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Duran Ş, Üstüntanir Dede AF, Dündar Orhan Y, Arslanyolu M. Genome-wide identification and in-silico analysis of papain-family cysteine protease encoding genes in Tetrahymena thermophila. Eur J Protistol 2024; 92:126033. [PMID: 38088016 DOI: 10.1016/j.ejop.2023.126033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 02/06/2024]
Abstract
Tetrahymena thermophila is a promising host for recombinant protein production, but its utilization in biotechnology is mostly limited due to the presence of intracellular and extracellular papain-family cysteine proteases (PFCPs). In this study, we employed bioinformatics approaches to investigate the T. thermophila PFCP genes and their encoded proteases (TtPFCPs), the most prominent protease family in the genome. Results from the multiple sequence alignment, protein modeling, and conserved motif analyses revealed that all TtPFCPs showed considerably high homology with mammalian cysteine cathepsins and contained conserved amino acid motifs. The total of 121 TtPFCP-encoding genes, 14 of which were classified as non-peptidase homologs, were found. Remaining 107 true TtPFCPs were divided into four distinct subgroups depending on their homology with mammalian lysosomal cathepsins: cathepsin L-like (TtCATLs), cathepsin B-like (TtCATBs), cathepsin C-like (TtCATCs), and cathepsin X-like (TtCATXs) PFCPs. The majority of true TtPFCPs (96 out of the total) were in TtCATL-like peptidase subgroup. Both phylogenetic and chromosomal localization analyses of TtPFCPs supported the hypothesis that TtPFCPs likely evolved through tandem gene duplication events and predominantly accumulated on micronuclear chromosome 5. Additionally, more than half of the identified TtPFCP genes are expressed in considerably low quantities compared to the rest of the TtPFCP genes, which are expressed at a higher level. However, their expression patterns fluctuate based on the stage of the life cycle. In conclusion, this study provides the first comprehensive in-silico analysis of TtPFCP genes and encoded proteases. The results would help designing an effective strategy for protease knockout mutant cell lines to discover biological function and to improve the recombinant protein production in T. thermophila.
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Affiliation(s)
- Şeyma Duran
- Department of Molecular Biology, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Ayça Fulya Üstüntanir Dede
- Department of Molecular Biology, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Yeliz Dündar Orhan
- Department of Advanced Technologies, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskişehir 26470, Türkiye.
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2
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Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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3
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Abrahim M, Machado E, Alvarez-Valín F, de Miranda AB, Catanho M. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes. Genome Biol Evol 2022; 14:6754225. [PMID: 36208292 PMCID: PMC9576210 DOI: 10.1093/gbe/evac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
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Affiliation(s)
- Mayla Abrahim
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Brazil
| | - Fernando Alvarez-Valín
- Unidad de Genómica Evolutiva, Sección Biomatemática, Universidad de la República del Uruguay, Montevideo, Uruguay
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4
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Rivi V, Batabyal A, Wiley B, Benatti C, Tascedda F, Blom JMC, Lukowiak K. Fluoride affects memory by altering the transcriptional activity in the central nervous system of Lymnaea stagnalis. Neurotoxicology 2022; 92:61-66. [PMID: 35907516 DOI: 10.1016/j.neuro.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022]
Abstract
Fluoride (F-), has been found to affect learning and memory in several species. In this study, we exposed an F--naïve, inbred strain of Lymnaea stagnalis to a concentration of F- similar to that naturally occurring in wild ponds. We found that the exposure to F- before the configural learning procedure obstructs the memory formation and blocks the configural learning-induced upregulation of CREB1, GRIN1, and HSP70 in snails' central ring ganglia. Along with altering the mRNA levels of these key genes for memory formation, a single acute F- exposure also upregulates Cytochrome c Oxidase, a major regulatory enzyme of the electron transport chain, which plays direct or indirect roles in reactive oxygen species production. As the central nervous system is sensitive to oxidative stress and consistent with previous studies from mammals, our results suggest a potential role of oxidative stress in memory impairment. To our knowledge, this is the first study investigating the neuronal mechanism of memory impairment in an invertebrate species that is exposed to natural F- levels.
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Affiliation(s)
- Veronica Rivi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Anuradha Batabyal
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada.
| | - Bevin Wiley
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Cristina Benatti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; Centre of Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Tascedda
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; Centre of Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy; CIB, Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Joan M C Blom
- Centre of Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy; Dept. of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Ken Lukowiak
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
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5
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Schulman LS. Apparent Power Laws Can Occur without Criticality. ENTROPY 2021; 23:e23111486. [PMID: 34828184 PMCID: PMC8624822 DOI: 10.3390/e23111486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022]
Abstract
Power laws often lead to the conclusion that self-organized criticality is at work. This is not the case, and power laws can also occur away from criticality or can occur for other reasons.
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6
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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7
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Garewal N, Goyal N, Pathania S, Kaur J, Singh K. Gauging the trends of pseudogenes in plants. Crit Rev Biotechnol 2021; 41:1114-1129. [PMID: 33993808 DOI: 10.1080/07388551.2021.1901648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pseudogenes, the debilitated parts of ancient genes, were previously scrapped off as junk or discarded genes with no functional significance. Pseudogenes have come under scrutiny for their functionality, since recent studies have unveiled their importance in the regulation of their corresponding parent genes and various biological mechanisms. Despite the enormous occurrence of pseudogenes in plants, the lack of experimental validation has contributed toward their unresolved roles in gene regulation. Contrarily, most of the studies associated with gene regulation have been mainly reported for humans, mice, and other mammalian genomes. Consequently, in order to present a cumulative report on plant-based pseudogenes research, an attempt has been made to assemble multiple studies presenting the pseudogene classification, the prediction and the determination of comparative accuracies of various computational pipelines, and recent trends in analyzing their biological functions, and regulatory mechanisms. This review represents the classical, as well as the recent advances on pseudogene identification and their potential roles in transcriptional regulation, which could possibly invigorate the quality of genome annotation, evolutionary analysis, and complexity surrounding the regulatory pathways in plants. Thus, when the ambiguous boundary girdling the pseudogenes eventually recedes on account of their explicit orchestration role, research in flora would no longer saunter compared to that on fauna.
