1
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Feng Q, Wang H, Shao Y, Xu X. Antizyme inhibitor family: biological and translational research implications. Cell Commun Signal 2024; 22:11. [PMID: 38169396 PMCID: PMC10762828 DOI: 10.1186/s12964-023-01445-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Metabolism of polyamines is of critical importance to physiological processes. Ornithine decarboxylase (ODC) antizyme inhibitors (AZINs) are capable of interacting with antizymes (AZs), thereby releasing ODC from ODC-AZs complex, and promote polyamine biosynthesis. AZINs regulate reproduction, embryonic development, fibrogenesis and tumorigenesis through polyamine and other signaling pathways. Dysregulation of AZINs has involved in multiple human diseases, especially malignant tumors. Adenosine-to-inosine (A-to-I) RNA editing is the most common type of post-transcriptional nucleotide modification in humans. Additionally, the high frequencies of RNA-edited AZIN1 in human cancers correlates with increase of cancer cell proliferation, enhancement of cancer cell stemness, and promotion of tumor angiogenesis. In this review, we summarize the current knowledge on the various contribution of AZINs related with potential cancer promotion, cancer stemness, microenvironment and RNA modification, especially underlying molecular mechanisms, and furthermore explored its promising implication for cancer diagnosis and treatment.
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Affiliation(s)
- Qiaohui Feng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, 110001, PR China
| | - Huijie Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China
| | - Youcheng Shao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China
| | - Xiaoyan Xu
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning Province, PR China.
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2
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Vindu A, Shin BS, Choi K, Christenson ET, Ivanov IP, Cao C, Banerjee A, Dever TE. Translational autoregulation of the S. cerevisiae high-affinity polyamine transporter Hol1. Mol Cell 2021; 81:3904-3918.e6. [PMID: 34375581 PMCID: PMC8500938 DOI: 10.1016/j.molcel.2021.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022]
Abstract
Polyamines, small organic polycations, are essential for cell viability, and their physiological levels are homeostatically maintained by post-transcriptional regulation of key biosynthetic enzymes. In addition to de novo synthesis, cells can also take up polyamines; however, identifying cellular polyamine transporters has been challenging. Here we show that the S. cerevisiae HOL1 mRNA is under translational control by polyamines, and we reveal that the encoded membrane transporter Hol1 is a high-affinity polyamine transporter and is required for yeast growth under limiting polyamine conditions. Moreover, we show that polyamine inhibition of the translation factor eIF5A impairs translation termination at a Pro-Ser-stop motif in a conserved upstream open reading frame on the HOL1 mRNA to repress Hol1 synthesis under conditions of elevated polyamines. Our findings reveal that polyamine transport, like polyamine biosynthesis, is under translational autoregulation by polyamines in yeast, highlighting the extensive control cells impose on polyamine levels.
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Affiliation(s)
- Arya Vindu
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Byung-Sik Shin
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Choi
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric T Christenson
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chune Cao
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas E Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Lambertos A, Peñafiel R. Polyamine biosynthesis in Xenopus laevis: the xlAZIN2/xlODC2 gene encodes a lysine/ornithine decarboxylase. PLoS One 2019; 14:e0218500. [PMID: 31509528 PMCID: PMC6738921 DOI: 10.1371/journal.pone.0218500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/26/2019] [Indexed: 11/29/2022] Open
Abstract
Ornithine decarboxylase (ODC) is a key enzyme in the biosynthesis of polyamines, organic cations that are implicated in many cellular processes. The enzyme is regulated at the post-translational level by an unusual system that includes antizymes (AZs) and antizyme inhibitors (AZINs). Most studies on this complex regulatory mechanism have been focused on human and rodent cells, showing that AZINs (AZIN1 and AZIN2) are homologues of ODC but devoid of enzymatic activity. Little is known about Xenopus ODC and its paralogues, in spite of the relevance of Xenopus as a model organism for biomedical research. We have used the information existing in different genomic databases to compare the functional properties of the amphibian ODC1, AZIN1 and AZIN2/ODC2, by means of transient transfection experiments of HEK293T cells. Whereas the properties of xlODC1 and xlAZIN1 were similar to those reported for their mammalian orthologues, the former catalyzing the decarboxylation of L-ornithine preferentially to that of L-lysine, xlAZIN2/xlODC2 showed important differences with respect to human and mouse AZIN2. xlAZIN2 did not behave as an antizyme inhibitor, but it rather acts as an authentic decarboxylase forming cadaverine, due to its higher affinity to L-lysine than to L-ornithine as substrate; so, in accordance with this, it should be named as lysine decarboxylase (LDC) or lysine/ornithine decarboxylase (LODC). In addition, AZ1 stimulated the degradation of xlAZIN2 by the proteasome, but the removal of the 21 amino acid C-terminal tail, with a sequence quite different to that of mouse or human ODC, made the protein resistant to degradation. Collectively, our results indicate that in Xenopus there is only one antizyme inhibitor (xlAZIN1) and two decarboxylases, xlODC1 and xlLDC, with clear preferences for L-ornithine and L-lysine, respectively.
