CEEM | Publications

2009

Leonard, Guy, Stevens, J.R., Richards, T.A. (2009) REFGEN and TREENAMER: Automated sequence data handling for phylogenetic analysis in the genomic era. Evolutionary Bioinformatics Online. 5, 1-4
Maralikova, B., Ali, V., Nakada-Tsukui, K., Nozaki, T., van der Giezen, M., Henze, K. and Tovar, J. (2009) Bacterial-type oxygen detoxification and iron-sulphur cluster assembly in amoebal relict mitochondria. Cell. Microbiol., in press.
Tsaousis, A.D., Stechmann, A., Hamblin, K.A., van der Giezen, M., Pérez-Brocal, V. and Clark C.G. (2009) The Blastocystis mitochondrion-like organelles. In: Anaerobic parasitic protozoa: Genomics and molecular biology. (C.G. Clark, P.J. Johnson, and R.D. Adam, Eds.), Caister Academic Press Ltd, Norwich, in press.
van der Giezen, M. (2009) Hydrogenosomes and mitosomes: conservation and evolution of functions. J. Euk. Microbiol. 56, 221-231.

2008

Standley, D.M., Lis, M., van der Giezen, M. and Nakamura, H. (2008) Structure-based functional annotation of protein sequences guided by comparative models. Optimization and Systems Biology 395-403.
Puthiyaveetil, S., Kavanagh, T. A., Cain, P., Sullivan, J. A., Newell, C. A., Gray, J. C., Robinson, C., van der Giezen, M., Rogers, M.B. and Allen, J.F. (2008) The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts. Proc. Natl. Acad. Sci. U.S.A. 105, 10061-10066.
Lee, R. C. H., Williams, B. A. P., Brown, A. M. V., Adamson, M. L., Keeling, P. J. and Fast, N. M. (2008) Alpha and Beta-Tubulin Phylogenies Support a Close Relationship between the Microsporidia Brachiola algerae and Antonospora locustae. J. Euk. Microbiol. in press.
Williams B.A., Lee R.C.H , Becnel J.J., Weiss L.M., Fast N.M., Keeling P.J. (2008) Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities. BMC Genomics. 29;9:200.
Hamblin, K., Standley, D. M., Rogers, M. B., Stechmann, A., Roger, A.J., Maytum, R. and van der Giezen, M. (2008) Localisation and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol. Microbiol. 68, 1395-1405.
Stechmann, A., Hamblin, K., Perez-Brocal, V., Gaston, D., Richmond, G.S., van der Giezen, M., Clark, C.G. and Roger, A.J. (2008) Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes. Curr. Biol. 18, 580-585.
joint first. van Grinsven, K.W.A., Rosnowsky, S., van Weelden, S.WH., Paetz, S., van der Giezen, M., Martin, W., van Hellemond, J.J., Tielens, A.G.M. and Henze, K. (2008) Acetate: succinate CoA-transferase in the hydrogenosomes of Trichomonas vaginalis: identification and characterization. J. Biol. Chem. 283, 1411-1418.
Williams B.A., Cali., A, Takvorian, P., Keeling, P.J. Distinct localisation patterns of two putative mitochondrial proteins in the microsporidian Encephalitozoon cuniculi. J. Eukaryot. Microbiol. 55, 131-133.

