@article {356,
	title = {Analysis of the genome of the sexually transmitted insect virus Helicoverpa zea nudivirus 2.},
	journal = {Viruses},
	volume = {4},
	year = {2012},
	month = {2012 Jan},
	pages = {28-61},
	abstract = {The sexually transmitted insect virus Helicoverpa zea nudivirus 2 (HzNV-2) was determined to have a circular double-stranded DNA genome of 231,621 bp coding for an estimated 113 open reading frames (ORFs). HzNV-2 is most closely related to the nudiviruses, a sister group of the insect baculoviruses. Several putative ORFs that share homology with the baculovirus core genes were identified in the viral genome. However, HzNV-2 lacks several key genetic features of baculoviruses including the late transcriptional regulation factor, LEF-1 and the palindromic hrs, which serve as origins of replication. The HzNV-2 genome was found to code for three ORFs that had significant sequence homology to cellular genes which are not generally found in viral genomes. These included a presumed juvenile hormone esterase gene, a gene coding for a putative zinc-dependent matrix metalloprotease, and a major facilitator superfamily protein gene; all of which are believed to play a role in the cellular proliferation and the tissue hypertrophy observed in the malformation of reproductive organs observed in HzNV-2 infected corn earworm moths, Helicoverpa zea.},
	keywords = {Amino Acid Sequence, Animals, Baculoviridae, Base Sequence, Biological Evolution, Consensus Sequence, DNA Viruses, Female, Genome, Viral, Insect Viruses, Molecular Sequence Data, Moths, Open Reading Frames, Phylogeny, Sequence Alignment, Sequence Homology, Species Specificity, Viral Proteins},
	issn = {1999-4915},
	doi = {10.3390/v4010028},
	author = {Burand, John P and Kim, Woojin and Afonso, Claudio L and Tulman, Edan R and Kutish, Gerald F and Lu, Zhiqiang and Rock, Daniel L}
}
@article {360,
	title = {Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade.},
	journal = {J Gen Virol},
	volume = {90},
	year = {2009},
	month = {2009 Feb},
	pages = {334-46},
	abstract = {Glossina pallidipes and Musca domestica salivary gland hypertrophy viruses (GpSGHV and MdSGHV) replicate in the nucleus of salivary gland cells causing distinct tissue hypertrophy and reduction of host fertility. They share general characteristics with the non-occluded insect nudiviruses, such as being insect-pathogenic, having enveloped, rod-shaped virions, and large circular double-stranded DNA genomes. MdSGHV measures 65x550 nm and contains a 124 279 bp genome (approximately 44 mol\% G+C content) that codes for 108 putative open reading frames (ORFs). GpSGHV, measuring 50x1000 nm, contains a 190 032 bp genome (28 mol\% G+C content) with 160 putative ORFs. Comparative genomic analysis demonstrates that 37 MdSGHV ORFs have homology to 42 GpSGHV ORFs, as some MdSGHV ORFs have homology to two different GpSGHV ORFs. Nine genes with known functions (dnapol, ts, pif-1, pif-2, pif-3, mmp, p74, odv-e66 and helicase-2), a homologue of the conserved baculovirus gene Ac81 and at least 13 virion proteins are present in both SGHVs. The amino acid identity ranged from 19 to 39 \% among ORFs. An (A/T/G)TAAG motif, similar to the baculovirus late promoter motif, was enriched 100 bp upstream of the ORF transcription initiation sites of both viruses. Six and seven putative microRNA sequences were found in MdSGHV and GpSGHV genomes, respectively. There was genome. Collinearity between the two SGHVs, but not between the SGHVs and the nudiviruses. Phylogenetic analysis of conserved genes clustered both SGHVs in a single clade separated from the nudiviruses and baculoviruses. Although MdSGHV and GpSGHV are different viruses, their pathology, host range and genome composition indicate that they are related.},
	keywords = {Animals, Chromosome Mapping, Conserved Sequence, Cytomegalovirus, DNA, Viral, Genes, Viral, Genome, Viral, Houseflies, Hypertrophy, Open Reading Frames, Salivary Glands, Tsetse Flies, Virion},
