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Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes

By Nadja Neumann, Daniel C. Jeffares and Anthony M. Poole

Abstract

The nuclear pore complex (NPC) facilitates transport between nucleus and cytoplasm. The protein constituents of the NPC, termed nucleoporins (Nups), are conserved across a wide diversity of eukaryotes. In apparent exception to this, no nucleoporin genes have been identified in nucleomorph genomes. Nucleomorphs, nuclear remnants of once free-living eukaryotes, took up residence as secondary endosymbionts in cryptomonad and chlorarachniophyte algae. As these genomes are highly reduced, Nup genes may have been lost, or relocated to the host nucleus. However, Nup genes are often poorly conserved between species, so absence may be an artifact of low sequence similarity. We therefore constructed an evolutionary bioinformatic screen to establish whether the apparent absence of Nup genes in nucleomorph genomes is due to genuine absence or the inability of current methods to detect homologues. We searched green plant (Arabidopsis and rice), green alga (Chlamydomonas reinhardtii) and red alga (Cyanidioschyzon merolae) genomes, plus two nucleomorph genomes (Bigelowiella natans and Guillardia theta) with profile hidden Markov models (HMMs) from curated alignments of known vertebrate/yeast Nups. Since the plant, algal and nucleomorph genomes all belong to the kingdom Plantae, and are evolutionarily distant from the outgroup (vertebrate/yeast) training set, we use the plant and algal genomes as internal positive controls for the sensitivity of the searches in nucleomorph genomes. We find numerous Nup homologues in all plant and free-living algal species, but none in either nucleomorph genome. BLAST searches using identified plant and algal Nups also failed to detect nucleomorph homologues. We conclude that nucleomorph Nup genes have either been lost, being replaced by host Nup genes, or, that nucleomorph Nup genes have been transferred to the host nucleus twice independently; once in the evolution of the red algal nucleomorph and once in the green algal nucleomorph

Topics: Original Research
Publisher: Libertas Academica
OAI identifier: oai:pubmedcentral.nih.gov:2674657
Provided by: PubMed Central
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    Citations

    1. (2004). A molecular timeline for the origin of photosynthetic eukaryotes.
    2. (2000). Analysis of the genome sequence of the fl owering plant Arabidopsis thaliana.
    3. (1998). cDNA cloning and analysis of the expression of nucleoporin p45.
    4. (2003). Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    5. (2004). Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle,
    6. (2006). Comparative rates of evolution in endosymbiotic nuclear genomes.
    7. (2006). Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature’s smallest nucleus.
    8. (2002). Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease.
    9. (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
    10. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    11. (2002). Genes for two mitochondrial ribosomal proteins in fl owering plants are derived from their chloroplast or cytosolic counterparts. Plant Cell,
    12. (2004). Genome evolution in yeasts.
    13. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.
    14. (1999). Horizontal gene transfer among genomes: the complexity hypothesis.
    15. (2002). Jam packed genomes--a preliminary, comparative analysis of nucleomorphs.
    16. (2005). Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics.
    17. (2003). Peering through the pore: nuclear pore complex structure, assembly, and function.
    18. (2006). Pfam: clans, web tools and services. Nucleic Acids Res.,
    19. (2004). Photosynthetic eukaryotes unite: endosymbiosis connects the dots.
    20. (2005). Plant organellar protein targeting: a traffi c plan still under construction.
    21. (2004). Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans.
    22. (2006). Protein targeting into the complex plastid of cryptophytes.
    23. (2003). Sequencing and comparison of yeast species to identify genes and regulatory elements.
    24. (1997). The CLUSTAL_X windows interface: fl exible strategies for multiple sequence alignment aided by quality analysis tools.
    25. (2002). The gene encoding Arabidopsis thaliana mitochondrial ribosomal protein S13 is a recent duplication of the gene encoding plastid S13.
    26. (2001). The highly reduced genome of an enslaved algal nucleus.
    27. (2005). The institute for genomic research Osa1 rice genome annotation database.
    28. (2005). The map-based sequence of the rice genome.
    29. (2006). The nuclear pore complex up close.
    30. (2004). The plant nuclear envelope.
    31. (2005). The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure. Genome Biol.,

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