2007

Akiyoshi, D.E., Weiss, L. M., Feng, X., Williams B.A., Keeling, P.J., Zhang, Q. and Tzipori, S. (2007) Analysis of the beta-tubulin genes from Enterocytozoon bieneusi isolates from a human and rhesus macaque. J. Eukaryot. Microbiol., 54, 38-41.
Allen, C.A., van der Giezen, M. and Allen, J.F. (2007) Origin, function, and transmission of mitochondria. In: Origin of mitochondria and hydrogenosomes. (W. Martin and M. Maeller, Eds), Springer, Berlin, 39-56.
Bass, D., Howe, A., Brown, N., Barton, H., Demidova, M., Michelle, H., Li, L., Sanders, H., Watkinson, S.C., Willcock, S. and Richards, T.A. (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc. Biol. Sci. 274, 3069-3077.
Bass, D., Richards, T.A., Matthai, L., Marsh, V. and Cavalier-Smith, T. (2007) DNA evidence for global dispersal and probable endemicity of protozoa. BMC Evol. Biol. 7, 162.
Ferguson, D.J., Campbell, S.A., Henriquez, F.L., Phan, L., Mui, E., Richards, T.A., Muench, S.P., Allary, M., Lu, J.Z., Prigge, S.T., Tomley, F., Shirley, M.W., Rice, D.W., McLeod, R. and Roberts, C.W. (2007) Enzymes of type II fatty acid synthesis and apicoplast differentiation and division in Eimeria tenella. Int. J. Parasitol. 37, 33-51.
Richards, T.A. and Talbot, N.J. (2007) Plant parasitic oomycetes such as Phytophthora species contain genes derived from three eukaryotic lineages. Plant Sig. & Behav. 2, 112-114.
Soanes, D.M., Richards, T.A. and Talbot, N.J. (2007) Insights from sequencing fungal and oomycete genomes: what can we learn about plant disease and the evolution of pathogenicity? Plant Cell. 19, 3318-26.
Tovar, J., Cox, S.S.E. and van der Giezen, M. (2007) A mitosome purification protocol based on Percoll density gradients and its use in validating the mitosomal nature of Entamoeba histolytica mitochondrial Hsp70. Meth. Mol. Biol. 390, 167-177.
Williams B.A., Haferkamp, I. and Keeling, P.J. (2007) An ADP/ATP-specific mitochondrial carrier protein in the microsporidian Antonospora locustae. J. Mol. Biol. 375, 1249-1257.
Protein targeting protocols, 2nd ed. (van der Giezen, M., Ed.) (2007), Humana Press.

2006

Burri, L., Williams B.A., Bursac, D., Lithgow, T. and Keeling, P.J. (2006) Microsporidian mitosomes retain elements of the general mitochondrial targeting system. Proc. Natl. Acad. Sci. U.S.A., 103, 15916-15920.
Cox S.S.E., van der Giezen M., Tarr S.J., Crompton M.R. and Tovar J. (2006) Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis. BMC Microbiol 6, 45.
Dacks J.B., Dyal P.L., Embley T.M. and van der Giezen M. (2006) Hydrogenosomal succinyl-CoA synthetase from the rumen-dwelling fungus Neocallimastix patriciarum; an energy-producing enzyme of mitochondrial origin. Gene 373, 75-82.
Richards, T.A., Dacks, J.B., Campbell, S.A., Blanchard, J.L., Foster, P.G., McLeod, R. and Roberts, C.W. (2006) Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot. Cell 5, 1517-1531.
Richards, T.A., Dacks, J.B., Jenkinson, J.M., Thornton, C.R. and Talbot, N.J. (2006) Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr. Biol. 16, 1857-1864.
Richards, T.A. and van der Giezen, M. (2006) Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes. Mol. Biol. Evol. 23, 1341-1344.
van der Giezen, M. (2006) Mitochondrial amazement. EMBO Rep. 7, 478.

2005

Brinkmann H., van der Giezen M., Zhou Y., Poncelin de Raucourt G. and Philippe H. (2005) An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst. Biol. 54, 743-757.
Chan K.W., Slotboom D.J., Cox S., Embley T.M., Fabre O., van der Giezen M., Harding M., Horner D.S., Kunji E.R., Lean-Avila G. and Tovar J. (2005) A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica. Curr. Biol. 15, 737-742.
Henriquez, F.L., Richards, T.A., Roberts, F., McLeod, R. and Roberts, C.W. (2005) The unusual mitochondrial compartment of Cryptosporidium parvum. Trends Parasitol. 21, 68-74.
Keeling, P.J., Fast, N.M., Law, J.S., Williams B.A. and Slamovits, C.H. (2005) Comparative genomics of microsporidia. Folia Parasitol (Praha), 52, 8-14.
Regoes A., Zourmpanou D., Lean-Avila D., van der Giezen M., Tovar J. and Hehl A.B. (2005) Protein import, replication and inheritance of a vestigial mitochondrion. J. Biol. Chem. 280, 30557-30563.
Richards, T.A. and Bass, D. (2005) Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis. Curr. Opin. Microbiol. 8, 240-252.
Richards, T.A. and Cavalier-Smith, T. (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436, 1113-1118.
Richards, T.A., Vepritskiy, A.A., Gouliamova, D. and Nierzwicki-Bauer, S.A. (2005) The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ. Microbiol. 7, 1413-1425.
van der Giezen M. (2005) Endosymbiosis: past and present. Heredity 95, 335-336.
van der Giezen M., Lean-Avila G. and Tovar J. (2005) Characterisation of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica. Microbiology 151, 3107-3115.
van der Giezen M. and Tovar J. (2005) Degenerate mitochondria. EMBO reports 6, 525-530.
van der Giezen M., Tovar J. and Clark C.G. (2005) Mitochondria-derived organelles in protists and fungi. Int. Rev. Cytol. 244,175-225.
Williams B.A. and Keeling, P.J. (2005) Microsporidian mitochondrial proteins: expression in Antonospora locustae spores and identification of genes coding for two further proteins. J. Eukaryot. Microbiol., 52, 271-276.
Williams B.A., Slamovits, C.H., Patron, N.J., Fast, N.M. and Keeling, P.J. (2005) A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc. Natl. Acad. Sci. U.S.A., 102, 10936-10941.

