1
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Bastolla U, Abia D, Piette O. PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score. Bioinformatics 2023; 39:btad630. [PMID: 37847775 PMCID: PMC10628387 DOI: 10.1093/bioinformatics/btad630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/01/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023] Open
Abstract
MOTIVATION Evolutionary inference depends crucially on the quality of multiple sequence alignments (MSA), which is problematic for distantly related proteins. Since protein structure is more conserved than sequence, it seems natural to use structure alignments for distant homologs. However, structure alignments may not be suitable for inferring evolutionary relationships. RESULTS Here we examined four protein similarity measures that depend on sequence and structure (fraction of aligned residues, sequence identity, fraction of superimposed residues, and contact overlap), finding that they are intimately correlated but none of them provides a complete and unbiased picture of conservation in proteins. Therefore, we propose the new hybrid protein sequence and structure similarity score PC_sim based on their main principal component. The corresponding divergence measure PC_div shows the strongest correlation with divergences obtained from individual similarities, suggesting that it infers accurate evolutionary divergences. We developed the program PC_ali that constructs protein MSAs either de novo or modifying an input MSA, using a similarity matrix based on PC_sim. The program constructs a starting MSA based on the maximal cliques of the graph of these PAs and it refines it through progressive alignments along the tree reconstructed with PC_div. Compared with eight state-of-the-art multiple structure or sequence alignment tools, PC_ali achieves higher or equal aligned fraction and structural scores, sequence identity higher than structure aligners although lower than sequence aligners, highest score PC_sim, and highest similarity with the MSAs produced by other tools and with the reference MSA Balibase. AVAILABILITY AND IMPLEMENTATION https://github.com/ugobas/PC_ali.
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Affiliation(s)
- Ugo Bastolla
- Centro de Biologia Molecular “Severo Ochoa” (CBMSO), CSIC-UAM Cantoblanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility CBMSO, CSIC-UAM Cantoblanco, 28049 Madrid, Spain
| | - Oscar Piette
- Centro de Biologia Molecular “Severo Ochoa” (CBMSO), CSIC-UAM Cantoblanco, 28049 Madrid, Spain
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2
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Duong HTT, Suzuki H, Katagiri S, Shibata M, Arai M, Yura K. Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin. Biophys Physicobiol 2022; 19:e190025. [PMID: 36160324 PMCID: PMC9465404 DOI: 10.2142/biophysico.bppb-v19.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Sequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.
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Affiliation(s)
- Ha T. T. Duong
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Hirofumi Suzuki
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Saki Katagiri
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Mayu Shibata
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Misae Arai
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
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3
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Ogawa S, Shimidzu H, Fukuda K, Tsunekawa N, Hirano T, Sato F, Yura K, Hasunuma T, Ochi K, Yamamoto M, Sakamoto W, Hashimoto K, Ogata H, Kanao T, Nemoto M, Inagaki K, Tamura T. Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory. Biosci Biotechnol Biochem 2021; 85:1275-1282. [PMID: 33710298 DOI: 10.1093/bbb/zbab011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022]
Abstract
Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, antiprotozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic-net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y, made moderate or even negative effects. To identify why the rif cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The 4 residues were located near the mRNA strand. Density functional theory-based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.
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Affiliation(s)
- Saori Ogawa
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hitomi Shimidzu
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koji Fukuda
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Naoki Tsunekawa
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Toshiyuki Hirano
- Institute of Industrial Science, The University of Tokyo, Komaba, Japan
| | - Fumitoshi Sato
- Institute of Industrial Science, The University of Tokyo, Komaba, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kozo Ochi
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Michio Yamamoto
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,RIKEN AIP, Tokyo, Japan
| | - Wataru Sakamoto
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro Hashimoto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Tadayoshi Kanao
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Michiko Nemoto
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kenji Inagaki
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Takashi Tamura
- The Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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4
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Yoshida MA, Imoto J, Kawai Y, Funahashi S, Minei R, Akizuki Y, Ogura A, Nakabayashi K, Yura K, Ikeo K. Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:760-771. [PMID: 33098466 PMCID: PMC7708342 DOI: 10.1007/s10126-020-10001-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/28/2020] [Indexed: 05/26/2023]
Abstract
Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.