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Affiliation(s)
- Ana Lambertos
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Rafael Peñafiel
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
- * E-mail:
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4
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Abstract
Polyamines are organic polycations that bind to a variety of cellular molecules, including nucleic acids. Within cells, polyamines contribute to both the efficiency and fidelity of protein synthesis. In addition to directly acting on the translation apparatus to stimulate protein synthesis, the polyamine spermidine serves as a precursor for the essential post-translational modification of the eukaryotic translation factor 5A (eIF5A), which is required for synthesis of proteins containing problematic amino acid sequence motifs, including polyproline tracts, and for termination of translation. The impact of polyamines on translation is highlighted by autoregulation of the translation of mRNAs encoding key metabolic and regulatory proteins in the polyamine biosynthesis pathway, including S-adenosylmethionine decarboxylase (AdoMetDC), antizyme (OAZ), and antizyme inhibitor 1 (AZIN1). Here, we highlight the roles of polyamines in general translation and also in the translational regulation of polyamine biosynthesis.
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Affiliation(s)
- Thomas E Dever
- From the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Ivaylo P Ivanov
- From the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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5
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Ramos-Molina B, Lambertos A, Peñafiel R. Antizyme Inhibitors in Polyamine Metabolism and Beyond: Physiopathological Implications. ACTA ACUST UNITED AC 2018; 6:medsci6040089. [PMID: 30304856 PMCID: PMC6313458 DOI: 10.3390/medsci6040089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 12/25/2022]
Abstract
The intracellular levels of polyamines, cationic molecules involved in a myriad of cellular functions ranging from cellular growth, differentiation and apoptosis, is precisely regulated by antizymes and antizyme inhibitors via the modulation of the polyamine biosynthetic and transport systems. Antizymes, which are mainly activated upon high polyamine levels, inhibit ornithine decarboxylase (ODC), the key enzyme of the polyamine biosynthetic route, and exert a negative control of polyamine intake. Antizyme inhibitors (AZINs), which are proteins highly homologous to ODC, selectively interact with antizymes, preventing their action on ODC and the polyamine transport system. In this review, we will update the recent advances on the structural, cellular and physiological functions of AZINs, with particular emphasis on the action of these proteins in the regulation of polyamine metabolism. In addition, we will describe emerging evidence that suggests that AZINs may also have polyamine-independent effects on cells. Finally, we will discuss how the dysregulation of AZIN activity has been implicated in certain human pathologies such as cancer, fibrosis or neurodegenerative diseases.
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Affiliation(s)
- Bruno Ramos-Molina
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain.
- Laboratory of Cellular and Molecular Endocrinology, Institute of Biomedical Research in Malaga (IBIMA), Virgen de la Victoria University Hospital, 29010 Málaga, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain.
| | - Ana Lambertos
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain.
- Biomedical Research Institute of Murcia (IMIB), 30120 Murcia, Spain.
| | - Rafael Peñafiel
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain.
- Biomedical Research Institute of Murcia (IMIB), 30120 Murcia, Spain.
