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Sun ZC, Jiang Z, Xu X, Li M, Zeng Q, Zhu Y, Wang S, Li Y, Tian XL, Hu C. Fish Paralog Proteins RNASEK-a and -b Enhance Type I Interferon Secretion and Promote Apoptosis. Front Immunol 2021; 12:762162. [PMID: 34880860 PMCID: PMC8645942 DOI: 10.3389/fimmu.2021.762162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Type I interferon and apoptosis elicit multifaceted effects on host defense and various diseases, such as viral infections and cancers. However, the gene/protein network regulating type I interferon and apoptosis has not been elucidated completely. In this study, we selected grass carp (Ctenopharyngodon idella) as an experimental model to investigate the modulation of RNASEK on the secretion of type I interferon and apoptosis. We first cloned two paralogs RNASEK-a and -b in grass carp, defined three exons in each gene, and found the length of both coding regions is 306 bp with 73.27% of protein homology. The protein sequences of the two paralogs are highly conserved across species. Two proteins were mainly localized in early and late endosomes and endoplasmic reticulum. Further, quantitative real-time PCR demonstrated that dsRNA poly I:C and grass carp reovirus upregulated RNASEK-a and -b in grass carp cells and tissues. Overexpression of RNASEK-a and -b individually induced type I interferon expression and the phosphorylation of IRF3/IRF7 shown by Western blot and immunofluorescent staining, increased Bax/Bcl-2 mRNA ratio, DNA fragmentations, TUNEL-positive cells, and the proportion of Annexin V-positive signals in flow cytometry, and activated eIF2α, opposite to that observed when RNASEK-a and -b were knocked down in multiple cell types. Taken together, we claim for the first time that fish paralog proteins RNASEK-a and -b enhance type I interferon secretion and promote apoptosis, which may be involved in the phosphorylation of IRF3/IRF7 and eIF2α, respectively. Our study reveals a previously unrecognized role of RNASEK as a new positive regulator of type I interferon and apoptosis.
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Affiliation(s)
- Zhi-Chao Sun
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China
| | - Zeyin Jiang
- College of Life Science, Nanchang University, Nanchang, China
| | - Xiaowen Xu
- College of Life Science, Nanchang University, Nanchang, China
| | - Meifeng Li
- College of Life Science, Nanchang University, Nanchang, China
| | - Qing Zeng
- College of Life Science, Nanchang University, Nanchang, China
| | - Ying Zhu
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China.,Blood Transfusion Department, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Shanghong Wang
- College of Life Science, Nanchang University, Nanchang, China
| | - Yuanyuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Li Tian
- College of Life Science, Nanchang University, Nanchang, China.,Human Aging Research Institute, Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang, China
| | - Chengyu Hu
- College of Life Science, Nanchang University, Nanchang, China
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2
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Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors. Nat Commun 2021; 12:4498. [PMID: 34301931 PMCID: PMC8302750 DOI: 10.1038/s41467-021-24681-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2',3'-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5'-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5'-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors. We identified Bombyx RNase Kappa (BmRNase κ) as a mitochondria-associated endoribonuclease which produces cP-RNAs during piRNA biogenesis. BmRNase κ-depletion elevated transposon levels and disrupted a piRNA-mediated sex determination in Bombyx embryos, indicating the crucial roles of BmRNase κ in piRNA biogenesis and embryonic development. Our results reveal a BmRNase κ-engaged piRNA biogenesis pathway, in which the generation of cP-RNAs promotes robust piRNA production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Keisuke Morichika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Natsuko Izumi
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ryuma Matsubara
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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3
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Abbas YM, Wu D, Bueler SA, Robinson CV, Rubinstein JL. Structure of V-ATPase from the mammalian brain. Science 2020; 367:1240-1246. [PMID: 32165585 DOI: 10.1126/science.aaz2924] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/12/2020] [Indexed: 12/16/2022]
Abstract
In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a Legionella pneumophila effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions.
