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Abe T, Akazawa Y, Toyoda A, Niki H, Baba T. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Front Microbiol 2020; 11:1486. [PMID: 32719664 PMCID: PMC7350273 DOI: 10.3389/fmicb.2020.01486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/08/2020] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
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Affiliation(s)
- Takashi Abe
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Yu Akazawa
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
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A natural occurring bifunctional CPD/(6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9. Appl Microbiol Biotechnol 2020; 104:7037-7050. [PMID: 32572574 DOI: 10.1007/s00253-020-10734-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/15/2020] [Accepted: 06/07/2020] [Indexed: 10/24/2022]
Abstract
Photolyases are flavoproteins that repair ultraviolet-induced DNA lesions (cyclobutane pyrimidine dimer or CPD, and pyrimidine (6-4) pyrimidone photoproducts or (6-4)-PPs), using blue light as an energy source. These enzymes are substrate specific, meaning that a specific photolyase repairs either a CPD or a (6-4)-PP. In this work, we produced a class II CPD-photolyase (called as PhrSph98) from the Antarctic bacterium Sphingomonas sp. UV9 by recombinant DNA technology and we purified the enzyme using immobilized metal affinity chromatography. By using an immunochemistry assay, with monoclonal antibodies against CPD and (6-4)-PP, we found that PhrSph98 repairs both DNA lesions. The result was confirmed by immunocytochemistry using immortalized non-tumorigenic human keratinocytes. Results from structure prediction, pocket computation, and molecular docking analyses showed that PhrSph98 has the two expected protein domains (light-harvesting antenna and a catalytic domain), a larger catalytic site as compared with photolyases produced by mesophilic organisms, and that both substrates fit the catalytic domain. The results obtained from predicted homology modeling suggest that the electron transfer pathway may occur following this pathway: Y389-W369-W390-F376-W381/FAD. The evolutionary reconstruction of PhrSph98 suggests that this is a missing link that reflects the transition of (6-4)-PP repair into the CPD repair ability for the class II CPD-photolyases. To the best of our knowledge, this is the first report of a naturally occurring bifunctional, CPD and (6-4)-PP, repairing enzyme. KEY POINTS: • We report the first described bifunctional CPD/(6-4)-photoproducts repairing enzyme. The bifunctional enzyme reaches the nuclei of keratinocyte and repairs the UV-induced DNA damage. The enzyme should be a missing link from an evolutionary point of view. The enzyme may have potential uses in the pharmaceutical and cosmetic industries.
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Vechtomova YL, Telegina TA, Kritsky MS. Evolution of Proteins of the DNA Photolyase/Cryptochrome Family. BIOCHEMISTRY (MOSCOW) 2020; 85:S131-S153. [DOI: 10.1134/s0006297920140072] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Corradi N. Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers. Annu Rev Microbiol 2015. [PMID: 26195306 DOI: 10.1146/annurev-micro-091014-104136] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microsporidia are eukaryotic parasites of many animals that appear to have adapted to an obligate intracellular lifestyle by modifying the morphology and content of their cells. Living inside other cells, they have lost many, or all, metabolic functions, resulting in genomes that are always gene poor and often very small. The minute content of microsporidian genomes led many to assume that these parasites are biochemically static and uninteresting. However, recent studies have demonstrated that these organisms can be surprisingly complex and dynamic. In this review I detail the most significant recent advances in microsporidian genomics and discuss how these have affected our understanding of many biological aspects of these peculiar eukaryotic intracellular pathogens.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada K1N 6N5;
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Abstract
Microsporidia are obligate intracellular parasites whose genomes have been shaped by an extreme lifestyle. Specifically, their obligate intracellular parasitism has resulted in the loss of many genes and biochemical pathways, but these reductive processes have been often offset by the acquisition of several genes by means of horizontal gene transfer (HGT). Until recently, these HGTs were all found to have derived from prokaryotic donors, but a recent study suggests that some species took advantage of this mechanism to acquire one gene from an animal, which they maintained in their genome for metabolic purposes. The gene encodes for a purine nucleoside phosphorylase, and shows a strong phylogenetic signal of arthropod origin. Here, we briefly review our current knowledge of HGTs discovered across microsporidian genomes and discuss the implications of the most recent findings in this research area for understanding the origin and evolution of this highly adapted group of intracellular parasites. A novel gene potentially transferred by means of HGT to one microsporidia is also reported.