	issn = {0022-1317},
	doi = {10.1099/vir.0.006783-0},
	author = {Garcia-Maruniak, Alejandra and Abd-Alla, Adly M M and Salem, Tamer Z and Parker, Andrew G and Lietze, Verena-Ulrike and van Oers, Monique M and Maruniak, James E and Kim, Woojin and Burand, John P and Cousserans, Fran{\c c}ois and Robinson, Alan S and Vlak, Just M and Bergoin, Max and Boucias, Drion G}
}
@article {698,
	title = {PIG-V involved in transferring the second mannose in glycosylphosphatidylinositol.},
	journal = {J Biol Chem},
	volume = {280},
	year = {2005},
	month = {2005 Mar 11},
	pages = {9489-97},
	abstract = {Glycosylphosphatidylinositol (GPI) is a glycolipid that anchors many proteins to the eukaryotic cell surface. The biosynthetic pathway of GPI is mediated by sequential additions of sugars and other components to phosphatidylinositol. Four mannoses in the GPI are transferred from dolichol-phosphate-mannose (Dol-P-Man) and are linked through different glycosidic linkages. Therefore, four Dol-P-Man-dependent mannosyltransferases, GPI-MT-I, -MT-II, -MT-III, and -MT-IV for the first, second, third, and fourth mannoses, respectively, are required for generation of GPI. GPI-MT-I (PIG-M), GPI-MT-III (PIG-B), and GPI-MT-IV (SMP3) were previously reported, but GPI-MT-II remains to be identified. Here we report the cloning of PIG-V involved in transferring the second mannose in the GPI anchor. Human PIG-V encodes a 493-amino acid, endoplasmic reticulum (ER) resident protein with eight putative transmembrane regions. Saccharomyces cerevisiae protein encoded in open reading frame YBR004c, which we termed GPI18, has 25\% amino acid identity to human PIG-V. Viability of the yeast gpi18 deletion mutant was restored by human PIG-V cDNA. PIG-V has two functionally important conserved regions facing the ER lumen. Taken together, we suggest that PIG-V is the second mannosyltransferase in GPI anchor biosynthesis.},
	keywords = {Amino Acid Sequence, Animals, Cell Line, Tumor, CHO Cells, Cloning, Molecular, Conserved Sequence, Cricetinae, DNA Primers, Glioma, Glycosylphosphatidylinositols, Humans, Mannose, Mannosyltransferases, Molecular Sequence Data, Open Reading Frames, Rats, Restriction Mapping, Saccharomyces cerevisiae, Sequence Alignment, Sequence Homology, Amino Acid},
	issn = {0021-9258},
	doi = {10.1074/jbc.M413867200},
	author = {Kang, Ji Young and Hong, Yeongjin and Ashida, Hisashi and Shishioh, Nobue and Murakami, Yoshiko and Morita, Yasu S and Maeda, Yusuke and Kinoshita, Taroh}
}
@article {562,
	title = {Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.},
	journal = {Science},
	volume = {302},
	year = {2003},
	month = {2003 Dec 12},
	pages = {1967-9},
	abstract = {The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.},
	keywords = {Acetates, Acetyl Coenzyme A, Aerobiosis, Anaerobiosis, Bacterial Proteins, Carbon, Chemotaxis, Chromosomes, Bacterial, Cytochromes c, Electron Transport, Energy Metabolism, Genes, Bacterial, Genes, Regulator, Genome, Bacterial, Geobacter, Hydrogen, Metals, Movement, Open Reading Frames, Oxidation-Reduction, Phylogeny},
	issn = {1095-9203},
	doi = {10.1126/science.1088727},
	author = {Meth{\'e}, B A and Nelson, K E and Eisen, J A and Paulsen, I T and Nelson, W and Heidelberg, J F and Wu, D and Wu, M and Ward, N and Beanan, M J and Dodson, R J and Madupu, R and Brinkac, L M and Daugherty, S C and DeBoy, R T and Durkin, A S and Gwinn, M and Kolonay, J F and Sullivan, S A and Haft, D H and Selengut, J and Davidsen, T M and Zafar, N and White, O and Tran, B and Romero, C and Forberger, H A and Weidman, J and Khouri, H and Feldblyum, T V and Utterback, T R and Van Aken, S E and Lovley, D R and Fraser, C M}
}
@article {780,
	title = {Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.},
	journal = {Mol Biol Evol},
	volume = {19},
	year = {2002},
	month = {2002 May},
	pages = {619-30},