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Affiliation(s)
- Yazan M Abbas
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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Afshar K, Dube FF, Najafabadi HS, Bonneil E, Thibault P, Salavati R, Bede JC. Insights into the insect salivary gland proteome: diet-associated changes in caterpillar labial salivary proteins. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:351-366. [PMID: 23353727 DOI: 10.1016/j.jinsphys.2013.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/05/2013] [Accepted: 01/07/2013] [Indexed: 06/01/2023]
Abstract
The primary function of salivary glands is fluid and protein secretion during feeding. Compared to mammalian systems, little is known about salivary protein secretion processes and the effect of diet on the salivary proteome in insect models. Therefore, the effect of diet nutritional quality on caterpillar labial salivary gland proteins was investigated using an unbiased global proteomic approach by nanoLC/ESI/tandem MS. Caterpillars of the beet armyworm, Spodoptera exigua Hübner, were fed one of three diets: an artificial diet containing their self-selected protein to carbohydrate (p:c) ratio (22p:20c), an artificial diet containing a higher nutritional content but the same p:c ratio (33p:30c) or the plant Medicago truncatula Gaertn. As expected, most identified proteins were associated with secretory processes and not influenced by diet. However, some diet-specific differences were observed. Nutrient stress-associated proteins, such as peptidyl-propyl cis-trans isomerase and glucose-regulated protein94/endoplasmin, and glyceraldehyde 3-phosphate dehydrogenase were identified in the labial salivary glands of caterpillars fed nutritionally poor diets, suggesting a link between nutritional status and vesicular exocytosis. Heat shock proteins and proteins involved in endoplasmic reticulum-associated protein degradation were also abundant in the labial salivary glands of these caterpillars. In comparison, proteins associated with development, such as arylphorin, were found in labial salivary glands of caterpillars fed 33p:30c. These results suggest that caterpillars fed balanced or nutritionally-poor diets have accelerated secretion pathways compared to those fed a protein-rich diet.
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Affiliation(s)
- Khashayar Afshar
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Qc, Canada H9X 3V9.
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McCormick M, Chen K, Ramaswamy P, Kenyon C. New genes that extend Caenorhabditis elegans' lifespan in response to reproductive signals. Aging Cell 2012; 11:192-202. [PMID: 22081913 DOI: 10.1111/j.1474-9726.2011.00768.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In Caenorhabditis elegans and Drosophila, removing germline stem cells increases lifespan. In C. elegans, this lifespan extension requires DAF-16, a FOXO transcription factor, and DAF-12, a nuclear hormone receptor. To better understand the regulatory relationships between DAF-16 and DAF-12, we used microarray analysis to identify downstream genes. We found that these two transcription factors influence the expression of distinct but overlapping sets of genes in response to loss of the germline. In addition, we identified several new genes that are required for loss of the germline to increase lifespan. One, phi-62, encodes a conserved, predicted RNA-binding protein. PHI-62 influences DAF-16-dependent transcription, possibly by collaborating with TCER-1, a putative transcription elongation factor, and FTT-2, a 14-3-3 protein known to bind DAF-16. Three other genes encode proteins involved in lipid metabolism; one is a triacylglycerol lipase, and another is an acyl-CoA reductase. These genes do not noticeably affect bulk fat storage levels; therefore, we propose a model in which they may influence production of a lifespan-extending signal or metabolite.
