@article {677,
	title = {ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.},
	journal = {Nucleic Acids Res},
	volume = {38},
	year = {2010},
	month = {2010 Jul},
	pages = {W529-33},
	abstract = {It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.},
	keywords = {Amino Acid Sequence, Base Sequence, Conserved Sequence, Evolution, Molecular, Internet, Nucleic Acid Conformation, Protein Conformation, Sequence Analysis, Sequence Homology, Amino Acid, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkq399},
	author = {Ashkenazy, Haim and Erez, Elana and Martz, Eric and Pupko, Tal and Ben-Tal, Nir}
}
@article {470,
	title = {Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.},
	journal = {BMC Genomics},
	volume = {9},
	year = {2008},
	month = {2008},
	pages = {471},
	abstract = {BACKGROUND: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells.

RESULTS: The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors sigma28 and sigma54 play a role in regulating the Geobacter chemotaxis gene expression.

CONCLUSION: The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Chemotaxis, Escherichia coli, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Geobacter, Membrane Proteins, Molecular Sequence Data, Multigene Family, Promoter Regions, Genetic, Sequence Alignment, Sequence Homology, Amino Acid},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-9-471},
	author = {Tran, Hoa T and Krushkal, Julia and Antommattei, Frances M and Lovley, Derek R and Weis, Robert M}
}
@article {692,
	title = {PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidylinositol mannoside in mycobacteria.},
	journal = {J Biol Chem},
	volume = {281},
	year = {2006},
	month = {2006 Sep 1},
	pages = {25143-55},
	abstract = {Phosphatidylinositol mannosides (PIMs) are a major class of glycolipids in all mycobacteria. AcPIM2, a dimannosyl PIM, is both an end product and a precursor for polar PIMs, such as hexamannosyl PIM (AcPIM6) and the major cell wall lipoglycan, lipoarabinomannan (LAM). The mannosyltransferases that convert AcPIM2 to AcPIM6 or LAM are dependent on polyprenol-phosphate-mannose (PPM), but have not yet been characterized. Here, we identified a gene, termed pimE that is present in all mycobacteria, and is required for AcPIM6 biosynthesis. PimE was initially identified based on homology with eukaryotic PIG-M mannosyltransferases. PimE-deleted Mycobacterium smegmatis was defective in AcPIM6 synthesis, and accumulated the tetramannosyl PIM, AcPIM4. Loss of PimE had no affect on cell growth or viability, or the biosynthesis of other intracellular and cell wall glycans. However, changes in cell wall hydrophobicity and plasma membrane organization were detected, suggesting a role for AcPIM6 in the structural integrity of the cell wall and plasma membrane. These defects were corrected by ectopic expression of the pimE gene. Metabolic pulse-chase radiolabeling and cell-free PIM biosynthesis assays indicated that PimE catalyzes the alpha1,2-mannosyl transfer for the AcPIM5 synthesis. Mutation of an Asp residue in PimE that is conserved in and required for the activity of human PIG-M resulted in loss of PIM-biosynthetic activity, indicating that PimE is the catalytic component. Finally, PimE was localized to a distinct membrane fraction enriched in AcPIM4-6 biosynthesis. Taken together, PimE represents the first PPM-dependent mannosyl-transferase shown to be involved in PIM biosynthesis, where it mediates the fifth mannose transfer.},
	keywords = {Amino Acid Sequence, Cell Proliferation, Cell Wall, Cell-Free System, Genome, Bacterial, Humans, Mannose, Mannosides, Mannosyltransferases, Molecular Sequence Data, Mycobacterium, Mycobacterium smegmatis, Phosphates, Phosphatidylinositols, Sequence Homology, Amino Acid},
	issn = {0021-9258},
	doi = {10.1074/jbc.M604214200},