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Affiliation(s)
- Naina Garewal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Neetu Goyal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | | | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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8
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Vandelle E, Colombo T, Regaiolo A, Maurizio V, Libardi T, Puttilli MR, Danzi D, Polverari A. Transcriptional Profiling of Three Pseudomonas syringae pv. actinidiae Biovars Reveals Different Responses to Apoplast-Like Conditions Related to Strain Virulence on the Host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:376-396. [PMID: 33356409 DOI: 10.1094/mpmi-09-20-0248-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pseudomonas syringae pv. actinidiae is a phytopathogen that causes devastating bacterial canker in kiwifruit. Among five biovars defined by genetic, biochemical, and virulence traits, P. syringae pv. actinidiae biovar 3 (Psa3) is the most aggressive and is responsible for the most recent reported outbreaks; however, the molecular basis of its heightened virulence is unclear. Therefore, we designed the first P. syringae multistrain whole-genome microarray, encompassing biovars Psa1, Psa2, and Psa3 and the well-established model P. syringae pv. tomato, and analyzed early bacterial responses to an apoplast-like minimal medium. Transcriptomic profiling revealed i) the strong activation in Psa3 of all hypersensitive reaction and pathogenicity (hrp) and hrp conserved (hrc) cluster genes, encoding components of the type III secretion system required for bacterial pathogenicity and involved in responses to environmental signals; ii) potential repression of the hrp/hrc cluster in Psa2; and iii) activation of flagellum-dependent cell motility and chemotaxis genes in Psa1. The detailed investigation of three gene families encoding upstream regulatory proteins (histidine kinases, their cognate response regulators, and proteins with diguanylate cyclase or phosphodiesterase domains) indicated that cyclic di-GMP may be a key regulator of virulence in P. syringae pv. actinidiae biovars. The gene expression data were supported by the quantification of biofilm formation. Our findings suggest that diverse early responses to the host apoplast, even among bacteria belonging to the same pathovar, can lead to different virulence strategies and may explain the differing outcomes of infections. Based on our detailed structural analysis of hrp operons, we also propose a revision of hrp cluster organization and operon regulation in P. syringae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elodie Vandelle
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Teresa Colombo
- National Research Council of Italy (CNR), Institute of Molecular Biology and Pathology (IBPM) c/o Department of Biochemical Sciences "A. Rossi Fanelli", "Sapienza" University of Rome, Rome, 00185, Italy
| | - Alice Regaiolo
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Vanessa Maurizio
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Tommaso Libardi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | | | - Davide Danzi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
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9
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Abstract
The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada.
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10
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Ahsan N, Wilson RS, Rao RSP, Salvato F, Sabila M, Ullah H, Miernyk JA. Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics. J Proteome Res 2020; 19:561-571. [PMID: 31967836 DOI: 10.1021/acs.jproteome.9b00550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.
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Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine , Brown University , Providence , Rhode Island 02903 , United States.,Center for Cancer Research Development, Proteomics Core Facility , Rhode Island Hospital , Providence , Rhode Island 02903 , United States
| | - Rashaun S Wilson
- Keck Mass Spectrometry & Proteomics Resource , Yale University , New Haven , Connecticut 06511 , United States
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center , Yenepoya University , Mangalore 575018 , India
| | - Fernanda Salvato
- Department of Plant and Microbial Biology, College of Agriculture and Life Sciences , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Mercy Sabila
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Hemayet Ullah
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Ján A Miernyk
- Division of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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11
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Chavarro-Portillo B, Soto CY, Guerrero MI. Mycobacterium leprae's evolution and environmental adaptation. Acta Trop 2019; 197:105041. [PMID: 31152726 DOI: 10.1016/j.actatropica.2019.105041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 11/24/2022]
Abstract
Leprosy is an ancient disease caused by the acid-fast bacillus Mycobacterium leprae, also known as Hansen's bacillus. M. leprae is an obligate intracellular microorganism with a marked Schwann cell tropism and is the only human pathogen capable of invading the superficial peripheral nerves. The transmission mechanism of M. leprae is not fully understood; however, the nasal mucosa is accepted as main route of M. leprae entry to the human host. The complete sequencing and the comparative genome analysis show that M. leprae underwent a genome reductive evolution process, as result of lifestyle change and adaptation to different environments; some of lost genes are homologous to those of host cells. Thus, M. leprae reduced its genome size to 3.3 Mbp, contributing to obtain the lowest GC content (approximately 58%) among mycobacteria. The M. leprae genome contains 1614 open reading frames coding for functional proteins, and 1310 pseudogenes corresponding to 41% of the genome, approximately. Comparative analyses to different microorganisms showed that M. leprae possesses the highest content of pseudogenes among pathogenic and non-pathogenic bacteria and archaea. The pathogen adaptation into host cells, as the Schwann cells, brought about the reduction of the genome and induced multiple gene inactivation. The present review highlights the characteristics of genome's reductive evolution that M. leprae experiences in the genetic aspects compared with other pathogens. The possible mechanisms of pseudogenes formation are discussed.
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12
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Avni E, Montoya D, Lopez D, Modlin R, Pellegrini M, Snir S. A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PLoS One 2018; 13:e0204322. [PMID: 30383852 PMCID: PMC6211624 DOI: 10.1371/journal.pone.0204322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/06/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of orthologs of Mycobacterium leprae pseudogenes in prokaryotes. The leprosy pathogen M. leprae is of particular interest since it contains an unusually large number of pseudogenes, comprising approximately 40% of its entire genome. The analysis is conducted in both broad and narrow phylogenetic ranges. RESULTS We have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain are used to assess the contributions of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes. CONCLUSIONS We conclude that, although it was reported that in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs.
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Affiliation(s)
- Eliran Avni
- Dept. of Evolutionary Biology and the Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dennis Montoya
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - David Lopez
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Robert Modlin
- Dept. of Microbiology, Immunology and Molecular Genetics, and Division of Dermatology, David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Matteo Pellegrini
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Sagi Snir
- Dept. of Evolutionary Biology and the Institute of Evolution, University of Haifa, Haifa, Israel
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13
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Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes (Basel) 2017; 8:genes8120366. [PMID: 29206165 PMCID: PMC5748684 DOI: 10.3390/genes8120366] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 11/16/2022] Open
Abstract
Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA. In small RNA, we discuss miRNA, transfer RNA, piwi-interacting RNA, small nucleolar RNA, small nuclear RNA, Y RNA, single recognition particle RNA, and 7SK RNA. We elaborate on the origin, detection method, and potential association with disease, putative functional mechanisms, and public resources for these non-coding RNAs. We aim to provide readers with a complete overview of non-coding RNAs and incite additional interest in non-coding RNA research.
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Affiliation(s)
- Jing Wang
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, TN 37232, USA.
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Yan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87102, USA.
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Rutter MT, Wieckowski YM, Murren CJ, Strand AE. Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana. J Evol Biol 2017; 30:1124-1135. [PMID: 28387971 DOI: 10.1111/jeb.13081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/09/2017] [Indexed: 01/05/2023]
Abstract
Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T-DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness-related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T-DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana.