2004

Campbell, S.A., Richards, T.A., Mui, E.J., Samuel, B.U., Coggins, J.R., McLeod, R. and Roberts, C.W. (2004) A complete shikimate pathway in Toxoplasma gondii: an ancient eukaryotic innovation. Int. J. Parasitol. 34, 5-13.
Roberts, C.W., Roberts, F., Henriquez, F.L., Akiyoshi, D., Samuel, B.U., Richards, T.A., Milhous, W., Kyle, D., McIntosh, L., Hill, G.C., Chaudhuri, M., Tzipori, S. and McLeod, R. (2004) Evidence for mitochondrial-derived alternative oxidase in the apicomplexan parasite Cryptosporidium parvum: a potential anti-microbial agent target. Int. J. Parasitol. 34, 297-308.
Slamovits, C.H., Williams B.A. and Keeling, P.J. (2004) Transfer of Nosema locustae (Microsporidia) to Antonospora locustae n. comb. based on molecular and ultrastructural data. J. Euk. Microbiol., 51, 207-213.
van der Giezen M., Cox S. and Tovar J. (2004). The iron-sulfur cluster assembly genes IscS and IscU of Entamoeba histolytica were acquired by horizontal gene transfer. BMC Evol. Biol. 4, 7.
van der Giezen M. and Tovar J. (2004). Hydrogenosomes, mitosomes and mitochondria; variations on a theme? In: Organelles, genomes and eukaryote phylogeny: An evolutionary synthesis in the age of genomics. (Horner, D.S. and R.P. Hirt, Eds.) CRC Press, pp 283-302.
Williams, B.A. and Hirt, R.P. (2004) RACE and RAGE cloning in parasitic microbial eukaryotes. Meth. Mol. Biol., 270, 151-172.

2003

Cammack R., Horner D.S., van der Giezen M., Kulda J. and Lloyd D. (2003). Iron-sulfur proteins in anaerobic eukaryotes. In: Biochemistry and physiology of anaerobic bacteria. (L. Ljungdahl, M.W.W. Adams, L.L. Barton, J.G. Ferry, and M.K. Johnson, Eds),Springer, New York, U.S.A., pp 113-127.
Embley T.M., van der Giezen M., Horner D.S., Dyal P.L. and P. Foster. (2003). Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Phil. Trans. R. Soc. Lond. 358, 191-204.
Embley T.M., van der Giezen M., Horner D.S., Dyal P.L., Bell S. and Foster P. (2003) Hydrogenosomes, mitochondria and early eukaryotic evolution. IUBMB Life, 55, 387-395.
Fast, N.M., Law, J.S., Williams B.A. and Keeling, P.J. (2003) Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution. Euk. Cell, 2, 1069-1075.
Richards, T.A., Hirt, R.P., Williams B.A. and Embley, T.M. (2003) Horizontal gene transfer and the evolution of parasitic protozoa. Protist 154, 17-32.
Tovar J., Lean-Avila G., Sa¡nchez L., Sutak R., Tachezy J., van der Giezen M., Herna¡ndez M., Maeller M. and Lucocq J.M.. (2003) Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 426, 172-176.
van der Giezen M., Birdsey G.M., Horner D.S., Lucocq J., Dyal P.L., Benchimol M., Danpure C.J. and Embley T.M. (2003). Fungal hydrogenosomes contain mitochondrial heat-shock proteins. Mol. Biol. Evol. 20, 1051-1061.
Williams B.A. and Keeling, P.J. (2003). Cryptic organelles in parasitic protists and fungi. Adv. Parasitol., 54, 9-68.