	author = {Morita, Yasu S and Sena, Chubert B C and Waller, Ross F and Kurokawa, Ken and Sernee, M Fleur and Nakatani, Fumiki and Haites, Ruth E and Billman-Jacobe, Helen and McConville, Malcolm J and Maeda, Yusuke and Kinoshita, Taroh}
}
@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 {774,
	title = {Quorum sensing in Staphylococci is regulated via phosphorylation of three conserved histidine residues.},
	journal = {J Biol Chem},
	volume = {279},
	year = {2004},
	month = {2004 Apr 9},
	pages = {14665-72},
	abstract = {Staphylococcus aureus cause infections by producing toxins, a process regulated by cell-cell communication (quorum sensing) through the histidine-phosphorylation of the target of RNAIII-activating protein (TRAP). We show here that TRAP is highly conserved in staphylococci and contains three completely conserved histidine residues (His-66, His-79, His-154) that are phosphorylated and essential for its activity. This was tested by constructing a TRAP(-) strain with each of the conserved histidine residues changed to alanine by site-directed mutagenesis. All mutants were tested for pathogenesis in vitro (expression of RNAIII and hemolytic activity) and in vivo (murine cellulitis model). Results show that RNAIII is not expressed in the TRAP(-) strain, that it is non hemolytic, and that it does not cause disease in vivo. These pathogenic phenotypes could be rescued in the strain containing the recovered traP, confirming the importance of TRAP in S. aureus pathogenesis. The phosphorylation of TRAP mutated in any of the conserved histidine residues was significantly reduced, and mutants defective in any one of these residues were non-pathogenic in vitro or in vivo, whereas those mutated in a non-conserved histidine residue (His-124) were as pathogenic as the wild type. These results confirm the importance of the three conserved histidine residues in TRAP activity. The phosphorylation pattern, structure, and gene organization of TRAP deviates from signaling molecules known to date, suggesting that TRAP belongs to a novel class of signal transducers.},
	keywords = {Amino Acid Sequence, Animals, Blotting, Northern, Cell Communication, DNA, Electrophoresis, Polyacrylamide Gel, Escherichia coli, Histidine, Mice, Molecular Sequence Data, Mutagenesis, Mutagenesis, Site-Directed, Mutation, Phenotype, Phosphorylation, Phylogeny, Plasmids, Protein Structure, Tertiary, RNA, Antisense, RNA, Bacterial, Sequence Homology, Amino Acid, Signal Transduction, Staphylococcus aureus, Time Factors},
	issn = {0021-9258},
	doi = {10.1074/jbc.M311106200},
	author = {Gov, Yael and Borovok, Ilya and Korem, Moshe and Singh, Vineet K and Jayaswal, Radheshyam K and Wilkinson, Brian J and Rich, Stephen M and Balaban, Naomi}
}
@article {576,
	title = {Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens.},
	journal = {Biochem J},
	volume = {369},
	year = {2003},
	month = {2003 Jan 1},
	pages = {153-61},
	abstract = {A 9.6 kDa periplasmic c -type cytochrome, designated PpcA, was purified from the Fe(III)-reducing bacterium Geobacter sulfurreducens and characterized. The purified protein is basic (pI 9.5), contains three haems and has an N-terminal amino acid sequence closely related to those of the previously described trihaem c (7) cytochromes of Geobacter metallireducens and Desulfuromonas acetoxidans. The gene encoding PpcA was identified from the G. sulfurreducens genome using the N-terminal sequence, and encodes a protein of 71 amino acids (molecular mass 9.58 kDa) with 49\% identity to the c (7) cytochrome of D. acetoxidans. In order to determine the physiological role of PpcA, a knockout mutant was prepared with a single-step recombination method. Acetate-dependent Fe(III) reduction was significantly inhibited in both growing cultures and cell suspensions of the mutant. When ppcA was expressed in trans, the full capacity for Fe(III) reduction with acetate was restored. The transfer of electrons from