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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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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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3
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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4
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Weisz F, Lalle M, Nohynkova E, Sannella AR, Dluhošová J, Cacciò SM. Testing the impact of Whole Genome Amplification on genome comparison using the polyploid flagellated Giardia duodenalis as a model. Exp Parasitol 2019; 207:107776. [PMID: 31628895 DOI: 10.1016/j.exppara.2019.107776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/03/2019] [Accepted: 10/13/2019] [Indexed: 11/27/2022]
Abstract
The availability of high quality genomic DNA in sufficient amounts to perform Next Generation Sequencing (NGS) experiments is challenging for pathogens that cannot be cultivated in vitro, as is the case for many parasites. Therefore, Whole Genome Amplification (WGA) of genomic DNA is used to overcome this limitation. In this study, we evaluated the effect of WGA using the intestinal flagellated protozoan Giardia duodenalis as a model, due to its genome compactness (12 Mb), the presence of two diploid nuclei with variable levels of allelic sequence heterogeneity (ASH), and the availability of reference genomes. We selected one isolate (ZX15) belonging to the same genetic group of the reference isolate WB, namely Assemblage A, sub-Assemblage AI. Genomic DNA from the ZX15 isolate (GEN dataset) and that obtained by WGA of 1 ng of the same genomic DNA (WGA dataset) were sequenced on a HiSeq Illumina platform. Trimmed reads from the GEN and WGA experiments were mapped against the WB reference genome, showing the presence of a very small number of mutations (846 and 752, respectively). The difference in the number of mutations is largely accounted by local variation in coverage and not by bias introduced by WGA. No significant difference were observed in the distribution of mutations in coding and non-coding regions, in the proportion of heterozygous mutations (ASH), or in the transition/transversion ratio of Single Nucleotide Variants within coding sequences. We conclude that the quantitative and qualitative impact of WGA on the identification of mutations is limited, and that this technique can be used to conduct comparative genomics studies.
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Affiliation(s)
- Filip Weisz
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic; Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Lalle
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eva Nohynkova
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic
| | - Anna Rosa Sannella
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Jana Dluhošová
- Institute of Immunology and Microbiology, First Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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5
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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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6
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Nawaz M, Malik MI, Hameed M, Zhou J. Research progress on the composition and function of parasite-derived exosomes. Acta Trop 2019; 196:30-36. [PMID: 31071298 DOI: 10.1016/j.actatropica.2019.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/04/2019] [Indexed: 12/20/2022]
Abstract
Parasites use excretory-secretory pathways to communicate with the host. Characterization of exosomes within the excretory-secretory products reveal by which parasites manipulate their hosts. Parasite derived exosomes provide a mechanistic framework for protein and miRNAs transfer. Transcriptomics and proteomics of parasite exosomes identified a large number of miRNAs and proteins being utilized by parasites in their survival, reproduction and development. Characterization of proteins and miRNAs in parasite secreted exosomes provide important information on host-parasite communication and forms the basis for future studies. In this review, we summarize recent advances in isolation and molecular characterization (protein and miRNAs) of parasite derived exosomes.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Muhammad Irfan Malik
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Muddassar Hameed
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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7
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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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8
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Emery SJ, Baker L, Ansell BRE, Mirzaei M, Haynes PA, McConville MJ, Svärd SG, Jex AR. Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis. Gigascience 2018; 7:4931738. [PMID: 29688452 PMCID: PMC5913674 DOI: 10.1093/gigascience/giy024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/06/2018] [Indexed: 01/20/2023] Open
Abstract
Background Metronidazole (Mtz) is the frontline drug treatment for multiple anaerobic pathogens, including the gastrointestinal protist, Giardia duodenalis. However, treatment failure is common and linked to in vivo drug resistance. In Giardia, in vitro drug-resistant lines allow controlled experimental interrogation of resistance mechanisms in isogenic cultures. However, resistance-associated changes are inconsistent between lines, phenotypic data are incomplete, and resistance is rarely genetically fixed, highlighted by reversion to sensitivity after drug selection ceases or via passage through the life cycle. Comprehensive quantitative approaches are required to resolve isolate variability, fully define Mtz resistance phenotypes, and explore the role of post-translational modifications therein. Findings We performed quantitative proteomics to describe differentially expressed proteins in 3 seminal Mtz-resistant lines compared to their isogenic, Mtz-susceptible, parental line. We also probed changes in post-translational modifications including protein acetylation, methylation, ubiquitination, and phosphorylation via immunoblotting. We quantified more than 1,000 proteins in each genotype, recording substantial genotypic variation in differentially expressed proteins between isotypes. Our data confirm substantial changes in the antioxidant network, glycolysis, and electron transport and indicate links between protein acetylation and Mtz resistance, including cross-resistance to deacetylase inhibitor trichostatin A in Mtz-resistant lines. Finally, we performed the first controlled, longitudinal study of Mtz resistance stability, monitoring lines after cessation of drug selection, revealing isolate-dependent phenotypic plasticity. Conclusions Our data demonstrate understanding that Mtz resistance must be broadened to post-transcriptional and post-translational responses and that Mtz resistance is polygenic, driven by isolate-dependent variation, and is correlated with changes in protein acetylation networks.