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Affiliation(s)
- M T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Y M Wieckowski
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - A E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
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15
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D'Apice MR, Novelli A, di Masi A, Biancolella M, Antoccia A, Gullotta F, Licata N, Minella D, Testa B, Nardone AM, Palmieri G, Calabrese E, Biancone L, Tanzarella C, Frontali M, Sangiuolo F, Novelli G, Pallone F. Deletion of REXO1L1 locus in a patient with malabsorption syndrome, growth retardation, and dysmorphic features: a novel recognizable microdeletion syndrome? BMC MEDICAL GENETICS 2015; 16:20. [PMID: 25927938 PMCID: PMC4422118 DOI: 10.1186/s12881-015-0164-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/12/2015] [Indexed: 12/27/2022]
Abstract
Background Copy number variations (CNVs) can contribute to genetic variation among individuals and/or have a significant influence in causing diseases. Many studies consider new CNVs’ effects on protein family evolution giving rise to gene duplicates or losses. “Unsuccessful” duplicates that remain in the genome as pseudogenes often exhibit functional roles. So, changes in gene and pseudogene number may contribute to development or act as susceptibility alleles of diseases. Case presentation We report a de novo heterozygous 271 Kb microdeletion at 8q21.2 region which includes the family of REXO1L genes and pseudogenes in a young man affected by global development delay, progeroid signs, and gastrointestinal anomalies. Molecular and cellular analysis showed that the REXO1L1 gene hemizygosity in a patient’s fibroblasts induces genetic instability and increased apoptosis after treatment with different DNA damage-induced agents. Conclusions The present results support the hypothesis that low copy gene number within REXO1L1 cluster could play a significant role in this complex clinical and cellular phenotype.
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Affiliation(s)
| | - Antonio Novelli
- Mendel Institute, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
| | | | - Michela Biancolella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | | | - Francesca Gullotta
- Department of Biology, "Roma Tre" University, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Norma Licata
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy. .,Department of Neuroscience, Psychiatry and Anaesthesiology, University of Messina, Messina, Italy.
| | - Daniela Minella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Barbara Testa
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | | | | | - Emma Calabrese
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
| | - Livia Biancone
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
| | | | | | - Federica Sangiuolo
- Fondazione Policlinico Tor Vergata, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy.
| | - Giuseppe Novelli
- Fondazione Policlinico Tor Vergata, Rome, Italy. .,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy. .,San Pietro Fatebenefratelli Hospital, Rome, Italy.
| | - Francesco Pallone
- Department of Internal Medicine, Gastrointestinal Unit, Tor Vergata University of Rome, Rome, Italy.
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16
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Abstract
Pseudogenes were once considered genomic fossils, but recent studies indicate that they may function as gene regulators through the generation of endogenous small interfering RNAs (esiRNAs), antisense RNAs, and decoys for microRNAs. In this review, we summarize pseudogene study methods, emphasizing relevant publicly available resources, and we describe a systematic pipeline to identify pseudogene-derived esiRNAs and their targets, which can lead to a deeper understanding of pseudogene function.
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Affiliation(s)
- Wen-Ling Chan
- Biomedical Informatics, Asia University, Taichung, Taiwan
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17
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Abstract
Pseudogenes are degraded fossil copies of genes. Here, we report a comparison of pseudogenes spanning three phyla, leveraging the completed annotations of the human, worm, and fly genomes, which we make available as an online resource. We find that pseudogenes are lineage specific, much more so than protein-coding genes, reflecting the different remodeling processes marking each organism's genome evolution. The majority of human pseudogenes are processed, resulting from a retrotranspositional burst at the dawn of the primate lineage. This burst can be seen in the largely uniform distribution of pseudogenes across the genome, their preservation in areas with low recombination rates, and their preponderance in highly expressed gene families. In contrast, worm and fly pseudogenes tell a story of numerous duplication events. In worm, these duplications have been preserved through selective sweeps, so we see a large number of pseudogenes associated with highly duplicated families such as chemoreceptors. However, in fly, the large effective population size and high deletion rate resulted in a depletion of the pseudogene complement. Despite large variations between these species, we also find notable similarities. Overall, we identify a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiting varying degrees of partial activity. In particular, we identify a consistent amount of transcription (∼15%) across all species, suggesting a uniform degradation process. Also, we see a uniform decay of pseudogene promoter activity relative to their coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activity, hinting at potential regulatory roles.
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18
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Abstract
The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Stewart Biology Building, 1205 Doctor Penfield Avenue, Montreal, QC, Canada, H3A 1B1,
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19
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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20
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Katju V. To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs. BMC Evol Biol 2013; 13:73. [PMID: 23530733 PMCID: PMC3637608 DOI: 10.1186/1471-2148-13-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/20/2013] [Indexed: 12/18/2022] Open
Abstract
Background Gene duplicates often exhibit asymmetric rates of molecular evolution in their early evolutionary existence. This asymmetry in rates is thought to signify the maintenance of the ancestral function by one copy and the removal of functional constraint on the other copy, enabling it to embark on a novel evolutionary trajectory. Here I focused on a large population of evolutionarily young gene duplicates (KS ≤ 0.14) in the Caenorhabditis elegans genome in order to conduct the first combined analysis of four predictors (evolutionary age, chromosomal location, structural resemblance between duplicates, and duplication span) which may be implicated in the asymmetric sequence divergence of paralogs at the nucleotide and amino acid level. In addition, I investigate if either paralog is equally likely to embark on a trajectory of accelerated sequence evolution or whether the derived paralog is more likely to exhibit faster sequence evolution. Results Three predictors (evolutionary age of duplicates, chromosomal location and duplication span) serve as major determinants of sequence asymmetry between C. elegans paralogs. Paralogs diverge asymmetrically in sequence with increasing evolutionary age, the relocation of one copy to a different chromosome and attenuated duplication spans that likely fail to capture the entire ancestral repertoire of coding sequence and regulatory elements. Furthermore, for paralogs residing on the same chromosome, opposite transcriptional orientation and increased genomic distance do not increase sequence asymmetry between paralogs. For a subset of duplicate pairs wherein the ancestral versus derived paralog could be distinguished, the derived paralogs are more likely to evolve at accelerated rates. Conclusions This genome-wide study of evolutionarily young duplicates stemming primarily from DNA-mediated small-scale duplication events demonstrates that genomic relocation to a new chromosome has important consequences for asymmetric divergence of paralogs, akin to paralogs arising from RNA-mediated duplication events. Additionally, the duplication span is negatively correlated with sequence rate asymmetry among paralogs, suggesting that attenuated duplication spans stemming from incomplete duplication of the ORF and/or ancestral regulatory elements further accelerate sequence divergence between paralogs. Cumulatively, derived copies exhibit accelerated rates of sequence evolution suggesting that they are primed for a divergent evolutionary trajectory by changes in structure and genomic context at inception.
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Affiliation(s)
- Vaishali Katju
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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21
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Translational recoding in archaea. Extremophiles 2012; 16:793-803. [DOI: 10.1007/s00792-012-0482-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/09/2012] [Indexed: 12/31/2022]
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22
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Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol 2012; 13:R51. [PMID: 22951037 PMCID: PMC3491395 DOI: 10.1186/gb-2012-13-9-r51] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/30/2012] [Accepted: 06/25/2012] [Indexed: 12/11/2022] Open
Abstract
Background Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. Results As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. Conclusions At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.