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Affiliation(s)
- Mark McCormick
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
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Kiritsi MN, Fragoulis EG, Sideris DC. Essential cysteine residues for human RNase κ catalytic activity. FEBS J 2012; 279:1318-26. [DOI: 10.1111/j.1742-4658.2012.08526.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Zhang S, Shukle R, Mittapalli O, Zhu YC, Reese JC, Wang H, Hua BZ, Chen MS. The gut transcriptome of a gall midge, Mayetiola destructor. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:1198-1206. [PMID: 20346948 DOI: 10.1016/j.jinsphys.2010.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 05/29/2023]
Abstract
The Hessian fly, Mayetiola destructor, is a serious pest of wheat and an experimental organism for the study of gall midge-plant interactions. In addition to food digestion and detoxification, the gut of Hessian fly larvae is also an important interface for insect-host interactions. Analysis of the genes expressed in the Hessian fly larval gut will enhance our understanding of the overall gut physiology and may also lead to the identification of critical molecules for Hessian fly-host plant interactions. Over 10,000 Expressed Sequence Tags (ESTs) were generated and assembled into 2007 clusters. The most striking feature of the Hessian fly larval transcriptome is the existence of a large number of transcripts coding for so-called small secretory proteins (SSP) with amino acids less than 250. Eleven of the 30 largest clusters were SSP transcripts with the largest cluster containing 11.3% of total ESTs. Transcripts coding for diverse digestive enzymes and detoxification proteins were also identified. Putative digestive enzymes included trypsins, chymotrypsins, cysteine proteases, aspartic protease, endo-oligopeptidase, aminopeptidases, carboxypeptidases, and alpha-amylases. Putative detoxification proteins included cytochrome P450s, glutathione S-transferases, peroxidases, ferritins, a catalase, peroxiredoxins, and others. This study represents the first global analysis of gut transcripts from a gall midge. The identification of a large number of transcripts coding for SSPs, digestive enzymes, detoxification proteins in the Hessian fly larval gut provides a foundation for future studies on the functions of these genes.
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Affiliation(s)
- Shize Zhang
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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8
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Alves-Silva J, Ribeiro JMC, Van Den Abbeele J, Attardo G, Hao Z, Haines LR, Soares MB, Berriman M, Aksoy S, Lehane MJ. An insight into the sialome of Glossina morsitans morsitans. BMC Genomics 2010; 11:213. [PMID: 20353571 PMCID: PMC2853526 DOI: 10.1186/1471-2164-11-213] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 03/30/2010] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Blood feeding evolved independently in worms, arthropods and mammals. Among the adaptations to this peculiar diet, these animals developed an armament of salivary molecules that disarm their host's anti-bleeding defenses (hemostasis), inflammatory and immune reactions. Recent sialotranscriptome analyses (from the Greek sialo = saliva) of blood feeding insects and ticks have revealed that the saliva contains hundreds of polypeptides, many unique to their genus or family. Adult tsetse flies feed exclusively on vertebrate blood and are important vectors of human and animal diseases. Thus far, only limited information exists regarding the Glossina sialome, or any other fly belonging to the Hippoboscidae. RESULTS As part of the effort to sequence the genome of Glossina morsitans morsitans, several organ specific, high quality normalized cDNA libraries have been constructed, from which over 20,000 ESTs from an adult salivary gland library were sequenced. These ESTs have been assembled using previously described ESTs from the fat body and midgut libraries of the same fly, thus totaling 62,251 ESTs, which have been assembled into 16,743 clusters (8,506 of which had one or more EST from the salivary gland library). Coding sequences were obtained for 2,509 novel proteins, 1,792 of which had at least one EST expressed in the salivary glands. Despite library normalization, 59 transcripts were overrepresented in the salivary library indicating high levels of expression. This work presents a detailed analysis of the salivary protein families identified. Protein expression was confirmed by 2D gel electrophoresis, enzymatic digestion and mass spectrometry. Concurrently, an initial attempt to determine the immunogenic properties of selected salivary proteins was undertaken. CONCLUSIONS The sialome of G. m. morsitans contains over 250 proteins that are possibly associated with blood feeding. This set includes alleles of previously described gene products, reveals new evidence that several salivary proteins are multigenic and identifies at least seven new polypeptide families unique to Glossina. Most of these proteins have no known function and thus, provide a discovery platform for the identification of novel pharmacologically active compounds, innovative vector-based vaccine targets, and immunological markers of vector exposure.