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Affiliation(s)
- Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Sciences, Shimane University, Oki, Japan.
| | - Junichi Imoto
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Fisheries Data Sciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuri Kawai
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Satomi Funahashi
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Ryuhei Minei
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Yuki Akizuki
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Atsushi Ogura
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan.
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
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5
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Makigaki S, Ishida T. Sequence alignment using machine learning for accurate template-based protein structure prediction. Bioinformatics 2020; 36:104-111. [PMID: 31197318 DOI: 10.1093/bioinformatics/btz483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Template-based modeling, the process of predicting the tertiary structure of a protein by using homologous protein structures, is useful if good templates can be found. Although modern homology detection methods can find remote homologs with high sensitivity, the accuracy of template-based models generated from homology-detection-based alignments is often lower than that from ideal alignments. RESULTS In this study, we propose a new method that generates pairwise sequence alignments for more accurate template-based modeling. The proposed method trains a machine learning model using the structural alignment of known homologs. It is difficult to directly predict sequence alignments using machine learning. Thus, when calculating sequence alignments, instead of a fixed substitution matrix, this method dynamically predicts a substitution score from the trained model. We evaluate our method by carefully splitting the training and test datasets and comparing the predicted structure's accuracy with that of state-of-the-art methods. Our method generates more accurate tertiary structure models than those produced from alignments obtained by other methods. AVAILABILITY AND IMPLEMENTATION https://github.com/shuichiro-makigaki/exmachina. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shuichiro Makigaki
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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6
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Garlid AO, Schaffer CT, Kim J, Bhatt H, Guevara-Gonzalez V, Ping P. TAZ encodes tafazzin, a transacylase essential for cardiolipin formation and central to the etiology of Barth syndrome. Gene 2019; 726:144148. [PMID: 31647997 DOI: 10.1016/j.gene.2019.144148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/12/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022]
Abstract
Tafazzin, which is encoded by the TAZ gene, catalyzes transacylation to form mature cardiolipin and shows preference for the transfer of a linoleic acid (LA) group from phosphatidylcholine (PC) to monolysocardiolipin (MLCL) with influence from mitochondrial membrane curvature. The protein contains domains and motifs involved in targeting, anchoring, and an active site for transacylase activity. Tafazzin activity affects many aspects of mitochondrial structure and function, including that of the electron transport chain, fission-fusion, as well as apoptotic signaling. TAZ mutations are implicated in Barth syndrome, an underdiagnosed and devastating disease that primarily affects male pediatric patients with a broad spectrum of disease pathologies that impact the cardiovascular, neuromuscular, metabolic, and hematologic systems.
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Affiliation(s)
- Anders O Garlid
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Physiology, University of California at Los Angeles, CA 90095, USA.
| | - Calvin T Schaffer
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Physiology, University of California at Los Angeles, CA 90095, USA
| | - Jaewoo Kim
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Physiology, University of California at Los Angeles, CA 90095, USA
| | - Hirsh Bhatt
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Physiology, University of California at Los Angeles, CA 90095, USA
| | - Vladimir Guevara-Gonzalez
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Mathematics, University of California at Los Angeles, CA 90095, USA
| | - Peipei Ping
- Cardiovascular Data Science Training Program at UCLA, University of California at Los Angeles, CA 90095, USA; Department of Physiology, University of California at Los Angeles, CA 90095, USA; Department of Medicine/Cardiology, University of California at Los Angeles, CA 90095, USA; Department of Bioinformatics, University of California at Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi), University of California at Los Angeles, CA 90095, USA.