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Ivanov IP, Shin BS, Loughran G, Tzani I, Young-Baird SK, Cao C, Atkins JF, Dever TE. Polyamine Control of Translation Elongation Regulates Start Site Selection on Antizyme Inhibitor mRNA via Ribosome Queuing. Mol Cell 2018; 70:254-264.e6. [PMID: 29677493 PMCID: PMC5916843 DOI: 10.1016/j.molcel.2018.03.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 02/06/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022]
Abstract
Translation initiation is typically restricted to AUG codons, and scanning eukaryotic ribosomes inefficiently recognize near-cognate codons. We show that queuing of scanning ribosomes behind a paused elongating ribosome promotes initiation at upstream weak start sites. Ribosomal profiling reveals polyamine-dependent pausing of elongating ribosomes on a conserved Pro-Pro-Trp (PPW) motif in an inhibitory non-AUG-initiated upstream conserved coding region (uCC) of the antizyme inhibitor 1 (AZIN1) mRNA, encoding a regulator of cellular polyamine synthesis. Mutation of the PPW motif impairs initiation at the uCC's upstream near-cognate AUU start site and derepresses AZIN1 synthesis, whereas substitution of alternate elongation pause sequences restores uCC translation. Impairing ribosome loading reduces uCC translation and paradoxically derepresses AZIN1 synthesis. Finally, we identify the translation factor eIF5A as a sensor and effector for polyamine control of uCC translation. We propose that stalling of elongating ribosomes triggers queuing of scanning ribosomes and promotes initiation by positioning a ribosome near the start codon.
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Affiliation(s)
- Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT57, Ireland.
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT57, Ireland
| | - Ioanna Tzani
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT57, Ireland
| | - Sara K Young-Baird
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chune Cao
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT57, Ireland
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Lambertos A, Ramos-Molina B, Cerezo D, López-Contreras AJ, Peñafiel R. The mouse Gm853 gene encodes a novel enzyme: Leucine decarboxylase. Biochim Biophys Acta Gen Subj 2017; 1862:365-376. [PMID: 29108956 DOI: 10.1016/j.bbagen.2017.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022]
Abstract
Ornithine decarboxylase (ODC) is a key enzyme in the biosynthesis of polyamines. ODC-antizyme inhibitors (AZINs) are homologous proteins of ODC, devoid of enzymatic activity but acting as regulators of polyamine levels. The last paralogue gene recently incorporated into the ODC/AZINs family is the murine Gm853, which is located in the same chromosome as AZIN2, and whose biochemical function is still unknown. By means of transfection assays of HEK293T cells with a plasmid containing the coding region of Gm853, we show here that unlike ODC, GM853 was a stable protein that was not able to decarboxylate l-ornithine or l-lysine and that did not act as an antizyme inhibitor. However, GM853 showed leucine decarboxylase activity, an enzymatic activity never described in animal cells, and by acting on l-leucine (Km=7.03×10-3M) it produced isopentylamine, an aliphatic monoamine with unknown function. The other physiological branched-chain amino acids, l-valine and l-isoleucine were poor substrates of the enzyme. Gm853 expression was mainly detected in the kidney, and as Odc, it was stimulated by testosterone. The conservation of Gm853 orthologues in different mammalian species, including primates, underlines the possible biological significance of this new enzyme. In this study, we describe for the first time a mammalian enzyme with leucine decarboxylase activity, therefore proposing that the gene Gm853 and its protein product should be named as leucine decarboxylase (Ldc, LDC).
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Affiliation(s)
- Ana Lambertos
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Bruno Ramos-Molina
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Spain
| | - David Cerezo
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Spain
| | - Andrés J López-Contreras
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Spain
| | - Rafael Peñafiel
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain.
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8
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Cassella L, Salvetti A, Iacopetti P, Ippolito C, Ghezzani C, Gimenez G, Ghigo E, Rossi L. Putrescine independent wound response phenotype is produced by ODC-like RNAi in planarians. Sci Rep 2017; 7:9736. [PMID: 28851936 PMCID: PMC5574924 DOI: 10.1038/s41598-017-09567-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/26/2017] [Indexed: 01/18/2023] Open
Abstract
Despite increasing evidence indicates polyamines as a convergence point for signaling pathways, including cell growth and differentiation, a unifying concept to interpret their role is still missing. The activity of ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis, is tightly regulated by a complex molecular machinery, and the demonstration of the existence of multiple ODC paralogs, lacking decarboxylation activity, suggests additional layers of complexity to the intricate ODC regulatory pathway. Because of their extraordinary regenerative abilities and abundance of stem cells, planarians have potential to contribute to our understanding of polyamine function in an in vivo context. We undertook a study on ODC function in planarians and we found six planarian ODCs (ODC1-6). Five out of six ODC homologs carry substitutions of key aminoacids for enzymatic activity, which makes them theoretically unable to decarboxylate ornithine. Silencing of ODC5 and 6 produced a complex phenotype, by prompting animals to an aberrant response, following chronic injury without tissue removal. Phenotype is neither rescued by putrescine, nor mimicked by difluoromethylornithine treatment. Moreover, the co-silencing of other genes of the ODC regulatory pathway did not modulate phenotype outcome or severity, thus suggesting that the function/s of these ODC-like proteins might be unrelated to decarboxylase activity and putrescine production.
