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Tushir S, Jhanwar P, Benda M, Horáčková V, Doležal P, Tatu U. In vivo Validation of Hsp90 Trans-splicing in Giardia lamblia: Highlighting the Role of Cis-elements. J Mol Biol 2024; 436:168440. [PMID: 38218367 DOI: 10.1016/j.jmb.2024.168440] [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: 10/23/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Giardia lambliacauses giardiasis, one of the most common human infectious diseases globally. Previous studies from our lab have shown that hsp90 gene ofGiardia is split into two halves, namely hspN and hspC. The independent pre-mRNAs of these split genes join by trans-splicing, producing a full-length Hsp90 (FlHsp90) mRNA. Genetic manipulation of the participating genes is necessary to understand the mechanism and significance of such trans-splicing based expression of Hsp90. In this study, we have performed transfection based exogenous expression of hspN and/or hspC in G. lamblia. We electroporated a plasmid containing the Avi-tagged hspN component of Hsp90 and examined its fate in G. lamblia. We show that the exogenously expressed hspN RNA gets trans-spliced to endogenously expressed hspC RNA, giving rise to a hybrid-FlHsp90. We highlight the importance of cis-elements in this trans-splicing reaction through mutational analysis. The episomal plasmid carrying deletions in the intronic region of hspN, showed inhibition of the trans-splicing reaction.Additionally, exogenous hspC RNA also followed the same fate as of exogenous hspN, while upon co-transfection with episomal hspN, they underwent trans-splicing with each other. Using eGFP as a test protein, we have shown that intronic sequences of hsp90 gene can guide trans-splicing mediated repair of any associated exonic sequences. Our study provides in vivo validation of Hsp90 trans-splicing, showing crucial role of cis-elements and importantly highlights the potential of hsp90 intronic sequences to function as a minimal splicing tool.
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Affiliation(s)
- Sheetal Tushir
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pratima Jhanwar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Martin Benda
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Vendula Horáčková
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Pavel Doležal
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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2
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Seabolt MH, Roellig DM, Konstantinidis KT. Spliceosomal introns in the diplomonad parasite Giardia duodenalis revisited. Microb Genom 2023; 9. [PMID: 37934076 DOI: 10.1099/mgen.0.001117] [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] [Indexed: 11/08/2023] Open
Abstract
Complete reference genomes, including correct feature annotations, are a fundamental aspect of genomic biology. In the case of protozoan species such as Giardia duodenalis, a major human and animal parasite worldwide, accurate genome annotation can deepen our understanding of the evolution of parasitism and pathogenicity by identifying genes underlying key traits and clinically relevant cellular mechanisms, and by extension, the development of improved prevention strategies and treatments. This study used bioinformatics analyses of Giardia mRNA libraries to characterize known introns and identify new intron candidates, working towards completion of the G. duodenalis assemblage A strain 'WB' genome and further elucidating Giardia's gene expression. By using a set of experimentally validated positive control loci to calibrate our intron detection pipeline, we were able to detect evidence of previously missed candidate splice junctions directly from expressed transcript data. These intron candidates were further studied in silico using NMDS (non-metric multidimensional scaling) clustering to determine shared characteristics and their relative importance such as secondary structure, splicing efficiency and motif conservation, and thus to refine intron models. Results from this study identified 34 new intron candidates, with several potential introns showing evidence that secondary structure of the mRNA molecule might play a more significant role in splicing than previously reported eukaryotic splicing activity mediated by a reduced spliceosome present in G. duodenalis.
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Affiliation(s)
- Matthew H Seabolt
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Leidos Inc., Reston, VA 20190, USA
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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González-Blanco G, García-Rivera G, Talmás-Rohana P, Orozco E, Galindo-Rosales JM, Vélez C, Salucedo-Cárdenas O, Azuara-Liceaga E, Rodríguez-Rodríguez MA, Nozaki T, Valdés J. An Unusual U2AF2 Inhibits Splicing and Attenuates the Virulence of the Human Protozoan Parasite Entamoeba histolytica. Front Cell Infect Microbiol 2022; 12:888428. [PMID: 35782149 PMCID: PMC9247205 DOI: 10.3389/fcimb.2022.888428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
E. histolytica is the etiological agent of intestinal amebiasis and liver abscesses, which still poses public health threat globally. Metronidazole is the drug of choice against amebiasis. However, metronidazole-resistant amoebic clinical isolates and strains have been reported recently, challenging the efforts for amebiasis eradication. In search of alternative treatments, E. histolytica transcriptomes have shown the association of genes involved in RNA metabolism with the virulence of the parasite. Among the upregulated genes in amoebic liver abscesses are the splicing factors EhU2AF2 and a paralog of EhSF3B1. For this reason and because EhU2AF2 contains unusual KH-QUA2 (84KQ) motifs in its lengthened C-terminus domain, here we investigated how the role of EhU2AF2 in pre-mRNA processing impacts the virulence of the parasite. We found that 84KQ is involved in splicing inhibition/intron retention of several virulence and non-virulence-related genes. The 84KQ domain interacts with the same domain of the constitutive splicing factor SF1 (SF1KQ), both in solution and when SF1KQ is bound to branchpoint signal RNA probes. The 84KQ–SF1KQ interaction prevents splicing complex E to A transition, thus inhibiting splicing. Surprisingly, the deletion of the 84KQ domain in EhU2AF2 amoeba transformants increased splicing and enhanced the in vitro and in vivo virulence phenotypes. We conclude that the interaction of the 84KQ and SF1KQ domains, probably involving additional factors, tunes down Entamoeba virulence by favoring intron retention.
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Affiliation(s)
- Gretter González-Blanco
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Patricia Talmás-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Ester Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - José Manuel Galindo-Rosales
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Cristina Vélez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Odila Salucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX, Mexico
| | - Mario Alberto Rodríguez-Rodríguez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
| | - Tomoyoshi Nozaki
- Laboratory of Biomedical Chemistry, Department of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), CDMX, Mexico
- *Correspondence: Jesús Valdés,
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4
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Bilodeau DY, Sheridan RM, Balan B, Jex AR, Rissland OS. Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia. RNA (NEW YORK, N.Y.) 2022; 28:668-682. [PMID: 35110372 PMCID: PMC9014877 DOI: 10.1261/rna.078793.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3' UTR of an mRNA, thus determining much of its post-transcriptional fate. Using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses an AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes with evidence of alternative polyadenylation. These results suggest that despite pared-down cleavage and polyadenylation machinery, 3' end formation still appears to be an important regulatory step for gene expression in G. lamblia.
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Affiliation(s)
- Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ryan M Sheridan
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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5
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Kumari A, Sedehizadeh S, Brook JD, Kozlowski P, Wojciechowska M. Differential fates of introns in gene expression due to global alternative splicing. Hum Genet 2022; 141:31-47. [PMID: 34907472 PMCID: PMC8758631 DOI: 10.1007/s00439-021-02409-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.
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Affiliation(s)
- Anjani Kumari
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Saam Sedehizadeh
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - John David Brook
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
- Department of Rare Human Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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6
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The role of nuclear organization in trans-splicing based expression of heat shock protein 90 in Giardia lamblia. PLoS Negl Trop Dis 2021; 15:e0009810. [PMID: 34559805 PMCID: PMC8494341 DOI: 10.1371/journal.pntd.0009810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/06/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
Hsp90 gene of G. lamblia has a split nature comprising two ORFs separated by 777 kb on chromosome 5. The ORFs of the split gene on chromosome 5 undergo transcription to generate independent pre-mRNAs that join by a unique trans-splicing reaction that remains partially understood. The canonical cis-acting nucleotide elements such as 5'SS-GU, 3'SS-AG, polypyrimidine tract and branch point adenine are present in the independent pre-mRNAs and therefore trans-splicing of Hsp90 must be assisted by spliceosomes in vivo. Using an approach of RNA-protein pull down, we show that an RNA helicase selectively interacts with HspN pre-mRNA. Our experiments involving high resolution chromosome conformation capture technology as well as DNA FISH show that the trans-spliced genes of Giardia are in three-dimensional spatial proximity in the nucleus. Altogether our study provides a glimpse into the in vivo mechanisms involving protein factors as well as chromatin structure to facilitate the unique inter-molecular post-transcriptional stitching of split genes in G. lamblia.
