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Shao Y, Yang S, Cheng L, Duan J, Li J, Kang J, Wang F, Liu J, Zheng F, Ma J, Zhang Y. Identification of chromosomal abnormalities in miscarriages by CNV-Seq. Mol Cytogenet 2024; 17:4. [PMID: 38369498 PMCID: PMC10875874 DOI: 10.1186/s13039-024-00671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVE The primary object of this study is to analyze chromosomal abnormalities in miscarriages detected by copy number variants sequencing (CNV-Seq), establish potential pathways or genes related to miscarriages, and provide guidance for birth health in the following pregnancies. METHODS This study enrolled 580 miscarriage cases with paired clinical information and chromosomal detection results analyzed by CNV-Seq. Further bioinformatic analyses were performed on validated pathogenic CNVs (pCNVs). RESULTS Of 580 miscarriage cases, three were excluded as maternal cell contamination, 357 cases showed abnormal chromosomal results, and the remaining 220 were normal, with a positive detection rate of 61.87% (357/577). In the 357 miscarriage cases, 470 variants were discovered, of which 65.32% (307/470) were pathogenic. Among all variants detected, 251 were numerical chromosomal abnormalities, and 219 were structural abnormalities. With advanced maternal age, the proportion of numerical abnormalities increased, but the proportion of structural abnormalities decreased. Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology analysis revealed that eleven pathways and 636 biological processes were enriched in pCNVs region genes. Protein-protein interaction analysis of 226 dosage-sensitive genes showed that TP53, CTNNB1, UBE3A, EP300, SOX2, ATM, and MECP2 might be significant in the development of miscarriages. CONCLUSION Our study provides evidence that chromosomal abnormalities contribute to miscarriages, and emphasizes the significance of microdeletions or duplications in causing miscarriages apart from numerical abnormalities. Essential genes found in pCNVs regions may account for miscarriages which need further validation.
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Affiliation(s)
- Yuqi Shao
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Saisai Yang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Lin Cheng
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Jie Duan
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Jin Li
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiawei Kang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Fang Wang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Juan Liu
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Fang Zheng
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jianhong Ma
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China
| | - Yuanzhen Zhang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, 430071, China.
- Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, 430071, China.
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MINCER ST, NIETHAMER TK, TENG T, BUSH JO, PERCIVAL CJ. Investigating the effects of compound paralogous EPHB receptor mutations on mouse facial development. Dev Dyn 2022; 251:1138-1155. [PMID: 35025117 PMCID: PMC9924224 DOI: 10.1002/dvdy.454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Variation in facial shape may arise from the combinatorial or overlapping actions of paralogous genes. Given its many members, and overlapping expression and functions, the EPH receptor family is a compelling candidate source of craniofacial morphological variation. We performed a detailed morphometric analysis of an allelic series of E14.5 Ephb1-3 receptor mutants to determine the effect of each paralogous receptor gene on craniofacial morphology. RESULTS We found that Ephb1, Ephb2, and Ephb3 genotypes significantly influenced facial shape, but Ephb1 effects were weaker than Ephb2 and Ephb3 effects. Ephb2-/- and Ephb3-/- mutations affected similar aspects of facial morphology, but Ephb3-/- mutants had additional facial shape effects. Craniofacial differences across the allelic series were largely consistent with predicted additive genetic effects. However, we identified a potentially important nonadditive effect where Ephb1 mutants displayed different morphologies depending on the combination of other Ephb paralogs present, where Ephb1+/- , Ephb1-/- , and Ephb1-/- ; Ephb3-/- mutants exhibited a consistent deviation from their predicted facial shapes. CONCLUSIONS This study provides a detailed assessment of the effects of Ephb receptor gene paralogs on E14.5 mouse facial morphology and demonstrates how the loss of specific receptors contributes to facial dysmorphology.
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Affiliation(s)
- Sarah T. MINCER
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Terren K. NIETHAMER
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Teng TENG
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey O. BUSH
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, United States of America,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America,Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher J. PERCIVAL
- Department of Anthropology, Stony Brook University, Stony Brook, New York, United States of America
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Sidorova A, Tverdislov V, Levashova N, Garaeva A. A model of autowave self-organization as a hierarchy of active media in the biological evolution. Biosystems 2020; 198:104234. [PMID: 32889101 DOI: 10.1016/j.biosystems.2020.104234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
Within the framework of the active media concept, we develop a biophysical model of autowave self-organization which is treated as a hierarchy of active media in the evolution of the biosphere. We also propose a mathematical model of the autowave process of speciation in a flow of mutations for the three main taxonometric groups (prokaryotes, unicellular and multicellular eukaryotes) with a naturally determined lower boundary of living matter (the appearance of prokaryotes) and an open upper boundary for the formation of new species. It is shown that the fluctuation-bifurcation description of the evolution for the formation of new taxonometric groups as a trajectory of transformation of small fluctuations into giant ones adequately reflects the process of self-organization during the formation of taxa. The major concepts of biological evolution, conditions of hierarchy formation as a fundamental manifestation of self-organization and complexity in the evolution of biological systems are considered.