acetate to anthraquinone 2,6-disulphonate (AQDS; a humic acid analogue) and to U(VI) was also compromised in the mutant, but acetate-dependent reduction of fumarate was not altered. The rates of reduction of Fe(III), AQDS, U(VI) and fumarate were also the same in the wild type and ppcA mutant when hydrogen was supplied as the electron donor. When taken together with previous studies on other electron transport proteins in G. sulfurreducens, these results suggest that PpcA serves as an intermediary electron carrier from acetate to terminal Fe(III) reductases in the outer membrane, and is also involved in the transfer of electrons from acetate to U(VI) and humics.},
	keywords = {Amino Acid Sequence, Base Sequence, Cytochrome c Group, DNA, Bacterial, Molecular Sequence Data, Periplasm, Proteobacteria, Sequence Homology, Amino Acid},
	issn = {0264-6021},
	doi = {10.1042/BJ20020597},
	author = {Lloyd, Jon R and Leang, Ching and Hodges Myerson, Allison L and Coppi, Maddalena V and Cuifo, Stacey and Methe, Barb and Sandler, Steven J and Lovley, Derek R}
}
@article {571,
	title = {OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {185},
	year = {2003},
	month = {2003 Apr},
	pages = {2096-103},
	abstract = {Microorganisms in the family Geobacteraceae are the predominant Fe(III)-reducing microorganisms in a variety of subsurface environments in which Fe(III) reduction is an important process, but little is known about the mechanisms for electron transport to Fe(III) in these organisms. The Geobacter sulfurreducens genome was found to contain a 10-kb chromosomal duplication consisting of two tandem three-gene clusters. The last genes of the two clusters, designated omcB and omcC, encode putative outer membrane polyheme c-type cytochromes which are 79\% identical. The role of the omcB and omcC genes in Fe(III) reduction in G. sulfurreducens was investigated. OmcB and OmcC were both expressed during growth with acetate as the electron donor and either fumarate or Fe(III) as the electron acceptor. OmcB was ca. twofold more abundant under both conditions. Disrupting omcB or omcC by gene replacement had no impact on growth with fumarate. However, the OmcB-deficient mutant was greatly impaired in its ability to reduce Fe(III) both in cell suspensions and under growth conditions. In contrast, the ability of the OmcC-deficient mutant to reduce Fe(III) was similar to that of the wild type. When omcB was reintroduced into the OmcB-deficient mutant, the capacity for Fe(III) reduction was restored in proportion to the level of OmcB production. These results indicate that OmcB, but not OmcC, has a major role in electron transport to Fe(III) and suggest that electron transport to the outer membrane is an important feature in Fe(III) reduction in this organism.},
	keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Bacterial Proteins, Cytochrome c Group, Deltaproteobacteria, Gene Expression Regulation, Bacterial, Iron, Molecular Sequence Data, Multigene Family, Mutation, Oxidation-Reduction, Sequence Homology, Amino Acid},
	issn = {0021-9193},
	author = {Leang, Ching and Coppi, M V and Lovley, D R}
}
@article {388,
	title = {Multiple mitochondrial DNA polymerases in Trypanosoma brucei.},
	journal = {Mol Cell},
	volume = {10},
	year = {2002},
	month = {2002 Jul},
	pages = {175-86},
	abstract = {Kinetoplast DNA (kDNA), the unusual mitochondrial DNA of Trypanosoma brucei, is a network containing thousands of catenated circles. Database searching for a kDNA replicative polymerase (pol) revealed no mitochondrial pol gamma homolog. Instead, we identified four proteins (TbPOLIA, IB, IC, and ID) related to bacterial pol I. Remarkably, all four localized to the mitochondrion. TbPOLIB and TbPOLIC localized beside the kDNA where replication occurs, and their knockdown by RNA interference caused kDNA network shrinkage. Furthermore, silencing of TbPOLIC caused loss of both minicircles and maxicircles and accumulation of minicircle replication intermediates, consistent with a role in replication. While typical mitochondria contain one DNA polymerase, pol gamma, trypanosome mitochondria contain five such enzymes, including the previously characterized pol beta.},