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7
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Emery-Corbin SJ, Hamey JJ, Ansell BRE, Balan B, Tichkule S, Stroehlein AJ, Cooper C, McInerney BV, Hediyeh-Zadeh S, Vuong D, Crombie A, Lacey E, Davis MJ, Wilkins MR, Bahlo M, Svärd SG, Gasser RB, Jex AR. Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia. Mol Biol Evol 2021; 37:3525-3549. [PMID: 32702104 PMCID: PMC7743719 DOI: 10.1093/molbev/msaa186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis-a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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Affiliation(s)
- Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Swapnil Tichkule
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Crystal Cooper
- Central Analytical Research Facility (CARF), Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Bernie V McInerney
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, Australia.,Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Melissa J Davis
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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8
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Mao JM, Wang Y, Yang L, Yao Q, Chen KP. An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence. Evol Bioinform Online 2021; 17:1176934320988558. [PMID: 33551639 PMCID: PMC7841239 DOI: 10.1177/1176934320988558] [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: 08/21/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022] Open
Abstract
Introns are highly variable in number and size. Sequence simulation is an
effective method to elucidate intron evolution patterns. Previously, we have
reported that introns are more likely to evolve through mutation-and-deletion
(MD) rather than through mutation-and-insertion (MI). In the present study, we
further studied evolution models by allowing insertion in the MD model and by
allowing deletion in the MI model at various frequencies. It was found that all
deletion-biased models with proper parameter settings could generate sequences
with attributes matchable to 16 invertebrate introns from the microphthalmia
transcription factor gene, whereas all insertion-biased models with any
parameter settings failed to generate such sequences. We conclude that the
examined invertebrate introns may have evolved from a longer ancestral sequence
in a deletion-biased pattern. The constructed models are useful for studying the
evolution of introns from other genes and/or from other taxonomic groups. (C++
scripts of all deletion- and insertion-biased models are available upon
request.)
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Affiliation(s)
- Jun-Ming Mao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yong Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Liu Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Qin Yao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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9
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Eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry. Int J Parasitol 2020; 51:225-239. [PMID: 33275945 DOI: 10.1016/j.ijpara.2020.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022]
Abstract
Diarrheal disease caused by Giardia duodenalis is highly prevalent, causing over 200 million cases globally each year. The processes that drive parasite virulence, host immune evasion and transmission involve coordinated gene expression and have been linked to epigenetic regulation. Epigenetic regulatory systems are eukaryote-conserved, including in deep branching excavates such as Giardia, with several studies already implicating histone post-translational modifications in regulation of its pathogenesis and life cycle. However, further insights into Giardia chromatin dynamics have been hindered by a lack of site-specific knowledge of histone modifications. Using mass spectrometry, we have provided the first known molecular map of histone methylation, acetylation and phosphorylation modifications in Giardia core histones. We have identified over 50 previously unreported histone modifications including sites with established roles in epigenetic regulation, and co-occurring modifications indicative of post-translational modification crosstalk. These demonstrate conserved histone modifications in Giardia which are equivalent to many other eukaryotes, and suggest that similar epigenetic mechanisms are in place in this parasite. Further, we used sequence, domain and structural homology to annotate putative histone enzyme networks in Giardia, highlighting representative chromatin modifiers which appear sufficient for identified sites, particularly those from H3 and H4 variants. This study is to our knowledge the first and most comprehensive, complete and accurate view of Giardia histone post-translational modifications to date, and a substantial step towards understanding their associations in parasite development and virulence.
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10
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Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. Genes (Basel) 2020; 11:genes11080937. [PMID: 32823766 PMCID: PMC7464555 DOI: 10.3390/genes11080937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution. A Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA, but not in cellulose synthases of other organisms. The recent discovery of another GH6 hydrolase-like gene (GH6-1) in tunicate genomes further raises the question of how tunicates acquired GH6. To examine the probable origin of these genes, we analyzed the phylogenetic relationship of GH6 proteins in tunicates and other organisms. Our analyses show that tunicate GH6s, the GH6-1 gene, and the GH6 part of the CesA gene, form two independent, monophyletic gene groups. We also compared their sequence signatures and exon splice sites. All tunicate species examined have shared splice sites in GH6-containing genes, implying ancient intron acquisitions. It is likely that the tunicate CesA and GH6-1 genes existed in the common ancestor of all extant tunicates.
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11
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Najdrová V, Stairs CW, Vinopalová M, Voleman L, Doležal P. The evolution of the Puf superfamily of proteins across the tree of eukaryotes. BMC Biol 2020; 18:77. [PMID: 32605621 PMCID: PMC7325665 DOI: 10.1186/s12915-020-00814-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat domains, each of which specifically recognizes a single RNA base. Recently, three diversified PufSF proteins have been described in model organisms, each of which is responsible for the maturation of ribosomal RNA or the translational regulation of mRNAs; however, less is known about the role of these proteins across eukaryotic diversity. RESULTS Here, we investigated the distribution and function of PufSF RBPs in the tree of eukaryotes. We determined that the following PufSF proteins are universally conserved across eukaryotes and can be broadly classified into three groups: (i) Nop9 orthologues, which participate in the nucleolar processing of immature 18S rRNA; (ii) 'classical' Pufs, which control the translation of mRNA; and (iii) PUM3 orthologues, which are involved in the maturation of 7S rRNA. In nearly all eukaryotes, the rRNA maturation proteins, Nop9 and PUM3, are retained as a single copy, while mRNA effectors ('classical' Pufs) underwent multiple lineage-specific expansions. We propose that the variation in number of 'classical' Pufs relates to the size of the transcriptome and thus the potential mRNA targets. We further distinguished full set of PufSF proteins in divergent metamonad Giardia intestinalis and initiated their cellular and biochemical characterization. CONCLUSIONS Our data suggest that the last eukaryotic common ancestor (LECA) already contained all three types of PufSF proteins and that 'classical' Pufs then underwent lineage-specific expansions.
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Affiliation(s)
- Vladimíra Najdrová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Martina Vinopalová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic.