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Affiliation(s)
- Baikang Pei
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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23
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The ecology of bacterial genes and the survival of the new. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:394026. [PMID: 22900231 PMCID: PMC3415099 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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24
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Abstract
Global change includes alterations in ocean temperature, oxygen availability, salinity, and pH, abiotic variables with strong and interacting influences on the physiology of all taxa. Physiological stresses resulting from changes in these four variables may cause broad biogeographic shifts as well as localized changes in distribution in mosaic habitats. To elucidate these causal linkages, I address the following questions: What types of physiological limitations can alter species' distributions and, in cases of extreme stress, cause extinctions? Which species are most threatened by these physiological challenges--and why? How do contents of genomes establish capacities to respond to global change, notably in the case of species that have evolved in highly stable habitats? How fully can phenotypic acclimatization offset abiotic stress? Can physiological measurements, including new molecular ("-omic") approaches, provide indices of the degree of sublethal stress an organism experiences? And can physiological evolution keep pace with global change?
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Affiliation(s)
- George N Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA.
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25
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Fan G, Li J. Regions identity between the genome of vertebrates and non-retroviral families of insect viruses. Virol J 2011; 8:511. [PMID: 22073942 PMCID: PMC3226645 DOI: 10.1186/1743-422x-8-511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 11/10/2011] [Indexed: 01/06/2023] Open
Abstract
Background The scope of our understanding of the evolutionary history between viruses and animals is limited. The fact that the recent availability of many complete insect virus genomes and vertebrate genomes as well as the ability to screen these sequences makes it possible to gain a new perspective insight into the evolutionary interaction between insect viruses and vertebrates. This study is to determine the possibility of existence of sequence identity between the genomes of insect viruses and vertebrates, attempt to explain this phenomenon in term of genetic mobile element, and try to investigate the evolutionary relationship between these short regions of identity among these species. Results Some of studied insect viruses contain variable numbers of short regions of sequence identity to the genomes of vertebrate with nucleotide sequence length from 28 bp to 124 bp. They are found to locate in multiple sites of the vertebrate genomes. The ontology of animal genes with identical regions involves in several processes including chromatin remodeling, regulation of apoptosis, signaling pathway, nerve system development and some enzyme-like catalysis. Phylogenetic analysis reveals that at least some short regions of sequence identity in the genomes of vertebrate are derived the ancestral of insect viruses. Conclusion Short regions of sequence identity were found in the vertebrates and insect viruses. These sequences played an important role not only in the long-term evolution of vertebrates, but also in promotion of insect virus. This typical win-win strategy may come from natural selection.
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Affiliation(s)
- Gaowei Fan
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, China
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26
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Suzuki K, Akama T, Kawashima A, Yoshihara A, Yotsu RR, Ishii N. Current status of leprosy: epidemiology, basic science and clinical perspectives. J Dermatol 2011; 39:121-9. [PMID: 21973237 DOI: 10.1111/j.1346-8138.2011.01370.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leprosy has affected humans for millennia and remains an important health problem worldwide, as evidenced by nearly 250 000 new cases detected every year. It is a chronic infectious disorder, caused by Mycobacterium leprae, that primarily affects the skin and peripheral nerves. Recent advances in basic science have improved our knowledge of the disease. Variation in the cellular immune response is the basis of a range of clinical manifestations. The introduction of multidrug therapy has significantly contributed to a decrease in the prevalence of the disease. However, leprosy control activities, including monitoring and prevention programs, must be maintained.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases Department of Dermatology, National Center for Global Health and Medicine, Tokyo, Japan.
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27
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Herrada A, Eguíluz VM, Hernández-García E, Duarte CM. Scaling properties of protein family phylogenies. BMC Evol Biol 2011; 11:155. [PMID: 21645345 PMCID: PMC3277297 DOI: 10.1186/1471-2148-11-155] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/06/2011] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with those of a set of species phylogenies. RESULTS The comparative analysis between protein and species phylogenies shows that both sets of phylogenies share a remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. CONCLUSIONS The invariance of the scaling properties at levels spanning from genes to species suggests that rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.
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Affiliation(s)
- Alejandro Herrada
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Emilio Hernández-García
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Carlos M Duarte
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, E-07190 Esporles, Spain
- Oceans Institute, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
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28
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Cai XH, Jaroszewski L, Wooley J, Godzik A. Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering. Proteins 2011; 79:2389-402. [PMID: 21671455 DOI: 10.1002/prot.23049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/12/2011] [Accepted: 03/13/2011] [Indexed: 12/14/2022]
Abstract
The protein universe can be organized in families that group proteins sharing common ancestry. Such families display variable levels of structural and functional divergence, from homogenous families, where all members have the same function and very similar structure, to very divergent families, where large variations in function and structure are observed. For practical purposes of structure and function prediction, it would be beneficial to identify sub-groups of proteins with highly similar structures (iso-structural) and/or functions (iso-functional) within divergent protein families. We compared three algorithms in their ability to cluster large protein families and discuss whether any of these methods could reliably identify such iso-structural or iso-functional groups. We show that clustering using profile-sequence and profile-profile comparison methods closely reproduces clusters based on similarities between 3D structures or clusters of proteins with similar biological functions. In contrast, the still commonly used sequence-based methods with fixed thresholds result in vast overestimates of structural and functional diversity in protein families. As a result, these methods also overestimate the number of protein structures that have to be determined to fully characterize structural space of such families. The fact that one can build reliable models based on apparently distantly related templates is crucial for extracting maximal amount of information from new sequencing projects.
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Affiliation(s)
- Xiao-Hui Cai
- Joint Center for Structural Genomics, Center for Research in Biological Systems, University of California, San Diego, California 92093-0446, USA
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29
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Detection of selection utilizing molecular phylogenetics: a possible approach. Genetica 2011; 139:639-48. [DOI: 10.1007/s10709-011-9560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 02/28/2011] [Indexed: 11/25/2022]
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30
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Koonin EV, Wolf YI. Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet 2011; 11:487-98. [PMID: 20548290 DOI: 10.1038/nrg2810] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Multiple constraints variously affect different parts of the genomes of diverse life forms. The selective pressures that shape the evolution of viral, archaeal, bacterial and eukaryotic genomes differ markedly, even among relatively closely related animal and bacterial lineages; by contrast, constraints affecting protein evolution seem to be more universal. The constraints that shape the evolution of genomes and phenomes are complemented by the plasticity and robustness of genome architecture, expression and regulation. Taken together, these findings are starting to reveal complex networks of evolutionary processes that must be integrated to attain a new synthesis of evolutionary biology.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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31
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Xu Q, Tian L, Zhang L, Liu N. Sodium channel genes and their differential genotypes at the L-to-F kdr locus in the mosquito Culex quinquefasciatus. Biochem Biophys Res Commun 2011; 407:645-9. [PMID: 21419752 DOI: 10.1016/j.bbrc.2011.03.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 03/14/2011] [Indexed: 12/19/2022]
Abstract
The para-type sodium channel in insects is the primary target of pyrethroid and DDT insecticides. However, modifications in the target protein structure such as point mutations or substitutions, resulting from single nucleotide polymorphisms (SNP), cause insensitivity of the insect's nervous system to pyrethroids and DDT and, in turn, result in insecticide resistance. Among these mutations, substitution of leucine to phenylalanine (L to F) in the 6th segment of domain II (IIS6) has been clearly associated with pyrethroid and DDT resistance in many insect species, including mosquitoes. Here, multiple copies of the sodium channel gene were identified in the mosquito Culex quinquefasciatus by Southern blot analysis and polymerase chain reaction (PCR) analysis. Two genomic DNA fragments of the mosquito sodium channel gene (509 and 181 bp) were detected by a single PCR primer pair. Sequence analysis indicated the lack of an intron sequence in the 181 bp sodium channel fragment. Single nucleotide polymorphism (SNP) analysis revealed a strong correlation among the frequencies of L-to-F allelic (T) expression at the RNA level, the frequencies and resistance allele (T) at the L-to-F site of the 509 bp genomic DNA fragment, which did include an intron sequence, and the levels of insecticide resistance. Taking together, this study, for the first time, not only revealed multiple copies of the sodium channel gene presented in the Culex mosquito genome but also suggested that the one with the intro sequence may be a functional copy of the sodium channel gene in the Culex mosquitoes.
