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He M, Wang J, Fan X, Liu X, Shi W, Huang N, Zhao F, Miao M. Genetic basis for the establishment of endosymbiosis in Paramecium. ISME JOURNAL 2019; 13:1360-1369. [PMID: 30647459 PMCID: PMC6474222 DOI: 10.1038/s41396-018-0341-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/28/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023]
Abstract
The single-celled ciliate Paramecium bursaria is an indispensable model for investigating endosymbiosis between protists and green-algal symbionts. To elucidate the mechanism of this type of endosymbiosis, we combined PacBio and Illumina sequencing to assemble a high-quality and near-complete macronuclear genome of P. bursaria. The genomic characteristics and phylogenetic analyses indicate that P. bursaria is the basal clade of the Paramecium genus. Through comparative genomic analyses with its close relatives, we found that P. bursaria encodes more genes related to nitrogen metabolism and mineral absorption, but encodes fewer genes involved in oxygen binding and N-glycan biosynthesis. A comparison of the transcriptomic profiles between P. bursaria with and without endosymbiotic Chlorella showed differential expression of a wide range of metabolic genes. We selected 32 most differentially expressed genes to perform RNA interference experiment in P. bursaria, and found that P. bursaria can regulate the abundance of their symbionts through glutamine supply. This study provides novel insights into Paramecium evolution and will extend our knowledge of the molecular mechanism for the induction of endosymbiosis between P. bursaria and green algae.
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Affiliation(s)
- Ming He
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xiaohui Liu
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenyu Shi
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Huang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Chan KHK, Chacko SA, Song Y, Cho M, Eaton CB, Wu WCH, Liu S. Genetic variations in magnesium-related ion channels may affect diabetes risk among African American and Hispanic American women. J Nutr 2015; 145:418-24. [PMID: 25733456 PMCID: PMC4336527 DOI: 10.3945/jn.114.203489] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Prospective studies consistently link low magnesium intake to higher type 2 diabetes (T2D) risk. OBJECTIVE We examined the association of common genetic variants [single nucleotide polymorphisms (SNPs)] in genes related to magnesium homeostasis with T2D risk and potential interactions with magnesium intake. METHODS Using the Women's Health Initiative-SNP Health Association Resource (WHI-SHARe) study, we identified 17 magnesium-related ion channel genes (583 SNPs) and examined their associations with T2D risk in 7287 African-American (AA; n = 1949 T2D cases) and 3285 Hispanic-American (HA; n = 611 T2D cases) postmenopausal women. We performed both single- and multiple-locus haplotype analyses. RESULTS Among AA women, carriers of each additional copy of SNP rs6584273 in cyclin mediator 1 (CNNM1) had 16% lower T2D risk [OR: 0.84; false discovery rate (FDR)-adjusted P = 0.02]. Among HA women, several variants were significantly associated with T2D risk, including rs10861279 in solute carrier family 41 (anion exchanger), member 2 (SLC41A2) (OR: 0.54; FDR-adjusted P = 0.04), rs7174119 in nonimprinted in Prader-Willi/Angelman syndrome 1 (NIPA1) (OR: 1.27; FDR-adjusted P = 0.04), and 2 SNPs in mitochondrial RNA splicing 2 (MRS2) (rs7738943: OR = 1.55, FDR-adjusted P = 0.01; rs1056285: OR = 1.48, FDR-adjusted P = 0.02). Even with the most conservative Bonferroni adjustment, two 2-SNP-haplotypes in SLC41A2 and MRS2 region were significantly associated with T2D risk (rs12582312-rs10861279: P = 0.0006; rs1056285-rs7738943: P = 0.002). Among women with magnesium intake in the lowest 30% (AA: ≤0.164 g/d; HA: ≤0.185 g/d), 4 SNP signals were strengthened [rs11590362 in claudin 19 (CLDN19), rs823154 in SLC41A1, rs5929706 and rs5930817 in membra; HA: ≥0.313 g/d), rs6584273 in CNNM1 (OR: 0.71; FDR-adjusted P = 0.04) and rs1800467 in potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) (OR: 2.50; FDR-adjusted P = 0.01) were significantly associated with T2D risk. CONCLUSIONS Our findings suggest important associations between genetic variations in magnesium-related ion channel genes and T2D risk in AA and HA women that vary by amount of magnesium intake.
