scholarly journals Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences

2011 ◽  
Vol 29 (3) ◽  
pp. 883-886 ◽  
Author(s):  
M. Toll-Riera ◽  
N. Rado-Trilla ◽  
F. Martys ◽  
M. M. Alba
Keyword(s):  
Low Complexity ◽  
Protein Coding ◽  
Coding Sequences ◽  
Novel Protein

Evolution of primate orphan proteins

2009 ◽  
Vol 37 (4) ◽  
pp. 778-782 ◽  
Author(s):  
Macarena Toll-Riera ◽  
Robert Castelo ◽  
Nicolás Bellora ◽  
M. Mar Albà
Keyword(s):  
Related Species ◽  
Sequence Divergence ◽  
Orphan Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Rapid Sequence ◽  
Adaptive Processes ◽  
Mechanisms Of Formation ◽  
Novel Protein

Genomes contain a large number of genes that do not have recognizable homologues in other species. These genes, found in only one or a few closely related species, are known as orphan genes. Their limited distribution implies that many of them are probably involved in lineage-specific adaptive processes. One important question that has remained elusive to date is how orphan genes originate. It has been proposed that they might have arisen by gene duplication followed by a period of very rapid sequence divergence, which would have erased any traces of similarity to other evolutionarily related genes. However, this explanation does not seem plausible for genes lacking homologues in very closely related species. In the present article, we review recent efforts to identify the mechanisms of formation of primate orphan genes. These studies reveal an unexpected important role of transposable elements in the formation of novel protein-coding genes in the genomes of primates.

scholarly journals De novoemergence of adaptive membrane proteins from thymine-rich intergenic sequences

2019 ◽  
Author(s):  
Nikolaos Vakirlis ◽  
Omer Acar ◽  
Brian Hsu ◽  
Nelson Castilho Coelho ◽  
S. Branden Van Oss ◽  
...  
Keyword(s):  
De Novo ◽  
Transmembrane Proteins ◽  
Protein Coding ◽  
Coding Sequences ◽  
Beneficial Effects ◽  
Protein Coding Genes ◽  
Evolutionary Innovation ◽  
Intergenic Sequences ◽  
Intergenic Regions ◽  
Novel Protein

SummaryRecent evidence demonstrates that novel protein-coding genes can arisede novofrom intergenic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of intergenic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Do intergenic translation events yield polypeptides with useful biochemical capacities? The answer to this question remains controversial. Here, we systematically characterized howde novoemerging coding sequences impact fitness. In budding yeast, overexpression of these sequences was enriched in beneficial effects, while their disruption was generally inconsequential. We found that beneficial emerging sequences have a strong tendency to encode putative transmembrane proteins, which appears to stem from a cryptic propensity for transmembrane signals throughout thymine-rich intergenic regions of the genome. These findings suggest that novel genes with useful biochemical capacities, such as transmembrane domains, tend to evolvede novowithin intergenic loci that already harbored a blueprint for these capacities.

scholarly journals The central role of RNA in the genetic programming of complex organisms

2010 ◽  
Vol 82 (4) ◽  
pp. 933-939 ◽  
Author(s):  
John S. Mattick
Keyword(s):  
Gene Expression ◽  
Control Gene ◽  
Animal Kingdom ◽  
Protein Coding ◽  
Coding Sequences ◽  
Protein Coding Genes ◽  
Control Gene Expression ◽  
Large Numbers ◽  
The Brain

Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the extent of genomic non-proteincoding sequences with increasing developmental complexity. These non-coding sequences are, in fact, transcribed in a regulated manner to produce large numbers of large and small non-protein-coding RNAs that control gene expression at many levels including chromatin architecture, post-transcriptional processing and translation. Moreover, many RNAs are edited, especially in the nervous system, which may be the basis of epigenome-environment interactions and the function of the brain.

scholarly journals Activation of Adenoviral Gene Expression by Protein IX Is Not Required for Efficient Virus Replication