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Affiliation(s)
- Alla Sidorova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vsevolod Tverdislov
- Head of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Natalia Levashova
- Department of Mathematics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Anastasia Garaeva
- Postgraduate Student of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Al-Salam A, Irwin DM. Evolution of the vertebrate insulin receptor substrate (Irs) gene family. BMC Evol Biol 2017; 17:148. [PMID: 28645244 PMCID: PMC5482937 DOI: 10.1186/s12862-017-0994-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/07/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Insulin receptor substrate (Irs) proteins are essential for insulin signaling as they allow downstream effectors to dock with, and be activated by, the insulin receptor. A family of four Irs proteins have been identified in mice, however the gene for one of these, IRS3, has been pseudogenized in humans. While it is known that the Irs gene family originated in vertebrates, it is not known when it originated and which members are most closely related to each other. A better understanding of the evolution of Irs genes and proteins should provide insight into the regulation of metabolism by insulin. RESULTS Multiple genes for Irs proteins were identified in a wide variety of vertebrate species. Phylogenetic and genomic neighborhood analyses indicate that this gene family originated very early in vertebrae evolution. Most Irs genes were duplicated and retained in fish after the fish-specific genome duplication. Irs genes have been lost of various lineages, including Irs3 in primates and birds and Irs1 in most fish. Irs3 and Irs4 experienced an episode of more rapid protein sequence evolution on the ancestral mammalian lineage. Comparisons of the conservation of the proteins sequences among Irs paralogs show that domains involved in binding to the plasma membrane and insulin receptors are most strongly conserved, while divergence has occurred in sequences involved in interacting with downstream effector proteins. CONCLUSIONS The Irs gene family originated very early in vertebrate evolution, likely through genome duplications, and in parallel with duplications of other components of the insulin signaling pathway, including insulin and the insulin receptor. While the N-terminal sequences of these proteins are conserved among the paralogs, changes in the C-terminal sequences likely allowed changes in biological function.
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Affiliation(s)
- Ahmad Al-Salam
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada.
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Tanz SK, Castleden I, Hooper CM, Small I, Millar AH. Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family. FRONTIERS IN PLANT SCIENCE 2014; 5:396. [PMID: 25161662 PMCID: PMC4130198 DOI: 10.3389/fpls.2014.00396] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/24/2014] [Indexed: 05/20/2023]
Abstract
Sub-functionalization during the expansion of gene families in eukaryotes has occurred in part through specific subcellular localization of different family members. To better understand this process in plants, compiled records of large-scale proteomic and fluorescent protein localization datasets can be explored and bioinformatic predictions for protein localization can be used to predict the gaps in experimental data. This process can be followed by targeted experiments to test predictions. The SUBA3 database is a free web-service at http://suba.plantenergy.uwa.edu.au that helps users to explore reported experimental data and predictions concerning proteins encoded by gene families and to define the experiments required to locate these homologous sets of proteins. Here we show how SUBA3 can be used to explore the subcellular location of the Deg protease family of ATP-independent serine endopeptidases (Deg1-Deg16). Combined data integration and new experiments refined location information for Deg1 and Deg9, confirmed Deg2, Deg5, and Deg8 in plastids and Deg 15 in peroxisomes and provide substantial experimental evidence for mitochondrial localized Deg proteases. Two of these, Deg3 and Deg10, additionally localized to the plastid, revealing novel dual-targeted Deg proteases in the plastid and the mitochondrion. SUBA3 is continually updated to ensure that researchers can use the latest published data when planning the experimental steps remaining to localize gene family functions.
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Affiliation(s)
- Sandra K. Tanz
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- *Correspondence: Sandra K. Tanz, The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia e-mail:
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Ian Small
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - A. Harvey Millar
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
- Centre for Comparative Analysis on Biomolecular Networks, The University of Western AustraliaPerth, WA, Australia
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Yu GX. RULEMINER: A KNOWLEDGE SYSTEM FOR SUPPORTING HIGH-THROUGHPUT PROTEIN FUNCTION ANNOTATIONS. J Bioinform Comput Biol 2011; 2:615-37. [PMID: 15617156 DOI: 10.1142/s0219720004000752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Revised: 03/23/2004] [Accepted: 03/24/2004] [Indexed: 11/18/2022]
Abstract
In this paper, we present RuleMiner, a knowledge system to facilitate a seamless integration of multi-sequence analysis tools and define profile-based rules for supporting high-throughput protein function annotations. This system consists of three essential components, Protein Function Groups (PFGs), PFG profiles and rules. The PFGs, established from an integrated analysis of current knowledge of protein functions from Swiss-Prot database and protein family-based sequence classifications, cover all possible cellular functions available in the database. The PFG profiles illustrate detailed protein features in the PFGs as in sequence conservations, the occurrences of sequence-based motifs, domains and species distributions. The rules, extracted from the PFG profiles, describe the clear relationships between these PFGs and all possible features. As a result, the RuleMiner is able to provide an enhanced capability for protein function analysis, such as results from the integrated sequence analysis tools for given proteins can be comparatively analyzed due to the clear feature-PFG relationships. Also, much needed guidance is readily available for such analysis. If the rules describe one-to-one (unique) relationships between the protein features and the PFGs, then these features can be utilized as unique functional identifiers and cellular functions of unknown proteins can be reliably determined. Otherwise, additional information has to be provided.
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Affiliation(s)
- Gong-Xin Yu
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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Arenas-Mena C. Indirect development, transdifferentiation and the macroregulatory evolution of metazoans. Philos Trans R Soc Lond B Biol Sci 2010; 365:653-69. [PMID: 20083640 PMCID: PMC2817142 DOI: 10.1098/rstb.2009.0253] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is proposed here that a biphasic life cycle with partial dedifferentiation of intermediate juvenile or larval stages represents the mainstream developmental mode of metazoans. Developmental plasticity of differentiated cells is considered the essential characteristic of indirect development, rather than the exclusive development of the adult from 'set-aside' cells. Many differentiated larval cells of indirect developers resume proliferation, partially dedifferentiate and contribute to adult tissues. Transcriptional pluripotency of differentiated states has premetazoan origins and seems to be facilitated by histone variant H2A.Z. Developmental plasticity of differentiated states also facilitates the evolution of polyphenism. Uncertainty remains about whether the most recent common ancestor of protostomes and deuterostomes was a direct or an indirect developer, and how the feeding larvae of bilaterians are related to non-feeding larvae of sponges and cnidarians. Feeding ciliated larvae of bilaterians form their primary gut opening by invagination, which seems related to invagination in cnidarians. Formation of the secondary gut opening proceeds by protostomy or deuterostomy, and gene usage suggests serial homology of the mouth and anus. Indirect developers do not use the Hox vector to build their ciliated larvae, but the Hox vector is associated with the construction of the reproductive portion of the animal during feeding-dependent posterior growth. It is further proposed that the original function of the Hox cluster was in gonad formation rather than in anteroposterior diversification.