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Affiliation(s)
- Samantha J Emery
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Louise Baker
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Mehdi Mirzaei
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, Australia
| | - Paul A Haynes
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Malcom J McConville
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Aaron R Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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9
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Proteomic diversity in a prevalent human-infective Giardia duodenalis sub-species. Int J Parasitol 2018; 48:817-823. [DOI: 10.1016/j.ijpara.2018.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 01/08/2023]
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10
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Singh M, Beri D, Nageshan RK, Chavaan L, Gadara D, Poojary M, Subramaniam S, Tatu U. A secreted Heat shock protein 90 of Trichomonas vaginalis. PLoS Negl Trop Dis 2018; 12:e0006493. [PMID: 29768419 PMCID: PMC5973626 DOI: 10.1371/journal.pntd.0006493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/29/2018] [Accepted: 05/03/2018] [Indexed: 11/18/2022] Open
Abstract
Trichomonas vaginalis is a causative agent of Trichomoniasis, a leading non-viral sexually transmitted disease worldwide. In the current study, we show Heat shock protein 90 is essential for its growth. Upon genomic analysis of the parasite, it was found to possess seven ORFs which could potentially encode Hsp90 isoforms. We identified a cytosolic Hsp90 homolog, four homologs which can align to truncated cytosolic Hsp90 gene products along with two Grp94 homologs (ER isoform of Hsp90). However, both Grp94 orthologs lacked an ER retention motif. In cancer cells, it is very well established that Hsp90 is secreted and regulates key clients involved in metastases, migration, and invasion. Since Trichomonas Grp94 lacks ER retention motif, we examined the possibility of its secretion. By using cell biology and biochemical approaches we show that the Grp94 isoform of Hsp90 is secreted by the parasite by the classical ER-Golgi pathway. This is the first report of a genome encoded secreted Hsp90 in a clinically important parasitic protozoan. Hsp90 is an essential chaperone in eukaryotes and it is often described as a master regulator of cellular homeostasis. In addition to its well-known functions inside the cell, extracellular Hsp90 has also been implicated in migration and invasion of tumor cells. We have, for the first time, identified the presence of an extracellular Hsp90 in a parasitic protozoan, Trichomonas vaginalis. The extracellular Hsp90 is a Grp94 homolog that lacks a canonical ER retention signal. Our analysis of Grp94 sequences from protozoa shows that it is uncommon for a Grp94 to lack ER retention signal. In the current study, we characterized the biochemical parameters and established the extracellular localization of this Hsp90 paralog. This secreted Hsp90 in Trichomonas can potentially modulate host-pathogen interaction.
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Affiliation(s)
- Meetali Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Divya Beri
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Leena Chavaan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Darshak Gadara
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mukta Poojary
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Suraj Subramaniam
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail:
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11
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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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12
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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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13
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Emery SJ, Lacey E, Haynes PA. Quantitative proteomics in Giardia duodenalis —Achievements and challenges. Mol Biochem Parasitol 2016; 208:96-112. [DOI: 10.1016/j.molbiopara.2016.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 12/31/2022]
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14
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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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15
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Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in Giardia duodenalis independent of host attachment. Sci Rep 2016; 6:20765. [PMID: 26867958 PMCID: PMC4751611 DOI: 10.1038/srep20765] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Giardia duodenalis is responsible for the majority of parasitic gastroenteritis in humans worldwide. Host-parasite interaction models in vitro provide insights into disease and virulence and help us to understand pathogenesis. Using HT-29 intestinal epithelial cells (IEC) as a model we have demonstrated that initial sensitisation by host secretions reduces proclivity for trophozoite attachment, while inducing virulence factors. Host soluble factors triggered up-regulation of membrane and secreted proteins, including Tenascins, Cathepsin-B precursor, cystatin, and numerous Variant-specific Surface Proteins (VSPs). By comparison, host-cell attached trophozoites up-regulated intracellular pathways for ubiquitination, reactive oxygen species (ROS) detoxification and production of pyridoxal phosphate (PLP). We reason that these results demonstrate early pathogenesis in Giardia involves two independent host-parasite interactions. Motile trophozoites respond to soluble secreted signals, which deter attachment and induce expression of virulence factors. Trophozoites attached to host cells, in contrast, respond by up-regulating intracellular pathways involved in clearance of ROS, thus anticipating the host defence response.
