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Fu Y, Liang F, Li C, Warren A, Shin MK, Li L. Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa. Microorganisms 2023; 11:1833. [PMID: 37513005 PMCID: PMC10384029 DOI: 10.3390/microorganisms11071833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.
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Affiliation(s)
- Yu Fu
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Congjun Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Mann Kyoon Shin
- Department of Biology, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
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Calow J, Behrens AJ, Mader S, Bockau U, Struwe WB, Harvey DJ, Cormann KU, Nowaczyk MM, Loser K, Schinor D, Hartmann MWW, Crispin M. Antibody production using a ciliate generates unusual antibody glycoforms displaying enhanced cell-killing activity. MAbs 2016; 8:1498-1511. [PMID: 27594301 PMCID: PMC5098438 DOI: 10.1080/19420862.2016.1228504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibody glycosylation is a key parameter in the optimization of antibody therapeutics. Here, we describe the production of the anti-cancer monoclonal antibody rituximab in the unicellular ciliate, Tetrahymena thermophila. The resulting antibody demonstrated enhanced antibody-dependent cell-mediated cytotoxicity, which we attribute to unusual N-linked glycosylation. Detailed chromatographic and mass spectrometric analysis revealed afucosylated, oligomannose-type glycans, which, as a whole, displayed isomeric structures that deviate from the typical human counterparts, but whose branches were equivalent to fragments of metabolic intermediates observed in human glycoproteins. From the analysis of deposited crystal structures, we predict that the ciliate glycans adopt protein-carbohydrate interactions with the Fc domain that closely mimic those of native complex-type glycans. In addition, terminal glucose structures were identified that match biosynthetic precursors of human glycosylation. Our results suggest that ciliate-based expression systems offer a route to large-scale production of monoclonal antibodies exhibiting glycosylation that imparts enhanced cell killing activity.
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Affiliation(s)
| | - Anna-Janina Behrens
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | | | | | - Weston B Struwe
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | - David J Harvey
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | - Kai U Cormann
- c Plant Biochemistry, Ruhr University Bochum , Bochum , Germany
| | - Marc M Nowaczyk
- c Plant Biochemistry, Ruhr University Bochum , Bochum , Germany
| | - Karin Loser
- d Department of Dermatology , University of Münster , Münster , Germany
| | - Daniel Schinor
- e Wessling GmbH, Pharmaanalytik Münster , Münster , Germany
| | | | - Max Crispin
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
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Yilmaz G, Arslanyolu M. Efficient expression of codon-adapted affinity tagged super folder green fluorescent protein for synchronous protein localization and affinity purification studies in Tetrahymena thermophila. BMC Biotechnol 2015; 15:22. [PMID: 25887423 PMCID: PMC4432788 DOI: 10.1186/s12896-015-0137-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 03/18/2015] [Indexed: 11/20/2022] Open
Abstract
Background A superior Green Fluorescent Protein (GFP) mutant, known as superfolder GFP (sfGFP), is more soluble, faster folding, and is the brightest of the known GFP mutants. This study aimed to create a codon-adapted sfGFP tag (TtsfGFP) for simultaneous protein localization and affinity purification in Tetrahymena thermophila. Results In vivo fluorescence spectroscopic analyses of clones carrying a codon-adapted and 6 × His tagged TtsfGFP cassette showed approximately 2–4-fold increased fluorescence emission compared with the control groups at 3 h. Fluorescence microscopy also revealed that TtsfGFP reached its emission maxima at 100 min, which was much earlier than controls expressing EGFP and sfGFP (240 min). A T. thermophila ATP-dependent DNA ligase domain containing hypothetical gene (H) was cloned into the 3' end of 6 × His-TtsfGFP to assess the affinity/localization dual tag feature. Fluorescence microscopy of the 6 × His-TtsfGFP-H clone confirmed its localization in the macro- and micronucleus of vegetative T. thermophila. Simultaneous affinity purification of TtsfGFP and TtsfGFP-H with Ni-NTA beads was feasible, as shown by Ni-NTA purified proteins analysis by SDS-PAGE and western blotting. Conclusions We successfully codon adapted the N-terminal 6 × His-TtsfGFP tag and showed that it could be used for protein localization and affinity purification simultaneously in T. thermophila. We believe that this dual tag will advance T. thermophila studies by providing strong visual traceability of the target protein in vivo and in vitro during recombinant production of heterologous and homologous proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0137-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gürkan Yilmaz
- Graduate School of Science, Department of Advance Technologies, Biotechnology Program, Anadolu University, Yunusemre Campus, Eskisehir, Turkey.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Science, Anadolu University, Yunusemre Campus, Eskisehir, Turkey.
