<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Burand, John P</style></author><author><style face="normal" font="default" size="100%">Kim, Woojin</style></author><author><style face="normal" font="default" size="100%">Afonso, Claudio L</style></author><author><style face="normal" font="default" size="100%">Tulman, Edan R</style></author><author><style face="normal" font="default" size="100%">Kutish, Gerald F</style></author><author><style face="normal" font="default" size="100%">Lu, Zhiqiang</style></author><author><style face="normal" font="default" size="100%">Rock, Daniel L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of the genome of the sexually transmitted insect virus Helicoverpa zea nudivirus 2.</style></title><secondary-title><style face="normal" font="default" size="100%">Viruses</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Viruses</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Baculoviridae</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Viruses</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Viral</style></keyword><keyword><style  face="normal" font="default" size="100%">Insect Viruses</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Moths</style></keyword><keyword><style  face="normal" font="default" size="100%">Open Reading Frames</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Viral Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">28-61</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22355451?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Heat-shock sigma factor RpoH from Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Heat-Shock Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">153</style></volume><pages><style face="normal" font="default" size="100%">838-46</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Recent studies with Myxococcus xanthus have suggested that homologues of the Escherichia coli heat-shock sigma factor, RpoH, may not be involved in the heat-shock response in this delta-proteobacterium. The genome of another delta-proteobacterium, Geobacter sulfurreducens, which is considered to be a representative of the Fe(III)-reducing Geobacteraceae that predominate in a diversity of subsurface environments, contains an rpoH homologue. Characterization of the G. sulfurreducens rpoH homologue revealed that it was induced by a temperature shift from 30 degrees C to 42 degrees C and that an rpoH-deficient mutant was unable to grow at 42 degrees C. The predicted heat-shock genes, hrcA, grpE, dnaK, groES and htpG, were heat-shock inducible in an rpoH-dependent manner, and comparison of promoter regions of these genes identified the consensus sequences for the -10 and -35 promoter elements. In addition, DNA elements identical to the CIRCE consensus sequence were found in promoters of rpoH, hrcA and groES, suggesting that these genes are regulated by a homologue of the repressor HrcA, which is known to bind the CIRCE element. These results suggest that the G. sulfurreducens RpoH homologue is the heat-shock sigma factor and that heat-shock response in G. sulfurreducens is regulated positively by RpoH as well as negatively by the HrcA/CIRCE system.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17322204?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jara, Mónica</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Campoy, Susana</style></author><author><style face="normal" font="default" size="100%">Fernández de Henestrosa, Antonio R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Barbé, Jordi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter sulfurreducens has two autoregulated lexA genes whose products do not bind the recA promoter: differing responses of lexA and recA to DNA damage.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Damage</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Polymerase beta</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Repair</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoretic Mobility Shift Assay</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Serine Endopeptidases</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">185</style></volume><pages><style face="normal" font="default" size="100%">2493-502</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Escherichia coli LexA protein was used as a query sequence in TBLASTN searches to identify the lexA gene of the delta-proteobacterium Geobacter sulfurreducens from its genome sequence. The results of the search indicated that G. sulfurreducens has two independent lexA genes designated lexA1 and lexA2. A copy of a dinB gene homologue, which in E. coli encodes DNA polymerase IV, is present downstream of each lexA gene. Reverse transcription-PCR analyses demonstrated that, in both cases, lexA and dinB constitute a single transcriptional unit. Electrophoretic mobility shift assays with purified LexA1 and LexA2 proteins have shown that both proteins bind the imperfect palindrome GGTTN(2)CN(4)GN(3)ACC found in the promoter region of both lexA1 and lexA2. This sequence is also present upstream of the Geobacter metallireducens lexA gene, indicating that it is the LexA box of this bacterial genus. This palindrome is not found upstream of either the G. sulfurreducens or the G. metallireducens recA genes. Furthermore, DNA damage induces expression of the lexA-dinB transcriptional unit but not that of the recA gene. However, the basal level of recA gene expression is dramatically higher than that of the lexA gene. Likewise, the promoters of the G. sulfurreducens recN, ruvAB, ssb, umuDC, uvrA, and uvrB genes do not contain the LexA box and are not likely to bind to the LexA1 or LexA2 proteins. G. sulfurreducens is the first bacterial species harboring a lexA gene for which a constitutive expression of its recA gene has been described.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12670973?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Brendel, V</style></author><author><style face="normal" font="default" size="100%">Brocchieri, L</style></author><author><style face="normal" font="default" size="100%">Sandler, S J</style></author><author><style face="normal" font="default" size="100%">Clark, A J</style></author><author><style face="normal" font="default" size="100%">Karlin, S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Evol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Evol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaeal Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Cycle Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Rad51 Recombinase</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">44</style></volume><pages><style face="normal" font="default" size="100%">528-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9115177?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Duran, E</style></author><author><style face="normal" font="default" size="100%">Komuniecki, R W</style></author><author><style face="normal" font="default" size="100%">Komuniecki, P R</style></author><author><style face="normal" font="default" size="100%">Wheelock, M J</style></author><author><style face="normal" font="default" size="100%">Klingbeil, M M</style></author><author><style face="normal" font="default" size="100%">Ma, Y C</style></author><author><style face="normal" font="default" size="100%">Johnson, K R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">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.</style></title><secondary-title><style face="normal" font="default" size="100%">J Biol Chem</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Biol. Chem.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Ascaris suum</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Cloning, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Complementary</style></keyword><keyword><style  face="normal" font="default" size="100%">Fatty Acid Desaturases</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Library</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Mitochondria</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotides, Antisense</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases Acting on CH-CH Group Donors</style></keyword><keyword><style  face="normal" font="default" size="100%">Poly A</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1993</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1993 Oct 25</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">268</style></volume><pages><style face="normal" font="default" size="100%">22391-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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' 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'-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.</style></abstract><issue><style face="normal" font="default" size="100%">30</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/7693666?dopt=Abstract</style></custom1></record></records></xml>