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12
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Hudson AJ, McWatters DC, Bowser BA, Moore AN, Larue GE, Roy SW, Russell AG. Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages. BMC Evol Biol 2019; 19:162. [PMID: 31375061 PMCID: PMC6679479 DOI: 10.1186/s12862-019-1488-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022] Open
Abstract
Background Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. Results We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to ‘long’ G. lamblia introns, RNA secondary structural potential is evident for ‘long’ (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S. salmonicida; cumulatively, illustrating significant snRNA differences within some diplomonads. Finally, we studied spliceosomal protein complements and find protein sets in Giardia, Spironucleus and Trepomonas sp. PC1 highly- reduced but well conserved across the clade, with between 44 and 62 out of 174 studied spliceosomal proteins detectable. Comparison with more distant relatives revealed a highly nested pattern, with the more intron-rich fornicate Kipferlia bialata retaining 87 total proteins including nearly all those observed in the diplomonad representatives, and the oxymonad Monocercomonoides retaining 115 total proteins including nearly all those observed in K. bialata. Conclusions Comparisons in diplomonad representatives and species of other closely-related metamonad groups indicates similar patterns of intron structural conservation and spliceosomal protein composition but significant divergence of snRNA structure in genomically-reduced species. Relative to other eukaryotes, loss of evolutionarily-conserved snRNA domains and common sets of spliceosomal proteins point to a more streamlined splicing mechanism, where intron sequences and structures may be functionally compensating for the minimalization of spliceosome components. Electronic supplementary material The online version of this article (10.1186/s12862-019-1488-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew J Hudson
- Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - David C McWatters
- Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Bradley A Bowser
- Molecular Cell Biology, University of California-Merced, Merced, CA, USA
| | - Ashley N Moore
- Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Graham E Larue
- Molecular Cell Biology, University of California-Merced, Merced, CA, USA
| | - Scott W Roy
- Molecular Cell Biology, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Anthony G Russell
- Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada. .,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.
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13
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Jo SS, Choi SS. Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns. Genome Biol Evol 2019; 11:786-797. [PMID: 30753418 PMCID: PMC6424223 DOI: 10.1093/gbe/evz033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/03/2023] Open
Abstract
We previously showed that the first intron of genes exhibits several interesting characteristics not seen in other introns: 1) it is the longest intron on average in almost all eukaryotes, 2) it presents the highest number of conserved sites, and 3) it exhibits the highest density of regulatory chromatin marks. Here, we expand on our previous study by integrating various multiomics data, leading to further evidence supporting the functionality of sites in the first intron. We first show that trait-associated single-nucleotide polymorphisms (TASs) are significantly enriched in the first intron. We also show that within the first intron, the density of epigenetic chromatin signals is higher near TASs than in distant regions. Furthermore, the distribution of several chromatin regulatory marks is investigated in relation to gene expression specificity (i.e., housekeeping vs. tissue-specific expression), essentiality (essential genes vs. nonessential genes), and levels of gene expression; housekeeping genes or essential genes contain greater proportions of active chromatin marks than tissue-specific genes or nonessential genes, and highly expressed genes exhibit a greater density of chromatin regulatory marks than genes with low expression. Moreover, we observe that genes carrying multiple first-intron TASs interact with each other within a large protein-protein interaction network, ultimately connecting to the UBC protein, a well-established protein involved in ubiquitination. We believe that our results shed light on the functionality of first introns as a genomic entity involved in gene expression regulation.
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Affiliation(s)
- Shin-Sang Jo
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Korea
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14
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Saghaug CS, Klotz C, Kallio JP, Brattbakk HR, Stokowy T, Aebischer T, Kursula I, Langeland N, Hanevik K. Genetic variation in metronidazole metabolism and oxidative stress pathways in clinical Giardia lamblia assemblage A and B isolates. Infect Drug Resist 2019; 12:1221-1235. [PMID: 31190910 PMCID: PMC6519707 DOI: 10.2147/idr.s177997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose: Treatment-refractory Giardia cases have increased rapidly within the last decade. No markers of resistance nor a standardized susceptibility test have been established yet, but several enzymes and their pathways have been associated with metronidazole (MTZ) resistant Giardia. Very limited data are available regarding genetic variation in these pathways. We aimed to investigate genetic variation in metabolic pathway genes proposed to be involved in MTZ resistance in recently acquired, cultured clinical isolates. Methods: Whole genome sequencing of 12 assemblage A2 and 8 assemblage B isolates was done, to decipher genomic variation in Giardia. Twenty-nine genes were identified in a literature search and investigated for their single nucleotide variants (SNVs) in the coding/non-coding regions of the genes, either as amino acid changing (non-synonymous SNVs) or non-changing SNVs (synonymous). Results: In Giardia assemblage B, several genes involved in MTZ activation or oxidative stress management were found to have higher numbers of non-synonymous SNVs (thioredoxin peroxidase, nitroreductase 1, ferredoxin 2, NADH oxidase, nitroreductase 2, alcohol dehydrogenase, ferredoxin 4 and ferredoxin 1) than the average variation. For Giardia assemblage A2, the highest genetic variability was found in the ferredoxin 2, ferredoxin 6 and in nicotinamide adenine dinucleotide phosphate (NADPH) oxidoreductase putative genes. SNVs found in the ferredoxins and nitroreductases were analyzed further by alignment and homology modeling. SNVs close to the iron-sulfur cluster binding sites in nitroreductase-1 and 2 and ferredoxin 2 and 4 could potentially affect protein function. Flavohemoprotein seems to be a variable-copy gene, due to higher, but variable coverage compared to other genes investigated. Conclusion: In clinical Giardia isolates, genetic variability is common in important genes in the MTZ metabolizing pathway and in the management of oxidative and nitrosative stress and includes high numbers of non-synonymous SNVs. Some of the identified amino acid changes could potentially affect the respective proteins important in the MTZ metabolism.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway
| | - Hans-Richard Brattbakk
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Hordaland, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
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15
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Iyer V, Chettiar ST, Grover M, Rajyaguru P, Nageshan RK, Tatu U. Giardia lamblia
Hsp90 pre‐
mRNA
s undergo self‐splicing to generate mature
RNA
in an
in vitro
trans‐splicing reaction. FEBS Lett 2019; 593:433-442. [DOI: 10.1002/1873-3468.13324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Vinithra Iyer
- Department of Biochemistry Indian Institute of Science Bangalore India
| | | | - Manish Grover
- Department of Biochemistry Indian Institute of Science Bangalore India
| | | | | | - Utpal Tatu
- Department of Biochemistry Indian Institute of Science Bangalore India
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16
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Wang SE, Amir AS, Nguyen T, Poole AM, Simoes-Barbosa A. Spliceosomal introns in Trichomonas vaginalis revisited. Parasit Vectors 2018; 11:607. [PMID: 30482228 PMCID: PMC6260720 DOI: 10.1186/s13071-018-3196-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The human protozoan parasite Trichomonas vaginalis is an organism of interest for understanding eukaryotic evolution. Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: only 62 putative introns have been annotated in this genome, and little or no experimental evidence exists to back up these predictions. Results This study revisited the 62 annotated introns of T. vaginalis derived from the genome sequencing plus previous publications. After experimental validation and a new genome-wide search, we confirmed the presence of introns in 32 genes and 18 others were concluded to be intronless. Sequence analyses classified the validated introns into two types, based on distinctive features such as length and conservation of splice site motifs. Conclusions Our study provides an updated list of intron-containing genes in the genome of T. vaginalis. Our findings suggests the existence of two intron ‘families’ spread among T. vaginalis protein-coding genes. Additional studies are needed to understand the functional separation of these two classes of introns and to assess the existence of further introns in the T. vaginalis genome. Electronic supplementary material The online version of this article (10.1186/s13071-018-3196-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Abdul S Amir
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tai Nguyen
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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17
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Xue M, Chen B, Ye Q, Shao J, Lyu Z, Wen J. Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications. Biol Direct 2018; 13:23. [PMID: 30621773 PMCID: PMC6545626 DOI: 10.1186/s13062-018-0226-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Background It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Actually the reverse question -- how the few introns can be retained under the evolutionary selection pressure of intron loss -- is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The situation that extremely few (eight) spliceosome-mediated cis-spliced introns present in the relatively simple genome of Giardia lamblia provides an excellent opportunity to explore this question. Results Our investigation found three types of distribution patterns of the few introns in the intron-containing genes: ancient intron in ancient gene, later-evolved intron in ancient gene, and later-evolved intron in later-evolved gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Without finding any special features or functional importance of these introns responsible for their retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with transcribable genes on their complementary strands, and that the introns just reside in the overlapping regions. Conclusions In Giardia’s evolution, despite constant evolutionary selection pressure of intron loss, intron gain can still occur in both ancient and later-evolved genes, but only a few introns are retained; at least the evolutionary retention of some of the introns might not be due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introns, but suggest that “functional constraint” of introns may not be necessarily directly associated with intron loss and gain, and that the real functions are probably still outside of our current knowledge. Reviewers This article was reviewed by Mikhail Gelfand, Michael Gray, and Igor Rogozin. Electronic supplementary material The online version of this article (10.1186/s13062-018-0226-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Xue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Bing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Qingqing Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jingru Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhangxia Lyu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jianfan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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18
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Bannerman BP, Kramer S, Dorrell RG, Carrington M. Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism. PLoS One 2018; 13:e0192633. [PMID: 29561870 PMCID: PMC5862402 DOI: 10.1371/journal.pone.0192633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/26/2018] [Indexed: 12/01/2022] Open
Abstract
The degree of conservation and evolution of cytoplasmic mRNA metabolism pathways across the eukaryotes remains incompletely resolved. In this study, we describe a comprehensive genome and transcriptome-wide analysis of proteins involved in mRNA maturation, translation, and mRNA decay across representative organisms from the six eukaryotic super-groups. We demonstrate that eukaryotes share common pathways for mRNA metabolism that were almost certainly present in the last eukaryotic common ancestor, and show for the first time a correlation between intron density and a selective absence of some Exon Junction Complex (EJC) components in eukaryotes. In addition, we identify pathways that have diversified in individual lineages, with a specific focus on the unique gene gains and losses in members of the Excavata and SAR groups that contribute to their unique gene expression pathways compared to other organisms.