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7
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Hosoda E, Hiraoka D, Hirohashi N, Omi S, Kishimoto T, Chiba K. SGK regulates pH increase and cyclin B-Cdk1 activation to resume meiosis in starfish ovarian oocytes. J Cell Biol 2019; 218:3612-3629. [PMID: 31537709 PMCID: PMC6829648 DOI: 10.1083/jcb.201812133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/19/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
Tight regulation of intracellular pH (pHi) is essential for biological processes. Fully grown oocytes, having a large nucleus called the germinal vesicle, arrest at meiotic prophase I. Upon hormonal stimulus, oocytes resume meiosis to become fertilizable. At this time, the pHi increases via Na+/H+ exchanger activity, although the regulation and function of this change remain obscure. Here, we show that in starfish oocytes, serum- and glucocorticoid-regulated kinase (SGK) is activated via PI3K/TORC2/PDK1 signaling after hormonal stimulus and that SGK is required for this pHi increase and cyclin B-Cdk1 activation. When we clamped the pHi at 6.7, corresponding to the pHi of unstimulated ovarian oocytes, hormonal stimulation induced cyclin B-Cdk1 activation; thereafter, oocytes failed in actin-dependent chromosome transport and spindle assembly after germinal vesicle breakdown. Thus, this SGK-dependent pHi increase is likely a prerequisite for these events in ovarian oocytes. We propose a model that SGK drives meiotic resumption via concomitant regulation of the pHi and cell cycle machinery.
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Affiliation(s)
- Enako Hosoda
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Daisaku Hiraoka
- Science and Education Center, Ochanomizu University, Tokyo, Japan
| | | | - Saki Omi
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takeo Kishimoto
- Science and Education Center, Ochanomizu University, Tokyo, Japan
| | - Kazuyoshi Chiba
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
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8
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Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na+-Driven Flagella. Structure 2017; 25:1540-1548.e3. [DOI: 10.1016/j.str.2017.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/15/2017] [Accepted: 08/15/2017] [Indexed: 01/24/2023]
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9
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Kawasaki Y, Oda H, Ito J, Niwa A, Tanaka T, Hijikata A, Seki R, Nagahashi A, Osawa M, Asaka I, Watanabe A, Nishimata S, Shirai T, Kawashima H, Ohara O, Nakahata T, Nishikomori R, Heike T, Saito MK. Identification of a High-Frequency Somatic NLRC4 Mutation as a Cause of Autoinflammation by Pluripotent Cell-Based Phenotype Dissection. Arthritis Rheumatol 2017; 69:447-459. [PMID: 27788288 DOI: 10.1002/art.39960] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/13/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To elucidate the genetic background of a patient with neonatal-onset multisystem inflammatory disease (NOMID) with no NLRP3 mutation. METHODS A Japanese male child diagnosed as having NOMID was studied. The patient did not have any NLRP3 mutation, even as low-frequency mosaicism. We performed whole-exome sequencing on the patient and his parents. Induced pluripotent stem cells (iPSCs) were established from the patient's fibroblasts. The iPSCs were then differentiated into monocyte lineage to evaluate the cytokine profile. RESULTS We established multiple iPSC clones from a patient with NOMID and incidentally found that the phenotypes of monocytes from iPSC clones were heterogeneous and could be grouped into disease and normal phenotypes. Because each iPSC clone was derived from a single somatic cell, we hypothesized that the patient had somatic mosaicism of an interleukin-1β-related gene. Whole-exome sequencing of both representative iPSC clones and the patient's blood revealed a novel heterozygous NLRC4 mutation, p.T177A (c.529A>G), as a specific mutation in diseased iPSC clones. Knockout of the NLRC4 gene using the clustered regularly interspaced short palindromic repeat/Cas9 system in a mutant iPSC clone abrogated the pathogenic phenotype. CONCLUSION Our findings indicate that the patient has somatic mosaicism of a novel NLRC4 mutation. To our knowledge, this is the first case showing that somatic mutation of NLRC4 causes autoinflammatory symptoms compatible with NOMID. The present study demonstrates the significance of prospective genetic screening combined with iPSC-based phenotype dissection for individualized diagnoses.
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Affiliation(s)
| | - Hirotsugu Oda
- Kyoto University, Kyoto, Japan, and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Ito
- Kyoto University, Kyoto, Japan
| | | | | | - Atsushi Hijikata
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Ryosuke Seki
- Kyoto University and Nippon Shinyaku Company, Ltd., Kyoto, Japan
| | | | | | | | | | | | - Tsuyoshi Shirai
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | | | - Osamu Ohara
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan, and Kazusa DNA Research Institute, Kisarazu, Japan
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10
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Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol 2017; 13:858-866. [PMID: 28581482 DOI: 10.1038/nchembio.2397] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.
