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Su H, Xu J, Li J, Yi Z. Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes. Mol Phylogenet Evol 2023; 184:107789. [PMID: 37105243 DOI: 10.1016/j.ympev.2023.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happen in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the increasement of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.
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Affiliation(s)
- Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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2
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Kissmehl R, Sehring IM, Wagner E, Plattner H. Immunolocalization of Actin in Paramecium Cells. J Histochem Cytochem 2016; 52:1543-59. [PMID: 15557210 DOI: 10.1369/jhc.4a6379.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have selected a conserved immunogenic region from several actin genes of Paramecium, recently cloned in our laboratory, to prepare antibodies for Western blots and immunolocalization. According to cell fractionation analysis, most actin is structure-bound. Immunofluorescence shows signal enriched in the cell cortex, notably around ciliary basal bodies (identified by anti-centrin antibodies), as well as around the oral cavity, at the cytoproct and in association with vacuoles (phagosomes) up to several μm in size. Subtle strands run throughout the cell body. Postembedding immunogold labeling/EM analysis shows that actin in the cell cortex emanates, together with the infraciliary lattice, from basal bodies to around trichocyst tips. Label was also enriched around vacuoles and vesicles of different size including “discoidal” vesicles that serve the formation of new phagosomes. By all methods used, we show actin in cilia. Although none of the structurally well-defined filament systems in Paramecium are exclusively formed by actin, actin does display some ordered, though not very conspicuous, arrays throughout the cell. F-actin may somehow serve vesicle trafficking and as a cytoplasmic scaffold. This is particularly supported by the postembedding/EM labeling analysis we used, which would hardly allow for any large-scale redistribution during preparation.
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Affiliation(s)
- Roland Kissmehl
- Department of Biology, University of Konstanz, PO Box 5560, 78457 Konstanz, Germany
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Yi Z, Huang L, Yang R, Lin X, Song W. Actin evolution in ciliates (Protist, Alveolata) is characterized by high diversity and three duplication events. Mol Phylogenet Evol 2015; 96:45-54. [PMID: 26721556 DOI: 10.1016/j.ympev.2015.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 01/13/2023]
Abstract
Ciliates possess two distinct nuclear genomes and unique genomic features, including highly fragmented chromosomes and extensive chromosomal rearrangements. Recent transcriptomic surveys have revealed that ciliates have several multi-copy genes providing an ideal template to study gene family evolution. Nonetheless, this process remains little studied in ciliated protozoa and consequently, the evolutionary patterns that govern it are not well understood. In this study, we focused on obtaining fine-scale information relative to ciliate species divergence for the first time. A total of 230 actin gene sequences were derived from this study, among which 217 were from four closely related Pseudokeronopsis species and 13 from other hypotrichous ciliates. Our investigation shows that: (1) At least three duplication events occurred in ciliates: diversification of three actin genes (Actin I, II, III) happened after the divergence of ciliate classes but before that of subclasses. And several recent and genus-specific duplications were followed within Actin I (Sterkiella, Oxytricha, Uroleptus, etc.), Actin II (Sterkiella), respectively. (2) Within the genus Pseudokeronopsis, Actin I gene duplication events happened after P. carnea and P. erythrina diverged. In contrast, in the morphologically similar species P. flava and P. rubra, the duplication event preceded diversification of the two species. The Actin II gene duplication events preceded divergence of the genus Pseudokeronopsis. (3) Phylogenetic analyses revealed that actin is suitable for resolving ciliate classes, but may not be used to infer lower taxon relationships.