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Affiliation(s)
- Qiang Xu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
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Zhang J, Guo C, Liu G, Li Z, Li X, Bao M. Genetic alteration with variable intron/exon organization amongst five PI-homoeologous genes in Platanus acerifolia. Gene 2011; 473:82-91. [DOI: 10.1016/j.gene.2010.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 11/04/2010] [Accepted: 11/12/2010] [Indexed: 11/27/2022]
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Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010; 330:1775-87. [PMID: 21177976 PMCID: PMC3142569 DOI: 10.1126/science.1196914] [Citation(s) in RCA: 761] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
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Affiliation(s)
- Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Zhi John Lu
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Eric L. Van Nostrand
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Chao Cheng
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Bradley I. Arshinoff
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada
| | - Tao Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Kevin Y. Yip
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Rebecca Robilotto
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andreas Rechtsteiner
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kohta Ikegami
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pedro Alves
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Aurelien Chateigner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Marc Perry
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mitzi Morris
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Raymond K. Auerbach
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Xin Feng
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Biomedical Engineering, State University of New York at Stonybrook, Stonybrook, NY 11794, USA
| | - Jing Leng
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Anne Vielle
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Wei Niu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Kahn Rhrissorrakrai
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Ashish Agarwal
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Roger P. Alexander
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Galt Barber
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Cathleen M. Brdlik
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Jennifer Brennan
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Adrian Carr
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ming-Sin Cheung
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Sergio Contrino
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | | | - Abby F. Dernburg
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Arshad Desai
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Lindsay Dick
- David Rockefeller Graduate Program, Rockefeller University, 1230 York Avenue New York, NY 10065, USA
| | - Andréa C. Dosé
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jiang Du
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA
| | - Thea Egelhofer
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sevinc Ercan
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ghia Euskirchen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Elise A. Feingold
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Reto Gassmann
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Peter J. Good
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Phil Green
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Francois Gullier
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Mark S. Guyer
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Lukas Habegger
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Ting Han
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Jorja G. Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Stefan R. Henz
- Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076 Tübingen, Germany
| | - Angie Hinrichs
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Heather Holster
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Tony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - A. Leo Iniguez
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Judith Janette
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Morten Jensen
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masaomi Kato
- Department of Molecular, Cellular and Developmental Biology, Post Office Box 208103, Yale University, New Haven, CT 06520, USA
| | - W. James Kent
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Ellen Kephart
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Vishal Khivansara
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Ekta Khurana
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John K. Kim
- Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
| | - Paulina Kolasinska-Zwierz
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Eric C. Lai
- Sloan-Kettering Institute, 1275 York Avenue, Post Office Box 252, New York, NY 10065, USA
| | - Isabel Latorre
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Amber Leahey
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Suzanna Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Paul Lloyd
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Lucas Lochovsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Rebecca F. Lowdon
- Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Sebastian D. Mackowiak
- Max-Delbrück-Centrum für Molekulare Medizin, Division of Systems Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
| | - Marco Mangone
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Sheldon McKay
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11542 USA
| | - Desirea Mecenas
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Gennifer Merrihew
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37232–8240, USA
| | - Andrew Muroyama
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - John I. Murray
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Siew-Loon Ooi
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Hoang Pham
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Taryn Phippen
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Elicia A. Preston
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Nikolaus Rajewsky
- Max-Delbrück-Centrum für Molekulare Medizin, Division of Systems Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Heidi Rosenbaum
- Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Kim Rutherford
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Peter Ruzanov
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Rajkumar Sasidharan
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andrea Sboner
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Paul Scheid
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hyunjin Shin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Chong Shou
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Frank J. Slack
- Department of Molecular, Cellular and Developmental Biology, Post Office Box 208103, Yale University, New Haven, CT 06520, USA
| | - Cindie Slightam
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - Richard Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - William C. Spencer
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37232–8240, USA
| | - E. O. Stinson
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Scott Taing
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Teruaki Takasaki
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Dionne Vafeados
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Ksenia Voronina
- Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA
| | - Guilin Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Nicole L. Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA
| | - Christina M. Whittle
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Beijing Wu
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - Koon-Kiu Yan
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Georg Zeller
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Zheng Zha
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Mei Zhong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Xingliang Zhou
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Susan Strome
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
- New York University, Abu Dhabi, United Arab Emirates
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Stuart K. Kim
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA
| | - LaDeana W. Hillier
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Fabio Piano
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
- New York University, Abu Dhabi, United Arab Emirates
| | - Michael Snyder
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11542 USA
| | - Jason D. Lieb
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA
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Khurana E, Lam HYK, Cheng C, Carriero N, Cayting P, Gerstein MB. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res 2010; 38:6997-7007. [PMID: 20615899 PMCID: PMC2978362 DOI: 10.1093/nar/gkq587] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Duplicated pseudogenes in the human genome are disabled copies of functioning parent genes. They result from block duplication events occurring throughout evolutionary history. Relatively recent duplications (with sequence similarity ≥90% and length ≥1 kb) are termed segmental duplications (SDs); here, we analyze the interrelationship of SDs and pseudogenes. We present a decision-tree approach to classify pseudogenes based on their (and their parents’) characteristics in relation to SDs. The classification identifies 140 novel pseudogenes and makes possible improved annotation for the 3172 pseudogenes located in SDs. In particular, it reveals that many pseudogenes in SDs likely did not arise directly from parent genes, but are the result of a multi-step process. In these cases, the initial duplication or retrotransposition of a parent gene gives rise to a ‘parent pseudogene’, followed by further duplication creating duplicated–duplicated or duplicated–processed pseudogenes, respectively. Moreover, we can precisely identify these parent pseudogenes by overlap with ancestral SD loci. Finally, a comparison of nucleotide substitutions per site in a pseudogene with its surrounding SD region allows us to estimate the time difference between duplication and disablement events, and this suggests that most duplicated pseudogenes in SDs were likely disabled around the time of the original duplication.