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Affiliation(s)
- Karine Bastard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Alain Perret
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Aline Mariage
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Thomas Bessonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Agnès Pinet-Turpault
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Pascal Bazire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Carine Vergne-Vaxelaire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Clémence Brewee
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Adrien Debard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Virginie Pellouin
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marielle Besnard-Gonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | | | - Claudine Médigue
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - David Vallenet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition (ICAN), Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Anne Zaparucha
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean Weissenbach
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marcel Salanoubat
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
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11
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Liou YF, Huang HL, Ho SY. A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area. BMC Bioinformatics 2016; 17:503. [PMID: 28155647 PMCID: PMC5259910 DOI: 10.1186/s12859-016-1368-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences. Methods The proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs. Results The RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones as prediction features. A hydrophobic spine composed of exposed hydrophobic residues of an α-helix was discovered by analyzing the PCPs of RSA predictors corresponding to hydrophobic residues. For example, the results of a molecular dynamics simulation of wild-type sequences and their mutants showed that proteins 1MOF and 2WRP_H16I (Protein Data Bank IDs), which have a perfectly hydrophobic spine, have more stable structures than 1MOF_I54D and 2WRP do (which do not have a perfectly hydrophobic spine). Conclusions We identified informative PCPs to design high-performance RSA predictors and to analyze these PCPs for identification of novel protein folding characteristics. A hydrophobic spine in a protein can help to stabilize exposed α-helices. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1368-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Fan Liou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hui-Ling Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
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Yamashita S, Hata A, Usui T, Oda H, Hijikata A, Shirai T, Kaneko N, Hata D. Novel AVPR2 mutation causing partial nephrogenic diabetes insipidus in a Japanese family. J Pediatr Endocrinol Metab 2016; 29:591-6. [PMID: 26974133 DOI: 10.1515/jpem-2015-0323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 12/30/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND X-linked recessive congenital nephrogenic diabetes insipidus (NDI) is caused by mutations of the arginine vasopressin type 2 receptor gene (AVPR2). More than 200 mutations of the AVPR2 gene with complete NDI have been reported although only 15 mutations with partial NDI has been reported to date. METHODS We herein report a Japanese kindred with partial NDI. The proband is an 8-year-old boy who was referred to our hospital for nocturnal enuresis. Water deprivation test and hypertonic saline test suggested partial renal antidiuretic hormone arginine vasopressin (AVP) resistance. RESULTS Analysis of genomic DNA revealed a novel missense mutation (p.L161P) in the patient. The patient's mother was heterozygous for the mutation. Three-dimensional (3-D) modeling study showed that L161P possibly destabilizes the transmembrane domain of the V2 receptor, resulting in its misfolding or mislocalization. CONCLUSIONS Distinguishing partial NDI from nocturnal enuresis is important. A clinical clue for diagnosis of partial NDI is an incompatibly high level of AVP despite normal serum osmolality.
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Tamura T, Tsunekawa N, Nemoto M, Inagaki K, Hirano T, Sato F. Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico. Sci Rep 2016; 6:19742. [PMID: 26818780 PMCID: PMC4730141 DOI: 10.1038/srep19742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022] Open
Abstract
Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni–Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions.
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Affiliation(s)
- Takashi Tamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.,Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan.,PRESTO, Japan Science and Technology Agency, Japan
| | - Naoki Tsunekawa
- Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan
| | - Michiko Nemoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenji Inagaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Toshiyuki Hirano
- Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan
| | - Fumitoshi Sato
- Institute of Industrial Science, the University of Tokyo, Komaba 153-8505, Japan
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14
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Aoto S, Yura K. Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins. Biophys Physicobiol 2015; 12:103-16. [PMID: 27493859 PMCID: PMC4736837 DOI: 10.2142/biophysico.12.0_103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/09/2015] [Indexed: 12/31/2022] Open
Abstract
We addressed the evolutionary trace of hetero-oligomer interfaces by comparing the structures of paralogous proteins; one of them is a monomer or homo-oligomer and the other is a hetero-oligomer. We found different trends in amino acid conservation pattern and hydrophobicity between homo-oligomer and hetero-oligomer. The degree of amino acid conservation in the interface of homo-oligomer has no obvious difference from that in the surface, whereas the degree of conservation is much higher in the interface of hetero-oligomer. The interface of homo-oligomer has a few very conserved residue positions, whereas the residue conservation in the interface of hetero-oligomer tends to be higher. In addition, the interface of hetero-oligomer has a tendency of being more hydrophobic compared with the one in homo-oligomer. We conjecture that these differences are related to the inherent symmetry in homo-oligomers that cannot exist in hetero-oligomers. Paucity of the structural data precludes statistical tests of these tendencies, yet the trend can be applied to the prediction of the interface of hetero-oligomer. We obtained putative interfaces of the subunits in CPSF (cleavage and polyadenylation specificity factor), one of the human pre-mRNA 3′-processing complexes. The locations of predicted interface residues were consistent with the known experimental data.