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Affiliation(s)
- Samantha J Emery
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, 2109, Australia
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ernest Lacey
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Hudson AJ, Stark MR, Fast NM, Russell AG, Rader SD. Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms. RNA Biol 2015; 12:1-8. [PMID: 26400738 PMCID: PMC4829280 DOI: 10.1080/15476286.2015.1094602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5′ splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms.
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Affiliation(s)
- Andrew J Hudson
- a Alberta RNA Research and Training Institute and Department of Biological Sciences ; University of Lethbridge ; Lethbridge , Alberta , Canada
| | - Martha R Stark
- b Department of Chemistry ; University of Northern British Columbia ; Prince George , British Columbia , Canada
| | - Naomi M Fast
- c Biodiversity Research Center and Department of Botany ; University of British Columbia ; Vancouver , British Columbia , Canada
| | - Anthony G Russell
- a Alberta RNA Research and Training Institute and Department of Biological Sciences ; University of Lethbridge ; Lethbridge , Alberta , Canada
| | - Stephen D Rader
- b Department of Chemistry ; University of Northern British Columbia ; Prince George , British Columbia , Canada
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Ankarklev J, Franzén O, Peirasmaki D, Jerlström-Hultqvist J, Lebbad M, Andersson J, Andersson B, Svärd SG. Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates. BMC Genomics 2015; 16:697. [PMID: 26370391 PMCID: PMC4570179 DOI: 10.1186/s12864-015-1893-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022] Open
Abstract
Background The diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. Comparative whole-genome analyses of three of these assemblages have shown that there is significant divergence at the inter-assemblage level, however little is currently known regarding variation at the intra-assemblage level. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic human patients, to study the biological and genetic diversity within assemblage A isolates. Results Several biological differences between the new and earlier characterized assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 [AS175] and AII-2 [AS98]) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of the Giardia reference isolate WB, an assemblage AI isolate. Our analyses indicate that the divergence between AI and AII is approximately 1 %, represented by ~100,000 single nucleotide polymorphisms (SNP) distributed over the chromosomes with enrichment in variable genomic regions containing surface antigens. The level of allelic sequence heterozygosity (ASH) in the two AII isolates was found to be 0.25–0.35 %, which is 25–30 fold higher than in the WB isolate and 10 fold higher than the assemblage AII isolate DH (0.037 %). 35 protein-encoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolate-specific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 8 members, localize to the variable regions of the genomes and show high sequence diversity between the assemblage A isolates. One of the families, Bactericidal/Permeability Increasing-like protein (BPIL), with eight members was characterized further and the proteins were shown to localize to the ER in trophozoites. Conclusions Giardia genomes are modular with highly conserved core regions mixed up by variable regions containing high levels of ASH, SNPs and variable surface antigens. There are significant genomic variations in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms and these differences mainly localize to the variable regions of the genomes. The large genetic differences within one assemblage of G. intestinalis strengthen the argument that the assemblages represent different Giardia species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1893-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Ankarklev
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, SE-171 77, Stockholm, Sweden. .,Science for Life Laboratory, KISP, Tomtebodavägen 23A, 171 65, Solna, Sweden.
| | - Dimitra Peirasmaki
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Marianne Lebbad
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82, Solna, Sweden.
| | - Jan Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, SE-171 77, Stockholm, Sweden. .,Science for Life Laboratory, KISP, Tomtebodavägen 23A, 171 65, Solna, Sweden.
