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Tao YT, Chen LX, Jin J, Du ZK, Li JM. Genome-wide identification and analysis of bZIP gene family reveal their roles during development and drought stress in Wheel Wingnut (Cyclocarya paliurus). BMC Genomics 2022; 23:743. [DOI: 10.1186/s12864-022-08978-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/30/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The bZIP gene family has important roles in various biological processes, including development and stress responses. However, little information about this gene family is available for Wheel Wingnut (Cyclocarya paliurus).
Results
In this study, we identified 58 bZIP genes in the C. paliurus genome and analyzed phylogenetic relationships, chromosomal locations, gene structure, collinearity, and gene expression profiles. The 58 bZIP genes could be divided into 11 groups and were unevenly distributed among 16 C. paliurus chromosomes. An analysis of cis-regulatory elements indicated that bZIP promoters were associated with phytohormones and stress responses. The expression patterns of bZIP genes in leaves differed among developmental stages. In addition, several bZIP members were differentially expressed under drought stress. These expression patterns were verified by RT-qPCR.
Conclusions
Our results provide insights into the evolutionary history of the bZIP gene family in C. paliurus and the function of these genes during leaf development and in the response to drought stress. In addition to basic genomic information, our results provide a theoretical basis for further studies aimed at improving growth and stress resistance in C. paliurus, an important medicinal plant.
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2
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Zhang SD, Ling LZ. Molecular Structure and Phylogenetic Analyses of the Plastomes of Eight Sorbus Sensu Stricto Species. Biomolecules 2022; 12:1648. [PMID: 36358998 PMCID: PMC9687737 DOI: 10.3390/biom12111648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 10/20/2023] Open
Abstract
Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and genetic markers. In this study, the chloroplast (cp) genomes of eight Sorbus s. str. species were characterized and compared with those of twelve released species in this genus. Our results indicated that the plastomes of the twenty Sorbus species had a conserved quadripartite structure, and 129 annotated genes had the same order and showed a good collinearity. Additionally, numerous SSRs were observed in the cp genome of each Sorbus species; most of the sequence variations appeared in non-coding regions, and four intergenic regions were identified as mutation spots. By contrast, protein-coding genes showed low variations under purifying selection. The phylogenetic and molecular-dating analysis showed that Sorbus was resolved into two major clades, in which S. americana forms one clade originating at 51.78 Ma, and the rest of Sorbus formed another clade, splitting at 36.77 Ma into two sister groups with high support values. These results provide a basis for further studying the phylogenetic relationship and biogeography of Sorbus species.
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Affiliation(s)
| | - Li-Zhen Ling
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui 553004, China
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3
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Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 ( TabZIP96) under Freezing Stress in Wheat ( Triticum aestivum). Int J Mol Sci 2022; 23:ijms23042351. [PMID: 35216467 PMCID: PMC8874521 DOI: 10.3390/ijms23042351] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 01/07/2023] Open
Abstract
The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.
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Mortz M, Dégletagne C, Romestaing C, Duchamp C. Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA. Genomics 2019; 112:1120-1127. [PMID: 31247329 DOI: 10.1016/j.ygeno.2019.06.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/01/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022]
Abstract
The mitochondrial genome (mt-DNA) functional repertoire has recently been enriched in mammals by the identification of functional small open reading frames (sORFs) embedded in ribosomal DNAs. Through comparative genomic analyses the presence of putatively functional sORFs was investigated in birds. Alignment of available avian mt-DNA sequences revealed highly conserved regions containing four putative sORFs that presented low insertion/deletion polymorphism rate (<0.1%) and preserved in frame start/stop codons in >80% of species. Detected sORFs included avian homologs of human Humanin and Short-Humanin-Like-Peptide 6 and two new sORFs not yet described in mammals. The amino-acid sequences of the four putative encoded peptides were strongly conserved among birds, with amino-acid p-distances (5.6 to 25.4%) similar to those calculated for typical avian mt-DNA-encoded proteins (14.8%). Conservation resulted from either drastic conservation of the nucleotide sequence or negative selection pressure. These data extend to birds the possibility that mitochondrial rDNA may encode small bioactive peptides.
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Affiliation(s)
- Mathieu Mortz
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Cyril Dégletagne
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Caroline Romestaing
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France
| | - Claude Duchamp
- Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, UMR 5023 CNRS, Université Claude Bernard Lyon 1, ENTPE, Villeurbanne Cedex, France.
