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1
Cao, Bang Phi, and Anh Thi Van Le. "Metal transporter encoding gene families in Fabaceae: II. Cation/H+ exchanger (CAX) encoding genes." Science and Technology Development Journal - Natural Sciences 1, T3 (September 30, 2017): 27–36. http://dx.doi.org/10.32508/stdjns.v1it3.462.
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The plant CAtion/H+ eXchangers (CAX) proteins belong to Ca2+/cation antiporter (CaCA) superfamily. By using in silico methods, the CAX encoding genes in the genome of six legume species have been identified in this work. In examined legume genomes, the CAX genes belong to a small multigenic family. The number of the CAX genes in these legume species is 17 (soybean), 6 (common bean and C. cajan), 5 (M. truncatula and C. arietinum) and 3 genes (L. japonicus), respectively. The legume CAX genes vary in genomic full-length ranging from 1,213 to 11,561 base pairs. All of the genes exhibit introns (from 4 to 11 introns). Their deduced full-length protein sequences range from 248 to 718 amino acids. Theoretical pI values of most (39/42) of legume CAX proteins were less than 7. The secondary structure modelling of protein exhibit transmembrane helix region (from 3 to 11 regions). Half of all (23/42) included 11 transmembrane helix regions. Based on phylogeny analysis, all of the legume CAX were divided into two groups, A and B, each consisting of two subgroups. The phylogeny suggested an ancient gene duplication in the genome of legumes ancestry. The recent gene duplication even was only detected in the soybean genome after the speciation. The expression analysis showed that all of 3 L. japonicus CAX genes expressed in all examined tissues. However, the expression of C. cajan CAX genes was not detected. For each of 4 remaining legumes, the CAX genes were differed in their expression level depending on studied tissues. The tissue-specific expressions of some CAX genes were observed in 5 out of the 6 legume species, except C. cajan.
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Koper, Teresa E., Amal F. El-Sheikh, Jeanette M. Norton, and Martin G. Klotz. "Urease-Encoding Genes in Ammonia-Oxidizing Bacteria." Applied and Environmental Microbiology 70, no. 4 (April 2004): 2342–48. http://dx.doi.org/10.1128/aem.70.4.2342-2348.2004.
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ABSTRACT Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the β-proteobacterium Nitrosospira sp. strain NpAV and the γ-proteobacterium Nitrosococcus oceani. In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively. Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani. Southern analyses revealed two copies of ureC in the Nitrosospira sp. strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani. The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB. In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several β-proteobacterial AOB. Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision. UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences. The UreC proteins from β-proteobacterial AOB formed a distinct monophyletic group. Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other β-proteobacteria. Instead, it appears that urease in β-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of γ- and β-proteobacteria that was initiated before their divergence during speciation. Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from β-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB. These gene sequences are the first publicly available for ure genes from autotrophic AOB.
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Mintz, Keith P., and Paula M. Fives-Taylor. "Identification of Genes Coding for Exported Proteins of Actinobacillus actinomycetemcomitans." Infection and Immunity 67, no. 11 (November 1, 1999): 6217–20. http://dx.doi.org/10.1128/iai.67.11.6217-6220.1999.
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ABSTRACT Random fusions of genomic DNA fragments to a partial gene encoding a signal sequence-deficient bacterial alkaline phosphatase were utilized to screen for exported proteins of Actinobacillus actinomycetemcomitans in Escherichia coli. Twenty-four PhoA+ clones were isolated and sequenced. Membrane localization signals in the form of signal sequences were deduced from most of these sequences. Several of the deduced amino acid sequences were found to be homologous to known exported or membrane-associated proteins. The complete genes corresponding to two of these sequences were isolated from an A. actinomycetemcomitans lambda phage library. One gene was found to be homologous to the outer membrane lipoprotein LolB. The second gene product had homology with a Haemophilus influenzae protein and was localized to the inner membrane of A. actinomycetemcomitans.
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Huang, Guozhong, Bingli Gao, Tom Maier, R. Allen, Eric L. Davis, Thomas J. Baum, and Richard S. Hussey. "A Profile of Putative Parasitism Genes Expressed in the Esophageal Gland Cells of the Root-knot Nematode Meloidogyne incognita." Molecular Plant-Microbe Interactions® 16, no. 5 (May 2003): 376–81. http://dx.doi.org/10.1094/mpmi.2003.16.5.376.