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Affiliation(s)
- Lucia Cassella
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy
| | - Paola Iacopetti
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy
| | - Chiara Ippolito
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy
| | - Claudio Ghezzani
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy
| | - Gregory Gimenez
- Otago Genomics & Bioinformatics Facility, Department of Biochemistry, University of Otago, PO Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Eric Ghigo
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13385, Marseille Cedex 05, France
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, via Volta 4, 56126, Pisa, Italy.
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9
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Characterization of an androgen-responsive, ornithine decarboxylase-related protein in mouse kidney. Biosci Rep 2017; 37:BSR20170163. [PMID: 28607032 PMCID: PMC5518511 DOI: 10.1042/bsr20170163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 01/26/2023] Open
Abstract
We have investigated and characterized a novel ornithine decarboxylase (ODC) related protein (ODCrp) also annotated as gm853. ODCrp shows 41% amino acid sequence identity with ODC and 38% with ODC antizyme inhibitor 1 (AZIN1). The Odcrp gene is selectively expressed in the epithelium of proximal tubuli of mouse kidney with higher expression in males than in females. Like Odc in mouse kidney, Odcrp is also androgen responsive with androgen receptor (AR)-binding loci within its regulatory region. ODCrp forms homodimers but does not heterodimerize with ODC. Although ODCrp contains 20 amino acid residues known to be necessary for the catalytic activity of ODC, no decarboxylase activity could be found with ornithine, lysine or arginine as substrates. ODCrp does not function as an AZIN, as it neither binds ODC antizyme 1 (OAZ1) nor prevents OAZ-mediated inactivation and degradation of ODC. ODCrp itself is degraded via ubiquination and mutation of Cys363 (corresponding to Cys360 of ODC) appears to destabilize the protein. Evidence for a function of ODCrp was found in ODC assays on lysates from transfected Cos-7 cells where ODCrp repressed the activity of endogenous ODC while Cys363Ala mutated ODCrp increased the enzymatic activity of endogenous ODC.
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Kafková L, Debler EW, Fisk JC, Jain K, Clarke SG, Read LK. The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex. J Biol Chem 2016; 292:2089-2100. [PMID: 27998975 DOI: 10.1074/jbc.m116.757112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/14/2016] [Indexed: 11/06/2022] Open
Abstract
Prozymes are catalytically inactive enzyme paralogs that dramatically stimulate the function of weakly active enzymes through complex formation. The two prozymes described to date reside in the polyamine biosynthesis pathway of the human parasite Trypanosoma brucei, an early branching eukaryote that lacks transcriptional regulation and regulates its proteome through posttranscriptional and posttranslational means. Arginine methylation is a common posttranslational modification in eukaryotes catalyzed by protein arginine methyltransferases (PRMTs) that are typically thought to function as homodimers. We demonstrate that a major T. brucei PRMT, TbPRMT1, functions as a heterotetrameric enzyme-prozyme pair. The inactive PRMT paralog, TbPRMT1PRO, is essential for catalytic activity of the TbPRMT1ENZ subunit. Mutational analysis definitively demonstrates that TbPRMT1ENZ is the cofactor-binding subunit and carries all catalytic activity of the complex. Our results are the first demonstration of an obligate heteromeric PRMT, and they suggest that enzyme-prozyme organization is expanded in trypanosomes as a posttranslational means of enzyme regulation.