	keywords = {Amino Acid Sequence, Animals, DNA, Kinetoplast, DNA-Directed DNA Polymerase, Mitochondria, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Protein Transport, RNA, Double-Stranded, RNA, Messenger, Sequence Homology, Amino Acid, Trypanosoma brucei brucei},
	issn = {1097-2765},
	author = {Klingbeil, Michele M and Motyka, Shawn A and Englund, Paul T}
}
@article {592,
	title = {Isolation and characterization of a soluble NADPH-dependent Fe(III) reductase from Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {183},
	year = {2001},
	month = {2001 Aug},
	pages = {4468-76},
	abstract = {NADPH is an intermediate in the oxidation of organic compounds coupled to Fe(III) reduction in Geobacter species, but Fe(III) reduction with NADPH as the electron donor has not been studied in these organisms. Crude extracts of Geobacter sulfurreducens catalyzed the NADPH-dependent reduction of Fe(III)-nitrilotriacetic acid (NTA). The responsible enzyme, which was recovered in the soluble protein fraction, was purified to apparent homogeneity in a four-step procedure. Its specific activity for Fe(III) reduction was 65 micromol. min(-1). mg(-1). The soluble Fe(III) reductase was specific for NADPH and did not utilize NADH as an electron donor. Although the enzyme reduced several forms of Fe(III), Fe(III)-NTA was the preferred electron acceptor. The protein possessed methyl viologen:NADP(+) oxidoreductase activity and catalyzed the reduction of NADP(+) with reduced methyl viologen as electron donor at a rate of 385 U/mg. The enzyme consisted of two subunits with molecular masses of 87 and 78 kDa and had a native molecular mass of 320 kDa, as determined by gel filtration. The purified enzyme contained 28.9 mol of Fe, 17.4 mol of acid-labile sulfur, and 0.7 mol of flavin adenine dinucleotide per mol of protein. The genes encoding the two subunits were identified in the complete sequence of the G. sulfurreducens genome from the N-terminal amino acid sequences derived from the subunits of the purified protein. The sequences of the two subunits had about 30\% amino acid identity to the respective subunits of the formate dehydrogenase from Moorella thermoacetica, but the soluble Fe(III) reductase did not possess formate dehydrogenase activity. This soluble Fe(III) reductase differs significantly from previously characterized dissimilatory and assimilatory Fe(III) reductases in its molecular composition and cofactor content.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Deltaproteobacteria, Ferric Compounds, FMN Reductase, Molecular Sequence Data, NADH, NADPH Oxidoreductases, NADP, Nitrilotriacetic Acid, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Solubility},
	issn = {0021-9193},
	doi = {10.1128/JB.183.15.4468-4476.2001},
	author = {Kaufmann, F and Lovley, D R}
}
@article {590,
	title = {Isolation, characterization and gene sequence analysis of a membrane-associated 89 kDa Fe(III) reducing cytochrome c from Geobacter sulfurreducens.},
	journal = {Biochem J},
	volume = {359},
	year = {2001},
	month = {2001 Oct 1},
	pages = {147-52},