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
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18
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Use of methanol as cryoprotectant and its effect on sox genes and proteins in chilled zebrafish embryos. Cryobiology 2015; 71:1-11. [DOI: 10.1016/j.cryobiol.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 01/01/2023]
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Peng Z, Yuan C, Zellmer L, Liu S, Xu N, Liao DJ. Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers. J Cancer 2015; 6:555-67. [PMID: 26000048 PMCID: PMC4439942 DOI: 10.7150/jca.11997] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine "two neighboring genes" as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of "consecutive reverse transcriptions (RTs)", i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.
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Affiliation(s)
- Zhiyu Peng
- 1. Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, P. R. China
| | - Chengfu Yuan
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Lucas Zellmer
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Siqi Liu
- 3. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Ningzhi Xu
- 4. Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P. R. China
| | - D Joshua Liao
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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Desai K, Spikings E, Zhang T. Short-Term Chilled Storage of Zebrafish (Danio rerio) Embryos in Cryoprotectant As an Alternative to Cryopreservation. Zebrafish 2015; 12:111-20. [DOI: 10.1089/zeb.2013.0961] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kunjan Desai
- Department of Neuroscience and Regenerative Medicine, Georgia Regents University, Augusta, Georgia
- Institute of Biomedical Science and Environmental Science and Technology, University of Bedfordshire, Luton, United Kingdom
| | - Emma Spikings
- Institute of Biomedical Science and Environmental Science and Technology, University of Bedfordshire, Luton, United Kingdom
| | - Tiantian Zhang
- Institute of Biomedical Science and Environmental Science and Technology, University of Bedfordshire, Luton, United Kingdom
- School of Applied Sciences, Bournemouth University, Poole, United Kingdom
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21
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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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Abstract
Trypanosomiasis is caused by Trypanosoma species which affect both human and animal populations and pose a major threat to developing countries. The incidence of animal trypanosomiasis is on the rise. Surra is a type of animal trypanosomiasis, caused by Trypanosoma evansi, and has been included in priority list B of significant diseases by the World Organization of Animal Health (OIE). Control of surra has been a challenge due to the lack of effective drugs and vaccines and emergence of resistance towards existing drugs. Our laboratory has previously implicated Heat shock protein 90 (Hsp90) from protozoan parasites as a potential drug target and successfully demonstrated efficacy of an Hsp90 inhibitor in cell culture as well as a pre-clinical mouse model of trypanosomiasis. This article explores the role of Hsp90 in the Trypanosoma life cycle and its potential as a drug target. It appears plausible that the repertoire of Hsp90 inhibitors available in academia and industry may have value for treatment of surra and other animal trypanosomiasis.
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Hsp90 inhibitors as new leads to target parasitic diarrheal diseases. Antimicrob Agents Chemother 2014; 58:4138-44. [PMID: 24820073 DOI: 10.1128/aac.02576-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Entamoeba histolytica and Giardia lamblia are anaerobic protozoan parasites that cause amebiasis and giardiasis, two of the most common diarrheal diseases worldwide. Current therapy relies on metronidazole, but resistance has been reported and the drug has significant adverse effects. Therefore, it is critical to search for effective, better-tolerated antiamebic and antigiardial drugs. We synthesized several examples of a recently reported class of Hsp90 inhibitors and evaluated these compounds as potential leads for antiparasitic chemotherapy. Several of these inhibitors showed strong in vitro activity against both E. histolytica and G. lamblia trophozoites. The inhibitors were rescreened to discriminate between amebicidal and giardicidal activity and general cytotoxicity toward a mammalian cell line. No mammalian cytotoxicity was found at >100 μM for 48 h for any of the inhibitors. To understand the mechanism of action, a competitive binding assay was performed using the fluorescent ATP analogue bis-ANS (4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid dipotassium salt) and recombinant E. histolytica Hsp90 preincubated in both the presence and absence of Hsp90 inhibitors. There was significant reduction in fluorescence compared to the level in the control, suggesting that E. histolytica Hsp90 is a selective target. The in vivo efficacy and safety of one Hsp90 inhibitor in a mouse model of amebic colitis and giardiasis was demonstrated by significant inhibition of parasite growth at a single oral dose of 5 mg/kg of body weight/day for 7 days and 10 mg/kg/day for 3 days. Considering the results for in vitro activity and in vivo efficacy, Hsp90 inhibitors represent a promising therapeutic option for amebiasis and giardiasis.