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Affiliation(s)
- Cesar Arenas-Mena
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA.
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Liao PC, Lin TP, Lan WC, Chung JD, Hwang SY. Duplication of the class I cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the {alpha}-crystallin domain in the genus Rhododendron (Ericaceae). ANNALS OF BOTANY 2010; 105:57-69. [PMID: 19887471 PMCID: PMC2794073 DOI: 10.1093/aob/mcp272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/11/2009] [Accepted: 10/05/2009] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Positive selection in the -crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation. METHODS A phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16.9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs. KEY RESULTS Two types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension. CONCLUSIONS Functional conservation of the ACD of Rhododendron CT1sHSP genes was inferred b
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Affiliation(s)
- Pei-Chun Liao
- Department of Life Science, Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Tsan-Piao Lin
- Institute of Plant Biology, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan
| | - Wei-Chieh Lan
- Graduate Institute of Biotechnology, Chinese Culture University, 55 Hwagang Road, Yangmingshan, Taipei 11114, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, 53 Nanhai Road, Taipei 10066, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
- For correspondence. E-mail
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Lin YH, Hwang SY, Hsu PY, Chiang YC, Huang CL, Wang CN, Lin TP. Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana. BMC PLANT BIOLOGY 2008; 8:111. [PMID: 18990244 PMCID: PMC2588587 DOI: 10.1186/1471-2229-8-111] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 11/07/2008] [Indexed: 05/08/2023]
Abstract
BACKGROUND CBF/DREB duplicate genes are widely distributed in higher plants and encode transcriptional factors, or CBFs, which bind a DNA regulatory element and impart responsiveness to low temperatures and dehydration. RESULTS We explored patterns of genetic variations of CBF1, -2, and -3 from 34 accessions of Arabidopsis thaliana. Molecular population genetic analyses of these genes indicated that CBF2 has much reduced nucleotide diversity in the transcriptional unit and promoter, suggesting that CBF2 has been subjected to a recent adaptive sweep, which agrees with reports of a regulatory protein of CBF2. Investigating the ratios of Ka/Ks between all paired CBF paralogus genes, high conservation of the AP2 domain was observed, and the major divergence of proteins was the result of relaxation in two regions within the transcriptional activation domain which was under positive selection after CBF duplication. With respect to the level of CBF gene expression, several mutated nucleotides in the promoters of CBF3 and -1 of specific ecotypes might be responsible for its consistently low expression. CONCLUSION We concluded from our data that important evolutionary changes in CBF1, -2, and -3 may have primarily occurred at the level of gene regulation as well as in protein function.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Gene Expression Regulation, Plant
- Gene Knockdown Techniques
- Gene Knockout Techniques
- Genes, Duplicate/genetics
- Genetics, Population
- Genome, Plant/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Genetic
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- Selection, Genetic
- Sequence Analysis, DNA
- Trans-Activators/chemistry
- Trans-Activators/genetics
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription, Genetic
- Transcriptional Activation/genetics
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Affiliation(s)
- Yen-Heng Lin
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Shih-Ying Hwang
- Department of Life Sciences, National Taiwan Normal University, Taipei 10610, Taiwan
| | - Po-Yen Hsu
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Chung Chiang
- Department of Life Science, Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Chun-Lin Huang
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Neng Wang
- Department of Life Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Tsan-Piao Lin
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
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10
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Crotwell PL, Mabee PM. Gene expression patterns underlying proximal-distal skeletal segmentation in late-stage zebrafish, Danio rerio. Dev Dyn 2008; 236:3111-28. [PMID: 17948314 DOI: 10.1002/dvdy.21352] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Timing and pattern of expression of ten candidate segmentation genes or gene pairs were reviewed or examined in developing median fins of late-stage zebrafish, Danio rerio. We found a general correspondence in timing and pattern of expression between zebrafish fin radial segmentation and tetrapod joint development, suggesting that molecular mechanisms underlying radial segmentation have been conserved over 400 million years of evolution. Gene co-expression during segmentation (5.5-6.5 mm SL) is similar between tetrapods and zebrafish: bmp2b, bmp4, chordin, and gdf5 in interradial mesenchyme and ZS; bapx1, col2a1, noggin3, and sox9a in chondrocytes. Surprisingly, wnt9a is not expressed in the developing median fins, though wnt9b is detected. In contrast to all other candidate segmentation genes we examined, bapx1 is not expressed in the caudal fin, which does not segment. Together, these data suggest a scenario of gene interactions underlying radial segmentation based on the patterns and timing of candidate gene expression.
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Affiliation(s)
- Patricia L Crotwell
- Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA
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11
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Jackson PJ, Douglas NR, Chai B, Binkley J, Sidow A, Barsh GS, Millhauser GL. Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins. CHEMISTRY & BIOLOGY 2006; 13:1297-305. [PMID: 17185225 PMCID: PMC2907901 DOI: 10.1016/j.chembiol.2006.10.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 09/20/2006] [Accepted: 10/11/2006] [Indexed: 10/23/2022]
Abstract
Agouti (ASIP) and Agouti-related protein (AgRP) are endogenous antagonists of melanocortin receptors that play critical roles in the regulation of pigmentation and energy balance, respectively, and which arose from a common ancestral gene early in vertebrate evolution. The N-terminal domain of ASIP facilitates antagonism by binding to an accessory receptor, but here we show that the N-terminal domain of AgRP has the opposite effect and acts as a prodomain that negatively regulates antagonist function. Computational analysis reveals similar patterns of evolutionary constraint in the ASIP and AgRP C-terminal domains, but fundamental differences between the N-terminal domains. These studies shed light on the relationships between regulation of pigmentation and body weight, and they illustrate how evolutionary structure function analysis can reveal both unique and common mechanisms of action for paralogous gene products.