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Affiliation(s)
| | - Sara A Chacko
- Division of General Medicine and Primary Care, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Yiqing Song
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN; Departments of
| | - Michele Cho
- Medicine and,Obstetrics and Gynecology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA
| | - Charles B Eaton
- Family Medicine,,Epidemiology, and,Center for Primary Care and Prevention, Memorial Hospital of Rhode Island, Pawtucket, RI
| | - Wen-Chih H Wu
- Medicine, Warren Alpert Medical School, Brown University, Providence, RI;,Vascular Research Laboratory, Providence US Department of Veterans Affairs Medical Center, Providence, RI; and
| | - Simin Liu
- Department of Epidemiology, and Departments of Medicine, Warren Alpert Medical School, Brown University, Providence, RI; Medicine and Obstetrics and Gynecology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA; Division of Endocrinology, Rhode Island Hospital, Providence, RI
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Hruby A, Ngwa JS, Renström F, Wojczynski MK, Ganna A, Hallmans G, Houston DK, Jacques PF, Kanoni S, Lehtimäki T, Lemaitre RN, Manichaikul A, North KE, Ntalla I, Sonestedt E, Tanaka T, van Rooij FJA, Bandinelli S, Djoussé L, Grigoriou E, Johansson I, Lohman KK, Pankow JS, Raitakari OT, Riserus U, Yannakoulia M, Zillikens MC, Hassanali N, Liu Y, Mozaffarian D, Papoutsakis C, Syvänen AC, Uitterlinden AG, Viikari J, Groves CJ, Hofman A, Lind L, McCarthy MI, Mikkilä V, Mukamal K, Franco OH, Borecki IB, Cupples LA, Dedoussis GV, Ferrucci L, Hu FB, Ingelsson E, Kähönen M, Kao WHL, Kritchevsky SB, Orho-Melander M, Prokopenko I, Rotter JI, Siscovick DS, Witteman JCM, Franks PW, Meigs JB, McKeown NM, Nettleton JA. Higher magnesium intake is associated with lower fasting glucose and insulin, with no evidence of interaction with select genetic loci, in a meta-analysis of 15 CHARGE Consortium Studies. J Nutr 2013; 143:345-53. [PMID: 23343670 PMCID: PMC3713023 DOI: 10.3945/jn.112.172049] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Favorable associations between magnesium intake and glycemic traits, such as fasting glucose and insulin, are observed in observational and clinical studies, but whether genetic variation affects these associations is largely unknown. We hypothesized that single nucleotide polymorphisms (SNPs) associated with either glycemic traits or magnesium metabolism affect the association between magnesium intake and fasting glucose and insulin. Fifteen studies from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium provided data from up to 52,684 participants of European descent without known diabetes. In fixed-effects meta-analyses, we quantified 1) cross-sectional associations of dietary magnesium intake with fasting glucose (mmol/L) and insulin (ln-pmol/L) and 2) interactions between magnesium intake and SNPs related to fasting glucose (16 SNPs), insulin (2 SNPs), or magnesium (8 SNPs) on fasting glucose and insulin. After adjustment for age, sex, energy intake, BMI, and behavioral risk factors, magnesium (per 50-mg/d increment) was inversely associated with fasting glucose [β = -0.009 mmol/L (95% CI: -0.013, -0.005), P < 0.0001] and insulin [-0.020 ln-pmol/L (95% CI: -0.024, -0.017), P < 0.0001]. No magnesium-related SNP or interaction between any SNP and magnesium reached significance after correction for multiple testing. However, rs2274924 in magnesium transporter-encoding TRPM6 showed a nominal association (uncorrected P = 0.03) with glucose, and rs11558471 in SLC30A8 and rs3740393 near CNNM2 showed a nominal interaction (uncorrected, both P = 0.02) with magnesium on glucose. Consistent with other studies, a higher magnesium intake was associated with lower fasting glucose and insulin. Nominal evidence of TRPM6 influence and magnesium interaction with select loci suggests that further investigation is warranted.
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Affiliation(s)
- Adela Hruby
- Tufts University Friedman School of Nutrition Science and Policy, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Julius S. Ngwa
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Frida Renström
- Department of Nutrition, Harvard School of Public Health, Boston, MA,Department of Clinical Sciences, Lund University, Malmö, Sweden,Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Mary K. Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Andrea Ganna
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Sweden
| | - Denise K. Houston
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Paul F. Jacques
- Tufts University Friedman School of Nutrition Science and Policy, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK,Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Terho Lehtimäki
- Fimlab Laboratories and University of Tampere, School of Medicine, and Tampere University Hospital, Tampere, Finland
| | - Rozenn N. Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Ani Manichaikul
- Center for Public Health Genomics, and Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC
| | - Ioanna Ntalla
- Clinical Research Branch, National Institute on Aging, Baltimore, MD
| | - Emily Sonestedt
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute on Aging, Baltimore, MD
| | - Frank J. A. van Rooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands
| | | | - Luc Djoussé
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Massachusetts Veterans Epidemiology and Research Information Center and Geriatric Research, Education, and Clinical Center, Boston Veterans Affairs Healthcare System, Boston, MA
| | - Efi Grigoriou
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | | | - Kurt K. Lohman
- Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, and Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Ulf Riserus
- Department of Public Health and Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Uppsala, Sweden
| | - Mary Yannakoulia
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - M. Carola Zillikens
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Neelam Hassanali
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Yongmei Liu
- Division of Public Health Sciences, Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Dariush Mozaffarian
- Department of Epidemiology and Nutrition, Harvard School of Public Health, Boston, MA; Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jorma Viikari
- Department of Medicine, University of Turku, and Turku University Hospital, Turku, Finland
| | - Christopher J. Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Vera Mikkilä
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kenneth Mukamal
- Division of General Medicine and Primary Care, Beth Israel Deaconess Medical Center, Boston, MA
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA,Framingham Heart Study, Framingham, MA
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, MD
| | - Frank B. Hu
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and University of Tampere, Tampere, Finland
| | - W. H. Linda Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | | | | | - Inga Prokopenko
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - David S. Siscovick
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA,Department of Epidemiology, University of Washington, Seattle, WA
| | - Jacqueline C. M. Witteman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands,Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden, The Netherlands
| | - Paul W. Franks
- Department of Nutrition, Harvard School of Public Health, Boston, MA,Department of Clinical Sciences, Lund University, Malmö, Sweden,Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - James B. Meigs
- Harvard Medical School and General Medicine Division, Clinical Epidemiology and Diabetes Research Units, Massachusetts General Hospital, Boston, MA; and
| | - Nicola M. McKeown
- Tufts University Friedman School of Nutrition Science and Policy, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA,To whom correspondence should be addressed. E-mail:
| | - Jennifer A. Nettleton
- Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health at The University of Texas Health Science Center–Houston, Houston, TX
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