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Affiliation(s)
- Lucie Kafková
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Erik W Debler
- the Laboratory of Cell Biology, The Rockefeller University, New York, New York 10065, and
| | - John C Fisk
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Kanishk Jain
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Laurie K Read
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214,
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11
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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12
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Rajput B, Murphy TD, Pruitt KD. RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates. Nucleic Acids Res 2015; 43:7270-9. [PMID: 26170238 PMCID: PMC4551939 DOI: 10.1093/nar/gkv713] [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: 05/22/2015] [Accepted: 07/01/2015] [Indexed: 12/29/2022] Open
Abstract
Polyamines are ubiquitous cations that are involved in regulating fundamental cellular processes such as cell growth and proliferation; hence, their intracellular concentration is tightly regulated. Antizyme and antizyme inhibitor have a central role in maintaining cellular polyamine levels. Antizyme is unique in that it is expressed via a novel programmed ribosomal frameshifting mechanism. Conventional computational tools are unable to predict a programmed frameshift, resulting in misannotation of antizyme transcripts and proteins on transcript and genomic sequences. Correct annotation of a programmed frameshifting event requires manual evaluation. Our goal was to provide an accurately curated and annotated Reference Sequence (RefSeq) data set of antizyme transcript and protein records across a broad taxonomic scope that would serve as standards for accurate representation of these gene products. As antizyme and antizyme inhibitor proteins are functionally connected, we also curated antizyme inhibitor genes to more fully represent the elegant biology of polyamine regulation. Manual review of genes for three members of the antizyme family and two members of the antizyme inhibitor family in 91 vertebrate organisms resulted in a total of 461 curated RefSeq records.
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Affiliation(s)
- Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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Stegehake D, Kurosinski MA, Schürmann S, Daniel J, Lüersen K, Liebau E. Polyamine-independent Expression of Caenorhabditis elegans Antizyme. J Biol Chem 2015; 290:18090-18101. [PMID: 26032421 DOI: 10.1074/jbc.m115.644385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 11/06/2022] Open
Abstract
Degradation of ornithine decarboxylase, the rate-limiting enzyme of polyamine biosynthesis, is promoted by the protein antizyme. Expression of antizyme is positively regulated by rising polyamine concentrations that induce a +1 translational frameshift required for production of the full-length protein. Antizyme itself is negatively regulated by the antizyme inhibitor. In our study, the regulation of Caenorhabditis elegans antizyme was investigated, and the antizyme inhibitor was identified. By applying a novel GFP-based method to monitor antizyme frameshifting in vivo, we show that the induction of translational frameshifting also occurs under stressful conditions. Interestingly, during starvation, the initiation of frameshifting was independent of polyamine concentrations. Because frameshifting was also prevalent in a polyamine auxotroph double mutant, a polyamine-independent regulation of antizyme frameshifting is suggested. Polyamine-independent induction of antizyme expression was found to be negatively regulated by the peptide transporter PEPT-1, as well as the target of rapamycin, but not by the daf-2 insulin signaling pathway. Stress-dependent expression of C. elegans antizyme occurred morely slowly than expression in response to increased polyamine levels, pointing to a more general reaction to unfavorable conditions and a diversion away from proliferation and reproduction toward conservation of energy. Interestingly, antizyme expression was found to drastically increase in aging individuals in a postreproductive manner. Although knockdown of antizyme did not affect the lifespan of C. elegans, knockdown of the antizyme inhibitor led to a significant reduction in lifespan. This is most likely caused by an increase in antizyme-mediated degradation of ornithine decarboxylase-1 and a resulting reduction in cellular polyamine levels.
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Affiliation(s)
- Dirk Stegehake
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany
| | - Marc-André Kurosinski
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany
| | - Sabine Schürmann
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany
| | - Jens Daniel
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany
| | - Kai Lüersen
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany
| | - Eva Liebau
- Department of Molecular Physiology, Institute for Animal Physiology, University of Muenster, 48143 Muenster, Germany.
