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Dermauw W, Van Leeuwen T, Feyereisen R. Diversity and evolution of the P450 family in arthropods. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 127:103490. [PMID: 33169702 DOI: 10.1016/j.ibmb.2020.103490] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 05/13/2023]
Abstract
The P450 family (CYP genes) of arthropods encodes diverse enzymes involved in the metabolism of foreign compounds and in essential endocrine or ecophysiological functions. The P450 sequences (CYPome) from 40 arthropod species were manually curated, including 31 complete CYPomes, and a maximum likelihood phylogeny of nearly 3000 sequences is presented. Arthropod CYPomes are assembled from members of six CYP clans of variable size, the CYP2, CYP3, CYP4 and mitochondrial clans, as well as the CYP20 and CYP16 clans that are not found in Neoptera. CYPome sizes vary from two dozen genes in some parasitic species to over 200 in species as diverse as collembolans or ticks. CYPomes are comprised of few CYP families with many genes and many CYP families with few genes, and this distribution is the result of dynamic birth and death processes. Lineage-specific expansions or blooms are found throughout the phylogeny and often result in genomic clusters that appear to form a reservoir of catalytic diversity maintained as heritable units. Among the many P450s with physiological functions, six CYP families are involved in ecdysteroid metabolism. However, five so-called Halloween genes are not universally represented and do not constitute the unique pathway of ecdysteroid biosynthesis. The diversity of arthropod CYPomes has only partially been uncovered to date and many P450s with physiological functions regulating the synthesis and degradation of endogenous signal molecules (including ecdysteroids) and semiochemicals (including pheromones and defense chemicals) remain to be discovered. Sequence diversity of arthropod P450s is extreme, and P450 sequences lacking the universally conserved Cys ligand to the heme have evolved several times. A better understanding of P450 evolution is needed to discern the relative contributions of stochastic processes and adaptive processes in shaping the size and diversity of CYPomes.
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Affiliation(s)
- Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871, Frederiksberg C, Copenhagen, Denmark.
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Disentangling the effects of selection and loss bias on gene dynamics. Proc Natl Acad Sci U S A 2017; 114:E5616-E5624. [PMID: 28652353 DOI: 10.1073/pnas.1704925114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.
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Wyroba E, Kwaśniak P, Miller K, Kobyłecki K, Osińska M. Site-directed mutagenesis, in vivo electroporation and mass spectrometry in search for determinants of the subcellular targeting of Rab7b paralogue in the model eukaryote Paramecium octaurelia. Eur J Histochem 2016; 60:2612. [PMID: 27349314 PMCID: PMC4933825 DOI: 10.4081/ejh.2016.2612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 11/25/2022] Open
Abstract
Protein products of paralogous genes resulting from whole genome duplication may acquire new functions. The role of post-translational modifications (PTM) in proper targeting of Paramecium Rab7b paralogue (distinct from that of Rab7a directly involved in phagocytosis) was studied using point mutagenesis, proteomic analysis and double immunofluorescence after in vivo electroporation of the mutagenized protein. Here we show that substitution of Thr200 by Ala diminished the incorporation of [P32] by 37% and of [C14-]UDP-glucose by 24% into recombinant Rab7b_200 in comparison to the non-mutagenized control. Double confocal imaging revealed that Rab7b_200 was mistargeted upon electroporation into living cells in contrast to non-mutagenized recombinant Rab7b correctly incorporated in the cytostome area. Using nano LC-MS/MS to compare the peptide map of Rab7b with that after deglycosylation with a mixture of five enzymes of different specificity we identified a peptide ion at m/z=677.63+ representing a glycan group attached to Thr200. Based on its mass and quantitative assays with [P32] and [C14]UDP-glucose, the suggested composition of the adduct attached to Thr200 is (Hex)1(HexNAc)1(Phos)3 or (HexNAc)1 (Deoxyhexose)1 (Phos)1 (HexA)1. These data indicate that PTM of Thr200 located in the hypervariable C-region of Paramecium octaurelia Rab7b is crucial for the proper localization/function of this protein. Moreover, the two Rab7 paralogues differ also in another PTM: substantially more phosphorylated amino acid residues are in Rab7b than in Rab7a.
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Affiliation(s)
- E Wyroba
- Nencki Institute of Experimental Biology of Polish Academy of Sciences.
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Sunil M, Hariharan AK, Nayak S, Gupta S, Nambisan SR, Gupta RP, Panda B, Choudhary B, Srinivasan S. The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. DNA Res 2014; 21:585-602. [PMID: 25071079 PMCID: PMC4263292 DOI: 10.1093/dnares/dsu021] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.
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Affiliation(s)
- Meeta Sunil
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Arun K Hariharan
- GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Soumya Nayak
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Saurabh Gupta
- GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Suran R Nambisan
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Ravi P Gupta
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Binay Panda
- GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
| | - Subhashini Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India
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Wong KC, Zhang Z. SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. ACTA ACUST UNITED AC 2014; 30:1112-1119. [PMID: 24389653 DOI: 10.1093/bioinformatics/btt769] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/13/2013] [Indexed: 11/12/2022]
Abstract
MOTIVATION The recent advances in genome sequencing have revealed an abundance of non-synonymous polymorphisms among human individuals; subsequently, it is of immense interest and importance to predict whether such substitutions are functional neutral or have deleterious effects. The accuracy of such prediction algorithms depends on the quality of the multiple-sequence alignment, which is used to infer how an amino acid substitution is tolerated at a given position. Because of the scarcity of orthologous protein sequences in the past, the existing prediction algorithms all include sequences of protein paralogs in the alignment, which can dilute the conservation signal and affect prediction accuracy. However, we believe that, with the sequencing of a large number of mammalian genomes, it is now feasible to include only protein orthologs in the alignment and improve the prediction performance. RESULTS We have developed a novel prediction algorithm, named SNPdryad, which only includes protein orthologs in building a multiple sequence alignment. Among many other innovations, SNPdryad uses different conservation scoring schemes and uses Random Forest as a classifier. We have tested SNPdryad on several datasets. We found that SNPdryad consistently outperformed other methods in several performance metrics, which is attributed to the exclusion of paralogous sequence. We have run SNPdryad on the complete human proteome, generating prediction scores for all the possible amino acid substitutions. AVAILABILITY AND IMPLEMENTATION The algorithm and the prediction results can be accessed from the Web site: http://snps.ccbr.utoronto.ca:8080/SNPdryad/ CONTACT: Zhaolei.Zhang@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ka-Chun Wong
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3G4 The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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Axelsen JB, Bernhardsson S, Sneppen K. One hub-one process: a tool based view on regulatory network topology. BMC SYSTEMS BIOLOGY 2008; 2:25. [PMID: 18318890 PMCID: PMC2292138 DOI: 10.1186/1752-0509-2-25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 03/04/2008] [Indexed: 11/25/2022]
Abstract
Background The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. Results To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We find that the topology of the regulatory network only show weak remnants of its history of network reorganizations, but strong features of co-regulated proteins associated to similar tasks. These functional correlations decreases strongly when one consider proteins separated by more than two steps in the regulatory network. The network topology primarily reflects the processes that is orchestrated by each individual hub, whereas there is nearly no remnants of the history of protein duplications. Conclusion Our results suggests that local topological features of regulatory networks, including broad degree distributions, emerge as an implicit result of matching a number of needed processes to a finite toolbox of proteins.
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Affiliation(s)
- Jacob Bock Axelsen
- Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial, Ctra de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain.
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