	abstract = {Geobacter sulfurreducens is capable of anaerobic respiration with Fe(III) as a terminal electron acceptor via a membrane-bound Fe(III) reductase activity associated with a large molecular mass cytochrome c. This cytochrome was purified by detergent extraction of the membrane fraction, Q-Sepharose ion-exchange chromatography, preparative electrophoresis, and MonoQ ion-exchange chromatography. Spectrophotometric analysis of the purified cytochrome reveals a c-type haem, with no evidence of haem a, haem b or sirohaem. The cytochrome has an M(r) of 89000 as determined by denaturing PAGE, and has an isoelectric point of 5.2 as determined by analytical isoelectric focusing. Dithionite-reduced cytochrome can donate electrons to Fe(III)-nitrilotriacetic acid and synthetic ferrihydrite, thus demonstrating that the cytochrome has redox and thermodynamic properties required for reduction of Fe(III). Analysis using cyclic voltammetry confirmed that the reduced cytochrome can catalytically transfer electrons to ferrihydrite, further demonstrating its ability to be an electron transport mediator in anaerobic Fe(III) respiration. Sequence analysis of a cloned chromosomal DNA fragment revealed a 2307 bp open reading frame (ferA) encoding a 768 amino acid protein corresponding to the 89 kDa cytochrome. The deduced amino acid sequence (FerA) translated from the open reading frame contained 12 putative haem-binding motifs, as well as a hydrophobic N-terminal membrane anchor sequence, a lipid-attachment site and an ATP/GTP-binding site. FerA displayed 20\% or less identity with amino acid sequences of other known cytochromes, although it does share some features with characterized polyhaem cytochromes c.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Chromatography, Ion Exchange, Cloning, Molecular, Cytochrome c Group, Deltaproteobacteria, DNA Primers, Electron Transport, Electrophoresis, Polyacrylamide Gel, Ferric Compounds, Gene Expression Regulation, Bacterial, Molecular Sequence Data, Molecular Weight, Nitrilotriacetic Acid, Oxidation-Reduction, Polymerase Chain Reaction, Sequence Homology, Amino Acid},
	issn = {0264-6021},
	author = {Magnuson, T S and Isoyama, N and Hodges-Myerson, A L and Davidson, G and Maroney, M J and Geesey, G G and Lovley, D R}
}
@article {794,
	title = {Plasmodium falciparum antigenic diversity: evidence of clonal population structure.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {94},
	year = {1997},
	month = {1997 Nov 25},
	pages = {13040-5},
	abstract = {Plasmodium falciparum, the agent of malignant malaria, is one of mankind{\textquoteright}s most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite{\textquoteright}s rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal--a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.},
	keywords = {Amino Acid Sequence, Animals, Antigens, Protozoan, Molecular Sequence Data, Phylogeny, Plasmodium falciparum, Polymorphism, Genetic, Protozoan Proteins, Recombination, Genetic, Sequence Homology, Amino Acid},
	issn = {0027-8424},
	author = {Rich, S M and Hudson, R R and Ayala, F J}
}
@article {391,
	title = {Identification of a novel dihydrolipoyl dehydrogenase-binding protein in the pyruvate dehydrogenase complex of the anaerobic parasitic nematode, Ascaris suum.},
	journal = {J Biol Chem},
	volume = {271},
	year = {1996},
	month = {1996 Mar 8},
	pages = {5451-7},
	abstract = {A novel dihydrolipoyl dehydrogenase-binding protein (E3BP) which lacks an amino-terminal lipoyl domain, p45, has been identified in the pyruvate dehydrogenase complex (PDC) of the adult parasitic nematode, Ascaris suum. Sequence at the amino terminus of p45 exhibited significant similarity with internal E3-binding domains of dihydrolipoyl transacetylase (E2) and E3BP. Dissociation and resolution of a pyruvate dehydrogenase-depleted adult A. suum PDC in guanidine hydrochloride resulted in two E3-depleted E2 core preparations which were either enriched or substantially depleted of p45. Following reconstitution, the p45-enriched E2 core exhibited enhanced E3 binding, whereas, the p45-depleted E2 core exhibited dramatically reduced E3 binding. Reconstitution of either the bovine kidney or A. suum PDCs with the A. suum E3 suggested that the ascarid E3 was more sensitive to NADH inhibition when bound to the bovine kidney core. The expression of p45 was developmentally regulated and p45 was most abundant in anaerobic muscle. In contrast, E3s isolated from anaerobic muscle or aerobic second-stage larvae were identical. These results suggest that during the transition to anaerobic metabolism, E3 remains unchanged, but it appears that a novel E3BP, p45, is expressed which may help to maintain the activity of the PDC in the face of the elevated intramitochondrial NADH/NAD+ ratios associated with anaerobiosis.},