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Aoi MC, Rourke BC. Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes. J Mol Evol 2011; 73:74-93. [PMID: 21915654 DOI: 10.1007/s00239-011-9457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 08/19/2011] [Indexed: 01/13/2023]
Abstract
Synonymous codon usage bias is a broadly observed phenomenon in bacteria, plants, and invertebrates and may result from selection. However, the role of selective pressures in shaping codon bias is still controversial in vertebrates, particularly for mammals. The myosin heavy-chain (MyHC) gene family comprises multiple isoforms of the major force-producing contractile protein in cardiac and skeletal muscles. Slow and fast genes are tandemly arrayed on separate chromosomes, and have distinct patterns of functionality and expression in muscle. We analyze both full-length MyHC genes (~5400 bp) and a larger collection of partial sequences at the 3' end (~500 bp). The MyHC isoforms are an interesting system in which to study codon usage bias because of their length, expression, and critical importance to organismal mobility. Codon bias and GC content differs among MyHC genes with regards to functional type, isoform, and position within the gene. Codon bias even varies by isoform within a species. We find evidence in favor of both chromosomal influences on nucleotide composition and selection against nonsense errors (SANE) acting on codon usage in MyHC genes. Intragenic variation in codon bias and elongation rate is significant, with a strong trend for increasing codon bias and elongation rate towards the 3' end of the gene, although the trend is dependent upon the degeneracy class of the codons. Therefore, patterns of codon usage in MyHC genes are consistent with models supporting SANE as a major force shaping codon usage.
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Affiliation(s)
- Mikio C Aoi
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
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Aldag I, Bockau U, Rossdorf J, Laarmann S, Raaben W, Herrmann L, Weide T, Hartmann MWW. Expression, secretion and surface display of a human alkaline phosphatase by the ciliate Tetrahymena thermophila. BMC Biotechnol 2011; 11:11. [PMID: 21281462 PMCID: PMC3042934 DOI: 10.1186/1472-6750-11-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/31/2011] [Indexed: 01/31/2023] Open
Abstract
Background Tetrahymena thermophila possesses many attributes that render it an attractive host for the expression of recombinant proteins. Surface proteins from the parasites Ichthyophthirius multifiliis and Plasmodium falciparum and avian influenza virus antigen H5N1 were displayed on the cell membrane of this ciliate. Furthermore, it has been demonstrated that T. thermophila is also able to produce a functional human DNase I. The present study investigates the heterologous expression of the functional human intestinal alkaline phosphatase (hiAP) using T. thermophila and thereby presents a powerful tool for the optimization of the ciliate-based expression system. Results Functional and full length human intestinal alkaline phosphatase was expressed by T. thermophila using a codon-adapted gene containing the native signal-peptide and GPI (Glycosylphosphatidylinositol) anchor attachment signal. HiAP activity in the cell extract of transformants suggested that the hiAP gene was successfully expressed. Furthermore, it was demonstrated that the enzyme was modified with N-glycosylation and localized on the surface membrane by the C-terminal GPI anchor. A C-terminally truncated version of hiAP lacking the GPI anchor signal peptide was secreted into the medium as an active enzyme. In a first approach to establish a high level expression system up to 14,000 U/liter were produced in a time frame of two days, which exceeds the production rate of other published expression systems for this enzyme. Conclusions With the expression of hiAP, not only a protein of commercial interest could be produced, but also a reporter enzyme that offers the possibility to analyze T. thermophila genes that play a role in the regulation of protein secretion. Additionally, the fact that ciliates do not secrete an endogenous alkaline phosphatase provides the possibility to use the truncated hiAP as a reporter enzyme, allowing the quantification of measures that will be necessary for further optimization of the host strains and the fermentation processes.