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Affiliation(s)
- Mohammed Selman
- Canadian Institute for Advanced Research; Department of Biology; University of Ottawa; Ottawa, ON Canada
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Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E. Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans. Genome Biol Evol 2014; 6:2289-300. [PMID: 25172905 PMCID: PMC4202319 DOI: 10.1093/gbe/evu178] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.
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Affiliation(s)
- Nicolas Parisot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France CNRS, UMR 6023, LMGE, Aubière, France
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Valérie Polonais
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Abdel Belkorchia
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Johan Panek
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Hicham El Alaoui
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - David G Biron
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Éric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Emmanuelle Lerat
- Université de Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France
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Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 2013; 29:329-38. [DOI: 10.1016/j.pt.2013.05.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022]
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Lee SC, Weiss LM, Heitman J. Generation of genetic diversity in microsporidia via sexual reproduction and horizontal gene transfer. Commun Integr Biol 2010; 2:414-7. [PMID: 19907704 DOI: 10.4161/cib.2.5.8846] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 01/06/2023] Open
Abstract
Microsporidia are obligate intracellular pathogens mainly infecting both vertebrate and invertebrate hosts. The group comprises approximately 150 genera with 1,200 species. Due to sequence divergence phylogenic reconstructions that are solely based on DNA sequence have been unprecise for these pathogens. Our previous study identified that three microsporidian genomes contained a putative sex-related locus similar to that of zygomycetes. In a comparison of genome architecture of the microsporidia to other fungi, Rhizopus oryzae, a zygomycete fungus, shared more common gene clusters with Encephalitozoon cuniculi, a microsporidian. This provides evidence supporting the hypothesis that microsporidia and zygomycete fungi may share a more recent common ancestor than other fungal lineages. Genetic recombination is an important outcome of sexual development. We describe genetic markers which will enable tests of whether sex occurs within E. cuniculi populations by analyzing tandem repeat DNA regions in three different isolates. Taken together, the phylogenetic relationship of microsporidia to fungi and the presence of a sex-related locus in their genomes suggest the microsporidia may have an extant sexual cycle. In addition, we describe recently reported evidence of horizontal gene transfer from Chlamydia to the E. cuniculi genome and show that these two obligate intracellular pathogens can infect the same host cells.
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Affiliation(s)
- Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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Idnurm A, Verma S, Corrochano LM. A glimpse into the basis of vision in the kingdom Mycota. Fungal Genet Biol 2010; 47:881-92. [PMID: 20451644 DOI: 10.1016/j.fgb.2010.04.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/20/2010] [Accepted: 04/27/2010] [Indexed: 12/21/2022]
Abstract
Virtually all organisms exposed to light are capable of sensing this environmental signal. In recent years the photoreceptors that mediate the ability of fungi to "see" have been identified in diverse species, and increasingly characterized. The small sizes of fungal genomes and ease in genetic and molecular biology manipulations make this kingdom ideal amongst the eukaryotes for understanding photosensing. The most widespread and conserved photosensory protein in the fungi is White collar 1 (WC-1), a flavin-binding photoreceptor that functions with WC-2 as a transcription factor complex. Other photosensory proteins in fungi include opsins, phytochromes and cryptochromes whose roles in fungal photobiology are not fully resolved and their distribution in the fungi requires further taxon sampling. Additional unknown photoreceptors await discovery. This review discusses the effects of light on fungi and the evolutionary processes that may have shaped the ability of species to sense and respond to this signal.
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Affiliation(s)
- Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
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Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr Opin Genet Dev 2009; 19:613-9. [PMID: 19897356 DOI: 10.1016/j.gde.2009.10.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/31/2009] [Accepted: 10/07/2009] [Indexed: 11/20/2022]
Abstract
Horizontal gene transfer (HGT) is known to have contributed to the content of eukaryotic genomes, but the direct effects of HGT on eukaryotic evolution are more obscure because many of the best supported cases involve a new gene replacing a functionally similar homologue. Here, several cases of HGT conferring a plausible adaptive advantage are reviewed to examine emerging trends in such transfer events. In particular, HGT seems to play an important role in adaptation to parasitism and pathogenesis, as well as to other specific environmental conditions such as anaerobiosis or nitrogen and iron limitation in marine environments. Most, but not all, of the functionally significant HGT to eukaryotes comes from bacteria, in part due to chance, but probably also because bacteria have greater metabolic diversity to offer.