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Affiliation(s)
- Saki Aoto
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo 112-8610, Japan; Centre for Informational Biology, Ochanomizu University, Bunkyo, Tokyo 112-8610, Japan; National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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15
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Hijikata A, Yura K, Ohara O, Go M. Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain. Meta Gene 2015; 4:92-106. [PMID: 25941633 PMCID: PMC4412953 DOI: 10.1016/j.mgene.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/03/2015] [Indexed: 10/26/2022] Open
Abstract
Tafazzin is a mitochondrial phospholipid transacylase, and its mutations cause Barth syndrome (BTHS). Human tafazzin gene produces four distinct alternatively spliced transcripts. To understand the molecular mechanisms of tafazzin deficiency, we performed an atomic resolution analysis of the influence of the BTHS mutations and of alternative splicing on the structure and function of tafazzin. From the three-dimensional (3D) homology modeling of tafazzin, we identified candidate amino acid residues that contribute to cardiolipin binding and to mitochondrial membrane associations that facilitate acyl-transfer reactions. Primate specific exon 5, which is alternatively spliced, is predicted to correspond to an intrinsically unstructured region in the protein. We proposed that this region should change the substrate-binding affinity and/or contribute to primate-specific molecular interactions. Exon 7, another alternatively spliced exon, encodes a region forming a part of the putative substrate-binding cleft, suggesting that the gene products lacking exon 7 will lose their substrate-binding ability. We demonstrate a clear localization of the BTHS mutations at residues responsible for membrane association, substrate binding, and the conformational stability of tafazzin. These findings provide new insights into the function of defective tafazzin and the pathogenesis of BTHS at the level of protein 3D structure and the evolution of alternatively spliced exons in primates.
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Affiliation(s)
- Atsushi Hijikata
- Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ; Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mitiko Go
- Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan ; Research Organization of Information and Systems, 4-3-13, Toranomon, Minatoku, Tokyo 105-0001, Japan
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16
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Kamijyo A, Yura K, Ogura A. Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure. Gene 2014; 555:73-9. [PMID: 25300250 DOI: 10.1016/j.gene.2014.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/16/2014] [Accepted: 10/02/2014] [Indexed: 12/30/2022]
Abstract
Eye-field transcription factors (EFTFs) are a set of genes that compose a regulatory network for eye development in animals, which are highly conserved among various animal phyla. To investigate the processes of conservation and diversification of the transcription factors for eye development, we examined the structural changes in the EFTF proteins by estimating the ancestral sequences with the available genome information. Among the different types of EFTFs, we selected otx2, tbx3, rx1, pax6, six3/6, lhx2 and nr2e1 because they are highly conserved in bilaterian animals. We searched the genome sequences of representative animal phyla for EFTF protein sequences. With deduced ancestral sequences and three-dimensional structures of EFTFs, we traced the evolutionary changes in amino acid residues and found that the DNA-binding domains were always more conserved than other regions, and that the other regions showed distinct evolutionary rates. The EFTF rx1, which resides at the pivotal part of the EFTF network, had a faster evolutionary rate than the others. These results indicated that the evolutionary rates of each protein in the EFTF network, which were expected to be consistent with each other to maintain the interactions in the network, were not constant among or within the factors, but rather, varied to a significant extent.
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Affiliation(s)
- Ai Kamijyo
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Ogura
- Department of Computer Bio-Science, Nagahama Institute of BioScience and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan.
