scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2020 ◽  
Author(s):  
Richard V. Miller ◽  
Rafik Neme ◽  
Derek M. Clay ◽  
Jananan S. Pathmanathan ◽  
Michael W. Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

AbstractThe germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2021 ◽  
Author(s):  
Richard V Miller ◽  
Rafik Neme ◽  
Derek M Clay ◽  
Jananan S Pathmanathan ◽  
Michael W Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

Abstract The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination.

scholarly journals You're one in a googol: optimizing genes for protein expression

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Mark Welch ◽  
Alan Villalobos ◽  
Claes Gustafsson ◽  
Jeremy Minshull
Keyword(s):  
Protein Expression ◽  
Dna Sequences ◽  
Ad Hoc ◽  
Protein Coding ◽  
Vast Number ◽  
Coding Sequences ◽  
Affect Expression ◽  
Continue Work ◽  
Existing Data ◽  
Rational Sequence

A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.

SOME HINTS ON OPEN READING FRAME STATISTICS — HOW ORF LENGTH DEPENDS ON SELECTION

1999 ◽  
Vol 10 (04) ◽  
pp. 635-643 ◽  
Author(s):  
AGNIESZKA GIERLIK ◽  
PAWEŁ MACKIEWICZ ◽  
MARIA KOWALCZUK ◽  
STANISŁAW CEBRAT ◽  
MIROSŁAW R. DUDEK
Keyword(s):  
Genetic Code ◽  
Dna Sequences ◽  
Nucleotide Composition ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Antisense Strand ◽  
Coding Sequences ◽  
Reading Frame ◽  
Intergenic Sequences ◽  
Reading Frames

Coding sequences of DNA generate Open Reading Frames (ORFs) inside them with much higher frequency than random DNA sequences do, especially in the antisense strand. This is a specific feature of the genetic code. Since coding sequences are selected for their length, the generated ORFs are indirect results of this selection and their length is also influenced by selection. That is why ORFs found in any genome, even much longer ones than those spontaneously generated in random DNA sequences, should be considered as two different sets of ORFs: The first one coding for proteins, the second one generated by the coding ORFs. Even intergenic sequences possess greater capacity for generating ORFs than random DNA sequences of the same nucleotide composition, which seems to be a premise that intergenic sequences were generated from coding sequences by recombinational mechanisms.

scholarly journals Concerted evolution at a multicopy locus in the protozoan parasite Theileria parva: extreme divergence of potential protein-coding sequences.

1997 ◽  
Vol 17 (3) ◽  
pp. 1666-1673 ◽  
Author(s):  
R Bishop ◽  
A Musoke ◽  
S Morzaria ◽  
B Sohanpal ◽  
E Gobright
Keyword(s):  
Concerted Evolution ◽  
Protozoan Parasite ◽  
Gene Families ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Theileria Parva ◽  
Gene Encoding ◽  
Additional Species ◽  
Protein Coding ◽  
Coding Sequences

Concerted evolution of multicopy gene families in vertebrates is recognized as an important force in the generation of biological novelty but has not been documented for the multicopy genes of protozoa. A multicopy locus, Tpr, which consists of tandemly arrayed open reading frames (ORFs) containing several repeated elements has been described for Theileria parva. Herein we show that probes derived from the 5'/N-terminal ends of ORFs in the genomic DNAs of T. parva Uganda (1,108 codons) and Boleni (699 codons) hybridized with multicopy sequences in homologous DNA but did not detect similar sequences in the DNA of 14 heterologous T. parva stocks and clones. The probe sequences were, however, protein coding according to predictive algorithms and codon usage. The 3'/C-terminal ends of the Uganda and Boleni ORFs exhibited 75% similarity and identity, respectively, to the previously identified Tpr1 and Tpr2 repetitive elements of T. parva Muguga. Tpr1-homologous sequences were detected in two additional species of Theileria. Eight different Tpr1-homologous transcripts were present in piroplasm mRNA from a single T. parva Muguga-infected animal. The Tpr1 and Tpr2 amino acid sequences contained six predicted membrane-associated segments. The ratio of synonymous to nonsynonymous substitutions indicates that Tpr1 evolves like protein-encoding DNA. The previously determined nucleotide sequence of the gene encoding the p67 antigen is completely identical in T. parva Muguga, Boleni, and Uganda, including the third base in codons. The data suggest that concerted evolution can lead to the radical divergence of coding sequences and that this can be a mechanism for the generation of novel genes.

scholarly journals Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate

2017 ◽  
Author(s):  
Sondos Samandi ◽  
Annie V. Roy ◽  
Vivian Delcourt ◽  
Jean-François Lucier ◽  
Jules Gagnon ◽  
...  
Keyword(s):  
Functional Relationship ◽  
Mitochondrial Fission ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Large Proteins ◽  
Small Proteins ◽  
Reading Frames

AbstractRecent studies in eukaryotes have 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 altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and evolutionary patterns indicate that altORFs are particularly constrained in CDSs that evolve slowly. Thousands of predicted alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. Protein domains and co-conservation analyses suggest a potential functional relationship between small and large proteins encoded in the same genes. 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 coding genes code for more than one protein that are often functionally related.