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Affiliation(s)
- Pilgrim J. Jackson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
| | - Nick R. Douglas
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
| | - Biaoxin Chai
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0682
| | - Jonathan Binkley
- Department of Pathology, Stanford University Medical Center, Stanford, California 94305
| | - Arend Sidow
- Department of Genetics, Stanford University Medical Center, Stanford, California 94305
- Department of Pathology, Stanford University Medical Center, Stanford, California 94305
| | - Gregory S. Barsh
- Department of Genetics, Stanford University Medical Center, Stanford, California 94305
- Department of Pediatrics, Stanford University Medical Center, Stanford, California 94305
| | - Glenn L. Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064
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Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem 2006; 281:36149-61. [PMID: 16990279 DOI: 10.1074/jbc.m605449200] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Haloacid dehalogenase (HAD)-like hydrolases are a vast superfamily of largely uncharacterized enzymes, with a few members shown to possess phosphatase, beta-phosphoglucomutase, phosphonatase, and dehalogenase activities. Using a representative set of 80 phosphorylated substrates, we characterized the substrate specificities of 23 soluble HADs encoded in the Escherichia coli genome. We identified small molecule phosphatase activity in 21 HADs and beta-phosphoglucomutase activity in one protein. The E. coli HAD phosphatases show high catalytic efficiency and affinity to a wide range of phosphorylated metabolites that are intermediates of various metabolic reactions. Rather than following the classical "one enzyme-one substrate" model, most of the E. coli HADs show remarkably broad and overlapping substrate spectra. At least 12 reactions catalyzed by HADs currently have no EC numbers assigned in Enzyme Nomenclature. Surprisingly, most HADs hydrolyzed small phosphodonors (acetyl phosphate, carbamoyl phosphate, and phosphoramidate), which also serve as substrates for autophosphorylation of the receiver domains of the two-component signal transduction systems. The physiological relevance of the phosphatase activity with the preferred substrate was validated in vivo for one of the HADs, YniC. Many of the secondary activities of HADs might have no immediate physiological function but could comprise a reservoir for evolution of novel phosphatases.
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Affiliation(s)
- Ekaterina Kuznetsova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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13
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Sharov AA. Genome increase as a clock for the origin and evolution of life. Biol Direct 2006; 1:17. [PMID: 16768805 PMCID: PMC1526419 DOI: 10.1186/1745-6150-1-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 06/12/2006] [Indexed: 11/25/2022] Open
Abstract
Background The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution. Results I propose a hypothesis that biological complexity increased exponentially during evolution. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution. A strong version of the exponential hypothesis is that the rate of complexity increase in early (pre-prokaryotic) evolution of life was at most the same (or even slower) than observed in the evolution of prokaryotes and eukaryotes. Conclusion The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis. If the strong exponential hypothesis is true, then the origin of life should be dated 10 billion years ago. Thus, the possibility of panspermia as a source of life on earth should be discussed on equal basis with alternative hypotheses of de-novo life origin. Panspermia may be proven if bacteria similar to terrestrial ones are found on other planets or satellites in the solar system. Reviewers This article was reviewed by Eugene V. Koonin, Chris Adami and Arcady Mushegian.
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Affiliation(s)
- Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging (NIA/NIH), 333 Cassell Dr., Baltimore, MD 21224, USA
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14
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Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H. Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evol Dev 2006; 8:30-45. [PMID: 16409381 DOI: 10.1111/j.1525-142x.2006.05073.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The MADS-box gene AGAMOUS (AG) plays a key role in determining floral meristem and organ identities. We identified three AG homologs, EScaAG1, EScaAG2, and EScaAGL11 from the basal eudicot Eschscholzia californica (California poppy). Phylogenetic analyses indicate that EScaAG1 and EScaAG2 are recent paralogs within the AG clade, independent of the duplication in ancestral core eudicots that gave rise to the euAG and PLENA (PLE) orthologs. EScaAGL11 is basal to core eudicot AGL11 orthologs in a clade representing an older duplication event after the divergence of the angiosperm and gymnosperm lineages. Detailed in situ hybridization experiments show that expression of EScaAG1 and EScaAG2 is similar to AG; however, both genes appear to be expressed earlier in floral development than described in the core eudicots. A thorough examination of available expression and functional data in a phylogenetic context for members of the AG and AGL11 clades reveals that gene expression has been quite variable throughout the evolutionary history of the AG subfamily and that ovule-specific expression might have evolved more than twice. Although sub- and neofunctionalization are inferred to have occurred following gene duplication, functional divergence among orthologs is evident, as is convergence, among paralogs sampled from different species. We propose that retention of multiple AG homologs in several paralogous lineages can be explained by the conservation of ancestral protein activity combined with evolutionarily labile regulation of expression in the AG and AGL11 clades such that the collective functions of the AG subfamily in stamen and carpel development are maintained following gene duplication.
