TY - JOUR AU - Gray, M. W. AU - Lang, B. F. AU - Burger, G. PY - 2004 DA - 2004// TI - Mitochondria of protists JO - Ann Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.37.110801.142526 DO - 10.1146/annurev.genet.37.110801.142526 ID - Gray2004 ER - TY - JOUR AU - Asin-Cayuela, J. AU - Gustafsson, C. M. PY - 2007 DA - 2007// TI - Mitochondrial transcription and its regulation in mammalian cells JO - Trends Biochem Sci VL - 32 UR - https://doi.org/10.1016/j.tibs.2007.01.003 DO - 10.1016/j.tibs.2007.01.003 ID - Asin-Cayuela2007 ER - TY - JOUR AU - Andersson, G. E. AU - Karlberg, O. AU - Canbäck, B. AU - Kurland, C. G. PY - 2003 DA - 2003// TI - On the origin of mitochondria: a genomics perspective JO - Phil Trans R Soc Lond B Biol Sci VL - 358 UR - https://doi.org/10.1098/rstb.2002.1193 DO - 10.1098/rstb.2002.1193 ID - Andersson2003 ER - TY - JOUR AU - Brown, J. R. PY - 2003 DA - 2003// TI - Ancient horizontal gene transfer JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1000 DO - 10.1038/nrg1000 ID - Brown2003 ER - TY - JOUR AU - Watkins, R. F. AU - Gray, M. W. PY - 2006 DA - 2006// TI - The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa JO - J Mol Evol VL - 63 UR - https://doi.org/10.1007/s00239-006-0031-0 DO - 10.1007/s00239-006-0031-0 ID - Watkins2006 ER - TY - JOUR AU - Moustafa, A. AU - Reyes-Prieto, A. AU - Bhattacharya, D. PY - 2008 DA - 2008// TI - Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions JO - PLoS One VL - 3 UR - https://doi.org/10.1371/journal.pone.0002205 DO - 10.1371/journal.pone.0002205 ID - Moustafa2008 ER - TY - JOUR AU - Woolfit, M. AU - Iturbe-Ormaetxe, I. AU - McGraw, E. A. AU - O’Neill, S. L. PY - 2009 DA - 2009// TI - An ancient horizontal gene transfer between mosquito and the endosymbiotic bacterium Wolbachia pipientis JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msn253 DO - 10.1093/molbev/msn253 ID - Woolfit2009 ER - TY - JOUR AU - McDonald, T. R. AU - Dietrich, F. S. AU - Lutzoni, F. PY - 2012 DA - 2012// TI - Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/msr123 DO - 10.1093/molbev/msr123 ID - McDonald2012 ER - TY - JOUR AU - Moran, Y. AU - Fredman, D. AU - Szczesny, P. AU - Grynberg, M. AU - Technau, U. PY - 2012 DA - 2012// TI - Recurrent horizontal transfer of bacterial toxin genes to eukaryotes JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss089 DO - 10.1093/molbev/mss089 ID - Moran2012 ER - TY - JOUR AU - Delannoy, E. AU - Stanley, W. A. AU - Bond, C. S. AU - Small, I. D. PY - 2007 DA - 2007// TI - Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles JO - Biochem Soc Trans VL - 35 UR - https://doi.org/10.1042/BST0351643 DO - 10.1042/BST0351643 ID - Delannoy2007 ER - TY - JOUR AU - Schmitz-Linneweber, C. AU - Small, I. PY - 2008 DA - 2008// TI - Pentatricopeptide repeat proteins: a socket set for organelle gene expression JO - Trends Plant Sci VL - 13 UR - https://doi.org/10.1016/j.tplants.2008.10.001 DO - 10.1016/j.tplants.2008.10.001 ID - Schmitz-Linneweber2008 ER - TY - JOUR AU - O’Toole, N. AU - Hattori, M. AU - Andres, C. AU - Iida, K. AU - Lurin, C. AU - Schmitz-Linneweber, C. AU - Sugita, M. AU - Small, I. PY - 2008 DA - 2008// TI - On the expansion of the pentatricopeptide repeat gene family in plants JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn057 