scholarly journals The Investigation of Perennial Sunflower Species (Helianthus L.) Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 982
Author(s):  
Maksim Makarenko ◽  
Alexander Usatov ◽  
Tatiana Tatarinova ◽  
Kirill Azarin ◽  
Alexey Kovalevich ◽  
...  
Keyword(s):  
Low Frequency ◽  
Blind Spot ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Perennial Species ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gene Profiles ◽  
Helianthus Species ◽  
Reading Frames

The genus Helianthus is a diverse taxonomic group with approximately 50 species. Most sunflower genomic investigations are devoted to economically valuable species, e.g., H. annuus, while other Helianthus species, especially perennial, are predominantly a blind spot. In the current study, we have assembled the complete mitogenomes of two perennial species: H. grosseserratus (273,543 bp) and H. strumosus (281,055 bp). We analyzed their sequences and gene profiles in comparison to the available complete mitogenomes of H. annuus. Except for sdh4 and trnA-UGC, both perennial sunflower species had the same gene content and almost identical protein-coding sequences when compared with each other and with annual sunflowers (H. annuus). Common mitochondrial open reading frames (ORFs) (orf117, orf139, and orf334) in sunflowers and unique ORFs for H. grosseserratus (orf633) and H. strumosus (orf126, orf184, orf207) were identified. The maintenance of plastid-derived coding sequences in the mitogenomes of both annual and perennial sunflowers and the low frequency of nonsynonymous mutations point at an extremely low variability of mitochondrial DNA (mtDNA) coding sequences in the Helianthus genus.

scholarly journals Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

2015 ◽  
Author(s):  
Anil Raj ◽  
Sidney H. Wang ◽  
Heejung Shim ◽  
Arbel Harpak ◽  
Yang I. Li ◽  
...  
Keyword(s):  
Significant Negative Correlation ◽  
Selective Constraint ◽  
Open Reading Frames ◽  
Sequence Information ◽  
The Novel ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Human Lymphoblastoid Cell ◽  
Reading Frames

AbstractAccurate annotation of protein coding regions is essential for understanding how genetic information is translated into biological functions. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,273 previously unannotated coding sequences, including 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. The novel sequences exhibit significant signatures of selective constraint in the reading frames of the inferred proteins, suggesting that many of these are functional. Nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Our work significantly expands the set of known coding regions in humans.

scholarly journals Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Anil Raj ◽  
Sidney H Wang ◽  
Heejung Shim ◽  
Arbel Harpak ◽  
Yang I Li ◽  
...  
Keyword(s):  
Selective Constraint ◽  
Open Reading Frames ◽  
The Novel ◽  
Drug Induced ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Human Lymphoblastoid Cell ◽  
Validation Rate ◽  
Reading Frames

Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans.

Rapid genomic changes in newly synthesized amphiploids ofTriticumandAegilops. II. Changes in low-copy coding DNA sequences

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 535-542 ◽  
Author(s):  
B Liu ◽  
J M Vega ◽  
M Feldman
Keyword(s):  
Dna Methylation ◽  
Dna Sequences ◽  
Gene Dosage ◽  
Restriction Enzymes ◽  
Noncoding Dna ◽  
Ploidy Levels ◽  
Coding Sequences ◽  
Genomic Changes ◽  
Cdna Sequences ◽  
Specific Sequences

We recently reported that formation of allopolyploid wheat was accompanied by rapid nonrandom changes in low-copy noncoding DNA sequences. In this report we show that following allopolyploidization, changes also occurred in coding sequences. Genomic DNA of nine different newly synthesized amphiploids of different ploidy levels and their parental lines was digested with five restriction enzymes and probed with 43 coding sequences. The sequences, 19 genomic and 24 cDNA sequences, are group (homoeologous) specific and represent the proximal and distal regions of the short and long arms of the seven homoeologous groups of the Triticeae. We revealed three types of changes: disappearance of a parental hybridization fragment(s), appearance of a novel fragment(s), and simultaneous disappearance of a parental fragment(s) and appearance of a novel fragment(s). No elimination of sequences took place, since in every sequence studied the parental hybridization fragments were present in at least one of the enzyme digests. Variations in pattern among individual plants of the same amphiploid, as well as between several synthetic and natural amphiploids, indicated that at least some of the genomic changes occurred at random. Intergenomic recombination was not the cause of the observed changes. Evidence was obtained, however, that changes were also brought about by DNA methylation. Methylation may cause inactivation of genes or modify their expression levels in some of the newly synthesized amphiploid plants, leading to genetic diploidization and gene-dosage compensation and thus increasing variation among individuals.Key words: wheat, allopolyploidy, DNA methylation, genetic diploidization, genome evolution, group (homoeologous) specific sequences.

scholarly journals Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome

2020 ◽  
Vol 36 (19) ◽  
pp. 4827-4832
Author(s):  
C S Casimiro-Soriguer ◽  
M M Rigual ◽  
A M Brokate-Llanos ◽  
M J Muñoz ◽  
A Garzón ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Supplementary Information ◽  
Protein Coding ◽  
Reading Frame ◽  
A Genome ◽  
Caenorhabditis Elegans Genome

Abstract Motivation Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance. Results AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes. Availability and implementation AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans. Supplementary information Supplementary data are available at Bioinformatics online.

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