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Affiliation(s)
- Ingo Aldag
- Cilian AG, Johann-Krane-Weg 42, Münster, Germany
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Weide T, Herrmann L, Bockau U, Niebur N, Aldag I, Laroy W, Contreras R, Tiedtke A, Hartmann MWW. Secretion of functional human enzymes by Tetrahymena thermophila. BMC Biotechnol 2006; 6:19. [PMID: 16542419 PMCID: PMC1431531 DOI: 10.1186/1472-6750-6-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 03/16/2006] [Indexed: 11/10/2022] Open
Abstract
Background The non-pathogenic ciliate Tetrahymena thermophila is one of the best-characterized unicellular eucaryotes used in various research fields. Previous work has shown that this unicellular organism provides many biological features to become a high-quality expression system, like multiplying to high cell densities with short generation times in bioreactors. In addition, the expression of surface antigens from the malaria parasite Plasmodium falciparum and the ciliate Ichthyophthirius multifiliis suggests that T. thermophila might play an important role in vaccine development. However, the expression of functional mammalian or human enzymes remains so far to be seen. Results We have been able to express a human enzyme in T. thermophila using expression modules that encode a fusion protein consisting of the endogenous phospholipase A1 precursor and mature human DNaseI. The recombinant human enzyme is active, indicating that also disulfide bridges are correctly formed. Furthermore, a detailed N-glycan structure of the recombinant enzyme is presented, illustrating a very consistent glycosylation pattern. Conclusion The ciliate expression system has the potential to become an excellent expression system. However, additional optimisation steps including host strain improvement as wells as measures to increase the yield of expression are necessary to be able to provide an alternative to the common E. coli and yeast-based systems as well as to transformed mammalian cell lines.
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Affiliation(s)
- Thomas Weide
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
| | - Lutz Herrmann
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
| | - Ulrike Bockau
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
- Institut für allgemeine Zoologie und Genetik, Universität Münster, Schlossplatz 5, D-48149 Münster, Germany
| | - Nadine Niebur
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
- Institut für allgemeine Zoologie und Genetik, Universität Münster, Schlossplatz 5, D-48149 Münster, Germany
| | - Ingo Aldag
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
| | - Wouter Laroy
- Department of Molecular Biology Research, Unit for Fundamental and Applied Molecular Biology, Ghent and Flanders Interuniversity Institute for Biotechnology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Roland Contreras
- Department of Molecular Biology Research, Unit for Fundamental and Applied Molecular Biology, Ghent and Flanders Interuniversity Institute for Biotechnology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Arno Tiedtke
- Institut für allgemeine Zoologie und Genetik, Universität Münster, Schlossplatz 5, D-48149 Münster, Germany
| | - Marcus WW Hartmann
- Cilian AG, Johann-Krane-Weg 42, D-48149 Münster, Germany
- Institut für allgemeine Zoologie und Genetik, Universität Münster, Schlossplatz 5, D-48149 Münster, Germany
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Lee SR, Collins K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem 2005; 280:42744-9. [PMID: 16272149 DOI: 10.1074/jbc.m510356200] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amino acid deprivation triggers dramatic physiological responses in all organisms, altering both the synthesis and destruction of RNA and protein. Here we describe, using the ciliate Tetrahymena thermophila, a previously unidentified response to amino acid deprivation in which mature transfer RNA (tRNA) is cleaved in the anticodon loop. We observed that anticodon loop cleavage affects a small fraction of most or all tRNA sequences. Accumulation of cleaved tRNA is temporally coordinated with the morphological and metabolic changes of adaptation to starvation. The starvation-induced endonucleolytic cleavage activity targets tRNAs that have undergone maturation by 5' and 3' end processing and base modification. Curiously, the majority of cleaved tRNAs lack the 3' terminal CCA nucleotides required for aminoacylation. Starvation-induced tRNA cleavage is inhibited in the presence of essential amino acids, independent of the persistence of other starvation-induced responses. Our findings suggest that anticodon loop cleavage may reduce the accumulation of uncharged tRNAs as part of a specific response induced by amino acid starvation.