DO - 10.1093/molbev/msn057 ID - O’Toole2008 ER - TY - JOUR AU - Hayes, M. L. AU - Mulligan, R. M. PY - 2011 DA - 2011// TI - Pentatricopeptide repeat proteins constrain genome evolution in chloroplasts JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr023 DO - 10.1093/molbev/msr023 ID - Hayes2011 ER - TY - JOUR AU - Hayes, M. AU - Giang, K. AU - Mulligan, R. PY - 2012 DA - 2012// TI - Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures JO - BMC Evol Biol VL - 12 UR - https://doi.org/10.1186/1471-2148-12-66 DO - 10.1186/1471-2148-12-66 ID - Hayes2012 ER - TY - JOUR AU - Hallam, S. J. AU - Putnam, N. AU - Preston, C. M. AU - Detter, J. C. AU - Rokhsar, D. AU - Richardson, P. M. AU - DeLong, E. F. PY - 2004 DA - 2004// TI - Reverse methanogenesis: testing the hypothesis with environmental genomics JO - Science VL - 305 UR - https://doi.org/10.1126/science.1100025 DO - 10.1126/science.1100025 ID - Hallam2004 ER - TY - JOUR AU - Choudhary, M. AU - Zanhua, X. AU - Fu, Y. AU - Kaplan, S. PY - 2007 DA - 2007// TI - Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II JO - J Bacteriol VL - 189 UR - https://doi.org/10.1128/JB.01498-06 DO - 10.1128/JB.01498-06 ID - Choudhary2007 ER - TY - JOUR AU - Knoop, V. AU - Rüdinger, M. PY - 2010 DA - 2010// TI - DYW-type PPR proteins in a heterolobosean protist: Plant RNA editing factors involved in an ancient horizontal gene transfer? JO - FEBS Lett VL - 584 UR - https://doi.org/10.1016/j.febslet.2010.09.041 DO - 10.1016/j.febslet.2010.09.041 ID - Knoop2010 ER - TY - JOUR AU - Zoschke, R. AU - Kroeger, T. AU - Belcher, S. AU - Schöttler, M. A. AU - Barkan, A. AU - Schmitz-Linneweber, C. PY - 2012 DA - 2012// TI - The Pentatricopeptide Repeat-SMR Protein ATP4 promotes translation of the chloroplast atpB/E mRNA JO - Plant J VL - 72 UR - https://doi.org/10.1111/j.1365-313X.2012.05081.x DO - 10.1111/j.1365-313X.2012.05081.x ID - Zoschke2012 ER - TY - JOUR AU - Zoschke, R. AU - Qu, Y. AU - Zubo, Y. O. AU - Börner, T. AU - Schmitz-Linneweber, C. PY - 2013 DA - 2013// TI - Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana JO - J Plant Res VL - 126 UR - https://doi.org/10.1007/s10265-012-0527-1 DO - 10.1007/s10265-012-0527-1 ID - Zoschke2013 ER - TY - JOUR AU - Manna, S. AU - Brewster, J. AU - Barth, C. PY - 2013 DA - 2013// TI - Identification of pentatricopeptide repeat proteins in the model organism Dictyostelium discoideum JO - Int J Genomics VL - 2013 UR - https://doi.org/10.1155/2013/586498 DO - 10.1155/2013/586498 ID - Manna2013 ER - TY - JOUR AU - Kim, S. AU - Suddath, F. AU - Quigley, G. AU - McPherson, A. AU - Sussman, J. AU - Wang, A. AU - Seeman, N. AU - Rich, A. PY - 1974 DA - 1974// TI - Three-dimensional tertiary structure of yeast phenylalanine transfer RNA JO - Science VL - 185 UR - https://doi.org/10.1126/science.185.4149.435 DO - 10.1126/science.185.4149.435 ID - Kim1974 ER - TY - JOUR AU - Robertus, J. AU - Ladner, J. E. AU - Finch, J. AU - Rhodes, D. AU - Brown, R. AU - Clark, B. AU - Klug, A. PY - 1974 DA - 1974// TI - Structure of yeast phenylalanine tRNA at 3 Å resolution JO - Nature VL - 250 UR - https://doi.org/10.1038/250546a0 DO - 10.1038/250546a0 ID - Robertus1974 ER - TY - JOUR AU - Salemink, P. AU - Yamane, T. AU - Hilbers, C. PY - 1977 DA - 1977// TI - Demonstration of a tertiary interaction in solution between the extra arm and the D-stem in two different transfer RNA’s by NMR JO - Nucleic Acids Res VL - 4 UR - https://doi.org/10.1093/nar/4.11.3727 DO - 10.1093/nar/4.11.3727 ID - Salemink1977 ER - TY - JOUR AU - Karpenahalli, M. R. AU - Lupas, A. N. AU - Söding, J. PY - 2007 DA - 2007// TI - TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-2 DO - 10.1186/1471-2105-8-2 ID - Karpenahalli2007 ER - TY - JOUR AU - Claros, M. G. AU - Vincens, P. PY - 1996 DA - 1996// TI - Computational method to predict mitochondrially imported proteins and their targeting sequences JO - Eur J Biochem VL - 241 UR - https://doi.org/10.1111/j.1432-1033.1996.00779.x DO - 10.1111/j.1432-1033.1996.00779.x ID - Claros1996 ER - TY - JOUR AU - Emanuelsson, O. AU - Brunak, S. AU - von Heijne, G. AU - Nielsen, H. PY - 2007 DA - 2007// TI - Locating proteins in the cell using TargetP, SignalP and related tools JO - Nat Protoc VL - 2 UR - https://doi.org/10.1038/nprot.2007.131 DO - 10.1038/nprot.2007.131 ID - Emanuelsson2007 ER - TY - JOUR AU - Tovar, J. AU - Fischer, A. AU - Clark, C. G. PY - 1999 DA - 1999// TI - The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica JO - Mol Microbiol VL - 32 UR - https://doi.org/10.1046/j.1365-2958.1999.01414.x DO - 10.1046/j.1365-2958.1999.01414.x ID - Tovar1999 ER - TY - JOUR AU - Morf, L. AU - Singh, U. PY - 2012 DA - 2012// TI - Entamoeba histolytica: a snapshot of current research and methods for genetic analysis JO - Curr Opin Microbiol VL - 15 UR - https://doi.org/10.1016/j.mib.2012.04.011 DO - 10.1016/j.mib.2012.04.011 ID - Morf2012 ER - TY - JOUR AU - León-Avila, G. AU - Tovar, J. PY - 2004 DA - 2004// TI - Mitosomes of Entamoeba histolytica are abundant mitochondrion-related remnant organelles that lack a detectable organellar genome JO - Microbiology VL - 150 UR - https://doi.org/10.1099/mic.0.26923-0 DO - 10.1099/mic.0.26923-0 ID - León-Avila2004 ER - TY - JOUR AU - Aguilera, P. AU - Barry, T. AU - Tovar, J. PY - 2008 DA - 2008// TI - Entamoeba histolytica mitosomes: Organelles in search of a function JO - Exp Parasitol VL - 118 UR - https://doi.org/10.1016/j.exppara.2007.08.004 DO - 10.1016/j.exppara.2007.08.004 ID - Aguilera2008 ER - TY - JOUR AU - Bai, C. AU - Tolias, P. P. PY - 1996 DA - 1996// TI - Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein JO - Mol Cell Biol VL - 16 UR - https://doi.org/10.1128/MCB.16.12.6661 DO - 10.1128/MCB.16.12.6661 ID - Bai1996 ER - TY - JOUR AU - Cheng, Y. AU - Kato, N. AU - Wang, W. AU - Li, J. AU - Chen, X. PY - 2003 DA - 2003// TI - Two RNA Binding Proteins, HEN4 and HUA1, Act in the Processing of AGAMOUS Pre-mRNA in Arabidopsis thaliana JO - Dev Cell VL - 4 UR - https://doi.org/10.1016/S1534-5807(02)00399-4 DO - 10.1016/S1534-5807(02)00399-4 ID - Cheng2003 ER - TY - JOUR AU - Ogura, K. AU - Kishimoto, N. AU - Mitani, S. AU - Gengyo-Ando, K. AU - Kohara, Y. PY - 2003 DA - 2003// TI - Translational control of maternal glp-1 mRNA by POS-1 and its interacting protein SPN-4 in Caenorhabditis elegans JO - Development VL - 130 UR - https://doi.org/10.1242/dev.00469 DO - 10.1242/dev.00469 ID - Ogura2003 ER - TY - JOUR AU - Lai, W. S. AU - Parker, J. S. AU - Grissom, S. F. AU - Stumpo, D. J. AU - Blackshear, P. J. PY - 2006 DA - 2006// TI - Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts JO - Mol Cell Biol VL - 26 UR - https://doi.org/10.1128/MCB.00945-06 DO - 10.1128/MCB.00945-06 ID - Lai2006 ER - TY - JOUR AU - Dereeper, A. AU - Guignon, V. AU - Blanc, G. AU - Audic, S. AU - Buffet, S. AU - Chevenet, F. AU - Dufayard, J. F. AU - Guindon, S. AU - Lefort, V. AU - Lescot, M. PY - 2008 DA - 2008// TI - Phylogeny.fr: robust phylogenetic analysis for the non-specialist JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn180 DO - 10.1093/nar/gkn180 ID - Dereeper2008 ER - TY - JOUR AU - Rogers, M. B. AU - Watkins, R. F. AU - Harper, J. T. AU - Durnford, D. G. AU - Gray, M. W. AU - Keeling, P. J. PY - 2007 DA - 2007// TI - A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-89 DO - 10.1186/1471-2148-7-89 ID - Rogers2007 ER - TY - JOUR AU - van Der Giezen, M. AU - Cox, S. AU - Tovar, J. PY - 2004 DA - 2004// TI - The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer JO - BMC Evol Biol VL - 4 UR - https://doi.org/10.1186/1471-2148-4-7 DO - 10.1186/1471-2148-4-7 ID - van Der Giezen2004 ER - TY - JOUR AU - Becker, B. AU - Hoef-Emden, K. AU - Melkonian, M. PY - 2008 DA - 2008// TI - Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-203 DO - 10.1186/1471-2148-8-203 ID - Becker2008 ER - TY - JOUR AU - Loftus, B. AU - Anderson, I. AU - Davies, R. AU - Alsmark, U. C. M. AU - Samuelson, J. AU - Amedeo, P. AU - Roncaglia, P. AU - Berriman, M. AU - Hirt, R. P. AU - Mann, B. J. PY - 2005 DA - 2005// TI - The genome of the protist parasite Entamoeba histolytica JO - Nature VL - 433 UR - https://doi.org/10.1038/nature03291 DO - 10.1038/nature03291 ID - Loftus2005 ER - TY - JOUR AU - Andersson, J. O. AU - Hirt, R. P. AU - Foster, P. G. AU - Roger, A. J. PY - 2006 DA - 2006// TI - Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes JO - BMC Evol Biol VL - 6 UR - https://doi.org/10.1186/1471-2148-6-27 DO - 10.1186/1471-2148-6-27 ID - Andersson2006 ER - TY - JOUR AU - Doolittle, W. PY - 1998 DA - 1998// TI - You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes JO - Trends Genet VL - 14 UR - https://doi.org/10.1016/S0168-9525(98)01494-2 DO - 10.1016/S0168-9525(98)01494-2 ID - Doolittle1998 ER - TY - JOUR AU - Horn, M. PY - 2008 DA - 2008// TI - Chlamydiae as symbionts in eukaryotes JO - Annu Rev Microbiol VL - 62 UR - https://doi.org/10.1146/annurev.micro.62.081307.162818 DO - 10.1146/annurev.micro.62.081307.162818 ID - Horn2008 ER - TY - JOUR AU - Zdobnov, E. M. AU - Apweiler, R. PY - 2001 DA - 2001// TI - InterProScan–an integration platform for the signature-recognition methods in InterPro JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.9.847 DO - 10.1093/bioinformatics/17.9.847 ID - Zdobnov2001 ER - TY - JOUR AU - Larkin, M. AU - Blackshields, G. AU - Brown, N. AU - Chenna, R. AU - McGettigan, P. AU - McWilliam, H. AU - Valentin, F. AU - Wallace, I. AU - Wilm, A. AU - Lopez, R. PY - 2007 DA - 2007// TI - Clustal W and Clustal X version 2.0 JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Jones, D. T. AU - Taylor, W. R. AU - Thornton, J. M. PY - 1992 DA - 1992// TI - The rapid generation of mutation data matrices from protein sequences JO - Comput Appl Biosci VL - 8 ID - Jones1992 ER -