Dual Function of DNA Sequences: Protein-Coding Sequences Function as Transcriptional Enhancers

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.

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Transcribed germline-limited coding sequences in Oxytricha trifallax

10.1101/2020.10.07.330092 ◽

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.

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Transcribed germline-limited coding sequences in Oxytricha trifallax

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab092 ◽

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.

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Selection of new biological activities from random nucleotide sequences: evolutionary and practical considerations

Genome ◽

10.1139/g89-021 ◽

1989 ◽

Vol 31 (1) ◽

pp. 112-117 ◽

Cited By ~ 11

Author(s):

Marshall S. Z. Horwitz ◽

Dipak K. Dube ◽

Lawrence A. Loeb

Keyword(s):

Dna Sequences ◽

Active Sites ◽

Biological Activities ◽

Regulatory Elements ◽

Biologically Active ◽

Protein Domain ◽

Protein Coding ◽

Coding Sequences ◽

Future Success ◽

Selection Of

Recent advances in the selection of biologically active DNA sequences from random populations are reviewed. Within the framework of evolution, forces are considered that have precluded the testing of all possible DNA sequences, purely with regard to their functionality as genetic regulatory elements or protein coding sequences. Examples are drawn from cassette mutagenesis of enzyme active sites, protein domain replacement by fusion with random genomic digests, and the selection of bacterial promoters from random DNA. Efforts to derive new activities are examined, and the likelihood of future success is evaluated.Key words: active DNA, nucleotide permutation, DNA evolution.

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Genome organisation in the murine sperm nucleus

Zygote ◽

10.1017/s0967199400002495 ◽

1995 ◽

Vol 3 (2) ◽

pp. 123-131 ◽

Cited By ~ 6

Author(s):

Carol Jennings ◽

Don Powell

Keyword(s):

Repetitive Dna ◽

Ribosomal Dna ◽

Dna Sequences ◽

Sperm Nucleus ◽

Genome Organisation ◽

Telomeric Dna ◽

Protein Coding ◽

Coding Sequences ◽

Restricted Domains

SummaryThe organisation of DNA sequences in the murine sperm nucleus was studied using in situ hybridisation of biotinylated DNA probes. The efficiency of this reaction was assessed using a dispersed repetitive DNA probe. Telomeric DNA was distributed around the nucleus. Centromeric and ribosomal DNA sequences occupied restricted domains in the sperm nucleus. DNA sequences for a transgene and a cluster of homeogenes occupied different, and rather less defined, domains. Together these results imply that both repetitive and protein-coding sequences are arranged in the nucleus in an ordered fashion.

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Faculty Opinions recommendation of Role of low-complexity sequences in the formation of novel protein coding sequences.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718030532.793494763 ◽

2014 ◽

Author(s):

Erich Bornberg-Bauer ◽

Magdalena Heberlein

Keyword(s):

Low Complexity ◽

Protein Coding ◽

Coding Sequences ◽

Novel Protein

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Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

Microbiology Resource Announcements ◽

10.1128/mra.00189-19 ◽

2019 ◽

Vol 8 (23) ◽

Author(s):

Si Chul Kim ◽

Hyo Jung Lee

Keyword(s):

South Korea ◽

Genome Sequence ◽

Yellow Sea ◽

Draft Genome ◽

The Yellow Sea ◽

Draft Genome Sequence ◽

Protein Coding ◽

Coding Sequences ◽

Gram Negative ◽

Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

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3P-301 A Codon-based Model for Evolution of Protein-coding DNA Sequences(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s174_1 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S174

Author(s):

Sanzo Miyazawa

Keyword(s):

Annual Meeting ◽

Dna Sequences ◽

Protein Coding ◽

Biophysical Society

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Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽

10.3390/insects11060326 ◽

2020 ◽

Vol 11 (6) ◽

pp. 326

Author(s):

Yu-Jun Wang ◽

Hua-Ling Wang ◽

Xiao-Wei Wang ◽

Shu-Sheng Liu

Keyword(s):

Gene Expression ◽

Slow Rate ◽

Species Complex ◽

Evolutionary Patterns ◽

Protein Coding ◽

Coding Sequences ◽

Species Comparisons ◽

Differential Gene ◽

Males And Females ◽

And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

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