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Corradi N, Haag KL, Pombert JF, Ebert D, Keeling PJ. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Genome Biol 2009; 10:R106. [PMID: 19807911 PMCID: PMC2784321 DOI: 10.1186/gb-2009-10-10-r106] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/02/2009] [Accepted: 10/06/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The highly compacted 2.9-Mb genome of Encephalitozoon cuniculi placed the microsporidia in the spotlight, encoding a mere 2,000 proteins and a highly reduced suite of biochemical pathways. This extreme level of reduction is not universal across the microsporidia, with genomes known to vary up to sixfold in size, suggesting that some genomes may harbor a gene content that is not as reduced as that of Enc. cuniculi. In this study, we present an in-depth survey of the large genome of Octosporea bayeri, a pathogen of Daphnia magna, with an estimated genome size of 24 Mb, in order to shed light on the organization and content of a large microsporidian genome. RESULTS Using Illumina sequencing, 898 Mb of O. bayeri genome sequence was generated, resulting in 13.3 Mb of unique sequence. We annotated a total of 2,174 genes, of which 893 encodes proteins with assigned function. The gene density of the O. bayeri genome is very low on average, but also highly uneven, so gene-dense regions also occur. The data presented here suggest that the O. bayeri proteome is well represented in this analysis and is more complex that that of Enc. cuniculi. Functional annotation of O. bayeri proteins suggests that this species might be less biochemically dependent on its host for its metabolism than its more reduced relatives. CONCLUSIONS The combination of the data presented here, together with the imminent annotated genome of Daphnia magna, will provide a wealth of genetic and genomic tools to study host-parasite interactions in an interesting model for pathogenesis.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, The Biodiversity Research Centre, University of British Columbia, University Boulevard, Vancouver, BC V6T 1Z4, Canada.
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mRNA processing in Antonospora locustae spores. Mol Genet Genomics 2008; 280:565-74. [PMID: 18818951 DOI: 10.1007/s00438-008-0387-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 09/14/2008] [Indexed: 10/21/2022]
Abstract
Microsporidia are a group of intracellular parasites characterized by highly reduced and compact genomes. The presence of a high gene density had several consequences for microsporidian genomes, including a high frequency of overlap between transcripts of adjacent genes. This phenomenon is apparently widespread in microsporidia, and strongly correlated with gene density. However, all analyses to date have focused on one or a few transcripts from many loci, so it is unclear how diverse the pool of transcripts at a given locus may be. To address this question, we characterized initiation and termination points from 62 transcripts in gene-dense regions in Antonospora locustae spores using both conventional and fluorescence-based RACE-PCR procedures. In parallel, we investigated the abundance and nature of transcripts along a 6 kb region surrounding the actin locus of A. locustae using northern blotting, RACE-PCR and previously characterised EST sequences. Overall, we confirmed previous suggestions that most transcripts in A. locustae spores overlap with the downstream gene, but that at the 5' end untranslated regions are very short and overlap is rare. From fluorescence-based RACE-PCR we show that transcription of most genes (31 out of 34) initiates at a single position, whereas 35% of loci analyzed with 3' RACE polyadenylate mRNA at several sites. Finally, we identified the presence of previously unsuspected and very large transcripts in A. locustae spores. Those transcripts were found to overlap up to four open reading frames in different strands, adding a novel layer of complexity in the mRNA transcription of this microsporidian species.
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Active DNA photolyase encoded by a baculovirus from the insect Chrysodeixis chalcites. DNA Repair (Amst) 2008; 7:1309-18. [PMID: 18547877 DOI: 10.1016/j.dnarep.2008.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
The genome of Chrysodeixis chalcites nucleopolyhedrovirus (ChchNPV) contains two open reading frames, Cc-phr1 and Cc-phr2, which encode putative class II CPD-DNA photolyases. CPD-photolyases repair UV-induced pyrimidine cyclobutane dimers using visible light as an energy source. Expression of Cc-phr2 provided photolyase deficient Escherichia coli cells with photoreactivating activity indicating that Cc-phr2 encodes an active photolyase. In contrast, Cc-phr1 did not rescue the photolyase deficiency. Cc-phr2 was overexpressed in E. coli and the resulting photolyase was purified till apparent homogeneity. Spectral measurements indicated the presence of FAD, but a second chromophore appeared to be absent. Recombinant Cc-phr2 photolyase was found to bind specifically F0 (8-hydroxy-7,8-didemethyl-5-deazariboflavin), which is an antenna chromophore present in various photolyases.. After reconstitution, FAD and F0 were present in approximately equimolar amounts. In reconstituted photolyase the F0 chromophore is functionally active as judged from the increase in the in vitro repair activity. This study demonstrates for the first time that a functional photolyase is encoded by an insect virus, which may have implications for the design of a new generation of baculoviruses with improved performance in insect pest control.