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Affiliation(s)
| | - Susanne Kramer
- Biozentrum, Lehrstuhl für Zell-und Entwicklungsbiologie, Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Richard G. Dorrell
- Institute of Biology, École Normale Supérieure, PSL Research University, Paris, France
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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19
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Wang Q, Wang Q, Zhou YL, Shan S, Cui HH, Xiao Y, Dong K, Khashaveh A, Sun L, Zhang YJ. Characterization and Comparative Analysis of Olfactory Receptor Co-Receptor Orco Orthologs Among Five Mirid Bug Species. Front Physiol 2018; 9:158. [PMID: 29556202 PMCID: PMC5845112 DOI: 10.3389/fphys.2018.00158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 01/08/2023] Open
Abstract
The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis, and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest. In the odorant detection pathway, olfactory receptor co-receptor (Orco) plays critical role in the perception of odors. In this study, we identified the full-length cDNA sequences encoding three putative Orcos (AsutOrco, AfasOrco, and LpraOrco) in bug species of A. suturalis, A. fasciaticollis, and L. pratensis based on homology cloning method. Next, sequence alignment, membrane topology and gene structure analysis showed that these three Orco orthologs together with previously reported AlinOrco and AlucOrco shared high amino acid identities and similar topology structure, but had different gene structure especially at the length and insertion sites of introns. Furthermore, the evolutional estimation on the ratios of non-synonymous to synonymous (Ka/Ks) revealed that Orco genes were under strong purifying selection, but the degrees of variation were significant different between genera. The results of quantitative real-time PCR experiments showed that these five Orco genes had a similar antennae-biased tissue expression pattern. Taking these data together, it is thought that Orco genes in the mirid species could share conserved olfaction roles but had different evolution rates. These findings would lay a foundation to further investigate the molecular mechanisms of evolutionary interactions between mirid bugs and their host plants, which might in turn contribute to the development of pest management strategy for mirid bugs.
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Affiliation(s)
- Qi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yan-Le Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,DanDong Entry-Exit Inspection and Quarantine Bureau, Dandong, China
| | - Shuang Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huan-Huan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Xiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kun Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Sun
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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20
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Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr Biol 2017; 27:569-575. [PMID: 28190732 DOI: 10.1016/j.cub.2016.12.057] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/17/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023]
Abstract
The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities-if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor's cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.
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Affiliation(s)
- Mark M Slabodnick
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - J Graham Ruby
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah B Reiff
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Sager Gosai
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ewa Witkowska
- Department of Ob/Gyn, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Graham E Larue
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Susan Fisher
- Department of Ob/Gyn, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - William Chu
- Department of Biology, Bradley University, Peoria, IL 61625, USA
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, IL 61625, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Joseph Derisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
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21
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Roy SW. Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia. PeerJ 2017; 5:e2861. [PMID: 28090405 PMCID: PMC5224939 DOI: 10.7717/peerj.2861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/03/2016] [Indexed: 11/21/2022] Open
Abstract
Background The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist Giardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the G. lambliatranscriptome and across diplomonad diversity in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions. Methods I leverage newly available transcriptomic data from G. lamblia and the related diplomonad Spironucleus salmonicidato search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns in G. lamblia, suggesting good sensitivity. Results Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron in G. lamblia, in the p68 helicase gene, and no cases in S. salmonicida. The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features of G. lamblia trans-spliced introns are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism. Discussion These results serve to circumscribe the role of trans-splicing in diplomonads both in terms of the number of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.
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Affiliation(s)
- Scott William Roy
- Department of Biology, San Francisco State University , San Francisco , CA , United States
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Interactions between Giardia duodenalis Sm proteins and their association with spliceosomal snRNAs. Parasitol Res 2016; 116:617-626. [DOI: 10.1007/s00436-016-5326-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/08/2016] [Indexed: 12/16/2022]
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Inhibición parcial de dos genes que codifican para proteínas spliceosomales en Giardia intestinalis. BIOMEDICA 2016; 36:128-36. [DOI: 10.7705/biomedica.v36i0.3068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 02/29/2016] [Indexed: 11/21/2022]
Abstract
<p><strong>Introducción.</strong> <em>Giardia intestinalis</em> es un organismo tempranamente divergente en el que recientemente se demostró la presencia de intrones. La maquinaria responsable de la remoción de intrones en eucariotes superiores es el spliceosoma, conformado por 5 ribonucleoproteínas. Cada una tiene un ARN pequeño nuclear, un set de 7 proteínas Sm (B, D1, D2, D3, E, F y G) y varias proteínas específicas. En <em>G. intestinalis</em>, se han identificado los genes de algunas proteínas del spliceosoma por bioinformática. Aunque se asume que el spliceosoma es el responsable del splicing en el parásito, su caracterización bioquímica no ha sido realizada.</p><p><strong>Objetivo.</strong> Inhibir dos genes que codifican para proteínas del spliceosoma de <em>G. intestinalis</em> con el fin de determinar si esta inhibición afecta el crecimiento o la enquistación del parásito.</p><p><strong>Materiales y métodos.</strong> Se clonaron en un vector específico para <em>G. intestinalis</em> secuencias antisentido de los genes que codifican para las proteínas spliceosomales SmB y SmD3 del parásito. Posteriormente se transfectó <em>G. intestinalis</em> con los vectores recombinantes y se seleccionaron aquellos parásitos que lo incorporaron. Se confirmó la disminución del mensajero por PCR en tiempo real y se evaluó el crecimiento y la enquistación en parásitos silvestres y transfectados.</p><p><strong>Resultados.</strong> Se observó una disminución del 40% y 70% en el mARN de SmB y SmD3, respectivamente. El crecimiento y la enquistación no se vieron afectados en estos parásitos.</p><p><strong>Conclusión. </strong>La disminución de SmB y SmD3 no afectan el parásito, indicando que el spliceosoma sigue siendo funcional o que el splicing no es una función vital del parásito.</p>
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Dey G, Meyer T. Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. Cell Syst 2015; 1:106-15. [PMID: 27135799 DOI: 10.1016/j.cels.2015.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 12/22/2022]
Abstract
Information about functional connections between genes can be derived from patterns of coupled loss of their homologs across multiple species. This comparative approach, termed phylogenetic profiling, has been successfully used to infer genetic interactions in bacteria and eukaryotes. Rapid progress in sequencing eukaryotic species has enabled the recent phylogenetic profiling of the human genome, resulting in systematic functional predictions for uncharacterized human genes. Importantly, groups of co-evolving genes reveal widespread modularity in the underlying genetic network, facilitating experimental analyses in human cells as well as comparative studies of conserved functional modules across species. This strategy is particularly successful in identifying novel metabolic proteins and components of multi-protein complexes. The targeted sequencing of additional key eukaryotes and the incorporation of improved methods to generate and compare phylogenetic profiles will further boost the predictive power and utility of this evolutionary approach to the functional analysis of gene interaction networks.