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Nageshan RK, Roy N, Ranade S, Tatu U. Trans-spliced heat shock protein 90 modulates encystation in Giardia lamblia. PLoS Negl Trop Dis 2014; 8:e2829. [PMID: 24786776 PMCID: PMC4006730 DOI: 10.1371/journal.pntd.0002829] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/13/2014] [Indexed: 01/22/2023] Open
Abstract
Background Hsp90 from Giardia lamblia is expressed by splicing of two independently transcribed RNA molecules, coded by genes named HspN and HspC located 777 kb apart. The reasons underlying such unique trans-splicing based generation of GlHsp90 remain unclear. Principle Finding In this study using mass-spectrometry we identify the sequence of the unique, junctional peptide contributed by the 5′ UTR of HspC ORF. This peptide is critical for the catalytic function of Hsp90 as it harbours an essential “Arg” in its sequence. We also show that full length GlHsp90 possesses all the functional hall marks of a canonical Hsp90 including its ability to bind and hydrolyze ATP. Using qRT-PCR as well as western blotting approach we find the reconstructed Hsp90 to be induced in response to heat shock. On the contrary we find GlHsp90 to be down regulated during transition from proliferative trophozoites to environmentally resistant cysts. This down regulation of GlHsp90 appears to be mechanistically linked to the encystation process as we find pharmacological inhibition of GlHsp90 function to specifically induce encystation. Significance Our results implicate the trans-spliced GlHsp90 from Giardia lamblia to regulate an essential stage transition in the life cycle of this important human parasite. Giardia lamblia is one of the most common causes of diarrhoea across the globe. The disease can result in fatalities especially in small children. The parasite is transmitted by contaminated food through faeco-oral route due to unhygienic habits. The parasite exhibits two stages during its lifecycle; namely cysts and trophozoites. Due to their environmentally resistant hardy nature cysts are transmitted through contaminated food into the human body. Upon entry into the human body they convert into active trophozoites and cause pathogenesis of the disease. In the course of infection within the host, some of the trophozoites convert back into cysts and are released in the environment through the faeces. The mechanisms and signals that convert the parasite from trophozoites to cysts are not yet known. Our study, for the first time, implicates heat shock protein 90 of the parasite in the conversion of trophozoites into cysts in the intestine of the infected human body. Hsp90 is famous for its ability to sense environmental changes and provide cues for stage-switch in related parasites. In addition to providing a glimpse into molecular mechanisms of stage inter-conversion, our results suggest potential new ways of treating this important human infection.
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Affiliation(s)
| | - Nainita Roy
- The Department of Biochemistry, Indian Institute of Sciences, Bangalore, India
| | - Shatakshi Ranade
- The Department of Biochemistry, Indian Institute of Sciences, Bangalore, India
| | - Utpal Tatu
- The Department of Biochemistry, Indian Institute of Sciences, Bangalore, India
- * E-mail:
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26
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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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Ülker B, Hommelsheim CM, Berson T, Thomas S, Chandrasekar B, Olcay AC, Berendzen KW, Frantzeskakis L. Reevaluation of the reliability and usefulness of the somatic homologous recombination reporter lines. THE PLANT CELL 2012; 24:4314-23. [PMID: 23144181 PMCID: PMC3531835 DOI: 10.1105/tpc.112.100404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 05/15/2012] [Accepted: 10/18/2012] [Indexed: 05/25/2023]
Abstract
A widely used approach for assessing genome instability in plants makes use of somatic homologous recombination (SHR) reporter lines. Here, we review the published characteristics and uses of SHR lines. We found a lack of detailed information on these lines and a lack of sufficient evidence that they report only homologous recombination. We postulate that instead of SHR, these lines might be reporting a number of alternative stress-induced stochastic events known to occur at transcriptional, posttranscriptional, and posttranslational levels. We conclude that the reliability and usefulness of the somatic homologous recombination reporter lines requires revision. Thus, more detailed information about these reporter lines is needed before they can be used with confidence to measure genome instability, including the complete sequences of SHR constructs, the genomic location of reporter genes and, importantly, molecular evidence that reconstituted gene expression in these lines is indeed a result of somatic recombination.
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Affiliation(s)
- Bekir Ülker
- Plant Molecular Engineering Group, Institute of Cellular and Molecular Botany, University of Bon, 53115 Bon, Germany.
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28
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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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Selection of a DNA barcode for Nectriaceae from fungal whole-genomes. SCIENCE CHINA-LIFE SCIENCES 2012; 55:80-8. [PMID: 22314494 DOI: 10.1007/s11427-012-4266-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 11/17/2011] [Indexed: 10/14/2022]
Abstract
A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intra- and inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra- and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intra- and inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.