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Affiliation(s)
- Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Lijuan Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Ran Yang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaofeng Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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Sabaneyeva EV, Derkacheva ME, Benken KA, Fokin SI, Vainio S, Skovorodkin IN. Actin-based mechanism of holospora obtusa trafficking in Paramecium caudatum. Protist 2009; 160:205-19. [PMID: 19231281 DOI: 10.1016/j.protis.2008.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 11/08/2008] [Indexed: 12/25/2022]
Abstract
Holospora obtusa, an alpha-proteobacterium, is an obligate endonuclear pathogen of the ciliate Paramecium caudatum. It is engulfed by the host cell in the course of phagocytosis but soon escapes from the phagosome and is transported across the host cell cytoplasm to the paramecium macronucleus. Electron microscopy reveals a comet-like tail resembling that of Listeria trailing after H. obtusa in the host cytoplasm. In this study we investigated the role of the host cell actin and Arp3 in the process of infection with Holospora. Cytochalasin D treatment significantly reduced the rate of nuclear infection. Using immunocytochemistry and experimental infection of GFP-actin-transfected paramecia we demonstrated that the Paramecium actin1-1 took part in the bacterial escape from the phagosome, its trafficking in the cytoplasm and entry into the host macronucleus. Rapid assembly/disassembly of actin filaments in P. caudatum led to quick loss of actin1-1 from the trails left by H. obtusa. Immunocytochemistry using anti-bovine Arp3 antibodies demonstrated the presence of Arp3 in these trails. Our data indicate that details of H. obtusa infection are rather similar to those of Listeria and Rickettsia.
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Affiliation(s)
- Elena V Sabaneyeva
- Department of Cytology and Histology, St.-Petersburg State University, 199034 St.-Petersburg, Russia
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MIEOG JC, VAN OPPEN MJH, BERKELMANS R, STAM WT, OLSEN JL. Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCR. Mol Ecol Resour 2009; 9:74-82. [DOI: 10.1111/j.1755-0998.2008.02222.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim OTP, Yura K, Go N, Harumoto T. Highly divergent actins from karyorelictean, heterotrich, and litostome ciliates. J Eukaryot Microbiol 2004; 51:227-33. [PMID: 15134260 DOI: 10.1111/j.1550-7408.2004.tb00551.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have cloned, sequenced, and characterized cDNA of actins from five ciliate species of three different classes of the phylum Ciliophora: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma japonicum, Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Loxodes striatus uses UGA as the stop codon and has numerous in-frame UAA and UAG, which are translated into glutamine. The other four species use UAA as the stop codon and have no in-frame UAG nor UGA. The putative amino acid sequences of the newly determined actin genes were found to be highly divergent as expected from previous findings of other ciliate actins. These sequences were also highly divergent from other ciliate actins, indicating that actin genes are highly diverse even within the phylum Ciliophora. Phylogenetic analysis showed high evolutionary rate of ciliate actins. Our results suggest that the evolutionary rate was accelerated because of the differences in molecular interactions.
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Affiliation(s)
- Oanh T P Kim
- The Division of Human Environmental Sciences, Graduate School of Human Culture, Nara Women's University, Kitauoyanishi-machi, Nara 630-8506, Japan
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Villalobo E, Morin L, Moch C, Lescasse R, Hanna M, Xiao W, Baroin-Tourancheau A. A homologue of CROC-1 in a ciliated protist (Sterkiella histriomuscorum) testifies to the ancient origin of the ubiquitin-conjugating enzyme variant family. Mol Biol Evol 2002; 19:39-48. [PMID: 11752188 DOI: 10.1093/oxfordjournals.molbev.a003980] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Resting cysts of Sterkiella histriomuscorum (Ciliophora, Oxytrichidae) have been shown to contain messenger RNA, one of which codes for a protein significantly similar to CROC-1. CROC-1 is a human regulatory protein capable of transactivating the promoter of c-fos and belongs to a newly characterized family of ubiquitin-conjugating enzyme (E2) variants (UEV). We have determined the corresponding macronuclear gene sequence, which is the first protistan UEV sequence available. The phylogenetic analysis indicates the deep separation and solid clustering of all the UEV sequences within the E2 tree showing the ancient origin of these regulatory genes and their high structural conservation during evolution. Furthermore, overexpression of the ciliate UEV is able to rescue the Saccharomyces cerevisiae mms2 null mutant from killing by DNA damaging agents, implying that the UEV family proteins are functionally conserved. In S. histriomuscorum, expression of UEV is correlated with the growth of the cells as transcripts are present in excysting and vegetative cells but are rapidly down-regulated during starvation. These data support the high conservation of the UEV family in eukaryotes, and a regulatory role of the gene is discussed in relation to known functions of UEVs. This analysis may promote the search for homologues of other regulatory genes (metazoan regulators of differentiation) in ciliates.