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Affiliation(s)
- Gautam Dey
- Chemical and Systems Biology, Stanford University, Stanford CA 94305, USA.
| | - Tobias Meyer
- Chemical and Systems Biology, Stanford University, Stanford CA 94305, USA.
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25
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Kamikawa R, Inagaki Y, Roger AJ, Hashimoto T. Splintrons inGiardia intestinalis. Commun Integr Biol 2014. [DOI: 10.4161/cib.15466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Kamikawa R, Inagaki Y, Hashimoto T. Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages. BMC Res Notes 2014; 7:413. [PMID: 24981682 PMCID: PMC4085374 DOI: 10.1186/1756-0500-7-413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. However, we anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the open reading frames (ORFs) in the Giardia genome. Consequently, comprehensive surveys of introns in ORFs for hypothetical proteins are critical for better understanding of the intron evolution in this organism. RESULTS In this study, we identified two novel cis-spliced introns in the draft genome data of G. intestinalis strain WB, by surveying the conserved sequence motifs shared amongst the previously known introns. G. intestinalis strains can be divided into phylogenetically distinct assemblages A-H, and all the introns identified in past studies are shared among the published genome data from strains WB, DH, GS, and P15 representing assemblages A1, A2, B, and E, respectively. Nevertheless one of the two novel introns identified in this study was found to be absent in strain P15. CONCLUSION By considering the organismal relationship among G. intestinalis assemblages A1, A2, B, and E, one of the two introns identified in this study has highly likely been lost after the divergence of the assemblages. On the basis of a sequence comparison between the intron-bearing loci in WB, DH, and GS genomes and the homologous but intron-free locus in P15 genome, we propose that the loss of this particular intron was mediated by integration of the DNA fragment reverse-transcribed from mature mRNAs.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu cho, Kyoto 606-8501, Japan.
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Park SG, Hannenhalli S, Choi SS. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics 2014; 15:526. [PMID: 24964727 PMCID: PMC4085337 DOI: 10.1186/1471-2164-15-526] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/18/2014] [Indexed: 01/04/2023] Open
Abstract
Background Genomes of higher eukaryotes have surprisingly long first introns and in some cases, the first introns have been shown to have higher conservation relative to other introns. However, the functional relevance of conserved regions in the first introns is poorly understood. Leveraging the recent ENCODE data, here we assess potential regulatory roles of conserved regions in the first intron of human genes. Results We first show that relative to other downstream introns, the first introns are enriched for blocks of highly conserved sequences. We also found that the first introns are enriched for several chromatin marks indicative of active regulatory regions and this enrichment of regulatory marks is correlated with enrichment of conserved blocks in the first intron; the enrichments of conservation and regulatory marks in first intron are not entirely explained by a general, albeit variable, bias for certain marks toward the 5’ end of introns. Interestingly, conservation as well as proportions of active regulatory chromatin marks in the first intron of a gene correlates positively with the numbers of exons in the gene but the correlation is significantly weakened in second introns and negligible beyond the second intron. The first intron conservation is also positively correlated with the gene’s expression level in several human tissues. Finally, a gene-wise analysis shows significant enrichments of active chromatin marks in conserved regions of first introns, relative to the conserved regions in other introns of the same gene. Conclusions Taken together, our analyses strongly suggest that first introns are enriched for active transcriptional regulatory signals under purifying selection. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-526) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sridhar Hannenhalli
- Department of Cell Biology and Molecular Genetics, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, MD 20742, USA.
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Zhao X, Li H, Bao T. Analysis on the interaction between post-spliced introns and corresponding protein coding sequences in ribosomal protein genes. J Theor Biol 2013; 328:33-42. [DOI: 10.1016/j.jtbi.2013.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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Franzén O, Jerlström-Hultqvist J, Einarsson E, Ankarklev J, Ferella M, Andersson B, Svärd SG. Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq. PLoS Comput Biol 2013; 9:e1003000. [PMID: 23555231 PMCID: PMC3610916 DOI: 10.1371/journal.pcbi.1003000] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/02/2013] [Indexed: 01/08/2023] Open
Abstract
Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E. We have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3′ UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology. Giardia is a single cell intestinal parasite and a common cause of diarrhea in humans and animals. Giardia is an unusual eukaryote by possessing two nuclei, a highly reduced genome and simple transcriptional apparatus. We have characterized the transcriptome of Giardia at single nucleotide resolution, which allowed the calculation of digital gene expression values for the complete set of genes. We performed a comparison of gene expression divergence across three genotypes. Most of the genes were transcribed, and the data were used to refine and correct gene models. Several gene expression differences were identified between the genotypes. A non-transcribed cluster of genes was detected on chromosome 5, likely representing a silenced region. The data also allowed mapping of transcript termini, which provided the first global view of 3′ untranslated regions in this parasite. This study also gives the first genome-wide evidence of transcription of allelic variants in Giardia. In this study, we provide novel insights into the transcriptome of an important human pathogen and model eukaryote. The findings reported here likely relate to the lifestyle of this parasite and its adaptation to parasitism. The data provide starting points for functional investigation of Giardia's biology and diplomonads generally.
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Affiliation(s)
- Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Elin Einarsson
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Johan Ankarklev
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Marcela Ferella
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Staffan G. Svärd
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
- * E-mail:
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Hammesfahr B, Odronitz F, Mühlhausen S, Waack S, Kollmar M. GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures. BMC Bioinformatics 2013; 14:77. [PMID: 23496949 PMCID: PMC3605371 DOI: 10.1186/1471-2105-14-77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol. Conclusions GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html.
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Affiliation(s)
- Björn Hammesfahr
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
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Koonin EV, Csuros M, Rogozin IB. Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:93-105. [PMID: 23139082 DOI: 10.1002/wrna.1143] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In eukaryotes, protein-coding sequences are interrupted by non-coding sequences known as introns. During mRNA maturation, introns are excised by the spliceosome and the coding regions, exons, are spliced to form the mature coding region. The intron densities widely differ between eukaryotic lineages, from 6 to 7 introns per kb of coding sequence in vertebrates, some invertebrates and green plants, to only a few introns across the entire genome in many unicellular eukaryotes. Evolutionary reconstructions using maximum likelihood methods suggest intron-rich ancestors for each major group of eukaryotes. For the last common ancestor of animals, the highest intron density of all extant and extinct eukaryotes was inferred, at 120-130% of the human intron density. Furthermore, an intron density within 53-74% of the human values was inferred for the last eukaryotic common ancestor. Accordingly, evolution of eukaryotic genes in all lines of descent involved primarily intron loss, with substantial gain only at the bases of several branches including plants and animals. These conclusions have substantial biological implications indicating that the common ancestor of all modern eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information NLM/NIH, Bethesda, MD, USA.