2004 ◽  
Vol 78 (10) ◽  
pp. 5032-5037 ◽  
Author(s):  
Kathy L. Sargent ◽  
Robert A. Meulenbroek ◽  
Robin J. Parks
Keyword(s):  
Minor Component ◽  
Transient Transfection ◽  
Minimal Effect ◽  
Protein Coding ◽  
Coding Sequences ◽  
Late Genes ◽  
Viral Promoters ◽  
Protein Ix ◽  
A Minor

ABSTRACT The adenovirus (Ad) protein IX (pIX) is a minor component of the Ad capsid and is in part responsible for virion stability; virions lacking pIX are heat labile and lose their infectivity if the DNA content is greater than ∼35 kb. More recently, pIX has been identified as a transcriptional activator and, in transient-transfection assays, was shown to enhance expression from the E1A, E4, and major late Ad promoters by as much as 70-fold. In this study, we examined the role of pIX's ability to activate transcription during Ad replication. In transient-transfection assays, pIX had a minimal effect on expression from the E1A promoter, increasing expression by only 1.4-fold. We used helper-dependent Ad vectors, which had all Ad protein coding sequences deleted with the exception of E1A and which had capsids that either contained or lacked pIX, to show that pIX derived from decapsidation of the infecting virion does not influence expression of E1A. Similarly, expression of pIX from the Ad genome did not alter the expression levels of E1A. Viruses that had pIX deleted showed a threefold reduction in virus yield and expression of late genes compared to those of a similar virus which encoded pIX. This phenotype could not be rescued by growing the virus in cells which constitutively express pIX. Our results indicate that, although pIX can affect transcription from a variety of viral promoters, it does not appear to play a significant role in activation of Ad promoters during normal Ad replication.

scholarly journals Frequent appearance of novel protein-coding sequences by frameshift translation

Genomics ◽  
2006 ◽  
Vol 88 (6) ◽  
pp. 690-697 ◽  
Author(s):  
Kohji Okamura ◽  
Lars Feuk ◽  
Tomàs Marquès-Bonet ◽  
Arcadi Navarro ◽  
Stephen W. Scherer
Keyword(s):  
Protein Coding ◽  
Coding Sequences ◽  
Novel Protein ◽  
Frameshift Translation

Computationally predicted virus responsive miRNAs in banana (Musa AAB)

2021 ◽  
Vol 16 (7) ◽  
pp. 150-179
Author(s):  
K.S.A. Mathew ◽  
Subramanian Athira ◽  
K.B. Soni ◽  
Alex Swapna ◽  
J. Sreekumar ◽  
...  
Keyword(s):  
Target Genes ◽  
Mature Mirnas ◽  
Musa Acuminata ◽  
Biological Processes ◽  
Bioinformatics Tool ◽  
Protein Coding ◽  
Coding Sequences ◽  
Blast Analysis

The bioinformatics tool NovoMIR was used to predict miRNAs in Musa acuminata genome. NovoMIR predicted 85 pre-miRNAs from the 11 chromosomes of Musa acuminata DH Pahang and BLAST analysis of the predicted pre-miRNAs against annotated miRNAs of miRBase identified 52 mature miRNAs belonging to 38 different families. psRNATarget server identified 124 protein-coding sequences as potential targets for 40 mature miRNAs. Based on the role of the target genes in biological processes related to biotic stress, five miRNAs were selected for analyzing their response to Banana bract mosaic virus (BBrMV) infection. Three-month-old in vitro raised banana plants of var. Nendran (Musa AAB) infected with BBrMV showed the presence of all the five selected miRNAs in both healthy and BBrMV infected plants. Expression analysis using RT-qPCR showed changes in the expression of miR-3900-5p, miR-2172-5p, miR-6928-5p and miR-971-5p and their targets during BBrMV infection.

scholarly journals New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140332 ◽  
Author(s):  
Aoife McLysaght ◽  
Daniele Guerzoni
Keyword(s):  
De Novo ◽  
Complex Structure ◽  
Protein Coding ◽  
Functional Roles ◽  
Protein Coding Genes ◽  
Evolutionary Innovation ◽  
New Genes ◽  
De Novo Genes ◽  
Novel Protein

The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces , Drosophila , Plasmodium , Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.

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