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Affiliation(s)
- Eduardo Villalobo
- Laboratoire de Biologie Cellulaire 4, (UPRES-A 8080), Bâtiment 444, Université Paris-Sud, 91405 Orsay Cedex, France
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Perez-Romero P, Villalobo E, Torres A. Different stop codon usage in two pseudohypotrich ciliates. FEMS Microbiol Lett 2001; 205:259-63. [PMID: 11750813 DOI: 10.1111/j.1574-6968.2001.tb10958.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Based on rRNA phylogeny, morphologic and morphogenetic characters, two major groups of hypotrich ciliates can be distinguished: euhypotrichs and pseudohypotrichs. Through the sequencing of actin genes, we show here that, interestingly, the pseudohypotrichs Dyophrys sp. and Euplotes vannus have a different stop codon usage. In fact, the stop codon usage of the former species resembles that of euhypotrichs. This unexpected result is used to discuss the origin and acquisition of genetic code deviations in ciliates.
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Affiliation(s)
- P Perez-Romero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080, Sevilla, Spain
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Villalobo E, Moch C, Perasso R, Baroin-Tourancheau A. Searching for excystment-regulated genes in Sterkiella histriomuscorum (Ciliophora, Oxytrichidae): a mRNA differential display analysis of gene expression in excysting cells. J Eukaryot Microbiol 2001; 48:382-90. [PMID: 11411848 DOI: 10.1111/j.1550-7408.2001.tb00328.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In the absence of food, the oxytrichid Sterkiella histriomuscorum transforms like many ciliates into resting cysts. When transferred back into feeding medium, the cyst re-transforms into a vegetative cell. The entry into and exit from the dormant cyst stage are complex developmental processes still poorly investigated at the molecular level. Assuming that these changes in state could involve changes in gene expression, we have used the technique of mRNA differential display to detect differentially expressed genes in cysts and two different stages of excysting cell. Variation in the temporal expression pattern of transcripts could be detected and, in using an inverse-PCR strategy on circularized macronuclear DNA, we have sequenced the macronuclear genes of three of the isolated cDNAs. which correspond to 1) a nucleotide-binding domain-encoding gene, 2) a DHHC-domain-carrying gene, and 3) a phosphatase type 2C-encoding gene. For the first two genes, Northern blot analyses supported an excystment-associated regulated gene expression. We discuss their possible role during excystment and we show that the combination of differential display and inverse PCR constitutes a powerful approach to isolate excystment-regulated genes in hypotrichs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Protozoan/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Molecular Sequence Data
- Oxytricha/genetics
- Oxytricha/growth & development
- Oxytricha/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
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Affiliation(s)
- E Villalobo
- Laboratoire de Biologie Cellulaire 4 (CNRS, UPRESA 8080), Université Paris-Sud, Orsay, France.
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Prescott DM, Dizick SJ. A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs. Nucleic Acids Res 2000; 28:4679-88. [PMID: 11095678 PMCID: PMC115164 DOI: 10.1093/nar/28.23.4679] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 50 non-coding bases immediately internal to the telomeric repeats in the two 5' ends of macronuclear DNA molecules of a group of hypotrichous ciliates are anomalous in composition, consisting of 61% purines and 39% pyrimidines, A>T (ratio of 44:32), and G>C (ratio of 17:7). These ratio imbalances violate parity rule 2, according to which A should equal T and G should equal C within a DNA strand and therefore pyrimidines should equal purines. The purine-rich and base ratio imbalances are in marked contrast to the rest of the non-coding parts of the molecules, which have the theoretically expected purine content of 50%, with A = T and G = C. The ORFs contain an average of 52% purines as a result of bias in codon usage. The 50 bases that flank the 5' ends of macronuclear sequences in micronuclear DNA (12 cases) consist of approximately 50% purines. Thus, the 50 bases in the 5' ends of macronuclear sequences in micronuclear DNA are islands of purine richness in which A>T and G>C. These islands may serve as signals for the excision of macronuclear molecules during macronuclear development. We have found no published reports of coding or non-coding native DNA with such anomalous base composition.
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Affiliation(s)
- D M Prescott
- University of Colorado, Department of Molecular, Cellular and Developmental Biology, Boulder, CO 80309-0347, USA.
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