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Affiliation(s)
- Laura M Zahn
- Department of Biology, The Huck Institutes of the Life Sciences, and the Institute for Molecular Genetics and Evolution, The Pennsylvania State University, University Park, PA 16802, USA
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15
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Yu GX, Glass EM, Karonis NT, Maltsev N. Knowledge-based voting algorithm for automated protein functional annotation†. Proteins 2005; 61:907-17. [PMID: 16252283 DOI: 10.1002/prot.20652] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Automated annotation of high-throughput genome sequences is one of the earliest steps toward a comprehensive understanding of the dynamic behavior of living organisms. However, the step is often error-prone because of its underlying algorithms, which rely mainly on a simple similarity analysis, and lack of guidance from biological rules. We present herein a knowledge-based protein annotation algorithm. Our objectives are to reduce errors and to improve annotation confidences. This algorithm consists of two major components: a knowledge system, called "RuleMiner," and a voting procedure. The knowledge system, which includes biological rules and functional profiles for each function, provides a platform for seamless integration of multiple sequence analysis tools and guidance for function annotation. The voting procedure, which relies on the knowledge system, is designed to make (possibly) unbiased judgments in functional assignments among complicated, sometimes conflicting, information. We have applied this algorithm to 10 prokaryotic bacterial genomes and observed a significant improvement in annotation confidences. We also discuss the current limitations of the algorithm and the potential for future improvement.
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Affiliation(s)
- G X Yu
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
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16
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Wirth B, Louis VL, Potier S, Souciet JL, Despons L. Paleogenomics or the Search for Remnant Duplicated Copies of the Yeast DUP240 Gene Family in Intergenic Areas. Mol Biol Evol 2005; 22:1764-71. [PMID: 15917500 DOI: 10.1093/molbev/msi170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. Using an original three-step method of analysis reported here, both slightly and highly degenerate DUP240 copies, called pseudo-open reading frames (ORFs) and relics, respectively, were detected in strain S288C. It was concluded that two previously annotated ORFs correspond, in fact, to pseudo-ORFs and three additional relics were identified in intergenic areas. Comparative intraspecies analysis of these degenerate DUP240 loci revealed that the two pseudo-ORFs are present in a nondegenerate state in some other strains. This suggests that within a given gene family different loci are the target of the gene erasure process, which is therefore strain dependent. Besides, the variable positions observed indicate that the relic sequence may diverge faster than the flanking regions. All in all, this study shows that short conserved protein motifs provide a useful tool for detecting and accurately mapping degenerate gene remnants. The present results also highlight the strong contribution of comparative genomics for gene relic detection because the possibility of finding short conserved protein motifs in intergenic regions (IRs) largely depends on the choice of the most closely related paralog or ortholog. By mapping new genetic components in previously annotated IRs, our study constitutes a further refinement step in the crucial stage of genome annotation and provides a strategy for retracing ancient chromosomal reshaping events and, hence, for deciphering genome history.
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Affiliation(s)
- Bénédicte Wirth
- Laboratoire de Dynamique, Evolution et Expression de Génomes de Microorganismes, FRE 2326 ULP/CNRS, Institut de Botanique, Strasbourg, France
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17
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Torgerson DG, Singh RS. Rapid evolution through gene duplication and subfunctionalization of the testes-specific alpha4 proteasome subunits in Drosophila. Genetics 2005; 168:1421-32. [PMID: 15579695 PMCID: PMC1448786 DOI: 10.1534/genetics.104.027631] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Evidence suggests that duplicated genes are retained at a much higher rate than originally thought and that functional divergence of gene copies is a major factor promoting their retention in the genome. We find that two Drosophila testes-specific alpha4 proteasome subunit genes (alpha4-t1 and alpha4-t2) have a higher polymorphism within species and are significantly more diverged between species than the somatic alpha4 gene. Our data suggest that following gene duplication, the alpha4-t1 gene experienced relaxed selective constraints, whereas the alpha4-t2 gene experienced positive selection acting on several codons. We report significant heterogeneity in evolutionary rates among all three paralogs at homologous codons, indicating that functional divergence has coincided with genic divergence. Reproductive subfunctionalization may allow for a more rapid evolution of reproductive traits and a greater specialization of testes function. Our data add to the increasing evidence that duplicated genes experience lower selective constraints and in some cases positive selection following duplication. Newly duplicated genes that are freer from selective constraints may provide a mechanism for developing new interactions and a pathway for the evolution of new genes.
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Affiliation(s)
- Dara G Torgerson
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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18
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Aguileta G, Bielawski JP, Yang Z. Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol 2005; 59:177-89. [PMID: 15486692 DOI: 10.1007/s00239-004-2612-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 02/16/2004] [Indexed: 11/26/2022]
Abstract
Different models of gene family evolution have been proposed to explain the mechanism whereby gene copies created by gene duplications are maintained and diverge in function. Ohta proposed a model which predicts a burst of nonsynonymous substitutions following gene duplication and the preservation of duplicates through positive selection. An alternative model, the duplication-degeneration-complementation (DDC) model, does not explicitly require the action of positive Darwinian selection for the maintenance of duplicated gene copies, although purifying selection is assumed to continue to act on both copies. A potential outcome of the DDC model is heterogeneity in purifying selection among the gene copies, due to partitioning of subfunctions which complement each other. By using the d(N)/ d(S) (omega) rate ratio to measure selection pressure, we can distinguish between these two very different evolutionary scenarios. In this study we investigated these scenarios in the beta-globin family of genes, a textbook example of evolution by gene duplication. We assembled a comprehensive dataset of 72 vertebrate beta-globin sequences. The estimated phylogeny suggested multiple gene duplication and gene conversion events. By using different programs to detect recombination, we confirmed several cases of gene conversion and detected two new cases. We tested evolutionary scenarios derived from Ohta's model and the DDC model by examining selective pressures along lineages in a phylogeny of beta-globin genes in eutherian mammals. We did not find significant evidence for an increase in the omega ratio following major duplication events in this family. However, one exception to this pattern was the duplication of gamma-globin in simian primates, after which a few sites were identified to be under positive selection. Overall, our results suggest that following gene duplications, paralogous copies of beta-globin genes evolved under a nonepisodic process of functional divergence.