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Affiliation(s)
- Suzanne R Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204, USA
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Gerber CA, Lopez AB, Shook SJ, Doerder FP. Polymorphism and selection at the SerH immobilization antigen locus in natural populations of Tetrahymena thermophila. Genetics 2002; 160:1469-79. [PMID: 11973302 PMCID: PMC1462060 DOI: 10.1093/genetics/160.4.1469] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The SerH locus of Tetrahymena thermophila is one of several paralogous loci with genes encoding variants of the major cell surface protein known as the immobilization antigen (i-ag). The locus is highly polymorphic, raising questions concerning functional equivalency and selective forces acting on its multiple alleles. Here, we compare the sequences and expression of SerH1, SerH3, SerH4, SerH5, and SerH6. The precursor i-ags are highly similar. They are rich in alanine, serine, threonine, and cysteine and they share nearly identical ER translocation and GPI addition signals. The locations of the 39 cysteines are highly conserved, particularly in the 3.5 central, imperfect tandem repeats in which 8 periodic cysteines punctuate alternating short and long stretches of amino acids. Hydrophobicity patterns are also conserved. Nevertheless, amino acid sequence identity is low, ranging from 60.7 to 82.9%. At the nucleotide level, from 9.7 to 26.7% of nucleotide sites are polymorphic in pairwise comparisons. Expression of each allele is regulated by temperature-sensitive mRNA stability. H mRNAs are stable at <36 degrees but are unstable at >36 degrees. The H5 mRNA, which is less affected by temperature, has a different arrangement of the putative mRNA destabilization motif AUUUA. Statistical analysis of SerH genes indicates that the multiple alleles are neutral. Significantly low ratios of the rates of nonsynonymous to synonymous amino acid substitutions suggest that the multiple alleles are subject to purifying (negative) selection enforcing constraints on structure.
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Affiliation(s)
- Carri A Gerber
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA
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Fillingham JS, Chilcoat ND, Turkewitz AP, Orias E, Reith M, Pearlman RE. Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila. J Eukaryot Microbiol 2002; 49:99-107. [PMID: 12043965 DOI: 10.1111/j.1550-7408.2002.tb00350.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To assess the utility of expressed sequence tag (EST) sequencing as a method of gene discovery in the ciliated protozoan Tetrahymena thermophila, we have sequenced either the 5' or 3' ends of 157 clones chosen at random from two cDNA libraries constructed from the mRNA of vegetatively growing cultures. Of 116 total non-redundant clones, 8.6% represented genes previously cloned in Tetrahymena. Fifty-two percent had significant identity to genes from other organisms represented in GenBank, of which 92% matched human proteins. Intriguing matches include an opioid-regulated protein, a glutamate-binding protein for an NMDA-receptor, and a stem-cell maintenance protein. Eleven-percent of the non-Tetrahymena specific matches were to genes present in humans and other mammals but not found in other model unicellular eukaryotes, including the completely sequenced Saccharomyces cerevisiae. Our data reinforce the fact that Tetrahymena is an excellent unicellular model system for studying many aspects of animal biology and is poised to become an important model system for genome-scale gene discovery and functional analysis.
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Doerder FP. Sequence and expression of the SerJ immobilization antigen gene of Tetrahymena thermophila regulated by dominant epistasis. Gene 2000; 257:319-26. [PMID: 11080598 DOI: 10.1016/s0378-1119(00)00380-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In ciliates, variable surface protein genes encoding the immobilization antigen (-ag) are expressed under different environmental conditions, including temperature and salt stress. These i-ags are GPI-linked and coat the entire external surface of the cell, including the cilia. In Tetrahymena thermophila-ag in natural isolates is the result of dominant epistasis masking the expression of the H i-ag ordinarily expressed at 20-36 degrees C. This report describes the expression and sequence of the Ser-ag. J is present on the cell surface up to 38 degrees C; above 38 degrees C SerSeranked by an A-rich 5' UTR and a 3' UTR containing putative mRNA destabilization motifs. The encoded J polypeptide consists of 438 amino acids and is rich in alanine, cysteine, serine and threonine. The N- and resemble signal peptide and GPI-anchor addition sites, respectively. The majority of the molecule consists of four imperfect repeats with 10 periodic cysteines per repeat in the pattern CX(6)CX(2)CX(21)CX(4)CX(13-15)CX(2)CX(18)CX(3)CX(11)CX(9-10). Although H i-ags encoded by paralogous SerH genes have 3.5 imperfect repeats with eight periodic cysteines per repeat, J nevertheless resembles H with respect to amino acid composition, codon usage, N- and C-termini, the arrangement of the cysteine periods, and regulation by mRNA stability. However, despite these similarities and epistasis, the evolutionary relationship between SerH and SerJ is unclear.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- Antigens, Protozoan
- Antigens, Surface/chemistry
- Antigens, Surface/genetics
- Base Sequence
- Blotting, Northern
- Cysteine/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- Epistasis, Genetic
- Gene Expression Regulation
- Molecular Sequence Data
- Protozoan Proteins
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repetitive Sequences, Amino Acid/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Temperature
- Tetrahymena thermophila/genetics
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Affiliation(s)
- F P Doerder
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA.
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