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9
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A hybrid-specific, polymerase chain reaction-based amplification approach for chromosomal walking. Anal Biochem 2009; 388:342-4. [DOI: 10.1016/j.ab.2009.02.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/25/2009] [Accepted: 02/25/2009] [Indexed: 11/21/2022]
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Rampias TN, Fragoulis EG, Sideris DC. Genomic structure and expression analysis of the RNase kappa family ortholog gene in the insect Ceratitis capitata. FEBS J 2008; 275:6217-27. [PMID: 19016845 DOI: 10.1111/j.1742-4658.2008.06746.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cc RNase is the founding member of the recently identified RNase kappa family, which is represented by a single ortholog in a wide range of animal taxonomic groups. Although the precise biological role of this protein is still unknown, it has been shown that the recombinant proteins isolated so far from the insect Ceratitis capitata and from human exhibit ribonucleolytic activity. In this work, we report the genomic organization and molecular evolution of the RNase kappa gene from various animal species, as well as expression analysis of the ortholog gene in C. capitata. The high degree of amino acid sequence similarity, in combination with the fact that exon sizes and intronic positions are extremely conserved among RNase kappa orthologs in 15 diverse genomes from sea anemone to human, imply a very significant biological function for this enzyme. In C. capitata, two forms of RNase kappa mRNA (0.9 and 1.5 kb) with various lengths of 3' UTR were identified as alternative products of a single gene, resulting from the use of different polyadenylation signals. Both transcripts are expressed in all insect tissues and developmental stages. Sequence analysis of the extended region of the longer transcript revealed the existence of three mRNA instability motifs (AUUUA) and five poly(U) tracts, whose functional importance in RNase kappa mRNA decay remains to be explored.
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Affiliation(s)
- Theodoros N Rampias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Athens, Greece
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Economopoulou MAI, Fragoulis EG, Sideris DC. Molecular cloning and characterization of the human RNase kappa, an ortholog of Cc RNase. Nucleic Acids Res 2007; 35:6389-98. [PMID: 17881363 PMCID: PMC2095791 DOI: 10.1093/nar/gkm718] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A novel protein family, designated hereafter as RNase κ (kappa) family, has been recently introduced with the characterization of the specific Cc RNase, isolated from the insect Ceratitis capitata. The human ortholog of this family consists of 98 amino acids and shares > 98% identity with its mammalian counterparts. This RNase is encoded by a single-copy gene found to be expressed in a wide spectrum of normal and cancer tissues. The cDNA of the human ribonuclease has been isolated and subcloned into a variety of prokaryotic expression vectors, but most efforts to express it caused a severe toxic effect. On the other hand, the expression of the human RNase by the use of the methylotrophic yeast Pichia pastoris system resulted in the production of a highly active recombinant enzyme. Using a 30-mer 5′-end-labeled RNA probe as substrate, the purified enzyme seems to preferentially cleave ApU and ApG phosphodiester bonds, while it hydrolyzes UpU bonds at a lower rate. Based on amino acid sequence alignment and substrate specificity data, as well as the complete resistance of the recombinant protein to the placental ribonuclease inhibitor, we concluded that the human RNase κ is a novel endoribonuclease distinct from other known ribonucleases.
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Ribeiro JMC, Alarcon-Chaidez F, Francischetti IMB, Mans BJ, Mather TN, Valenzuela JG, Wikel SK. An annotated catalog of salivary gland transcripts from Ixodes scapularis ticks. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2006; 36:111-29. [PMID: 16431279 DOI: 10.1016/j.ibmb.2005.11.005] [Citation(s) in RCA: 275] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 11/04/2005] [Accepted: 11/04/2005] [Indexed: 05/06/2023]
Abstract
Over 8000 expressed sequence tags from six different salivary gland cDNA libraries from the tick Ixodes scapularis were analyzed. These libraries derive from feeding nymphs infected or not with the Lyme disease agent, Borrelia burgdorferi, from unfed adults, and from adults feeding on a rabbit for 6-12 h, 18-24 h, and 3-4 days. Comparisons of the several libraries led to identification of several significantly differentially expressed transcripts. Additionally, over 500 new predicted protein sequences are described, including several novel gene families unique to ticks; no function can be presently ascribed to most of these novel families. Among the housekeeping-associated transcripts, we highlight those enzymes associated with post translation modification of amino acids, particularly those forming sulfotyrosine, hydroxyproline, and carboxyl-glutamic acid. Results support the hypothesis that gene duplication, most possibly including genome duplications, is a major player in tick evolution.
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Affiliation(s)
- José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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