increase of the protein content and of P and Mg in the grain was also observed. The results indicated that the mineral nitrogen source could be replaced by inoculation of the seeds with Rhizobium tropici combined with Co + Mo leaf spray.

Computational discovery of small open reading frames in Bacillus lehensis

2015 ◽  
Author(s):  
Nurhafizhoh Zainuddin ◽  
Rosli Md. Illias ◽  
Nor Muhammad Mahadi ◽  
Mohd Firdaus-Raih
Keyword(s):  
Open Reading Frames ◽  
Computational Discovery ◽  
Reading Frames ◽  
Small Open Reading Frames

scholarly journals The product of the H19 gene may function as an RNA.

1990 ◽  
Vol 10 (1) ◽  
pp. 28-36 ◽  
Author(s):  
C I Brannan ◽  
E C Dees ◽  
R S Ingram ◽  
S M Tilghman
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Translation Termination ◽  
Sedimentation Coefficient ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Translational Machinery ◽  
H19 Gene ◽  
Reading Frames ◽  
Small Open Reading Frames

The mouse H19 gene was identified as an abundant hepatic fetal-specific mRNA under the transcriptional control of a trans-acting locus termed raf. The protein this gene encoded was not apparent from an analysis of its nucleotide sequence, since the mRNA contained multiple translation termination signals in all three reading frames. As a means of assessing which of the 35 small open reading frames might be important to the function of the gene, the human H19 gene was cloned and sequenced. Comparison of the two homologs revealed no conserved open reading frame. Cellular fractionation showed that H19 RNA is cytoplasmic but not associated with the translational machinery. Instead, it is located in a particle with a sedimentation coefficient of approximately 28S. Despite the fact that it is transcribed by RNA polymerase II and is spliced and polyadenylated, we suggest that the H19 RNA is not a classical mRNA. Instead, the product of this unusual gene may be an RNA molecule.

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