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Corradi N, Gangaeva A, Keeling PJ. Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi. Genomics 2008; 91:388-93. [PMID: 18280697 DOI: 10.1016/j.ygeno.2007.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 11/26/2007] [Accepted: 12/17/2007] [Indexed: 11/30/2022]
Abstract
Microsporidia are highly adapted parasites related to fungi with compact, gene-dense genomes. It has previously been shown in the microsporidian Antonospora locustae that transcripts from any given gene overlap with adjacent genes at a high frequency, perhaps due to the compact nature of its genome. However, it is still not known if this phenomenon is widespread among microsporidia or conserved between species, or even whether it is strictly correlated with compaction. To address these questions, we performed a comparison of transcription profiles in two microsporidian species, A. locustae and Encephalitozoon cuniculi. Transcription overlap was characterized at many A. locustae loci representing a range of gene densities, to determine if overlapping transcription correlates with the length of intergenic spacers. In parallel, we examined the first cases of transcription overlap in E. cuniculi. Using regions of the genome where the order of genes is conserved between A. locustae and E. cuniculi, we identified the transcriptional processing points in both species to determine how the process changes through evolutionary time. We show that there is little conservation of processing points between species and indeed that the process differs in important ways in the two genomes. Overall, A. locustae transcripts generally start just upstream of the start codon, but terminate well within or beyond downstream genes. In contrast, E. cuniculi transcripts often initiate within upstream genes, but more frequently terminate prior to the downstream gene. This process appears to have predictable characteristics within a given genome, but to be relatively flexible between species, presenting further challenges to the study of gene expression in these obligately intracellular parasites.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, Canada
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Yamamoto A, Hirouchi T, Mori T, Teranishi M, Hidema J, Morioka H, Kumagai T, Yamamoto K. Biochemical and biological properties of DNA photolyases derived from utraviolet-sensitive rice cultivars. Genes Genet Syst 2008; 82:311-9. [PMID: 17895582 DOI: 10.1266/ggs.82.311] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Class I and class II CPD photolyases are enzymes which repair pyrimidine dimers using visible light. A detailed characterization of class I CPD photolyases has been carried out, but little is known about the class II enzymes. Photolyases from rice are suitable for functional analyses because systematic breeding for long periods in Asian countries has led to the selection of naturally occurring mutations in the CPD photolyase gene. We report the biochemical characterization of rice mutant CPD photolyases purified as GST-form from Escherichia coli. We identified three amino acid changes, Gln126Arg, Gly255Ser, and Gln296His, among which Gln but not His at 296 is important for complementing phr-defective E. coli, binding UV-damage in E. coli, and binding thymine dimers in vitro. The photolyase with Gln at 296 has an apoenzyme:FAD ratio of 1 : 0.5 and that with His at 296 has an apoenzyme:FAD ratio of 1 : 0.12-0.25, showing a role for Gln at 296 in the binding of FAD not in the binding of thymine dimer. Concerning Gln or Arg at 126, the biochemical activity of the photolyases purified from E. coli and complementing activity for phr-defective E. coli are similarly proficient. However, the sensitivity to UV of cultivars differs depending on whether Gln or Arg is at 126. The role of Gln and Arg at 126 for photoreactivation in rice is discussed.
