Publications: R. Thane Papke

• 2023

• Neighboring inteins interfere with one another's homing capacity.
  Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U
  PNAS nexus (2023) 2(11):pgad354 PMC419797 10.1101/GR.849004
• Archaeal Tubulin-like Proteins Modify Cell Shape in during Early Biofilm Development.
  Cooper A, Makkay AM, Papke RT
  Genes (2023) 14(10): PMC8406309 10.1016/j.cub.2012.05.056

• 2021

• The Evolutionary Origins of Extreme Halophilic Archaeal Lineages.
  Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP
  Genome biology and evolution (2021) 13(8): PMC8350355 10.1093/gbe/evab166
• Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus.
  Hua Z, Ouellette M, Makkay AM, Papke RT, Zhaxybayeva O
  The ISME journal (2021) 15(10):2853-2864 PMC8443641 10.1038/s41396-021-00960-8
• Adaptation reduces competitive dominance and alters community assembly.
  Nadeau CP, Farkas TE, Makkay AM, Papke RT, Urban MC
  Proceedings. Biological sciences (2021) 288(1945):20203133 PMC7935105 10.1098/rspb.2020.3133

• 2020

• Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.
  Makkay AM, Louyakis AS, Ram-Mohan N, Gophna U, Gogarten JP, Papke RT
  Scientific reports (2020) 10(1):22297 PMC7749143 10.1038/s41598-020-79296-w
• Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.
  Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL
  Nature microbiology (2020) 6(1):136 PMC7752755 10.1038/s41564-020-00827-2
• Roadmap for naming uncultivated Archaea and Bacteria.
  Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL
  Nature microbiology (2020) 5(8):987-994 PMC7381421 10.1073/pnas.1720115115
• Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum.
  Pyatibratov MG, Syutkin AS, Quax TEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV
  MicrobiologyOpen (2020) 9(7):e1047 PMC7349177 10.1002/mbo3.1047

• 2019

• Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21.
  Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP
  Microbiology resource announcements (2019) 8(12): PMC6430316 10.1128/MRA.00096-19
• The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.
  Fullmer MS, Ouellette M, Louyakis AS, Papke RT, Gogarten JP
  Genes (2019) 10(3): PMC6471742 10.3390/genes10030233

• 2018

• Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006.
  Corral P, de la Haba RR, Infante-Domínguez C, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A
  Int. J. Syst. Evol. Microbiol. (2018) 68(11):3657-3665 10.1099/ijsem.0.003005
• Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.
  Méheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E
  Genome Biol. (2018) 19(1):75 (PMC5992828) 10.1186/s13059-018-1454-9
• Genotypic and Lipid Analyses of Strains From the Archaeal Genus Reveal Insights Into Their Taxonomy, Divergence, and Population Structure.
  de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT
  Front Microbiol (2018) 9:512 (PMC5890160) 10.3389/fmicb.2018.00512
• Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.
  Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U
  Genes (Basel) (2018) 9(3): (PMC5867893) 10.3390/genes9030172
• Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.
  Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT
  Genes (Basel) (2018) 9(3): (PMC5867850) 10.3390/genes9030129

• 2017

• Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus .
  López-Hermoso C, de la Haba RR, Sánchez-Porro C, Papke RT, Ventosa A
  Front Microbiol (2017) 8:1107 (PMC5479898)
• Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea.
  Prunetti L, Graf M, Blaby IK, Peil L, Makkay AM, Starosta AL, Papke RT, Oshima T, Wilson DN, de Crécy-Lagard V
  Archaea (2017) 2016:7316725 (PMC5178350)

• 2016

• Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel.
  Ram-Mohan N, Oren A, Papke RT
  Extremophiles (2016) 20(5):747-57

• 2015

• Microbial diversity of hypersaline environments: a metagenomic approach.
  Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT
  Curr. Opin. Microbiol. (2015) 25:80-7
• Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions.
  Chimileski S, Papke RT
  Front Microbiol (2015) 6:362 (PMC4419858)
• Horizontal gene transfer, dispersal and haloarchaeal speciation.
  Papke RT, Corral P, Ram-Mohan N, de la Haba RR, Sánchez-Porro C, Makkay A, Ventosa A
  Life (Basel) (2015) 5(2):1405-26 (PMC4500145)
• Preface to the proceedings of Halophiles 2013.
  Papke RT
  Front Microbiol (2015) 6:341 (PMC4406061)
• Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.
  Ouellette M, Jackson L, Chimileski S, Papke RT
  Front Microbiol (2015) 6:251 (PMC4389544)
• Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake.
  Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A
  Int. J. Syst. Evol. Microbiol. (2015) 65(Pt 6):1770-8

• 2014

• Viruses of haloarchaea.
  Luk AW, Williams TJ, Erdmann S, Papke RT, Cavicchioli R
  Life (Basel) (2014) 4(4):681-715 (PMC4284463)
• Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer.
  Chimileski S, Franklin MJ, Papke RT
  BMC Biol. (2014) 12:65 (PMC4180959)
• Inteins as indicators of gene flow in the halobacteria.
  Soucy SM, Fullmer MS, Papke RT, Gogarten JP
  Front Microbiol (2014) 5:299 (PMC4071816)
• Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach.
  Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A
  Front Microbiol (2014) 5:196 (PMC4021199)
• Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.
  Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT
  Front Microbiol (2014) 5:143 (PMC3988388)
• Population and genomic analysis of the genus Halorubrum.
  Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT
  Front Microbiol (2014) 5:140 (PMC3990103)
• DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.
  Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J
  PLoS ONE (2014) 9(4):e94819 (PMC3986227)
• Extracellular DNA metabolism in Haloferax volcanii.
  Chimileski S, Dolas K, Naor A, Gophna U, Papke RT
  Front Microbiol (2014) 5:57 (PMC3929857)
• Dihydroxyacetone metabolism in Haloferax volcanii.
  Ouellette M, Makkay AM, Papke RT
  Front Microbiol (2014) 4:376 (PMC3863723)