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Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF. A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA. J Biol Chem 2015; 290:17863-17878. [PMID: 25998126 PMCID: PMC4505036 DOI: 10.1074/jbc.m115.647065] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 01/06/2023] Open
Abstract
The protein antizyme is a negative regulator of cellular polyamine concentrations from yeast to mammals. Synthesis of functional antizyme requires programmed +1 ribosomal frameshifting at the 3′ end of the first of two partially overlapping ORFs. The frameshift is the sensor and effector in an autoregulatory circuit. Except for Saccharomyces cerevisiae antizyme mRNA, the frameshift site alone only supports low levels of frameshifting. The high levels usually observed depend on the presence of cis-acting stimulatory elements located 5′ and 3′ of the frameshift site. Antizyme genes from different evolutionary branches have evolved different stimulatory elements. Prior and new multiple alignments of fungal antizyme mRNA sequences from the Agaricomycetes class of Basidiomycota show a distinct pattern of conservation 5′ of the frameshift site consistent with a function at the amino acid level. As shown here when tested in Schizosaccharomyces pombe and mammalian HEK293T cells, the 5′ part of this conserved sequence acts at the nascent peptide level to stimulate the frameshifting, without involving stalling detectable by toe-printing. However, the peptide is only part of the signal. The 3′ part of the stimulator functions largely independently and acts at least mostly at the nucleotide level. When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general. A conserved RNA secondary structure 3′ of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting.
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Affiliation(s)
- Martina M Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330.
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15
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Jia J, Delhon G, Tulman ER, Diel DG, Osorio FA, Wen X, Kutish GF, Rock DL. Novel gammaherpesvirus functions encoded by bovine herpesvirus 6 (bovine lymphotropic virus). J Gen Virol 2014; 95:1790-1798. [PMID: 24836671 DOI: 10.1099/vir.0.066951-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The genus Macavirus of the subfamily Gammaherpesvirinae includes viruses that infect lymphoid cells of domestic and wild ruminants and swine, causing asymptomatic latent infections in reservoir hosts. Here, we describe the genome of bovine herpesvirus 6 (BoHV-6), a macavirus ubiquitous in healthy cattle populations. The BoHV-6 genome exhibited architecture conserved in macaviruses, including a repetitive H-DNA region and unique 141 kbp L-DNA region predicted to encode 77 genes. BoHV-6 encoded, in variable genomic regions, a novel complement of genes relative to other characterized macaviruses, probably contributing to distinctive aspects of BoHV-6 infection biology and host range. Most notably, BoHV-6 encoded the first herpesviral protein (Bov2.b2) similar to cellular ornithine decarboxylase, an enzyme that catalyses the first and rate-limiting step in the biosynthesis of polyamines. Bov2.b2 conceivably mediates a novel mechanism by which BoHV-6 promotes cell-cycle-dependent viral replication.
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Affiliation(s)
- J Jia
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.,Laboratory of Animal Infectious Disease and Microarray/Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Animal Veterinary Medicine, Sichuan Agricultural University, Yaan, Sichuan 625014, PR China
| | - G Delhon
- School of Veterinary Medicine & Biomedical Sciences and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
| | - E R Tulman
- Department of Pathobiology and Veterinary Science and Center of Excellence for Vaccine Research, University of Connecticut, Storrs, CT, USA
| | - D G Diel
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - F A Osorio
- School of Veterinary Medicine & Biomedical Sciences and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
| | - X Wen
- Laboratory of Animal Infectious Disease and Microarray/Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Animal Veterinary Medicine, Sichuan Agricultural University, Yaan, Sichuan 625014, PR China
| | - G F Kutish
- Department of Pathobiology and Veterinary Science and Center of Excellence for Vaccine Research, University of Connecticut, Storrs, CT, USA
| | - D L Rock
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
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16
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Nguyen S, Jones DC, Wyllie S, Fairlamb AH, Phillips MA. Allosteric activation of trypanosomatid deoxyhypusine synthase by a catalytically dead paralog. J Biol Chem 2013; 288:15256-67. [PMID: 23525104 PMCID: PMC3663545 DOI: 10.1074/jbc.m113.461137] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Polyamine biosynthesis is a key drug target in African trypanosomes. The “resurrection drug” eflornithine (difluoromethylornithine), which is used clinically to treat human African trypanosomiasis, inhibits the first step in polyamine (spermidine) biosynthesis, a highly regulated pathway in most eukaryotic cells. Previously, we showed that activity of a key trypanosomatid spermidine biosynthetic enzyme, S-adenosylmethionine decarboxylase, is regulated by heterodimer formation with a catalytically dead paralog (a prozyme). Here, we describe an expansion of this prozyme paradigm to the enzyme deoxyhypusine synthase, which is required for spermidine-dependent hypusine modification of a lysine residue in the essential translation factor eIF5A. Trypanosoma brucei encodes two deoxyhypusine synthase paralogs, one that is catalytically functional but grossly impaired, and the other is inactive. Co-expression in Escherichia coli results in heterotetramer formation with a 3000-fold increase in enzyme activity. This functional complex is also present in T. brucei, and conditional knock-out studies indicate that both DHS genes are essential for in vitro growth and infectivity in mice. The recurrent evolution of paralogous, catalytically dead enzyme-based activating mechanisms may be a consequence of the unusual gene expression in the parasites, which lack transcriptional regulation. Our results suggest that this mechanism may be more widely used by trypanosomatids to control enzyme activity and ultimately influence pathogenesis than currently appreciated.