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Affiliation(s)
- Gabriela Aguileta
- Department of Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, England
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19
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Newcomb RD, Gleeson DM, Yong CG, Russell RJ, Oakeshott JG. Multiple mutations and gene duplications conferring organophosphorus insecticide resistance have been selected at the Rop-1 locus of the sheep blowfly, Lucilia cuprina. J Mol Evol 2005; 60:207-20. [PMID: 15785849 DOI: 10.1007/s00239-004-0104-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2004] [Accepted: 09/09/2004] [Indexed: 11/27/2022]
Abstract
Sequences of the esterase gene alpha E7 were compared across 41 isogenic (IV) strains of the sheep blowfly, Lucilia cuprina, and one strain of the sibling species, L. sericata. The 1.2-kb region sequenced includes sites of two insecticide resistance mutations. Gly137Asp confers resistance to organophosphorus insecticides (OPs), particularly preferring diethyl OPs such as diazinon, while Trp251Leu prefers dimethyl OPs, and particularly malathion, with the additional presence of carboxylester moieties. We found that there are just eight haplotypes among the 41 chromosomes studied: two Gly137Asp containing haplotypes, two Trp251Leu containing haplotypes, and four susceptible haplotypes, including the L. sericata sequence. While phylogenetic analysis of these haplotypes suggests that the Asp137 and Leu251 mutations each arose at least twice, evidence for recombination was detected across the region, therefore single origins for these resistance mutations cannot be ruled out. Levels of linkage disequilibrium in the data are high and significant hitchhiking is indicated by Fay and Wu' s H test but not the Tajima test. A test of haplotype diversity indicates a paucity of diversity compared with neutral expectations. Both these results are consistent with a very recent selective sweep at the Lc alphaE7 locus. Interestingly, gene duplications of three different combinations of OP resistant haplotypes were identified in seven of the isogenic (IV) strains. All three types of duplication involve an Asp137 and a Trp251 haplotype. To examine whether more haplotypes existed before the hypothesised selective sweep, fragments of alpha E7 surrounding the resistance mutations were amplified from pinned material dating back to before OPs were used. Four new sequence haplotypes, not sampled in the survey of extant haplotypes, were obtained that are all associated with susceptibility. This is suggestive of a higher historical level of susceptible allelic diversity at this locus.
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Affiliation(s)
- Richard D Newcomb
- Gene Technologies Sector, The Horticulture and Food Research Institute of New Zealand, Private Bag 92169 Auckland, New Zealand.
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20
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Sun ES, Molini BJ, Barrett LK, Centurion-Lara A, Lukehart SA, Van Voorhis WC. Subfamily I Treponema pallidum repeat protein family: sequence variation and immunity. Microbes Infect 2005; 6:725-37. [PMID: 15207819 DOI: 10.1016/j.micinf.2004.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Accepted: 04/05/2004] [Indexed: 10/26/2022]
Abstract
A 12-membered Treponema pallidum repeat (Tpr) protein family has been identified in T. pallidum subsp. pallidum, the causative agent of syphilis. The subfamily I Tpr proteins (C, D, F, and I) possess conserved sequence at the N- and C-termini and central regions that differentiate the members. These proteins may be important in the immune response during syphilis infection and in protective immunity. Strong antibody responses have been observed toward some of the subfamily I Tpr proteins during infection with different syphilis isolates. Some sequence variation has also been identified in one subfamily I Tpr member, TprD, among T. pallidum subsp. pallidum isolates. In this study, we examined sequences in the remaining subfamily I Tpr proteins among strains. Both TprF and TprI were conserved among T. pallidum subsp. pallidum isolates. While some heterogeneity was identified in TprC. We further examined the immune response and protective capacity of TprF protein in this paper. We demonstrate that the N-terminal conserved region of the subfamily I Tpr proteins elicits strong antibody and T-cell responses during infection, and immunization with this region attenuates syphilitic lesion development upon infectious challenge.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Bacterial/blood
- Antigenic Variation
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/immunology
- Colony Count, Microbial
- Conserved Sequence
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Disease Models, Animal
- Genes, Bacterial
- Immunization
- Lymphocyte Activation
- Molecular Sequence Data
- Polymorphism, Genetic
- Rabbits
- Sequence Alignment
- Sequence Analysis, DNA
- Syphilis, Cutaneous/immunology
- Syphilis, Cutaneous/microbiology
- Syphilis, Cutaneous/pathology
- Treponema pallidum/genetics
- Treponema pallidum/immunology
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Affiliation(s)
- Eileen S Sun
- Department of Pathobiology, University of Washington, Box 357185, 1959 NE Pacific Street, Seattle, WA 98195, USA
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21
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Jordan IK, Wolf YI, Koonin EV. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004; 4:22. [PMID: 15238160 PMCID: PMC481058 DOI: 10.1186/1471-2148-4-22] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 07/06/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene duplication is an important mechanism that can lead to the emergence of new functions during evolution. The impact of duplication on the mode of gene evolution has been the subject of several theoretical and empirical comparative-genomic studies. It has been shown that, shortly after the duplication, genes seem to experience a considerable relaxation of purifying selection. RESULTS Here we demonstrate two opposite effects of gene duplication on evolutionary rates. Sequence comparisons between paralogs show that, in accord with previous observations, a substantial acceleration in the evolution of paralogs occurs after duplication, presumably due to relaxation of purifying selection. The effect of gene duplication on evolutionary rate was also assessed by sequence comparison between orthologs that have paralogs (duplicates) and those that do not (singletons). It is shown that, in eukaryotes, duplicates, on average, evolve significantly slower than singletons. Eukaryotic ortholog evolutionary rates for duplicates are also negatively correlated with the number of paralogs per gene and the strength of selection between paralogs. A tally of annotated gene functions shows that duplicates tend to be enriched for proteins with known functions, particularly those involved in signaling and related cellular processes; by contrast, singletons include an over-abundance of poorly characterized proteins. CONCLUSIONS These results suggest that whether or not a gene duplicate is retained by selection depends critically on the pre-existing functional utility of the protein encoded by the ancestral singleton. Duplicates of genes of a higher biological import, which are subject to strong functional constraints on the sequence, are retained relatively more often. Thus, the evolutionary trajectory of duplicated genes appears to be determined by two opposing trends, namely, the post-duplication rate acceleration and the generally slow evolutionary rate owing to the high level of functional constraints.