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Affiliation(s)
- Ekta Khurana
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gene array. Genetics 2010; 186:263-76. [PMID: 20551443 DOI: 10.1534/genetics.110.116392] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tandemly arrayed genes that belong to gene families characterize genomes of many organisms. Gene duplication and subsequent relaxation of selection can lead to the establishment of paralogous cluster members that may evolve along different trajectories. Here, we report on the structural variation in MADS AFFECTING FLOWERING 2 (MAF2) gene, one member of the tandemly duplicated cluster of MADS-box-containing transcription factors in Arabidopsis thaliana. The altered gene structure at the MAF2 locus is present as a moderate-frequency polymorphism in Arabidopsis and leads to the extensive diversity in transcript patterns due to alternative splicing. Rearrangements at the MAF2 locus are associated with an early flowering phenotype in BC(5) lines. The lack of suppression of flowering time in a MAF2-insertion line expressing the MAF2-specific artificial miRNA suggests that these MAF2 variants are behaving as loss-of-function alleles. The variation in gene architecture is also associated with segregation distortion, which may have facilitated the spread and the establishment of the corresponding alleles throughout the Eurasian range of the A. thaliana population.
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McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One 2010; 5:e11029. [PMID: 20543958 PMCID: PMC2882956 DOI: 10.1371/journal.pone.0011029] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/19/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Wolbachia are among the most abundant symbiotic microbes on earth; they are present in about 66% of all insect species, some spiders, mites and crustaceans, and most filarial nematode species. Infected filarial nematodes, including many pathogens of medical and veterinary importance, depend on Wolbachia for proper development and survival. The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free. METHODOLOGY/PRINCIPAL FINDINGS We used 454 pyrosequencing to survey the genomes of two distantly related Wolbachia-free filarial species, Acanthocheilonema viteae and Onchocerca flexuosa. This screen identified 49 Wolbachia-like DNA sequences in A. viteae and 114 in O. flexuosa. qRT-PCR reactions detected expression of 30 Wolbachia-like sequences in A. viteae and 56 in O. flexuosa. Approximately half of these appear to be transcribed from pseudogenes. In situ hybridization showed that two of these pseudogene transcripts were specifically expressed in developing embryos and testes of both species. CONCLUSIONS/SIGNIFICANCE These results strongly suggest that the last common ancestor of extant filarial nematodes was infected with Wolbachia and that this former endosymbiont contributed to their genome evolution. Horizontally transferred Wolbachia DNA may explain the ability of some filarial species to live and reproduce without the endosymbiont while other species cannot.
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Affiliation(s)
- Samantha N. McNulty
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Makedonka Mitreva
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - John Martin
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bo Wu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Paul J. Davis
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sanjay Kumar
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barton E. Slatko
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Gary J. Weil
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Somero GN. The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'. ACTA ACUST UNITED AC 2010; 213:912-20. [PMID: 20190116 DOI: 10.1242/jeb.037473] [Citation(s) in RCA: 965] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Physiological studies can help predict effects of climate change through determining which species currently live closest to their upper thermal tolerance limits, which physiological systems set these limits, and how species differ in acclimatization capacities for modifying their thermal tolerances. Reductionist studies at the molecular level can contribute to this analysis by revealing how much change in sequence is needed to adapt proteins to warmer temperatures--thus providing insights into potential rates of adaptive evolution--and determining how the contents of genomes--protein-coding genes and gene regulatory mechanisms--influence capacities for adapting to acute and long-term increases in temperature. Studies of congeneric invertebrates from thermally stressful rocky intertidal habitats have shown that warm-adapted congeners are most susceptible to local extinctions because their acute upper thermal limits (LT(50) values) lie near current thermal maxima and their abilities to increase thermal tolerance through acclimation are limited. Collapse of cardiac function may underlie acute and longer-term thermal limits. Local extinctions from heat death may be offset by in-migration of genetically warm-adapted conspecifics from mid-latitude 'hot spots', where midday low tides in summer select for heat tolerance. A single amino acid replacement is sufficient to adapt a protein to a new thermal range. More challenging to adaptive evolution are lesions in genomes of stenotherms like Antarctic marine ectotherms, which have lost protein-coding genes and gene regulatory mechanisms needed for coping with rising temperature. These extreme stenotherms, along with warm-adapted eurytherms living near their thermal limits, may be the major 'losers' from climate change.
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Affiliation(s)
- G N Somero
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA.
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Harrison PM, Khachane A, Kumar M. Genomic assessment of the evolution of the prion protein gene family in vertebrates. Genomics 2010; 95:268-77. [DOI: 10.1016/j.ygeno.2010.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 02/16/2010] [Accepted: 02/24/2010] [Indexed: 02/09/2023]
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Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010; 75:193-239, xii-xiii. [PMID: 17124868 DOI: 10.1002/9780471224464.ch3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein engineering holds great promise for the development of new biosensors, diagnostics, therapeutics, and agents for bioremediation. Despite some remarkable successes in experimental and computational protein design, engineered proteins rarely achieve the efficiency or specificity of natural enzymes. Current protein design methods utilize evolutionary concepts, including mutation, recombination, and selection, but the inability to fully recapitulate the success of natural evolution suggests that some evolutionary principles have not been fully exploited. One aspect of protein engineering that has received little attention is how to select the most promising proteins to serve as templates, or scaffolds, for engineering. Two evolutionary concepts that could provide a rational basis for template selection are the conservation of catalytic mechanisms and functional promiscuity. Knowledge of the catalytic motifs responsible for conserved aspects of catalysis in mechanistically diverse superfamilies could be used to identify promising templates for protein engineering. Second, protein evolution often proceeds through promiscuous intermediates, suggesting that templates which are naturally promiscuous for a target reaction could enhance protein engineering strategies. This review explores these ideas and alternative hypotheses concerning protein evolution and engineering. Future research will determine if application of these principles will lead to a protein engineering methodology governed by predictable rules for designing efficient, novel catalysts.
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Affiliation(s)
- Margaret E Glasner
- Department of Biopharmaceutical Sciences, University of California-San Francisco, San Francisco, CA 94143, USA
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Lafontaine I, Dujon B. Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis. BMC Genomics 2010; 11:260. [PMID: 20412590 PMCID: PMC2876123 DOI: 10.1186/1471-2164-11-260] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 04/22/2010] [Indexed: 12/20/2022] Open
Abstract
Background Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only the genome of the S. cerevisiae reference strain has been analyzed so far for pseudogenes. Results We present here the first comparative analysis of pseudogenes within the fully sequenced and annotated genomes of eight yeast species, spanning the entire phylogenetic range of Hemiascomycetes. A total of 871 pseudogenes were found, out of which mutational degradation patterns and consequences on the genetic repertoire of each species could be identified. We found that most pseudogenes in yeasts originate from mutational degradation of gene copies formed after species-specific duplications but duplications of pseudogenes themselves are also encountered. In all yeasts, except in Y. lipolytica, pseudogenes tend to cluster in subtelomeric regions where they can outnumber the number of functional genes from 3 to 16 times. Pseudogenes are generally not conserved between the yeast species studied (except in two cases), consistent with their large evolutionary distances, but tend to be conserved among S. cerevisiae strains. Reiterated pseudogenization of some genes is often observed in different lineages and may affect functions essential in S. cerevisiae, which are, therefore, lost in other species. Although a variety of functions are affected by pseudogenization, there is a bias towards functions involved in the adaptation of the yeasts to their environment, and towards genes of unknown functions. Conclusions Our work illustrates for the first time the formation of pseudogenes in different branches of hemiascomycetous yeasts, showing their limited conservation and how they testify for the adaptation of the yeasts functional repertoires.