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5
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Annibalini G, Bielli P, De Santi M, Agostini D, Guescini M, Sisti D, Contarelli S, Brandi G, Villarini A, Stocchi V, Sette C, Barbieri E. MIR retroposon exonization promotes evolutionary variability and generates species-specific expression of IGF-1 splice variants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:757-68. [DOI: 10.1016/j.bbagrm.2016.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/07/2016] [Accepted: 03/23/2016] [Indexed: 12/18/2022]
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6
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Arquez M, Colgan D, Castro LR. Sequence and comparison of mitochondrial genomes in the genus Nerita (Gastropoda: Neritimorpha: Neritidae) and phylogenetic considerations among gastropods. Mar Genomics 2014; 15:45-54. [PMID: 24798873 DOI: 10.1016/j.margen.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
In the present study, we determined the mitochondrial DNA (mtDNA) sequence of three Neritas, Nerita versicolor, Nerita tessellata, and Nerita fulgurans. We present an analysis of the features of their gene content and genome organization and compare these within the genus Nerita, and among the main gastropod groups. The new sequences were used in a phylogenetic analysis including all available gastropod mitochondrial genomes. Genomic lengths were quite conserved, being 15,866bp for N. versicolor, 15,741bp for N. tessellata and 15,343bp for N. fulgurans. Intergenic regions were generally short; genes are transcribed from both strands and have a nucleotide composition high in A and T. The high similarity in nucleotide content of the different sequences, gene composition, as well as an identical genomic organization among the Nerita species compared in this study, indicates a high degree of conservation within this diverse genus. Values of Ka/Ks of the 13 protein coding genes (PCGs) of Nerita species ranged from 0 to 0.18, and suggested different selection pressures in gene sequences. Bayesian phylogenetic analyses using concatenated DNA sequences of the 13 PCGs and the two rRNAs, and of amino acid sequences strongly supported Neritimorpha and Vetigastropoda as sister groups.
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Affiliation(s)
- Moises Arquez
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
| | - Donald Colgan
- The Australian Museum, 6 College Street, Sydney 2010, Australia.
| | - Lyda R Castro
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
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7
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Shabalina SA, Spiridonov NA, Kashina A. Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 2013; 41:2073-94. [PMID: 23293005 PMCID: PMC3575835 DOI: 10.1093/nar/gks1205] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA.
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8
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Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 2012; 46:871-83. [PMID: 22749400 PMCID: PMC3437557 DOI: 10.1016/j.molcel.2012.05.039] [Citation(s) in RCA: 283] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/11/2012] [Accepted: 05/16/2012] [Indexed: 02/09/2023]
Abstract
Alternative inclusion of exons increases the functional diversity of proteins. Among alternatively spliced exons, tissue-specific exons play a critical role in maintaining tissue identity. This raises the question of how tissue-specific protein-coding exons influence protein function. Here we investigate the structural, functional, interaction, and evolutionary properties of constitutive, tissue-specific, and other alternative exons in human. We find that tissue-specific protein segments often contain disordered regions, are enriched in posttranslational modification sites, and frequently embed conserved binding motifs. Furthermore, genes containing tissue-specific exons tend to occupy central positions in interaction networks and display distinct interaction partners in the respective tissues, and are enriched in signaling, development, and disease genes. Based on these findings, we propose that tissue-specific inclusion of disordered segments that contain binding motifs rewires interaction networks and signaling pathways. In this way, tissue-specific splicing may contribute to functional versatility of proteins and increases the diversity of interaction networks across tissues.
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Affiliation(s)
- Marija Buljan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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9
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Abstract
To detect positive Darwinian selection it is thought essential to compare two sequences. Despite its defects, "the comparative method rules." However, genes evolving rapidly under positive selection conflict more with internal forces (the genome phenotype) than genes evolving slowly under negative selection. In particular, there is conflict with stem-loop potential. The conflict between protein-encoding potential (primary information) and stem-loop potential (secondary information) permits detection of positive selection in a single sequence. The degree to which secondary information is compromised provides a measure of the speed of transmission of primary information. Thus, the sovereignty of the comparative method is challenged not only by its own defects, but also by the availability of a single-sequence method. However, while of limited utility for positive selection, the comparative method casts new light on Darwin's great question — the origin of species. Comparison of rates of synonymous and non-synonymous mutation suggests that branching into new species begins with synonymous mutations.