2002

Davidson E.A., van der Giezen M., Horner D.S., Embley T.M. and Howe C.J. (2002) An [Fe] hydrogenase from the anaerobic hydrogenosome-containing fungus Neocallimastix frontalis L2. Gene 296, 45-52.
van der Giezen M. (2002). Strange fungi with even stranger insides. Mycologist 16, 129-131.
van der Giezen M., Slotboom D.J., Horner D.S., Dyal P.L., Harding M., Xue G.-P., Embley T.M. and Kunji E.R.S. (2002) Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. EMBO J. 21, 572-579.
Williams B.A., Hirt, R.P., Lucocq, J.M. and Embley, T.M. (2002) A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature, 418, 865-869.

2001

Baker, R.H., Ashwell, R.I.S., Richards, T.A., Fowler, K., Chapman, T. and Pomiankowski, A. (2001) Effects of multiple mating and male eye span on female reproductive output in the stalk-eyed fly, Cyrtodiopsis dalmanni. Behav. Ecol. 12, 732-739.

2000

Gasc, A., Giammarinaro, P., Ton-Hoang, B., Geslin, P., van der Giezen, M., and Sicard, M. (2000) Structural organization of the Streptococcus pneumoniae chromosome and relatedness of penicillin-sensitive and -resistant strains in type 9V. In: Streptococcus pneumoniae, molecular biology and mechanisms of disease. (Tomasz, A. Ed), Mary Ann Liebert, Larchmont, NY, USA., 25-32.

1999

Bray, R.A., Littlewood, D.T., Herniou, E.A., Williams, B.A. and Henderson, R.E. (1999) Digenean parasites of deep-sea teleosts: a review and case studies of intrageneric phylogenies. Parasitology, 119, S125-144. 1998

1998

van der Giezen, M., Kiel, J.A.K.W., Sjollema, K.A. and R.A. Prins. (1998) The hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis is targeted to mitochondria of the methylotrophic yeast Hansenula polymorpha. Curr. Genet. 33, 131-135.

1997

Biagini, G.A., van der Giezen, M., Hill, B., Winters, C. and Lloyd, D. (1997) Ca2+ accumulation in the hydrogenosomes of Neocallimastix frontalis L2: A mitochondrial-like physiological role. FEMS Microbiol. Lett.149:227-232.
Gasc, A., Giammarinaro, P., Ton-Hoang, B., Geslin, P., van der Giezen, M., and Sicard, M. (1997) Structural organization of the Streptococcus pneumoniae chromosome and relatedness of penicillin-sensitive and -resistant strains in type 9V. Microb. Drug Resist. 3, 65-72.
van der Giezen, M., Rechinger, K.B., Svendsen, I., Durand, R., Hirt, R.P., Fasvre, M., Embley, T.M. and Prins, R.A. (1997) A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: evidence for the hypothesis that hydrogenosomes are modified mitochondria. Mol. Microbiol. 23, 11-21.
van der Giezen, M., Sjollema, K.A., Artz, R.R.E., Alkema, W. and Prins, R.A. (1997) Hydrogenosomes in the anaerobic fungus Neocallimastix frontalis have a double membrane but lack an associated organelle genome. FEBS Lett. 408, 147-150.

1996

Brondijk, T.H.C., Durand, R., van der Giezen, M., Gottschal, J.C., Prins, R.A. and Fasvre, M. (1996) scsB, a cDNA encoding the hydrogenosomal protein beta-succinyl-CoA synthetase from the anaerobic fungus Neocallimastix frontalis. Mol. Gen. Genet. 253, 315-323.

1994

Prins, R.A., Marvin-Sikkema, F.D., van der Giezen, M. and Gottschal, J.C. (1994) Hydrogenosomes of the anaerobic fungus Neocallimastix sp. L2. In: Micro-organisms in ruminant nutrition. (Prins, R.A. and C.S. Stewart, Eds). Nottingham University Press, Nottingham, UK. 179-194.
van der Giezen, M., Gottschal, J.C. and Prins, R.A. (1994) The evolutionary origin of hydrogenosomes from anaerobic fungi. In: Micro-organisms in ruminant nutrition. (Prins, R.A. and C.S. Stewart, Eds). Nottingham University Press, Nottingham, UK. 195-208.