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17
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Takasawa K, Ono M, Hijikata A, Matsubara Y, Katsumata N, Takagi M, Morio T, Ohara O, Kashimada K, Mizutani S. Two novel HSD3B2 missense mutations with diverse residual enzymatic activities for Δ5-steroids. Clin Endocrinol (Oxf) 2014; 80:782-9. [PMID: 24372086 DOI: 10.1111/cen.12394] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/22/2013] [Accepted: 12/17/2013] [Indexed: 02/03/2023]
Abstract
CONTEXT Classical 3β-hydroxysteroid dehydrogenase (3β-HSD) deficiency (3β-HSDD) is caused by loss-of-function mutations in the HSD3B2 gene encoding type II 3β-HSD, which has a key role in steroid biosynthesis, converting Δ5-steroids to Δ4-steroids in adrenal glands and gonads. PATIENT A patient (46, XX) was found to have elevated 17-hydroxyprogesterone (17-OHP) [203 nmol/l (normal range: 2·94 ± 0·9 nmol/l)] by newborn screening. Endocrinological examination revealed dramatically increased Δ5-steroids [e.g. 17-OH pregnenolone: 910 nmol/l (normal range: 12·6 ± 10·5 nmol/l)]. The patient had virilization of external genitalia with labial fusion, suggesting classical 3β-HSDD. METHODS AND RESULTS Consistent with the endocrinological data, the patient was a compound heterozygote for two novel missense mutations (p.Y190C and p.S218P) that were identified in HSD3B2. Both Y190 and S218 are conserved among mammals. The mutant proteins had severely impaired residual enzymatic activity in vitro, although both mutants retained higher activity for 17-OH pregnenolone than for the other Δ5-steroids. In a three-dimensional model of the enzyme based on the known structures of similar proteins, both mutations were located extremely close to the predicted substrate-binding pocket. This suggests that the mutations can cause a local conformational change in the substrate-binding pocket, leading to alterations of the binding affinities for Δ5-steroids. CONCLUSIONS We identified two novel missense mutations of HSD3B2 that resulted in unbalanced residual enzymatic activities for Δ5-steroids. As a potential novel mechanism, we propose that the mutations, which differently affect the activity towards different substrates, the effects of these mutations provide novel insights into the pathophysiology of 3β-HSDD.
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Affiliation(s)
- Kei Takasawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
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Sakuma M, Imada K, Okumura Y, Uchiya KI, Yamashita N, Ogawa K, Hijikata A, Shirai T, Homma M, Nikai T. X-ray structure analysis and characterization of AFUEI, an elastase inhibitor from Aspergillus fumigatus. J Biol Chem 2013; 288:17451-9. [PMID: 23640894 DOI: 10.1074/jbc.m112.433987] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elastase from Aspergillus sp. is an important factor for aspergillosis. AFUEI is an inhibitor of the elastase derived from Aspergillus fumigatus. AFUEI is a member of the I78 inhibitor family and has a high inhibitory activity against elastases of Aspergillus fumigatus and Aspergillus flavus, human neutrophil elastase and bovine chymotrypsin, but does not inhibit bovine trypsin. Here we report the crystal structure of AFUEI in two crystal forms. AFUEI is a wedge-shaped protein composed of an extended loop and a scaffold protein core. The structure of AFUEI shows remarkable similarity to serine protease inhibitors of the potato inhibitor I family, although they are classified into different inhibitor families. A structural comparison with the potato I family inhibitors suggests that the extended loop of AFUEI corresponds to the binding loop of the potato inhibitor I family, and AFUEI inhibits its cognate proteases through the same mechanism as the potato I family inhibitors.