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Affiliation(s)
- DONALD R. FORSDYKE
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L3N6, Canada
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10
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Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 2011; 21:1916-28. [PMID: 21994248 DOI: 10.1101/gr.108753.110] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes--especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.
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Affiliation(s)
- Michael F Lin
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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11
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Hutter B, Bieg M, Helms V, Paulsen M. Divergence of imprinted genes during mammalian evolution. BMC Evol Biol 2010; 10:116. [PMID: 20429903 PMCID: PMC2875234 DOI: 10.1186/1471-2148-10-116] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 04/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In contrast to the majority of mammalian genes, imprinted genes are monoallelically expressed with the choice of the active allele depending on its parental origin. Due to their special inheritance patterns, maternally and paternally expressed genes might be under different evolutionary pressure. Here, we aimed at assessing the evolutionary history of imprinted genes. RESULTS In this study, we investigated the conservation of imprinted genes in vertebrate genomes and their exposition to natural selection. In a genome-wide comparison, orthologs of imprinted genes show a stronger divergence on cDNA and protein level in mammals. This pattern is most pronounced for maternally expressed genes in rodents in comparison to their non-rodent orthologs. The divergence is not attributable to increased mutation of CpG positions. It is contrasted by strong conservation of paternally expressed genes in mouse and rat. Interestingly, we found that the early divergence of imprinted genes was accompanied by an unusually strict conservation of their paralogs. CONCLUSIONS The apparent degeneration of maternally expressed genes may reflect a relaxation of selective pressure due to counteracting effects on maternal and embryonic fitness. Functional redundancy provided by the presence of highly conserved (non-imprinted) paralogs may have facilitated the divergence. Moreover, intensification of imprinting in modern rodents seems to have shifted the evolutionary fate of imprinted genes towards strong purifying selection.
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Affiliation(s)
- Barbara Hutter
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
| | - Matthias Bieg
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Lehrstuhl für Computational Biology, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
| | - Martina Paulsen
- Lehrstuhl für Genetik/Epigenetik, Universität des Saarlandes, Postfach 151150, D-66041 Saarbrücken, Germany
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12
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Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res 2009; 38:1071-85. [PMID: 19969543 PMCID: PMC2831330 DOI: 10.1093/nar/gkp1124] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) in teleosts, we discover a set of 38 candidate cis-regulatory coding exons (RCEs) with predicted target genes. These elements demonstrate evolutionary separation of overlapping protein-coding and regulatory information after WGD in teleosts. We present evidence that the corresponding mammalian exons are still under both coding and non-coding selection pressure, are more conserved than other protein coding exons in the host gene and several control sets, and share key characteristics with highly conserved non-coding elements in the same regions. Their dual function is corroborated by existing experimental data. Additionally, we show examples of human exon remnants stemming from the vertebrate 2R WGD. Our findings suggest that long-range cis-regulatory inputs for developmental genes are not limited to non-coding regions, but can also overlap the coding sequence of unrelated genes. Thus, exonic regulatory elements in GRBs might be functionally equivalent to those in non-coding regions, calling for a re-evaluation of the sequence space in which to look for long-range regulatory elements and experimentally test their activity.
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Affiliation(s)
- Xianjun Dong
- Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
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13
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Fishman SL, Branch AD. The quasispecies nature and biological implications of the hepatitis C virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2009; 9:1158-67. [PMID: 19666142 PMCID: PMC2790008 DOI: 10.1016/j.meegid.2009.07.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/24/2009] [Accepted: 07/31/2009] [Indexed: 12/18/2022]
Abstract
Many RNA viruses exist as a cloud of closely related sequence variants called a quasispecies, rather than as a population of identical clones. In this article, we explain the quasispecies nature of RNA viral genomes, and briefly review the principles of quasispecies dynamics and the differences with classical population genetics. We then discuss the current methods for quasispecies analysis and conclude with the biological implications of this phenomenon, focusing on the hepatitis C virus.
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Affiliation(s)
- Sarah L Fishman
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
| | - Andrea D Branch
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
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14
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Wang Q, Barr I, Guo F, Lee C. Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene. RNA (NEW YORK, N.Y.) 2008; 14:2478-88. [PMID: 18974280 PMCID: PMC2590956 DOI: 10.1261/rna.1252608] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 09/24/2008] [Indexed: 05/20/2023]
Abstract
RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 2'-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.