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Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG. Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia. Nucleic Acids Res 2012; 40:10995-1008. [PMID: 23019220 PMCID: PMC3510501 DOI: 10.1093/nar/gks887] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discovery of a conserved 12 nt RNA processing sequence motif found in the 3' end regions of a large number of G. lamblia ncRNA genes. RNA end mapping and other experiments indicate the motif serves to mediate ncRNA 3' end formation from mono- and di-cistronic RNA precursor transcripts. Remarkably, we find the motif is also utilized in the processing pathway of all four previously identified trans-spliced G. lamblia introns, revealing a common RNA processing pathway for ncRNAs and trans-spliced introns in this organism. Motif sequence conservation then allowed for the bioinformatic and experimental identification of additional G. lamblia ncRNAs, including new U1 and U6 spliceosomal snRNA candidates. The U6 snRNA candidate was then used as a tool to identity novel U2 and U4 snRNAs, based on predicted phylogenetically conserved snRNA-snRNA base-pairing interactions, from a set of previously identified G. lamblia ncRNAs without assigned function. The Giardia snRNAs retain the core features of spliceosomal snRNAs but are sufficiently evolutionarily divergent to explain the difficulties in their identification. Most intriguingly, all of these snRNAs show structural features diagnostic of U2-dependent/major and U12-dependent/minor spliceosomal snRNAs.
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Affiliation(s)
- Andrew J Hudson
- Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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Li W, Saraiya AA, Wang CC. The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lamblia. Cell Microbiol 2012; 14:1455-73. [PMID: 22568619 PMCID: PMC3422372 DOI: 10.1111/j.1462-5822.2012.01811.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 04/27/2012] [Indexed: 12/21/2022]
Abstract
In the current investigation, we analysed all the known small nucleolar RNAs (snoRNAs) in the deeply branching protozoan parasite Giardia lamblia for potential microRNAs (miRNAs) that might be derived from them. Two putative miRNAs have since been identified by Northern blot, primer extension, 3' RACE and co-immunoprecipitation with Giardia Argonaute (GlAgo), and designated miR6 and miR10. Giardia Dicer (GlDcr) is capable of processing the snoRNAs into the corresponding miRNAs in vitro. Potential miR6 and miR10 binding sites in Giardia genome were predicted bio-informatically. A miR6 binding site was found at the 3' untranslated regions (UTR) of 44 variant surface protein (vsp) genes, whereas a miR10 binding site was identified at the 3' end of 159 vsp open-reading frames. Thirty-three of these vsp genes turned out to contain binding sites for both miR6 and miR10. A reporter mRNA tagged with the 3' end of vsp1267, which contains the target sites for both miRNAs, was translationally repressed by both miRNAs in Giardia. Episomal expression of an N-terminal c-myc tagged VSP1267 was found significantly repressed by introducing either miR6 or miR10 into the cells and the repressive effects were additive. When the 2'-O-methyl antisense oligos (ASOs) of either miR6 or miR10 was introduced, however, there was an enhancement of tagged VSP1267 expression suggesting an inhibition of the repressive effects of endogenous miR6 or miR10 by the ASOs. Of the total 220 vsp genes in Giardia, we have now found 178 of them carrying putative binding sites for all the miRNAs that have been currently identified, suggesting that miRNAs are likely the regulators of VSP expression in Giardia.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
| | - Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
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Abstract
In this review, the current status of genomic and proteomic research on Giardia is examined in terms of evolutionary biology, phylogenetic relationships and taxonomy. The review also describes how characterising genetic variation in Giardia from numerous hosts and endemic areas has provided a better understanding of life cycle patterns, transmission and the epidemiology of Giardia infections in humans, domestic animals and wildlife. Some progress has been made in relating genomic information to the phenotype of Giardia, and as a consequence, new information has been obtained on aspects of developmental biology and the host-parasite relationship. However, deficiencies remain in our understanding of pathogenesis and host specificity, highlighting the limitations of currently available genomic datasets.
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Korneta I, Magnus M, Bujnicki JM. Structural bioinformatics of the human spliceosomal proteome. Nucleic Acids Res 2012; 40:7046-65. [PMID: 22573172 PMCID: PMC3424538 DOI: 10.1093/nar/gks347] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258-338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540-683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome.
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Affiliation(s)
- Iga Korneta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw PL-02-109, Poland
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Rogozin IB, Carmel L, Csuros M, Koonin EV. Origin and evolution of spliceosomal introns. Biol Direct 2012; 7:11. [PMID: 22507701 PMCID: PMC3488318 DOI: 10.1186/1745-6150-7-11] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/15/2012] [Indexed: 12/31/2022] Open
Abstract
Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers’ Reports section.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information NLM/NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
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Saraiya AA, Li W, Wang CC. A microRNA derived from an apparent canonical biogenesis pathway regulates variant surface protein gene expression in Giardia lamblia. RNA (NEW YORK, N.Y.) 2011; 17:2152-64. [PMID: 22033329 PMCID: PMC3222128 DOI: 10.1261/rna.028118.111] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 09/13/2011] [Indexed: 05/19/2023]
Abstract
We have previously shown that a snoRNA-derived microRNA, miR2, in Giardia lamblia potentially regulates the expression of 22 variant surface protein (VSP) genes. Here, we identified another miRNA, miR4, also capable of regulating the expression of several VSPs but derived from an unannotated open reading frame (ORF) rather than a snoRNA, suggesting a canonical miRNA biogenesis pathway in Giardia. miR4 represses expression of a reporter containing two miR4 antisense sequences at the 3' UTR without causing a corresponding decrease in the mRNA level. This repression requires the presence of the Giardia Argonaute protein (GlAgo) and is reversed by 2' O-methylated antisense oligo to miR4, suggesting an RNA-induced silencing complex (RISC)-mediated mechanism. Furthermore, in vivo and in vitro evidence suggested that the Giardia Dicer protein (GlDcr) is required for miR4 biogenesis. Coimmunoprecipitation of miR4 with GlAgo further verified miR4 as a miRNA. A total of 361 potential target sites for miR4 were bioinformatically identified in Giardia, out of which 69 (32.7%) were associated with VSP genes. miR4 reduces the expression of a reporter containing two copies of the target site from VSP (GL50803_36493) at the 3' UTR. Sixteen of the 69 VSP genes were further found to contain partially overlapping miR2 and miR4 targeting sites. Expression of a reporter carrying the two overlapping sites was inhibited by either miR2 or miR4, but the inhibition was neither synergistic nor additive, suggesting a complex mechanism of miRNA regulation of VSP expression and the presence of a rich miRNAome in Giardia.
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Affiliation(s)
- Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
| | - Wei Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
- Corresponding author.E-mail .
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Kamikawa R, Inagaki Y, Hashimoto T. A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis. Biophys Rev 2011; 3:193-197. [PMID: 28510047 DOI: 10.1007/s12551-011-0058-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/29/2011] [Indexed: 11/30/2022] Open
Abstract
Although spliceosomal introns are an abundant landmark in eukaryotic genomes, the nuclear genome of the divergent eukaryote Giardia intestinalis, the causative agent of giardiasis, has been considered as "intron-poor" with only five canonical (cis-spliced) introns. However, three research groups (including ours) have independently reported a novel class of spliceosomal introns in the G. intestinalis genome. Three protein-coding genes are split into pieces in the G. intestinalis genome, and each of the partial coding regions was independently transcribed into polyadenylated premature mRNAs (pre-mRNAs). The two pre-mRNAs directly interact with each other by an intermolecular-stem structure formed between their non-coding portions, and are then processed into mature mRNAs by spliceosome-mediated trans-splicing. Here, we summarize the recently published works on split introns ("splintrons") in the G. intestinalis genome, and then provide our speculation on the functional property of the Giardia spliceosomes based on the putative ratio of splintrons to canonical introns. Finally, we discuss a scenario for the transition from typical GT-AG boundaries to non-typical AT-AC boundaries in a particular splintron of Giardia.