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MESH Headings
- Animals
- Base Composition/genetics
- DNA/genetics
- DNA, Archaeal/genetics
- DNA, Bacterial/genetics
- Evolution, Molecular
- Genes/genetics
- Genes/physiology
- Genes, Archaeal/genetics
- Genes, Archaeal/physiology
- Genes, Bacterial/genetics
- Genes, Bacterial/physiology
- Genes, Duplicate/genetics
- Genes, Duplicate/physiology
- Genes, Fungal/genetics
- Genes, Fungal/physiology
- Genes, Insect/genetics
- Genes, Insect/physiology
- Gram-Negative Bacteria/genetics
- Gram-Positive Bacteria/genetics
- Humans
- Mice
- Mutation/genetics
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- I King Jordan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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22
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Dart S, Kron P, Mable BK. Characterizing polyploidy inArabidopsis lyratausing chromosome counts and flow cytometry. ACTA ACUST UNITED AC 2004. [DOI: 10.1139/b03-134] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protocols were developed for both chromosome counts and flow cytometry to assess ploidy level and DNA content for populations of Arabidopsis lyrata L. sampled from Europe (Arabidopsis lyrata subsp. petraea), North America (Arabidopsis lyrata subsp. lyrata), and Japan (Arabidopsis lyrata subsp. kawasakiana). Ploidy variation within this species is not clear, with previous studies having documented both diploid and tetraploid populations. Chromosome counts in this study confirmed ploidy expectations for all populations examined. Individuals from Iceland and North America were diploid (2n = 2x = 16), whereas those from Japanese and Austrian populations were tetraploid (2n = 4x = 32). Flow cytometry was also used successfully to distinguish between ploidy levels, but the need to calibrate DNA content measures with chromosome counts was demonstrated by a deviation from the expected 2:1 ratio between tetraploid and diploid values among European populations (A. lyrata subsp. petraea). This deviation might be explained by a hybrid (allopolyploid) origin or by genomic changes following polyploidization, emphasizing the dynamic nature of polyploid genomes. Variation in DNA content among families was found only for North American populations, but these individuals were sampled from a broader geographic range than those from other regions.Key words: cytogenetics, flow cytometry, polyploidy, Arabidopsis lyrata, genome size, chromosome counts.
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23
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Hyle JW, Shaw RJ, Reines D. Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast. J Biol Chem 2003; 278:28470-8. [PMID: 12746440 PMCID: PMC3367515 DOI: 10.1074/jbc.m303736200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IMP dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo synthesis of GTP. Yeast with mutations in the transcription elongation machinery are sensitive to inhibitors of this enzyme such as 6-azauracil and mycophenolic acid, at least partly because of their inability to transcriptionally induce IMPDH. To understand the molecular basis of this drug-sensitive phenotype, we have dissected the expression and function of a four-gene family in yeast called IMD1 through IMD4. We show here that these family members are distinct, despite a high degree of amino acid identity between the proteins they encode. Extrachromosomal copies of IMD1, IMD3, or IMD4 could not rescue the drug-sensitive phenotype of IMD2 deletants. When overexpressed, IMD3 or IMD4 weakly compensated for deletion of IMD2. IMD1 is transcriptionally silent and bears critical amino acid substitutions compared with IMD2 that destroy its function, offering strong evidence that it is a pseudogene. The simultaneous deletion of all four IMD genes was lethal unless growth media were supplemented with guanine. This suggests that there are no other essential functions of the IMPDH homologs aside from IMP dehydrogenase activity. Although neither IMD3 nor IMD4 could confer drug resistance to cells lacking IMD2, either alone was sufficient to confer guanine prototrophy. The special function of IMD2 was provided by its ability to be transcriptionally induced and the probable intrinsic drug resistance of its enzymatic activity.
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Affiliation(s)
| | | | - Daniel Reines
- To whom correspondence should be addressed: Dept. of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd., Rollins Research Center, Rm. 4023, Atlanta, GA 30322. Tel.: 404-727-3361; Fax: 404-727-3452;
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24
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Kopp A, Graze RM, Xu S, Carroll SB, Nuzhdin SV. Quantitative trait loci responsible for variation in sexually dimorphic traits in Drosophila melanogaster. Genetics 2003; 163:771-87. [PMID: 12618413 PMCID: PMC1462463 DOI: 10.1093/genetics/163.2.771] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To understand the mechanisms of morphological evolution and species divergence, it is essential to elucidate the genetic basis of variation in natural populations. Sexually dimorphic characters, which evolve rapidly both within and among species, present attractive models for addressing these questions. In this report, we map quantitative trait loci (QTL) responsible for variation in sexually dimorphic traits (abdominal pigmentation and the number of ventral abdominal bristles and sex comb teeth) in a natural population of Drosophila melanogaster. To capture the pattern of genetic variation present in the wild, a panel of recombinant inbred lines was created from two heterozygous flies taken directly from nature. High-resolution mapping was made possible by cytological markers at the average density of one per 2 cM. We have used a new Bayesian algorithm that allows QTL mapping based on all markers simultaneously. With this approach, we were able to detect small-effect QTL that were not evident in single-marker analyses. Our results show that at least for some sexually dimorphic traits, a small number of QTL account for the majority of genetic variation. The three strongest QTL account for >60% of variation in the number of ventral abdominal bristles. Strikingly, a single QTL accounts for almost 60% of variation in female abdominal pigmentation. This QTL maps to the chromosomal region that Robertson et al. have found to affect female abdominal pigmentation in other populations of D. melanogaster. Using quantitative complementation tests, we demonstrate that this QTL is allelic to the bric a brac gene, whose expression has previously been shown to correlate with interspecific differences in pigmentation. Multiple bab alleles that confer distinct phenotypes appear to segregate in natural populations at appreciable frequencies, suggesting that intraspecific and interspecific variation in abdominal pigmentation may share a similar genetic basis.