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Zaphiropoulos PG. Trans-splicing in Higher Eukaryotes: Implications for Cancer Development? Front Genet 2011; 2:92. [PMID: 22303386 PMCID: PMC3268641 DOI: 10.3389/fgene.2011.00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 12/07/2011] [Indexed: 12/28/2022] Open
Abstract
Trans-splicing, the possibility of exons from distinct pre-mRNAs to join together, is still a concept in gene expression that is generally regarded of limited significance. However, recent work has provided evidence that in human tumors trans-splicing events may precede chromosomal rearrangements. In fact, it has been suggested that the trans-spliced molecules could act as “guides” that facilitate the genomic translocation. This perspective highlights the development of the ideas of trans-splicing in higher eukaryotes during the last 25 years, from a bizarre phenomenon to a biological event that is attaining stronger recognition.
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Roy N, Nageshan RK, Ranade S, Tatu U. Heat shock protein 90 from neglected protozoan parasites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:707-11. [PMID: 22198098 DOI: 10.1016/j.bbamcr.2011.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 01/15/2023]
Abstract
Significant advances have been made in our understanding of heat shock protein 90 (Hsp90) in terms of its structure, biochemical characteristics, post-translational modifications, interactomes, regulation and functions. In addition to yeast as a model several new systems have now been examined including flies, worms, plants as well as mammalian cells. This review discusses themes emerging out of studies reported on Hsp90 from infectious disease causing protozoa. A common theme of sensing and responding to host cell microenvironment emerges out of analysis of Hsp90 in Malaria, Trypanosmiasis as well as Leishmaniasis. In addition to their functional roles, the potential of Hsp90 from these infectious disease causing organisms to serve as drug targets and the current status of this drug development endeavor are discussed. Finally, a unique and the only known example of a split Hsp90 gene from another disease causing protozoan Giardia lamblia and its evolutionary significance are discussed. Clearly studies on Hsp90 from protozoan parasites promise to reveal important new paradigms in Hsp90 biology while exploring its potential as an anti-infective drug target. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).
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Affiliation(s)
- Nainita Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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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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Abstract
Some genes in the candidate early-branching eukaryote Giardia lamblia occur in separate pieces, transcribed from non-contiguous chromosomal locations. The pre-mRNAs from the separate pieces apparently find each other by regions of complementarity and are subsequently spliced together by the spliceosome. Could genes in pieces, transcribed into separate pre-mRNAs, have been an early feature of spliceosomal evolution?
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Affiliation(s)
- Thomas Blumenthal
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
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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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Lauwaet T, Smith AJ, Reiner DS, Romijn EP, Wong CCL, Davids BJ, Shah SA, Yates JR, Gillin FD. Mining the Giardia genome and proteome for conserved and unique basal body proteins. Int J Parasitol 2011; 41:1079-92. [PMID: 21723868 DOI: 10.1016/j.ijpara.2011.06.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/25/2011] [Accepted: 06/01/2011] [Indexed: 12/27/2022]
Abstract
Giardia lamblia is a flagellated protozoan parasite and a major cause of diarrhoea in humans. Its microtubular cytoskeleton mediates trophozoite motility, attachment and cytokinesis, and is characterised by an attachment disk and eight flagella that are each nucleated in a basal body. To date, only 10 giardial basal body proteins have been identified, including universal signalling proteins that are important for regulating mitosis or differentiation. In this study, we have exploited bioinformatics and proteomic approaches to identify new Giardia basal body proteins and confocal microscopy to confirm their localisation in interphase trophozoites. This approach identified 75 homologs of conserved basal body proteins in the genome including 65 not previously known to be associated with Giardia basal bodies. Thirteen proteins were confirmed to co-localise with centrin to the Giardia basal bodies. We also demonstrate that most basal body proteins localise to additional cytoskeletal structures in interphase trophozoites. This might help to explain the roles of the four pairs of flagella and Giardia-specific organelles in motility and differentiation. A deeper understanding of the composition of the Giardia basal bodies will contribute insights into the complex signalling pathways that regulate its unique cytoskeleton and the biological divergence of these conserved organelles.
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Affiliation(s)
- Tineke Lauwaet
- Department of Pathology, University of California San Diego, San Diego, CA 92103, USA.
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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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