	keywords = {Amino Acid Sequence, Anaerobiosis, Animals, Ascaris suum, Binding Sites, Carrier Proteins, Dihydrolipoamide Dehydrogenase, Electrophoresis, Polyacrylamide Gel, Flavin-Adenine Dinucleotide, Helminth Proteins, Kinetics, Larva, Molecular Sequence Data, NAD, Oxidation-Reduction, Pyruvate Dehydrogenase Complex, Sequence Homology, Amino Acid},
	issn = {0021-9258},
	author = {Klingbeil, M M and Walker, D J and Arnette, R and Sidawy, E and Hayton, K and Komuniecki, P R and Komuniecki, R}
}
@article {392,
	title = {Characterization of cDNA clones for the 2-methyl branched-chain enoyl-CoA reductase. An enzyme involved in branched-chain fatty acid synthesis in anaerobic mitochondria of the parasitic nematode Ascaris suum.},
	journal = {J Biol Chem},
	volume = {268},
	year = {1993},
	month = {1993 Oct 25},
	pages = {22391-6},
	abstract = {The 2-methyl branched-chain enoyl-CoA reductase plays a pivotal role in the reversal of beta-oxidation operating in anaerobic mitochondria of the parasitic nematode Ascaris suum. An affinity-purified polyclonal anti-serum against the reductase was used to screen a cDNA library constructed in lambda gt11 with poly(A)+ RNA from adult A. suum muscle. A 1.2-kilobase partial cDNA clone was isolated, subcloned, and sequenced in both directions. Additional sequence at the 5{\textquoteright} end of the mRNA was determined by the RACE (rapid amplification of cDNA ends) procedure. Nucleotide sequence analysis of the cDNAs revealed the 22-nucleotide trans-spliced leader sequence characteristic of many nematode mRNAs, an open reading frame of 1236 nucleotides and a 3{\textquoteright}-untranslated sequence of 109 nucleotides including a short poly(A) tail 14 nucleotides from a polyadenylation signal (AATAAA). The open reading frame encoded a 396-amino acid sequence (M(r) 43,046) including a 16-amino acid leader peptide. Two-dimensional gel electrophoresis of the purified reductase yielded multiple spots with two distinct but overlapping amino-terminal amino acid sequences. Both sequences overlapped with the sequence predicted from the mRNA, and one of the sequences was identical to the predicted sequence. Comparison of the ascarid sequence with that of mammalian acyl-CoA dehydrogenases revealed a high degree of sequence identity, suggesting that these enzymes may have evolved from a common ancestral gene even though the ascarid enzyme functions as a reductase, not as a dehydrogenase. Immunoblotting of A. suum larval stages and adult tissues with antisera that cross-reacted with each of the spots separated on two-dimensional gels suggested that the reductase was only found in adult muscle. Northern blotting using the partial cDNA revealed a hybridization band of about 1.5 kilobases and also suggested that the enzyme was tissue-specific and developmentally regulated in agreement with the results of the immunoblotting.},
	keywords = {Amino Acid Sequence, Anaerobiosis, Animals, Ascaris suum, Base Sequence, Cloning, Molecular, Consensus Sequence, DNA, DNA Primers, DNA, Complementary, Fatty Acid Desaturases, Gene Library, Humans, Mitochondria, Molecular Sequence Data, Oligonucleotides, Antisense, Oxidoreductases, Oxidoreductases Acting on CH-CH Group Donors, Poly A, RNA, RNA, Messenger, Sequence Homology, Amino Acid},
	issn = {0021-9258},
	author = {Duran, E and Komuniecki, R W and Komuniecki, P R and Wheelock, M J and Klingbeil, M M and Ma, Y C and Johnson, K R}
}