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Affiliation(s)
- Artyom Kopp
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
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25
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Yu JK, Holland ND, Holland LZ. An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolution. Dev Dyn 2002; 225:289-97. [PMID: 12412011 DOI: 10.1002/dvdy.10173] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During amphioxus development, the neural plate is bordered by cells expressing many genes with homologs involved in vertebrate neural crest induction. However, these amphioxus cells evidently lack additional genetic programs for the cell delaminations, migrations, and differentiations characterizing definitive vertebrate neural crest. We characterize an amphioxus winged helix/forkhead gene (AmphiFoxD) closely related to vertebrate FoxD genes. Phylogenetic analysis indicates that the AmphiFoxD is basal to vertebrate FoxD1, FoxD2, FoxD3, FoxD4, and FoxD5. One of these vertebrate genes (FoxD3) consistently marks neural crest during development. Early in amphioxus development, AmphiFoxD is expressed medially in the anterior neural plate as well as in axial (notochordal) and paraxial mesoderm; later, the gene is expressed in the somites, notochord, cerebral vesicle (diencephalon), and hindgut endoderm. However, there is never any expression in cells bordering the neural plate. We speculate that an AmphiFoxD homolog in the common ancestor of amphioxus and vertebrates was involved in histogenic processes in the mesoderm (evagination and delamination of the somites and notochord); then, in the early vertebrates, descendant paralogs of this gene began functioning in the presumptive neural crest bordering the neural plate to help make possible the delaminations and cell migrations that characterize definitive vertebrate neural crest.
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Affiliation(s)
- Jr-Kai Yu
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0202, USA.
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Nembaware V, Crum K, Kelso J, Seoighe C. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res 2002; 12:1370-6. [PMID: 12213774 PMCID: PMC186655 DOI: 10.1101/gr.270902] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2002] [Accepted: 06/25/2002] [Indexed: 11/24/2022]
Abstract
Using a large set of orthologous human and mouse gene pairs, we have characterized genes that have been retained in duplicate in human over timescales comparable to the time of speciation of human and mouse. Orthologous gene pairs for which a paralogous gene has been present for much or all of the time since speciation show an increased rate of nonsynonymous substitution. We have related rate of divergence to functional classification using the Gene Ontology terms. Protein function was found, in some cases, to have a larger impact on rate of evolution than the presence or absence of a paralog. No evidence was found that genes that have been retained in duplicate are weighted toward any functional categories. An increase in the ratio of nonsynonymous to synonymous changes following duplication has previously been reported. However, because amino acid sequences include conservative as well as more freely evolving sites, the ratio of nonsynonymous to synonymous changes tends to be higher for closely related pairs. By measuring the divergence of orthologs only and comparing between genes for which a paralogous gene is either present or absent, we have compared gene pairs that share a common divergence time. We have also found that shorter genes have a higher probability of being found duplicated in the human genome, possibly reflecting a mutational effect.
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Affiliation(s)
- Victoria Nembaware
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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27
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Abstract
The duplication-degeneration-complementation model of duplicate gene preservation by subfunctionalisation is currently the best explanation for the high level of retention of duplicate genes in early vertebrate evolution. But a direct test of the applicability of this model to such ancient evolutionary events may be difficult. More likely, recent duplications in other lineages will allow us to establish general principles concerning the fate of genes of different types that are duplicated in different ways. These principles may be then extrapolated to understanding the early evolution of the vertebrates.
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Affiliation(s)
- Francoise Mazet
- School of Animal and Microbial Sciences, University of Reading, Whiteknights, UK.
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Bishop PN, Takanosu M, Le Goff M, Mayne R. The role of the posterior ciliary body in the biosynthesis of vitreous humour. Eye (Lond) 2002; 16:454-60. [PMID: 12101453 DOI: 10.1038/sj.eye.6700199] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Recently, several groups have published new information regarding the origins and structure of the vitreous humour, and the inner limiting lamina (ILL) of the retina. This short article provides an overview of this new information. It is proposed that vitreous proteins are derived from several different cell types with the posterior half of the non-pigmented ciliary epithelium being prominent in the expression of several connective tissue macromolecules. In addition, some basement membrane macromolecules are also expressed by the ciliary body and may subsequently be assembled on the surface of the Müller cells to form the ILL. New data suggest that the posterior half of the non-pigmented ciliary epithelium has substantial secretory activity and is likely to play a pivotal role in eye development.
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Affiliation(s)
- P N Bishop
- Wellcome Trust Centre for Cell-Matrix Research School of Biological Sciences and Research Group in Eye & Vision Sciences, The Medical School University of Manchester, Manchester, UK
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29
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Riechmann JL. Transcriptional regulation: a genomic overview. THE ARABIDOPSIS BOOK 2002; 1:e0085. [PMID: 22303220 PMCID: PMC3243377 DOI: 10.1199/tab.0085] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription.
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Affiliation(s)
- José Luis Riechmann
- Mendel Biotechnology, 21375 Cabot Blvd., Hayward, CA 94545, USA
- California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125
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