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Affiliation(s)
- Ayumi Yamamoto
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Liu F, Lu J, Hu W, Wang SY, Cui SJ, Chi M, Yan Q, Wang XR, Song HD, Xu XN, Wang JJ, Zhang XL, Zhang X, Wang ZQ, Xue CL, Brindley PJ, McManus DP, Yang PY, Feng Z, Chen Z, Han ZG. New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathog 2006; 2:e29. [PMID: 16617374 PMCID: PMC1435792 DOI: 10.1371/journal.ppat.0020029] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 03/06/2006] [Indexed: 11/20/2022] Open
Abstract
Schistosomiasis remains a serious public health problem with an estimated 200 million people infected in 76 countries. Here we isolated ~ 8,400 potential protein-encoding cDNA contigs from Schistosoma japonicum after sequencing circa 84,000 expressed sequence tags. In tandem, we undertook a high-throughput proteomics approach to characterize the protein expression profiles of a number of developmental stages (cercariae, hepatic schistosomula, female and male adults, eggs, and miracidia) and tissues at the host-parasite interface (eggshell and tegument) by interrogating the protein database deduced from the contigs. Comparative analysis of these transcriptomic and proteomic data, the latter including 3,260 proteins with putative identities, revealed differential expression of genes among the various developmental stages and sexes of S. japonicum and localization of putative secretory and membrane antigens, enzymes, and other gene products on the adult tegument and eggshell, many of which displayed genetic polymorphisms. Numerous S. japonicum genes exhibited high levels of identity with those of their mammalian hosts, whereas many others appeared to be conserved only across the genus Schistosoma or Phylum Platyhelminthes. These findings are expected to provide new insights into the pathophysiology of schistosomiasis and for the development of improved interventions for disease control and will facilitate a more fundamental understanding of schistosome biology, evolution, and the host-parasite interplay. Schistosomiasis remains a major public health problem in the developing world. Schistosoma japonicum, the Oriental blood fluke, causes intestinal schistosomiasis in China and the Philippines. Knowledge of the genome and proteome of this worm should improve understanding of biomedical aspects of schistosomiasis. This study represents the first major attempt to characterize the majority of the expressed genes and proteins of a human blood fluke through rigorous, high-throughput genomic and proteomic methodologies. The findings of this study provide a unique resource of numerous schistosome genes and information on protein profiles of the different developmental stages of S. japonicum. Many of the newly discovered proteins are localized on the surface of the worm and its eggs, and they are likely to be involved in the pathogenesis of schistosomiasis. Furthermore, genetic variants found in many of these new genes likely reflect the ability of this important human pathogen to adapt and respond to environmental pressures and the capacity of the parasite to respond to anti-schistosomal therapies. Comparison of these S. japonicum genes with those from mammals and other organisms will facilitate advances in the understanding of blood fluke biology and evolution.
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Affiliation(s)
- Feng Liu
- Chinese National Human Genome Center at Shanghai, Shanghai, China
- Proteomic Center and Department of Chemistry, Fudan University, Shanghai, China
| | - Jiong Lu
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Sheng-Yue Wang
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shu-Jian Cui
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Ming Chi
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Qing Yan
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Xin-Rong Wang
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Huai-Dong Song
- State Key Laboratory of Medical Genomics, Shanghai Second Medical University, Shanghai, China
| | - Xue-Nian Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Ju-Jun Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Xiang-Lin Zhang
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Xin Zhang
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhi-Qin Wang
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Chun-Liang Xue
- Department of Parasitology, Shanghai Second Medical University, Shanghai, China
| | - Paul J Brindley
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Donald P McManus
- Queensland Institute of Medical Research and Australian Center for International Health and Nutrition, Brisbane, Queensland, Australia
| | - Peng-Yuan Yang
- Proteomic Center and Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Zhu Chen
- Chinese National Human Genome Center at Shanghai, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Second Medical University, Shanghai, China
| | - Ze-Guang Han
- Chinese National Human Genome Center at Shanghai, Shanghai, China
- * To whom correspondence should be addressed. E-mail:
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Keeling PJ, Slamovits CH. Causes and effects of nuclear genome reduction. Curr Opin Genet Dev 2005; 15:601-8. [PMID: 16188433 DOI: 10.1016/j.gde.2005.09.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 09/14/2005] [Indexed: 10/25/2022]
Abstract
Eukaryotic nuclear genomes are generally considered to be large and gene-sparse, but extreme reduction has taken place several times, resulting in small genomes with a high gene-density. This process involves losing genes, compacting those that remain, or often both. Recently sequenced nuclear genomes include several that have converged to similar gene-densities by many means: variation in numbers and lengths of genes, intergenic regions and introns all contribute, but not equally in any given genome. Genomes of microsporidia and nucleomorphs have taken compaction much further, and in these hyper-compacted genomes there is evidence that some basic processes such as gene expression might be affected by genome form. In these genomes, normally weak forces might become more significant drivers of genome evolution.
