A reference translatome map reveals two modes of protein evolution

Ribosome profiling experiments demonstrate widespread translation of eukaryotic genomes outside of annotated protein-coding genes. However, it is unclear how much of this "noncanonical" translation contributes biologically relevant microproteins rather than insignificant translational noise. Here, we developed an integrative computational framework (iRibo) that leverages hundreds of ribosome profiling experiments to detect signatures of translation with high sensitivity and specificity. We deployed iRibo to construct a reference translatome in the model organism S. cerevisiae. We identified ~19,000 noncanonical translated elements outside of the ~5,400 canonical yeast protein-coding genes. Most (65%) of these non-canonical translated elements were located on transcripts annotated as non-coding, or entirely unannotated, while the remainder were located on the 5' and 3' ends of mRNA transcripts. Only 14 non-canonical translated elements were evolutionarily conserved. In stark contrast with canonical protein-coding genes, the great majority of the yeast noncanonical translatome appeared evolutionarily transient and showed no signatures of selection. Yet, we uncovered phenotypes for 53% of a representative subset of evolutionarily transient translated elements. The iRibo framework and reference translatome described here provide a foundation for further investigation of a largely unexplored, but biologically significant, evolutionarily transient translatome.

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New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

10.21203/rs.3.rs-1201297/v1 ◽

2021 ◽

Author(s):

Fangfang Huang ◽

Yingru Jiang ◽

Tiantian Chen ◽

Haoran Li ◽

Mengjia Fu ◽

...

Keyword(s):

Functional Genomics ◽

Rice Genome ◽

Model Organism ◽

Gene Families ◽

Food Crop ◽

Protein Coding ◽

Protein Coding Genes ◽

Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

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Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels

10.1101/2021.03.25.436978 ◽

2021 ◽

Author(s):

Yuta Hiragori ◽

Hiro Takahashi ◽

Noriya Hayashi ◽

Shun Sasaki ◽

Kodai Nakao ◽

...

Keyword(s):

Regulatory Peptides ◽

Inhibitory Effect ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Regulatory Sequences ◽

Dependent Manner ◽

Protein Coding ◽

Genome Wide ◽

Evolutionarily Conserved ◽

Upstream Open Reading Frames

Upstream open reading frames (uORFs) are short ORFs found in the 5′-UTRs of many eukaryotic transcripts and can influence the translation of protein-coding main ORFs (mORFs). Recent genome-wide ribosome profiling studies have revealed that thousands of uORFs initiate translation at non-AUG start codons. However, the physiological significance of these non-AUG uORFs has so far been demonstrated for only a few of them. It is conceivable that physiologically important non-AUG uORFs are evolutionarily conserved across species. In this study, using a combination of bioinformatics and experimental approaches, we searched the Arabidopsis genome for non-AUG-initiated uORFs with conserved sequences that control the expression of the mORF-encoded proteins. As a result, we identified four novel regulatory non-AUG uORFs. Among these, two exerted repressive effects on mORF expression in an amino acid sequence-dependent manner. These two non-AUG uORFs are likely to encode regulatory peptides that cause ribosome stalling, thereby enhancing their repressive effects. In contrast, one of the identified regulatory non-AUG uORFs promoted mORF expression by alleviating the inhibitory effect of a downstream AUG-initiated uORF. These findings provide insights into the mechanisms that enable non-AUG uORFs to play regulatory roles despite their low translation initiation efficiencies.

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A de novo evolved gene in the house mouse regulates female pregnancy cycles

eLife ◽

10.7554/elife.44392 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 4

Author(s):

Chen Xie ◽

Cemalettin Bekpen ◽

Sven Künzel ◽

Maryam Keshavarz ◽

Rebecca Krebs-Wheaton ◽

...