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Affiliation(s)
- Ingrid Lafontaine
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, Paris, France.
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Gamper HA, van der Heijden MGA, Kowalchuk GA. Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology. THE NEW PHYTOLOGIST 2010; 185:67-82. [PMID: 19863727 DOI: 10.1111/j.1469-8137.2009.03058.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form symbiotic associations with the roots of most plants, thereby mediating nutrient and carbon fluxes, plant performance, and ecosystem dynamics. Although considerable effort has been expended to understand the keystone ecological position of AM symbioses, most studies have been limited in scope to recording organism occurrences and identities, as determined from morphological characters and (mainly) ribosomal sequence markers. In order to overcome these restrictions and circumvent the shortcomings of culture- and phylogeny-based approaches, we propose a shift toward plant and fungal protein-encoding genes as more immediate indicators of mycorrhizal contributions to ecological processes. A number of candidate target genes, involved in the uptake of phosphorus and nitrogen, carbon cycling, and overall metabolic activity, are proposed. We discuss the advantages and disadvantages of future protein-encoding gene marker and current (phylo-) taxonomic approaches for studying the impact of AM fungi on plant growth and ecosystem functioning. Approaches based on protein-encoding genes are expected to open opportunities to advance the mechanistic understanding of ecological roles of mycorrhizas in natural and managed ecosystems.
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Affiliation(s)
- Hannes A Gamper
- Botanical Institute, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.
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Abstract
Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function.
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Affiliation(s)
- Anne E Osbourn
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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Khachane AN, Harrison PM. Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 2009; 10:435. [PMID: 19754956 PMCID: PMC2753554 DOI: 10.1186/1471-2164-10-435] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 09/15/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcribed pseudogenes are copies of protein-coding genes that have accumulated indicators of coding-sequence decay (such as frameshifts and premature stop codons), but nonetheless remain transcribed. Recent experimental evidence indicates that transcribed pseudogenes may regulate the expression of homologous genes, through antisense interference, or generation of small interfering RNAs (siRNAs). Here, we assessed the genomic evidence for such transcribed pseudogenes of potential functional importance, in the human genome. The most obvious indicators of such functional importance are significant evidence of conservation and selection pressure. RESULTS A variety of pseudogene annotations from multiple sources were pooled and filtered to obtain a subset of sequences that have significant mid-sequence disablements (frameshifts and premature stop codons), and that have clear evidence of full-length mRNA transcription. We found 1750 such transcribed pseudogene annotations (TPAs) in the human genome (corresponding to approximately 11.5% of human pseudogene annotations). We checked for syntenic conservation of TPAs in other mammals (rhesus monkey, mouse, rat, dog and cow). About half of the human TPAs are conserved in rhesus monkey, but strikingly, very few in mouse (approximately 3%). The TPAs conserved in rhesus monkey show evidence of selection pressure (relative to surrounding intergenic DNA) on: (i) their GC content, and (ii) their rate of nucleotide substitution. This is in spite of distributions of Ka/Ks (ratios of non-synonymous to synonymous substitution rates), congruent with a lack of protein-coding ability. Furthermore, we have identified 68 human TPAs that are syntenically conserved in at least two other mammals. Interestingly, we observe three TPA sequences conserved in dog that have intermediate character (i.e., evidence of both protein-coding ability and pseudogenicity), and discuss the implications of this. CONCLUSION Through evolutionary analysis, we have identified candidate sequences for functional human transcribed pseudogenes, and have pinpointed 68 strong candidates for further investigation as potentially functional transcribed pseudogenes across multiple mammal species.
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Affiliation(s)
- Amit N Khachane
- Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1 Canada.
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Kellermann V, van Heerwaarden B, Sgro CM, Hoffmann AA. Fundamental Evolutionary Limits in Ecological Traits Drive Drosophila Species Distributions. Science 2009; 325:1244-6. [DOI: 10.1126/science.1175443] [Citation(s) in RCA: 334] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Morais DD, Harrison PM. Genomic evidence for non-random endemic populations of decaying exons from mammalian genes. BMC Genomics 2009; 10:309. [PMID: 19594905 PMCID: PMC2718932 DOI: 10.1186/1471-2164-10-309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 07/13/2009] [Indexed: 11/13/2022] Open
Abstract
Background Functional diversification of genes in mammalian genomes is engendered by a number of processes, e.g., gene duplication and alternative splicing. Gene duplication is classically discussed as leading to neofunctionalization (generation of new functions), subfunctionalization (generation of a varied function), or pseudogenization (loss of the gene and its function). Results Here, we focus on the process of pseudogenization, but specifically for individual exons from genes. It is at present unclear to what extent pseudogenization of individual exon duplications affects gene evolution, i.e., is it a random phenomenon, or is it associated with specific types of genes and encoded proteins, and positions in gene structures? We gathered genomic evidence for pseudogenic exons (ΨEs, i.e., exons disabled by frameshifts and premature stop codons), to examine for significant trends in their distribution across four mammalian genomes (specifically human, cow, mouse and rat). Across these four genomes, we observed a consistent population of ΨEs, associated with 0.4–1.0% of genes. These ΨE populations exhibit codon substitution patterns that are typical of an endemic population of decaying sequences. In human, ΨEs have significant over-representation for functional categories related to 'ion binding' and 'nucleic-acid binding', compared to duplicated exons in general. Also, ΨEs tend to be associated with some protein domains that are abundant generally, e.g., Zinc-finger and immunoglobulin protein domains, but not others, e.g., EGF-like domains. Positionally, ΨEs are also significantly associated with the 5' end of genes, but despite this, individual stop codons are positioned so that there is significant avoidance of potential targeting to nonsense-mediated decay. In human, ΨEs are often associated with alternative splicing (in 22 out of 284 genes with ΨEs in their milieu), and can have different parts of their sequence differentially spliced in alternative transcripts. Some unusual cases of ΨEs embedded within 5' and 3' non-coding exons are observed. Conclusion Our results indicate the types of genes that harbour ΨEs, and demonstrate that ΨEs have non-random distribution within gene structures. These ΨEs may function in gene regulation through generation of transcribed pseudogenes, or regulatory alternate transcripts.
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Affiliation(s)
- David Delima Morais
- Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1, Canada.