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Affiliation(s)
- Mayuko Sakuma
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya 464-8602, Japan
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Takai T, Higaki K, Aguilar-Moncayo M, Mena-Barragán T, Hirano Y, Yura K, Yu L, Ninomiya H, García-Moreno MI, Sakakibara Y, Ohno K, Nanba E, Ortiz Mellet C, García Fernández JM, Suzuki Y. A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis. Mol Ther 2013; 21:526-32. [PMID: 23337983 DOI: 10.1038/mt.2012.263] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Lysosomal β-galactosidase (β-Gal) deficiency causes a group of disorders that include neuronopathic GM1 gangliosidosis and non-neuronopathic Morquio B disease. We have previously proposed the use of small molecule ligands of β-Gal as pharmacological chaperones (PCs) for the treatment of GM1 gangliosidosis brain pathology. Although it is still under development, PC therapy has yielded promising preclinical results in several lysosomal diseases. In this study, we evaluated the effect of bicyclic 1-deoxygalactonojirimycin (DGJ) derivative of the sp(2)-iminosugar type, namely 5N,6S-(N'-butyliminomethylidene)-6-thio-1- deoxygalactonojirimycin (6S-NBI-DGJ), as a novel PC for human mutant β-Gal. In vitro, 6S-NBI-DGJ had the ability to inhibit the activity of human β-Gal in a competitive manner and was able to protect this enzyme from heat-induced degradation. Computational analysis supported that the rigid glycone bicyclic core of 6S-NBI-DGJ binds to the active site of the enzyme, with the aglycone N'-butyl substituent, in a precise E-orientation, located at a hydrophobic region nearby. Chaperone potential profiling indicated significant increases of enzyme activity in 24 of 88 β-Gal mutants, including four common mutations. Finally, oral administration of 6S-NBI-DGJ ameliorated the brain pathology of GM1 gangliosidosis model mice. These results suggest that 6S-NBI-DGJ is a novel PC that may be effective on a broad range of β-Gal mutants.
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Suzuki S, Yanai H, Kanagawa M, Tamura S, Watanabe Y, Fuse K, Baba S, Sampei GI, Kawai G. Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 68:14-9. [PMID: 22232163 DOI: 10.1107/s1744309111048184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 11/14/2011] [Indexed: 11/10/2022]
Abstract
The crystal structure of PurL from Thermus thermophilus HB8 (TtPurL; TTHA1519) was determined in complex with an adenine nucleotide, PO(4)(3-) and Mg(2+) at 2.35 Å resolution. TtPurL consists of 29 α-helices and 28 β-strands, and one loop is disordered. TtPurL consists of four domains, A1, A2, B1 and B2, and the structures of the A1-B1 and A2-B2 domains were almost identical to each other. Although the sequence identity between TtPurL and PurL from Thermotoga maritima (TmPurL) is higher than that between TtPurL and the PurL domain of the large PurL from Salmonella typhimurium (StPurL), the secondary structure of TtPurL is much more similar to that of StPurL than to that of TmPurL.
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Affiliation(s)
- Sakiko Suzuki
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
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Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus. J Bacteriol 2011; 194:607-16. [PMID: 22101842 DOI: 10.1128/jb.06173-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carbon catabolite repression (CCR) is a widespread phenomenon in many bacteria that is defined as the repression of catabolic enzyme activities for an unfavorable carbon source by the presence of a preferable carbon source. In Streptomyces, secondary metabolite production often is negatively affected by the carbon source, indicating the involvement of CCR in secondary metabolism. Although the CCR mechanism in Streptomyces still is unclear, glucokinase is presumably a central player in CCR. SgGlkA, a glucokinase from S. griseus, belongs to the ROK family glucokinases, which have two consensus sequence motifs (1 and 2). Here, we report the crystal structures of apo-SgGlkA, SgGlkA in complex with glucose, and SgGlkA in complex with glucose and adenylyl imidodiphosphate (AMPPNP), which are the first structures of an ROK family glucokinase. SgGlkA is divided into a small α/β domain and a large α+β domain, and it forms a dimer-of-dimer tetrameric configuration. SgGlkA binds a β-anomer of glucose between the two domains, and His157 in consensus sequence 1 plays an important role in the glucose-binding mechanism and anomer specificity of SgGlkA. In the structures of SgGlkA, His157 forms an HC3-type zinc finger motif with three cysteine residues in consensus sequence 2 to bind a zinc ion, and it forms two hydrogen bonds with the C1 and C2 hydroxyls of glucose. When the three structures are compared, the structure of SgGlkA is found to be modified by the binding of substrates. The substrate-dependent conformational changes of SgGlkA may be related to the CCR mechanism in Streptomyces.
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