• 2013

• Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.
  Papke RT, de la Haba RR, Infante-Domínguez C, Pérez D, Sánchez-Porro C, Lapierre P, Ventosa A
  Genome Announc (2013) 1(4): (PMC3695434)
• Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.
  de la Haba RR, Sánchez-Porro C, León MJ, Papke RT, Ventosa A
  Genome Announc (2013) 1(3): (PMC3662824)
• Cell sorting analysis of geographically separated hypersaline environments.
  Zhaxybayeva O, Stepanauskas R, Mohan NR, Papke RT
  Extremophiles (2013) 17(2):265-75

• 2012

• Quantifying homologous replacement of loci between haloarchaeal species.
  Williams D, Gogarten JP, Papke RT
  Genome Biol Evol (2012) 4(12):1223-44 (PMC3542582)
• Low species barriers in halophilic archaea and the formation of recombinant hybrids.
  Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U
  Curr. Biol. (2012) 22(15):1444-8
• Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales.
  Andam CP, Harlow TJ, Papke RT, Gogarten JP
  BMC Evol. Biol. (2012) 12:85 (PMC3436685)
• Ecology. How bacterial lineages emerge.
  Papke RT, Gogarten JP
  Science (2012) 336(6077):45-6
• New abundant microbial groups in aquatic hypersaline environments.
  Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F
  Sci Rep (2012) 1:135 (PMC3216616)

• 2011

• Multilocus sequence analysis of the family Halomonadaceae.
  de la Haba RR, Márquez MC, Papke RT, Ventosa A
  Int. J. Syst. Evol. Microbiol. (2011) 62(Pt 3):520-38
• A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.
  Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A
  Int. J. Syst. Evol. Microbiol. (2011) 61(Pt 12):2984-95
• In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.
  Naor A, Lazary R, Barzel A, Papke RT, Gophna U
  PLoS ONE (2011) 6(1):e15833 (PMC3024317)
• Ancient origins determine global biogeography of hot and cold desert cyanobacteria.
  Bahl J, Lau MC, Smith GJ, Vijaykrishna D, Cary SC, Lacap DC, Lee CK, Papke RT, Warren-Rhodes KA, Wong FK, McKay CP, Pointing SB
  Nat Commun (2011) 2:163 (PMC3105302)

• 2009

• Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.
  Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP
  Genome Biol Evol (2009) 1:325-39 (PMC2817427)

• 2008

• Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.
  Sharma AK, Zhaxybayeva O, Papke RT, Doolittle WF
  Environ. Microbiol. (2008) 10(4):1039-56

• 2007

• Genomic plasticity in prokaryotes: the case of the square haloarchaeon.
  Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F
  ISME J (2007) 1(3):235-45
• Searching for species in haloarchaea.
  Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF
  Proc. Natl. Acad. Sci. U.S.A. (2007) 104(35):14092-7 (PMC1955782)
• Evolution of rhodopsin ion pumps in haloarchaea.
  Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT
  BMC Evol. Biol. (2007) 7:79 (PMC1885257)

• 2006

• Genomics and the bacterial species problem.
  Doolittle WF, Papke RT
  Genome Biol. (2006) 7(9):116 (PMC1794555)
• Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
  Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT
  Genome Res. (2006) 16(9):1099-108 (PMC1557764)
• Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species.
  Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT
  BMC Genomics (2006) 7:171 (PMC1560387)

• 2005

• The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.
  Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbø CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F
  Proc. Natl. Acad. Sci. U.S.A. (2005) 102(50):18147-52 (PMC1312414)
• Archaeal diversity along a soil salinity gradient prone to disturbance.
  Walsh DA, Papke RT, Doolittle WF
  Environ. Microbiol. (2005) 7(10):1655-66

• 2004

• Frequent recombination in a saltern population of Halorubrum.
  Papke RT, Koenig JE, Rodríguez-Valera F, Doolittle WF
  Science (2004) 306(5703):1928-9
• The importance of physical isolation to microbial diversification.
  Papke RT, Ward DM
  FEMS Microbiol. Ecol. (2004) 48(3):293-303

• 2003

• Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern.
  Papke RT, Douady CJ, Doolittle WF, Rodríguez-Valera F
  Environ. Microbiol. (2003) 5(11):1039-45
• Lateral gene transfer and the origins of prokaryotic groups.
  Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbø CL, Case RJ, Doolittle WF
  Annu. Rev. Genet. (2003) 37:283-328
• Phage evolution: new worlds of genomic diversity.
  Papke RT, Doolittle WF
  Curr. Biol. (2003) 13(15):R606-7
• Geographical isolation in hot spring cyanobacteria.
  Papke RT, Ramsing NB, Bateson MM, Ward DM
  Environ. Microbiol. (2003) 5(8):650-9

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