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Affiliation(s)
- Suong Nguyen
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9041, USA
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17
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Structural insight into DFMO resistant ornithine decarboxylase from Entamoeba histolytica: an inkling to adaptive evolution. PLoS One 2013; 8:e53397. [PMID: 23326423 PMCID: PMC3543441 DOI: 10.1371/journal.pone.0053397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Background Polyamine biosynthetic pathway is a validated therapeutic target for large number of infectious diseases including cancer, giardiasis and African sleeping sickness, etc. α-Difluoromethylornithine (DFMO), a potent drug used for the treatment of African sleeping sickness is an irreversible inhibitor of ornithine decarboxylase (ODC), the first rate limiting enzyme of polyamine biosynthesis. The enzyme ODC of E. histolytica (EhODC) has been reported to exhibit resistance towards DFMO. Methodology/Principal Finding The basis for insensitivity towards DFMO was investigated by structural analysis of EhODC and conformational modifications at the active site. Here, we report cloning, purification and crystal structure determination of C-terminal truncated Entamoeba histolytica ornithine decarboxylase (EhODCΔ15). Structure was determined by molecular replacement method and refined to 2.8 Å resolution. The orthorhombic crystal exhibits P212121 symmetry with unit cell parameters a = 76.66, b = 119.28, c = 179.28 Å. Functional as well as evolutionary relations of EhODC with other ODC homologs were predicted on the basis of sequence analysis, phylogeny and structure. Conclusions/Significance We determined the tetrameric crystal structure of EhODCΔ15, which exists as a dimer in solution. Insensitivity towards DFMO is due to substitution of key substrate binding residues in active site pocket. Additionally, a few more substitutions similar to antizyme inhibitor (AZI), a non-functional homologue of ODCs, were identified in the active site. Here, we establish the fact that EhODC sequence has conserved PLP binding residues; in contrast few substrate binding residues are mutated similar to AZI. Further sequence analysis and structural studies revealed that EhODC may represent as an evolutionary bridge between active decarboxylase and inactive AZI.
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Adrain C, Freeman M. New lives for old: evolution of pseudoenzyme function illustrated by iRhoms. Nat Rev Mol Cell Biol 2012; 13:489-98. [PMID: 22781900 DOI: 10.1038/nrm3392] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Large-scale sequencing of genomes has revealed that most enzyme families include inactive homologues. These pseudoenzymes are often well conserved, implying a selective pressure to retain them during evolution, and therefore that they have significant function. Mechanistic insights and evolutionary lessons are now emerging from the study of a broad range of such 'dead' enzymes. The recently discovered iRhoms - inactive homologues of rhomboid proteases - have joined derlins and other members of the rhomboid-like clan in regulating the fate of proteins as they pass through the secretory pathway. There is a strong case that dead enzymes, which have been rather overlooked, may be a rich source of biological regulators.
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Affiliation(s)
- Colin Adrain
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Paśko Ł, Ericson PGP, Elzanowski A. Phylogenetic utility and evolution of indels: a study in neognathous birds. Mol Phylogenet Evol 2011; 61:760-71. [PMID: 21843647 DOI: 10.1016/j.ympev.2011.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 07/28/2011] [Accepted: 07/30/2011] [Indexed: 11/25/2022]
Abstract
Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.
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Affiliation(s)
- Łukasz Paśko
- Institute of Zoology, University of Wrocław, 21 Sienkiewicz Street, PL-50-335 Wrocław, Poland
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