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Kim JM, Kim BG, Oh SJ. Evolutionary Signature of Information Transfer Complexity in Cellular Membrane Proteomes. Genomics Inform 2009. [DOI: 10.5808/gi.2009.7.2.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Meisel RP. Evolutionary dynamics of recently duplicated genes: Selective constraints on diverging paralogs in the Drosophila pseudoobscura genome. J Mol Evol 2009; 69:81-93. [PMID: 19536449 DOI: 10.1007/s00239-009-9254-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 05/06/2009] [Accepted: 05/26/2009] [Indexed: 01/12/2023]
Abstract
Duplicated genes produce genetic variation that can influence the evolution of genomes and phenotypes. In most cases, for a duplicated gene to contribute to evolutionary novelty it must survive the early stages of divergence from its paralog without becoming a pseudogene. I examined the evolutionary dynamics of recently duplicated genes in the Drosophila pseudoobscura genome to understand the factors affecting these early stages of evolution. Paralogs located in closer proximity have higher sequence identity. This suggests that gene conversion occurs more often between duplications in close proximity or that there is more genetic independence between distant paralogs. Partially duplicated genes have a higher likelihood of pseudogenization than completely duplicated genes, but no single factor significantly contributes to the selective constraints on a completely duplicated gene. However, DNA-based duplications and duplications within chromosome arms tend to produce longer duplication tracts than retroposed and inter-arm duplications, and longer duplication tracts are more likely to contain a completely duplicated gene. Therefore, the relative position of paralogs and the mechanism of duplication indirectly affect whether a duplicated gene is retained or pseudogenized.
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Affiliation(s)
- Richard P Meisel
- Department of Biology, The Pennsylvania State University, University Park, 16802, USA.
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Bier A, Oviedo-Landaverde I, Zhao J, Mamane Y, Kandouz M, Batist G. Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target. Mol Cancer Ther 2009; 8:786-93. [PMID: 19372551 DOI: 10.1158/1535-7163.mct-08-0930] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Connexin43 (Cx43) is often deregulated in breast cancer tissue compared with normal adjacent tissue. Stable reexpression of Cx43 in cancer slows growth and renders the cells more sensitive to cytotoxic chemotherapeutics. Pseudogenes are often considered nonfunctional copies of DNA. The Cx43 pseudogene (PsiCx43) possesses all the features of an expressed gene and is exclusively transcribed in breast cancer cell lines and not in normal cells. PsiCx43 can be translated in vivo, and its protein exhibits growth-suppressive behavior similar to Cx43. We showed that PsiCx43 binds to the polyribosomes in breast cancer cells and that exogenous expression of PsiCx43 induces translational inhibition of Cx43. Furthermore, PsiCx43 is translated and binds more efficiently to the translational machinery than does Cx43 in an in vitro system. Following knockdown of PsiCx43 in breast cancer cells, we observed an increase in Cx43 RNA and protein. This results in increased cellular sensitivity to cytotoxic chemotherapy. Our results show that PsiCx43 acts as a posttranscriptional regulator of Cx43 in breast cancer cells, and that this represents an example of the regulation of genes by pseudogenes with potential therapeutic implications in cancer.
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Affiliation(s)
- Andrew Bier
- Department of Oncology, Segal Cancer Centre, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, and Department of Biochemistry and McGill Cancer Centre, McGill University, Montreal, Quebec, Canada H3T 1E2
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Koziol U, Iriarte A, Castillo E, Soto J, Bello G, Cajarville A, Roche L, Marín M. Characterization of a putative hsp70 pseudogene transcribed in protoscoleces and adult worms of Echinococcus granulosus. Gene 2009; 443:1-11. [PMID: 19460422 DOI: 10.1016/j.gene.2009.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 05/06/2009] [Accepted: 05/06/2009] [Indexed: 11/25/2022]
Abstract
Searching for hsp70 genes in Echinococcus granulosus, a divergent cytoplasmic hsp70-like sequence (EgpsiHsp70) was isolated, possessing a small truncation in the region coding for the C-terminal glycine-rich linker and EEVD-Ct motif. Southern Blot analyses of E. granulosus, and in silico analyses of E. multilocularis indicate that this truncated sequence is repeated several times in both genomes, in some cases containing clear cut features of pseudogenization. Phylogenetic analyses and comparison of surrounding regions indicate that all these copies originated by successive genomic duplications of one originally truncated copy. These copies are diverging at an increased rate compared to functional cytoplasmic hsp70 genes, and ratios of non-synonymous over synonymous substitutions rates (dN/dS) point to a relaxation of sequence constraint, suggesting that these sequences are pseudogenes. Interestingly, RT-PCR demonstrates that EgpsiHsp70 is transcribed in protoscoleces and adult individuals of E. granulosus. We suggest that this sequence does not code for a functional polypeptide, although some features are unexpected for a sequence evolving under a strictly neutral mode. Transcription could either be vestigial or have a specific, non-coding function.
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Affiliation(s)
- Uriel Koziol
- Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Iguá 4225, 11400, Montevideo, Uruguay.
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Rajashekar B, Kohler A, Johansson T, Martin F, Tunlid A, Ahrén D. Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases. THE NEW PHYTOLOGIST 2009; 183:365-379. [PMID: 19453435 DOI: 10.1111/j.1469-8137.2009.02860.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The ectomycorrhizal fungus Laccaria bicolor has the largest genome of all fungi yet sequenced. The large genome size is partly a result of an expansion of gene family sizes. Among the largest gene families are protein kinases and RAS small guanosine triphosphatases (GTPases), which are key components of signal transduction pathways. Comparative genomics and phylogenetic analyses were used to examine the evolution of the two largest families of protein kinases and RAS small GTPases in L. bicolor. Expression levels in various tissues and growth conditions were inferred from microarray data. The two families possessed a large number of young duplicates (paralogs) that had arisen in the Laccaria lineage following the separation from the saprophyte Coprinopsis cinerea. The protein kinase paralogs were dispersed in many small clades and the majority were pseudogenes. By contrast, the RAS paralogs were found in three large groups of RAS1-, RAS2- and RHO1-like GTPases with few pseudogenes. Duplicates of protein kinases and RAS small GTPase have either retained, gained or lost motifs found in the coding regions of their ancestors. Frequent outcomes during evolution were the formation of pseudogenes (nonfunctionalization) or proteins with novel structures and expression patterns (neofunctionalization).
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Affiliation(s)
- Balaji Rajashekar
- Department of Microbial Ecology, Ecology Building, Lund University, SE-223 62, Lund, Sweden
| | - Annegret Kohler
- UMR1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - Tomas Johansson
- Department of Microbial Ecology, Ecology Building, Lund University, SE-223 62, Lund, Sweden
| | - Francis Martin
- UMR1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - Anders Tunlid
- Department of Microbial Ecology, Ecology Building, Lund University, SE-223 62, Lund, Sweden
| | - Dag Ahrén
- Department of Microbial Ecology, Ecology Building, Lund University, SE-223 62, Lund, Sweden
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