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Affiliation(s)
- Qi Wang
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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15
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Revisiting horizontal transfer of transposable elements in Drosophila. Heredity (Edinb) 2008; 100:545-54. [DOI: 10.1038/sj.hdy.6801094] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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16
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Ludwig A, Valente VLDS, Loreto ELS. Multiple invasions of Errantivirus in the genus Drosophila. INSECT MOLECULAR BIOLOGY 2008; 17:113-124. [PMID: 18353101 DOI: 10.1111/j.1365-2583.2007.00787.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Aiming to contribute to the knowledge of the evolutionary history of Errantivirus, a phylogenetic analysis of the env gene sequences of Errantivirus gypsy, gtwin, gypsy2, gypsy3, gypsy4 and gypsy6 was carried out in 33 Drosophilidae species. Most sequences were obtained from in silico searches in the Drosophila genomes. The complex evolutionary pattern reported by other authors for the gypsy retroelement was also observed in the present study, including vertical transmission, ancestral polymorphism, stochastic loss and horizontal transfer. Moreover, the elements gypsy2, gypsy3, gypsy4 and gypsy6 were shown to have followed an evolutionary model that is similar to gypsy. Fifteen new possible cases of horizontal transfer were suggested. The infectious potential of these elements may help elucidate the evolutionary scenario described in the present study.
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Affiliation(s)
- A Ludwig
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
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17
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Ke S, Zhang XHF, Chasin LA. Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res 2008; 18:533-43. [PMID: 18204002 DOI: 10.1101/gr.070268.107] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have used comparative genomics to characterize the evolutionary behavior of predicted splicing regulatory motifs. Using base substitution rates in intronic regions as a calibrator for neutral change, we found a strong avoidance of synonymous substitutions that disrupt predicted exonic splicing enhancers or create predicted exonic splicing silencers. These results attest to the functionality of the hexameric motif set used and suggest that they are subject to purifying selection. We also found that synonymous substitutions in constitutive exons tend to create exonic splicing enhancers and to disrupt exonic splicing silencers, implying positive selection for these splicing promoting events. We present evidence that this positive selection is the result of splicing-positive events compensating for splicing-negative events as well as for mutations that weaken splice-site sequences. Such compensatory events include nonsynonymous mutations, synonymous mutations, and mutations at splice sites. Compensation was also seen from the fact that orthologous exons tend to maintain the same number of predicted splicing motifs. Our data fit a splicing compensation model of exon evolution, in which selection for splicing-positive mutations takes place to counter the effect of an ongoing splicing-negative mutational process, with the exon as a whole being conserved as a unit of splicing. In the course of this analysis, we observed that synonymous positions in general are conserved relative to intronic sequences, suggesting that messenger RNA molecules are rich in sequence information for functions beyond protein coding and splicing.
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Affiliation(s)
- Shengdong Ke
- Department of Biological Sciences Columbia University New York, New York 10027, USA
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18
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Parmley JL, Hurst LD. How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations? J Mol Evol 2007; 64:646-55. [PMID: 17557167 DOI: 10.1007/s00239-006-0207-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 03/07/2007] [Indexed: 12/14/2022]
Abstract
One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (K (A)) to the corresponding figure for synonymous substitutions (K (S)). A ratio (K (A)/K (S)) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic K (A)/K (S) peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with K (A)/K (S) > 1 from more than 1000 long mouse-rat orthologues. Approximately one K (A)/K (S) > 1 peak is found per 12-15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low K (S) values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic K (S) are rare. As so few K (A)/K (S) peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.
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Affiliation(s)
- Joanna L Parmley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:36-49. [PMID: 18380339 DOI: 10.1007/978-0-387-77374-2_3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Prior to genomics, studies of alternative splicing primarily focused on the function and mechanism of alternative splicing in individual genes and exons. This has changed dramatically since the late 1990s. High-throughput genomics technologies, such as EST sequencing and microarrays designed to detect changes in splicing, led to genome-wide discoveries and quantification of alternative splicing in a wide range of species from human to Arabidopsis. Consensus estimates of AS frequency in the human genome grew from less than 5% in mid-1990s to as high as 60-74% now. The rapid growth in sequence and microarray data for alternative splicing has made it possible to look into the global impact of alternative splicing on protein function and evolution of genomes. In this chapter, we review recent research on alternative splicing's impact on proteomic complexity and its role in genome evolution.