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Affiliation(s)
- Ryoma Kamikawa
- Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Yuji Inagaki
- Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Tetsuo Hashimoto
- Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
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A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol 2011; 7:e1002150. [PMID: 21935348 PMCID: PMC3174169 DOI: 10.1371/journal.pcbi.1002150] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 06/21/2011] [Indexed: 11/19/2022] Open
Abstract
Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6–7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing. In eukaryotes, protein-coding genes are interrupted by non-coding introns. The intron densities widely differ, from 6–7 introns per kilobase of coding sequence in vertebrates, some invertebrates and plants, to only a few introns across the entire genome in many unicellular forms. We applied a robust statistical methodology, Markov Chain Monte Carlo, to reconstruct the history of intron gain and loss throughout the evolution of eukaryotes using a set of 245 homologous genes from 99 genomes that represent the diversity of eukaryotes. Intron-rich ancestors were confidently inferred for each major eukaryotic group including 53% to 74% of the human intron density for the last eukaryotic common ancestor, and 120% to 130% of the human value for the last common ancestor of animals. Evolution of eukaryotic genes involved primarily intron loss, with substantial gain only at the bases of several major branches including plants and animals. Thus, the common ancestor of all extant eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. The line of descent from the last common ancestor to mammals was an uninterrupted intron-rich state that, given the error-prone splicing in intron-rich organisms, was conducive to the elaboration of functional alternative splicing.
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Cohen NE, Shen R, Carmel L. The role of reverse transcriptase in intron gain and loss mechanisms. Mol Biol Evol 2011; 29:179-86. [PMID: 21804076 DOI: 10.1093/molbev/msr192] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Intron density is highly variable across eukaryotic species. It seems that different lineages have experienced considerably different levels of intron gain and loss events, but the reasons for this are not well known. A large number of mechanisms for intron loss and gain have been suggested, and most of them have at least some level of indirect support. We therefore figured out that the variability in intron density can be a reflection of the fact that different mechanisms are active in different lineages. Quite a number of these putative mechanisms, both for intron loss and for intron gain, postulate that the enzyme reverse transcriptase (RT) has a key role in the process. In this paper, we lay out three predictions whose approval or falsification gives indication for the involvement of RT in intron gain and loss processes. Testing these predictions requires data on the intron gain and loss rates of individual genes along different branches of the eukaryotic phylogenetic tree. So far, such rates could not be computed, and hence, these predictions could not be rigorously evaluated. Here, we use a maximum likelihood algorithm that we have devised in the past, Evolutionary Reconstruction by Expectation Maximization, which allows the estimation of such rates. Using this algorithm, we computed the intron loss and gain rates of more than 300 genes in each branch of the phylogenetic tree of 19 eukaryotic species. Based on that we found only little support for RT activity in intron gain. In contrast, we suggest that RT-mediated intron loss is a mechanism that is very efficient in removing introns, and thus, its levels of activity may be a major determinant of intron number. Moreover, we found that intron gain and loss rates are negatively correlated in intron-poor species but are positively correlated for intron-rich species. One explanation to this is that intron gain and loss mechanisms in intron-rich species (like metazoans) share a common mechanistic component, albeit not a RT.
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Affiliation(s)
- Noa E Cohen
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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Kamikawa R, Inagaki Y, Roger AJ, Hashimoto T. Splintrons in Giardia intestinalis: Spliceosomal introns in a split form. Commun Integr Biol 2011; 4:454-6. [PMID: 21966569 DOI: 10.4161/cib.4.4.15466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 03/13/2011] [Indexed: 11/19/2022] Open
Abstract
The divergent eukaryotic unicellular organism Giardia intestinalis is an intestinal parasite in humans and various animals. An analysis of a draft genome sequence suggested that G. intestinalis has a much simpler genome organization and gene repertoire than those of other model eukaryotic organisms (e.g., Arabidopsis and human). This general picture of the G. intestinalis genome seemingly agrees with the fact that only four spliceosomal (cis-spliced) introns have been identified in this organism to date. We have recently shown that G. intestinalis possesses a unique gene expression system incorporating spliceosome-mediated trans-splicing. Some protein-coding genes in G. intestinalis are split into multiple pieces in the genome and each gene fragment is independently transcribed. Two particular pre-mRNAs directly interact with each other by forming an intermolecular-stem structure and are then trans-spliced into a mature mRNA by spliceosomes. We believe that this trans-splicing secondarily arose from the system that excises canonical (cis-splicing) introns. Based on these findings, we suspect that similar phenomena-split genes and post-transcriptional assemblage of their transcripts via trans-splicing-may be prevalent in more distinct eukaryotic lineages than previously known, particularly in organisms possessing "intron-poor" genomes.
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Affiliation(s)
- Ryoma Kamikawa
- Center for Computational Sciences and Institute of Biological Sciences; University of Tsukuba; Ibaraki, Japan
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42
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Smith A, Johnson P. Gene expression in the unicellular eukaryote Trichomonas vaginalis. Res Microbiol 2011; 162:646-54. [DOI: 10.1016/j.resmic.2011.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 03/02/2011] [Indexed: 02/01/2023]
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Roy SW, Hudson AJ, Joseph J, Yee J, Russell AG. Numerous fragmented spliceosomal introns, AT-AC splicing, and an unusual dynein gene expression pathway in Giardia lamblia. Mol Biol Evol 2011; 29:43-9. [PMID: 21482665 DOI: 10.1093/molbev/msr063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Spliceosomal introns are hallmarks of eukaryotic genomes, dividing coding regions into separate exons, which are joined during mRNA intron removal catalyzed by the spliceosome. With few known exceptions, spliceosomal introns are cis-spliced, that is, removed from one contiguous pre-mRNA transcript. The protistan intestinal parasite Giardia lamblia exhibits one of the most reduced eukaryotic genomes known, with short intergenic regions and only four known spliceosomal introns. Our genome-wide search for additional introns revealed four unusual cases of spliceosomal intron fragmentation, with consecutive exons of conserved protein-coding genes being dispersed to distant genomic sites. Independent transcripts are trans-spliced to yield contiguous mature mRNAs. Most strikingly, a dynein heavy chain subunit is both interrupted by two fragmented introns and also predicted to be assembled as two separately translated polypeptides, a remarkably complex expression pathway for a nuclear-encoded sequence. For each case, we observe extensive base-pairing potential between intron halves. This base pairing provides both a rationale for the in vivo association of independently transcribed mRNAs transcripts and the apparent specificity of splicing. Similar base-pairing potential in two cis-spliced G. lamblia introns suggests an evolutionary pathway whereby intron fragmentation of cis-spliced introns is permissible and a preliminary evolutionary step to complete gene fission. These results reveal remarkably complex genome dynamics in a severely genomically reduced parasite.