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Affiliation(s)
- Patrick J Keeling
- Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
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19
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Keeling PJ, Fast NM, Law JS, Williams BAP, Slamovits CH. Comparative genomics of microsporidia. Folia Parasitol (Praha) 2005; 52:8-14. [PMID: 16004359 DOI: 10.14411/fp.2005.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microsporidia have been known for some time to possess among the smallest genomes of any eukaryote. There is now a completely sequenced microsporidian genome, as well as several other large-scale sequencing efforts, so the nature of these genomes is becoming apparent. This paper reviews some of the characteristics of microsporidian genomes in general, and some of the recent discoveries made through comparative genomic analyses. In general, microsporidian genomes are both reduced and compacted. Reduction takes place through gene loss, which is understandable in obligate intracellular parasites that rely on their host for many metabolites. Compaction is a more complex process, and is as yet not fully understood. It is clear from genomes surveyed thus far that the remaining genes are tightly packed and that there is little non-coding sequence, resulting in some extraordinary arrangements, including overlapping genes. Compaction also seems to affect certain aspects of genome evolution, like the frequency of rearrangements. The force behind this compaction is not known, and is especially interesting in light of the fact that surveys of genomes that are significantly different in size yield similar complements of protein-coding genes. There are some interesting exceptions, including catalase, photolyase and some mitochondrial proteins, but the rarity of these raises an interesting question as to what accounts for the significant differences seen in the genome sizes among microsporidia.
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Affiliation(s)
- Patrick J Keeling
- Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
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20
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Williams BAP, Slamovits CH, Patron NJ, Fast NM, Keeling PJ. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc Natl Acad Sci U S A 2005; 102:10936-41. [PMID: 16037215 PMCID: PMC1182411 DOI: 10.1073/pnas.0501321102] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene density of eukaryotic nuclear genomes is generally low relative to prokaryotes, but several eukaryotic lineages (many parasites or endosymbionts) have independently evolved highly compacted, gene-dense genomes. The best studied of these are the microsporidia, highly adapted fungal parasites, and the nucleomorphs, relict nuclei of endosymbiotic algae found in cryptomonads and chlorarachniophytes. These systems are now models for the effects of compaction on the form and dynamics of the nuclear genome. Here we report a large-scale investigation of gene expression from compacted eukaryotic genomes. We have conducted EST surveys of the microsporidian Antonospora locustae and nucleomorphs of the cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. In all three systems we find a high frequency of mRNA molecules that encode sequence from more than one gene. There is no bias for these genes to be on the same strand, so it is unlikely that these mRNAs represent operons. Instead, compaction appears to have reduced the intergenic regions to such an extent that control elements like promoters and terminators have been forced into or beyond adjacent genes, resulting in long untranslated regions that encode other genes. Normally, transcriptional overlap can interfere with expression of a gene, but these genomes cope with high frequencies of overlap and with termination signals within expressed genes. These findings also point to serious practical difficulties in studying expression in compacted genomes, because many techniques, such as arrays or serial analysis of gene expression will be misleading.
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Affiliation(s)
- Bryony A P Williams
- Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
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21
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Affiliation(s)
- Patrick J Keeling
- Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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Texier C, Brosson D, El Alaoui H, Méténier G, Vivarès CP. Post-genomics of microsporidia, with emphasis on a model of minimal eukaryotic proteome: a review. Folia Parasitol (Praha) 2005; 52:15-22. [PMID: 16004360 DOI: 10.14411/fp.2005.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The genome sequence of the microsporidian parasite Encephalitozoon cuniculi Levaditi, Nicolau et Schoen, 1923 contains about 2,000 genes that are representative of a non-redundant potential proteome composed of 1,909 protein chains. The purpose of this review is to relate some advances in the characterisation of this proteome through bioinformatics and experimental approaches. The reduced diversity of the set of E. cuniculi proteins is perceptible in all the compilations of predicted domains, orthologs, families and superfamilies, available in several public databases. The phyletic patterns of orthologs for seven eukaryotic organisms support an extensive gene loss in the fungal clade, with additional deletions in E. cuniculi. Most microsporidial orthologs are the smallest ones among eukaryotes, justifying an interest in the use of these compacted proteins to better discriminate between essential and non-essential regions. The three components of the E. cuniculi mRNA capping apparatus have been especially well characterized and the three-dimensional structure of the cap methyltransferase has been elucidated following the crystallisation of the microsporidial enzyme Ecm1. So far, our mass spectrometry-based analyses of the E. cuniculi spore proteome has led to the identification of about 170 proteins, one-quarter of these having no clearly predicted function. Immunocytochemical studies are in progress to determine the subcellular localisation of microsporidia-specific proteins. Post-translational modifications such as phosphorylation and glycosylation are expected to be soon explored.
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Affiliation(s)
- Catherine Texier
- Equipe de Parasitologie Moléculaire et Cellulaire, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Université Blaise Pascal (Clermont 2), Complexe Universitaire des Cézeaux, 63177-Aubière , France
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