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Affiliation(s)
- Yi Xing
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, USA
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20
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Kalamegham R, Sturgill D, Siegfried E, Oliver B. Drosophila mojoless, a retroposed GSK-3, has functionally diverged to acquire an essential role in male fertility. Mol Biol Evol 2006; 24:732-42. [PMID: 17179138 PMCID: PMC2292417 DOI: 10.1093/molbev/msl201] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Retroposition is increasingly recognized as an important mechanism for the acquisition of new genes. We show that a glycogen synthase kinase-3 gene, shaggy (sgg), retroposed at least 50 MYA in the Drosophila genus to generate a new gene, mojoless (mjl). We have extensively analyzed the function of mjl and examined its functional divergence from the parental gene sgg in Drosophila melanogaster. Unlike Sgg, which is expressed in many tissues of both sexes, Mjl is expressed specifically in the male germ line, where it is required for male germ line survival. Our analysis indicates that mjl has acquired a specific function in the maintenance of male germ line viability. However, it has not completely lost its ancestral biochemical function and can partially compensate for loss of the parental gene sgg when ectopically expressed in somatic cells. We postulate that mjl has undergone functional diversification and is now under stabilizing selection in the Drosophila genus.
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Affiliation(s)
- Rasika Kalamegham
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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21
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Zhang XHF, Chasin LA. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci U S A 2006; 103:13427-32. [PMID: 16938881 PMCID: PMC1569180 DOI: 10.1073/pnas.0603042103] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Orthologous gene structures in eight vertebrate species were compared on a genomic scale to detect the birth and maturation of new internal exons during the course of evolution. We found that 40% of new human exons are alternatively spliced, and most of these are cassette exons (exons that are either included or skipped in their entirety) with low inclusion rates. This proportion decreases steadily as older and older exons are examined, even as splicing efficiency increases. Remarkably, the great majority of new cassette exons are composed of highly repeated sequences, especially Alu. Many new cassette exons are 5' untranslated exons; the proportion that code for protein increases steadily with age. New protein-coding exons evolve at a high rate, as evidenced by the initially high substitution rates (K(s) and K(a)), as well as the SNP density compared with older exons. This dynamic picture suggests that de novo recruitment rather than shuffling is the major route by which exons are added to genes, and that species-specific repeats could play a significant role in recent evolution.
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Affiliation(s)
- Xiang H.-F. Zhang
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Lawrence A. Chasin
- Department of Biological Sciences, Columbia University, New York, NY 10027
- To whom correspondence should be addressed. E-mail:
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Xing Y, Lee C. Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet 2006; 7:499-509. [PMID: 16770337 DOI: 10.1038/nrg1896] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide analyses of alternative splicing have established its nearly ubiquitous role in gene regulation in many organisms. Genome sequencing and comparative genomics have made it possible to look in detail at the evolutionary history of specific alternative exons or splice sites, resulting in a flurry of publications in recent years. Here, we consider how alternative splicing has contributed to the evolution of modern genomes, and discuss constraints on evolution associated with alternative splicing that might have important medical implications.
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Affiliation(s)
- Yi Xing
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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Ermakova EO, Nurtdinov RN, Gelfand MS. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics 2006; 7:84. [PMID: 16620375 PMCID: PMC1459143 DOI: 10.1186/1471-2164-7-84] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 04/18/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways. RESULTS A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (dN), the rate of synonymous substitutions (dS), and their ratio (omega = dN/dS) appear to be significantly higher in alternatively spliced coding regions compared to constitutive regions. When N-terminal, internal and C-terminal alternatives are analysed separately, C-terminal alternatives appear to make the main contribution to the observed difference. The effects become even more pronounced in a subset of fast evolving genes. CONCLUSION These results provide evidence of weaker purifying selection and/or stronger positive selection in alternative regions and thus one more confirmation of accelerated evolution in alternative regions. This study corroborates the theory that alternative splicing serves as a testing ground for molecular evolution.
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Affiliation(s)
- Ekaterina O Ermakova
- Department of Bioengineering and Bioinformatics, Moscow State University, Vorob'evy gory, 1-73, 119992, Moscow, Russia
- Research and Training Center "Bioinformatics", Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per. 19, 127994, Moscow, Russia
| | - Ramil N Nurtdinov
- Department of Bioengineering and Bioinformatics, Moscow State University, Vorob'evy gory, 1-73, 119992, Moscow, Russia
| | - Mikhail S Gelfand
- Department of Bioengineering and Bioinformatics, Moscow State University, Vorob'evy gory, 1-73, 119992, Moscow, Russia
- Research and Training Center "Bioinformatics", Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per. 19, 127994, Moscow, Russia
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