	abstract = {Mobile elements that use reverse transcriptase to make new copies of themselves are found in all major lineages of eukaryotes. The non-long terminal repeat (non-LTR) retrotransposons have been suggested to be the oldest of these eukaryotic elements. Phylogenetic analysis of non-LTR elements suggests that they have predominantly undergone vertical transmission, as opposed to the frequent horizontal transmissions found for other mobile elements. One prediction of this vertical model of inheritance is that the oldest lineages of eukaryotes should exclusively harbor the oldest lineages of non-LTR retrotransposons. Here we characterize the non-LTR retrotransposons present in one of the most primitive eukaryotes, the diplomonad Giardia lamblia. Two families of elements were detected in the WB isolate of G. lamblia currently being used for the genome sequencing project. These elements are clearly distinct from all other previously described non-LTR lineages. Phylogenetic analysis indicates that these Genie elements (for Giardia early non-LTR insertion element) are among the oldest known lineages of non-LTR elements consistent with strict vertical descent. Genie elements encode a single open reading frame with a carboxyl terminal endonuclease domain. Genie 1 is site specific, as seven to eight copies are present in a single tandem array of a 771-bp repeat near the telomere of one chromosome. The function of this repeat is not known. One additional, highly divergent, element within the Genie 1 lineage is not located in this tandem array but is near a second telomere. Four different telomere addition sites could be identified within or near the Genie elements on each of these chromosomes. The second lineage of non-LTR elements, Genie 2, is composed of about 10 degenerate copies. Genie 2 elements do not appear to be site specific in their insertion. An unusual aspect of Genie 2 is that all copies contain inverted repeats up to 172 bp in length.},
	keywords = {Animals, Base Sequence, DNA, Protozoan, Evolution, Molecular, Giardia lamblia, Long Interspersed Nucleotide Elements, Molecular Sequence Data, Open Reading Frames, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Homology, Nucleic Acid, Telomere},
	issn = {0737-4038},
	author = {Burke, William D and Malik, Harmit S and Rich, Stephen M and Eickbush, Thomas H}
}
@article {831,
	title = {Replication fork assembly at recombination intermediates is required for bacterial growth.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {96},
	year = {1999},
	month = {1999 Mar 30},
	pages = {3552-5},
	abstract = {PriA, a 3{\textquoteright} --> 5{\textquoteright} DNA helicase, directs assembly of a primosome on some bacteriophage and plasmid DNAs. Primosomes are multienzyme replication machines that contribute both the DNA-unwinding and Okazaki fragment-priming functions at the replication fork. The role of PriA in chromosomal replication is unclear. The phenotypes of priA null mutations suggest that the protein participates in replication restart at recombination intermediates. We show here that PriA promotes replication fork assembly at a D loop, an intermediate formed during initiation of homologous recombination. We also show that DnaC810, encoded by a naturally arising intergenic suppressor allele of the priA2::kan mutation, bypasses the need for PriA during replication fork assembly at D loops in vitro. These findings underscore the essentiality of replication fork restart at recombination intermediates under normal growth conditions in bacteria.},
	keywords = {Bacteria, Bacteriophage phi X 174, Base Sequence, DNA Polymerase III, DNA Replication, DNA-Binding Proteins, Escherichia coli, Molecular Sequence Data, Oligodeoxyribonucleotides, Open Reading Frames, Recombination, Genetic, Replication Protein A, Templates, Genetic},
	issn = {0027-8424},
	author = {Liu, J and Xu, L and Sandler, S J and Marians, K J}
}