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Affiliation(s)
- Scott W Roy
- Department of Biology, Stanford University, USA
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Split Introns in the Genome of Giardia intestinalis Are Excised by Spliceosome-Mediated trans-Splicing. Curr Biol 2011; 21:311-5. [DOI: 10.1016/j.cub.2011.01.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 12/06/2010] [Accepted: 01/10/2011] [Indexed: 11/20/2022]
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Nageshan RK, Roy N, Hehl AB, Tatu U. Post-transcriptional repair of a split heat shock protein 90 gene by mRNA trans-splicing. J Biol Chem 2011; 286:7116-22. [PMID: 21209094 DOI: 10.1074/jbc.c110.208389] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heat shock protein 90 participates in diverse biological processes ranging from protein folding, cell cycle, signal transduction and development to evolution in all eukaryotes. It is also critically involved in regulating growth of protozoa such as Dictyostelium discoideum, Leishmania donovani, Plasmodium falciparum, Trypanosoma cruzi, and Trypanosoma evansi. Selective inhibition of Hsp90 has also been explored as an intervention strategy against important human diseases such as cancer, malaria, or trypanosomiasis. Giardia lamblia, a simple protozoan parasite of humans and animals, is an important cause of diarrheal disease with significant morbidity and some mortality in tropical countries. Here we show that the G. lamblia cytosolic hsp90 (glhsp90) is split in two similar sized fragments located 777 kb apart on the same scaffold. Intrigued by this unique arrangement, which appears to be specific for the Giardiinae, we have investigated the biosynthesis of GlHsp90. We used genome sequencing to confirm the split nature of the giardial hsp90. However, a specific antibody raised against the peptide detected a product with a mass of about 80 kDa, suggesting a post-transcriptional rescue of the genomic defect. We show evidence for the joining of the two independent Hsp90 transcripts in-trans to one long mature mRNA presumably by RNA splicing. The splicing junction carries hallmarks of classical cis-spliced introns, suggesting that the regular cis-splicing machinery may be sufficient for repair of the open reading frame. A complementary 26-nt sequence in the "intron" regions adjacent to the splice sites may assist in positioning the two pre-mRNAs for processing. This is the first example of post-transcriptional rescue of a split gene by trans-splicing.
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Affiliation(s)
- Rishi Kumar Nageshan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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Abstract
The eukaryotic intestinal parasite Giardia intestinalis was first described in 1681, when Antonie van Leeuwenhoek undertook a microscopic examination of his own diarrhoeal stool. Nowadays, although G. intestinalis is recognized as a major worldwide contributor to diarrhoeal disease in humans and other mammals, the disease mechanisms are still poorly understood. Owing to its reduced complexity and proposed early evolutionary divergence, G. intestinalis is used as a model eukaryotic system for studying many basic cellular processes. In this Review we discuss recent discoveries in the molecular cell biology and pathogenesis of G. intestinalis.
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Xiao Y, Yin J, Jiang N, Xiang M, Hao L, Lu H, Sang H, Liu X, Xu H, Ankarklev J, Lindh J, Chen Q. Seroepidemiology of human Toxoplasma gondii infection in China. BMC Infect Dis 2010; 10:4. [PMID: 20055991 PMCID: PMC2818656 DOI: 10.1186/1471-2334-10-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 01/07/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Toxoplasmosis is an important zoonotic parasitic disease worldwide. In immune competent individuals, Toxoplasma gondii preferentially infects tissues of central nervous systems, which might be an adding factor of certain psychiatric disorders. Congenital transmission of T. gondii during pregnancy has been regarded as a risk factor for the health of newborn infants. While in immune-compromised individuals, the parasite can cause life-threatening infections. This study aims to investigate the prevalence of T. gondii infection among clinically healthy individuals and patients with psychiatric disorders in China and to identify the potential risk factors related to the vulnerability of infection in the population. METHODS Serum samples from 2634 healthy individuals and 547 patients with certain psychiatric disorders in Changchun and Daqing in the northeast, and in Shanghai in the south of China were examined respectively for the levels of anti-T. gondii IgG by indirect ELISA and a direct agglutination assay. Prevalence of T. gondii infection in the Chinese population in respect of gender, age, residence and health status was systematically analyzed. RESULTS The overall anti-T. gondii IgG prevalence in the study population was 12.3%. In the clinically healthy population 12.5% was sero-positive and in the group with psychiatric disorders 11.3% of these patients were positive with anti-T. gondii IgG. A significant difference (P = 0.004) was found between male and female in the healthy population, the seroprevalence was 10.5% in men versus 14.3% in women. Furthermore, the difference of T. gondii infection rate between male and female in the 20-19 year's group was more obvious, with 6.4% in male population and 14.6% in female population. CONCLUSION A significant higher prevalence of T. gondii infection was observed in female in the clinically healthy population. No correlation was found between T. gondii infection and psychiatric disorders in this study. Results suggest that women are more exposed to T. gondii infection than men in China. The data argue for deeper investigations for the potential risk factors that threat the female populations.
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Affiliation(s)
- Yue Xiao
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Jigang Yin
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Ning Jiang
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Mei Xiang
- The Second Hospital of Jilin University, Ziqiang Street 218, Changchun 10041, PR China
| | - Lili Hao
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, Dong Dan San Tiao, Beijing 100730, PR China
| | - Huijun Lu
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Hong Sang
- The Sixth Hospital of Changchun City, North Round Road 4596, Changchun 130040, PR China
| | - Xianying Liu
- The Second Hospital of Jilin University, Ziqiang Street 218, Changchun 10041, PR China
| | - Huiji Xu
- Changzheng Hospital, Shanghai, Fengyang Road 415, Shanghai 200003, PR China
| | - Johan Ankarklev
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
| | - Johan Lindh
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
| | - Qijun Chen
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, Dong Dan San Tiao, Beijing 100730, PR China
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
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Abstract
Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a population-genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.
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Affiliation(s)
- Wenli Li
- Biology Department, Indiana University, Bloomington, IN 47405, USA
| | | | - Way Sung
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Michael Lynch
- Biology Department, Indiana University, Bloomington, IN 47405, USA
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Skelly DA, Ronald J, Connelly CF, Akey JM. Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences. Genome Biol Evol 2009; 1:466-78. [PMID: 20333215 PMCID: PMC2839277 DOI: 10.1093/gbe/evp046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2009] [Indexed: 11/12/2022] Open
Abstract
Introns are a ubiquitous feature of eukaryotic genomes, and the dynamics of intron evolution between species has been extensively studied. However, comparatively few analyses have focused on the evolutionary forces shaping patterns of intron variation within species. To better understand the population genetic characteristics of introns, we performed an extensive population genetics analysis on key intron splice sequences obtained from 38 strains of Saccharomyces cerevisiae. As expected, we found that purifying selection is the dominant force governing intron splice sequence evolution in yeast, formally confirming that intron-containing alleles are a mutational liability. In addition, through extensive coalescent simulations, we obtain quantitative estimates of the strength of purifying selection (2Nes ≈ 19) and use diffusion approximations to provide insights into the evolutionary dynamics and sojourn times of newly arising splice sequence mutations in natural yeast populations. In contrast to previous functional studies, evolutionary analyses comparing the prevalence of introns in essential and nonessential genes suggest that introns in nonribosomal protein genes are functionally important and tend to be actively maintained in natural populations of S. cerevisiae. Finally, we demonstrate that heritable variation in splicing efficiency is common in intron-containing genes with splice sequence polymorphisms. More generally, our study highlights the advantages of population genomics analyses for exploring the forces that have generated extant patterns of genome variation and for illuminating basic biological processes.
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Affiliation(s)
- Daniel A Skelly
- Department of Genome Sciences, University of Washington, USA
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50
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Splicing in the eukaryotic ancestor: form, function and dysfunction. Trends Ecol Evol 2009; 24:447-55. [DOI: 10.1016/j.tree.2009.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 12/11/2022]
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