Molecular and functional characterization of two DELLA protein-coding genes in litchi

Gene ◽  
2020 ◽  
Vol 738 ◽  
pp. 144455
Author(s):  
Yi Wang ◽  
Shae He ◽  
Yongzan Wei ◽  
Chen Dong ◽  
Liqin Liu ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Protein Coding ◽  
Della Protein ◽  
Protein Coding Genes

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Protein Coding ◽  
Core Promoters ◽  
Protein Coding Genes ◽  
The Core ◽  
Cell Type Specific ◽  
Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

scholarly journals Computer programs for the characterization of protein coding genes

1984 ◽  
Vol 12 (1Part1) ◽  
pp. 281-285 ◽  
Author(s):  
G. Pierno ◽  
N. Barni ◽  
M. Candurro ◽  
M. Cipollaro ◽  
A. Franzè ◽  
...  
Keyword(s):  
Computer Programs ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6866 ◽  
Author(s):  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Zhenyi Li ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A New Species ◽  
High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

scholarly journals Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 57 ◽  
Author(s):  
Jonathan F Schmitz ◽  
Erich Bornberg-Bauer
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
Divergence Times ◽  
Protein Coding ◽  
Future Studies ◽  
Functional Studies ◽  
Protein Coding Genes ◽  
Open Questions ◽  
Bona Fide

Over the last few years, there has been an increasing amount of evidence for the de novo emergence of protein-coding genes, i.e. out of non-coding DNA. Here, we review the current literature and summarize the state of the field. We focus specifically on open questions and challenges in the study of de novo protein-coding genes such as the identification and verification of de novo-emerged genes. The greatest obstacle to date is the lack of high-quality genomic data with very short divergence times which could help precisely pin down the location of origin of a de novo gene. We conclude that, while there is plenty of evidence from a genetics perspective, there is a lack of functional studies of bona fide de novo genes and almost no knowledge about protein structures and how they come about during the emergence of de novo protein-coding genes. We suggest that future studies should concentrate on the functional and structural characterization of de novo protein-coding genes as well as the detailed study of the emergence of functional de novo protein-coding genes.

scholarly journals Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Tasleem Akhtar ◽  
Ghazanfar Ali ◽  
Nuzhat Shafi ◽  
Wasim Akhtar ◽  
Abdul Hameed Khan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nadh Dehydrogenase ◽  
Mitochondrial Protein ◽  
Coi Gene ◽  
Nadh Dehydrogenase Subunit ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
High Bootstrap ◽  
Atpase 6

The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.

scholarly journals Structural and functional characterization of a putative de novo gene in Drosophila

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andreas Lange ◽  
Prajal H. Patel ◽  
Brennen Heames ◽  
Adam M. Damry ◽  
Thorsten Saenger ◽  
...  
Keyword(s):  
De Novo ◽  
Functional Characterization ◽  
Comparative Genomic ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Ancestral Sequences ◽  
De Novo Gene ◽  
Genomic Studies ◽  
Biochemical Genetic

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.

scholarly journals Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Sondos Samandi ◽  
Annie V Roy ◽  
Vivian Delcourt ◽  
Jean-François Lucier ◽  
Jules Gagnon ◽  
...  
Keyword(s):  
Mitochondrial Fission ◽  
Functional Characterization ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Protein Coding ◽  
Small Proteins ◽  
Conservation Patterns ◽  
Extreme Conservation

Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins.

scholarly journals Functional Characterization of a Trypanosoma brucei TATA-Binding Protein-Related Factor Points to a Universal Regulator of Transcription in Trypanosomes

2004 ◽  
Vol 24 (21) ◽  
pp. 9610-9618 ◽  
Author(s):  
Jia-peng Ruan ◽  
George K. Arhin ◽  
Elisabetta Ullu ◽  
Christian Tschudi
Keyword(s):  
Trypanosoma Brucei ◽  
Binding Protein ◽  
Functional Characterization ◽  
Tata Binding Protein ◽  
Related Factor ◽  
Protein Coding ◽  
Pol Ii ◽  
Protein Coding Genes ◽  
Pol I ◽  
Rna Genes

ABSTRACT Transcriptional mechanisms remain poorly understood in trypanosomatid protozoa. In particular, there is no knowledge about the function of basal transcription factors, and there is an apparent rarity of promoters for protein-coding genes transcribed by RNA polymerase (Pol) II. Here we describe a Trypanosoma brucei factor related to the TATA-binding protein (TBP). Although this TBP-related factor (TBP-related factor 4 [TRF4]) has about 31% identity to the TBP core domain, several key residues involved in TATA box binding are not conserved. Depletion of the T. brucei TRF4 (TbTRF4) by RNA interference revealed an essential role in RNA Pol I, II, and III transcription. Using chromatin immunoprecipitation, we further showed that TRF4 is recruited to the Pol I-transcribed procyclic acidic repetitive genes, Pol II-transcribed spliced leader RNA genes, and Pol III-transcribed U-snRNA and 7SL RNA genes, thus supporting a role for TbTRF4 in transcription performed by all three nuclear RNA polymerases. Finally, a search for TRF4 binding sites in the T. brucei genome led to the identification of such sites in the 3′ portion of certain protein-coding genes, indicating a unique aspect of Pol II transcription in these organisms.

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