Keyword(s):

House Mouse ◽

De Novo ◽

Specific Protein ◽

Ribosome Profiling ◽

Mass Spectrometry Data ◽

Preimplantation Embryos ◽

Protein Coding ◽

Reading Frame ◽

Protein Coding Genes ◽

New Genes

The de novo emergence of new genes has been well documented through genomic analyses. However, a functional analysis, especially of very young protein-coding genes, is still largely lacking. Here, we identify a set of house mouse-specific protein-coding genes and assess their translation by ribosome profiling and mass spectrometry data. We functionally analyze one of them, Gm13030, which is specifically expressed in females in the oviduct. The interruption of the reading frame affects the transcriptional network in the oviducts at a specific stage of the estrous cycle. This includes the upregulation of Dcpp genes, which are known to stimulate the growth of preimplantation embryos. As a consequence, knockout females have their second litters after shorter times and have a higher infanticide rate. Given that Gm13030 shows no signs of positive selection, our findings support the hypothesis that a de novo evolved gene can directly adopt a function without much sequence adaptation.

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Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

mBio ◽

10.1128/mbio.01730-18 ◽

2018 ◽

Vol 9 (5) ◽

Cited By ~ 14

Author(s):

Daniel Dar ◽

Rotem Sorek

Keyword(s):

Expression Patterns ◽

Noncoding Rnas ◽

Large Set ◽

Rna Structures ◽

Protein Coding ◽

Small Noncoding Rnas ◽

Coding Regions ◽

Protein Coding Genes ◽

Evolutionarily Conserved ◽

Intergenic Regions

ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

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EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.059360-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 689-691 ◽

Cited By ~ 94

Author(s):

Yoon-Seong Jeon ◽

Kihyun Lee ◽

Sang-Cheol Park ◽

Bong-Soo Kim ◽

Yong-Joon Cho ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequences ◽

Relevant Information ◽

Biological Information ◽

Sequence Alignments ◽

Protein Coding ◽

Structure Information ◽

Biologically Relevant ◽

Molecular Sequence ◽

Protein Coding Genes

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA- and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

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Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

10.1101/047308 ◽

2016 ◽

Cited By ~ 6

Author(s):

Chia-Yi Cheng ◽

Vivek Krishnakumar ◽

Agnes Chan ◽

Seth Schobel ◽

Christopher D. Town

Keyword(s):

Arabidopsis Thaliana ◽

Small Rna ◽

Noncoding Rna ◽

Model Organism ◽

Housekeeping Genes ◽

Flowering Plant ◽

Small Nuclear Rna ◽

Rna Seq ◽

Protein Coding ◽

Protein Coding Genes

ABSTRACTThe flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, noncoding RNA, and small RNA. The most recent annotation update (TAIR10) released more than five years ago had a profound impact on Arabidopsis research. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-seq libraries from 113 datasets and constructed 48,359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of noncoding RNA including small RNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and microRNA using published datasets and in-house analytic results. Altogether, we identified 738 novel protein-coding genes, 508 novel transcribed regions, 5051 non-coding genes, and 35846 small-RNA loci that formerly eluded annotation. Analysis on the splicing events and RNA-seq based expression profile revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

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The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota

Journal of Bacteriology ◽

10.1128/jb.187.14.4992-4999.2005 ◽

2005 ◽

Vol 187 (14) ◽

pp. 4992-4999 ◽

Cited By ~ 189

Author(s):

Lanming Chen ◽

Kim Brügger ◽

Marie Skovgaard ◽

Peter Redder ◽

Qunxin She ◽

...

Keyword(s):

Genome Stability ◽

Excision Repair ◽

Carbon Sources ◽

Model Organism ◽

Conjugative Plasmid ◽

Sulfolobus Acidocaldarius ◽

Repair System ◽

Protein Coding ◽

Modification System ◽

Protein Coding Genes

ABSTRACT Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of three Sulfolobus genome sequences. Of the protein-coding genes, 305 are exclusive to S. acidocaldarius and 866 are specific to the Sulfolobus genus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization of S. acidocaldarius differ radically from those of Sulfolobus solfataricus and Sulfolobus tokodaii. The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of other Sulfolobus species. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes for Sulfolobus, are incorporated into a public Sulfolobus database which can be accessed at http://dac.molbio.ku.dk/dbs/Sulfolobus .

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