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Identifying parasitism genes encoding proteins secreted from a nematode's esophageal gland cells and injected through its stylet into plant tissue is the key to understanding the molecular basis of nematode parasitism of plants. Meloidogyne incognita parasitism genes were cloned by microaspirating the cytoplasm from the esophageal gland cells of different parasitic stages to provide mRNA to create a gland cell-specific cDNA library by long-distance reverse-transcriptase polymerase chain reaction. Of 2,452 cDNA clones sequenced, deduced protein sequences of 185 cDNAs had a signal peptide for secretion and, thus, could have a role in root-knot nematode parasitism of plants. High-throughput in situ hybridization with cDNA clones encoding signal peptides resulted in probes of 37 unique clones specifically hybridizing to transcripts accumulating within the subventral (13 clones) or dorsal (24 clones) esophageal gland cells of M. incognita. In BLASTP analyses, 73% of the predicted proteins were novel proteins. Those with similarities to known proteins included a pectate lyase, acid phosphatase, and hypothetical proteins from other organisms. Our cell-specific analysis of genes encoding secretory proteins provided, for the first time, a profile of putative parasitism genes expressed in the M. incognita esophageal gland cells throughout the parasitic cycle.
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Osaki, Makoto, Daisuke Takamatsu, Yoshihiro Shimoji, and Tsutomu Sekizaki. "Characterization of Streptococcus suis Genes Encoding Proteins Homologous to Sortase of Gram-Positive Bacteria." Journal of Bacteriology 184, no. 4 (February 15, 2002): 971–82. http://dx.doi.org/10.1128/jb.184.4.971-982.2002.
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ABSTRACT Many surface proteins which are covalently linked to the cell wall of gram-positive bacteria have a consensus C-terminal motif, Leu-Pro-X-Thr-Gly (LPXTG). This sequence is cleaved, and the processed protein is attached to an amino group of a cross-bridge in the peptideglycan by a specific enzyme called sortase. Using the type strain of Streptococcus suis, NCTC 10234, we found five genes encoding proteins that were homologous to sortases of other bacteria and determined the nucleotide sequences of the genetic regions. One gene, designated srtA, was linked to gyrA, as were the sortase and sortase-like genes of other streptococci. Three genes, designated srtB, srtC, and srtD, were tandemly clustered in a different location, where there were three segments of directly repeated sequences of approximately 110 bp in close vicinity. The remaining gene, designated srtE, was located separately on the chromosome with a pseudogene which may encode a transposase. The deduced amino acid sequences of the five Srt proteins showed 18 to 31% identity with the sortases of Streptococcus gordonii and Staphylococcus aureus, except that SrtA of S. suis had 65% identity with that of S. gordonii. Isogenic mutants deficient for srtA, srtBCD, or srtE were generated by allelic exchanges. The protein fraction which was released from partially purified cell walls by digestion with N-acetylmuramidase was profiled by two-dimensional gel electrophoresis. More than 15 of the protein spots were missing in the profile of the srtA mutant compared with that of the parent strain, and this phenotype was completely complemented by srtA cloned from S. suis. Four genes encoding proteins corresponding to such spots were identified and sequenced. The deduced translational products of the four genes possessed the LPXTG motif in their C-terminal regions. On the other hand, the protein spots that were missing in the srtA mutant appeared in the profiles of the srtBCD and srtE mutants. These results provide evidence that the cell wall sorting system involving srtA is also present in S. suis.
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Dorsey, Caleb W., Marcelo E. Tolmasky, Jorge H. Crosa, and Luis A. Actis. "Genetic organization of an Acinetobacter baumannii chromosomal region harbouring genes related to siderophore biosynthesis and transport." Microbiology 149, no. 5 (May 1, 2003): 1227–38. http://dx.doi.org/10.1099/mic.0.26204-0.
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The Acinetobacter baumannii 8399 clinical isolate secretes dihydroxybenzoic acid (DHBA) and a high-affinity catechol siderophore, which is different from other bacterial iron chelators already characterized. Complementation assays with enterobactin-deficient Escherichia coli strains led to the isolation of a cosmid clone containing A. baumannii 8399 genes required for the biosynthesis and activation of DHBA. Accordingly, the cloned fragment harbours a dhbACEB polycistronic operon encoding predicted proteins highly similar to several bacterial proteins required for DHBA biosynthesis from chorismic acid. Genes encoding deduced proteins related to the E. coli Fes and the Bacillus subtilis DhbF proteins, and a putative Yersinia pestis phosphopantetheinyl transferase, all of them involved in the assembly and utilization of catechol siderophores in other bacteria, were found next to the dhbACEB locus. This A. baumannii 8399 gene cluster also contained the om73, p45 and p114 predicted genes encoding proteins potentially involved in transport of ferric siderophore complexes. The deduced products of the p114 and p45 genes are putative membrane proteins that belong to the RND and MFS efflux pump proteins, respectively. Interestingly, P45 is highly related to the E. coli P43 (EntS) protein that participates in the secretion of enterobactin. Although P114 is similar to other bacterial efflux pump proteins involved in antibiotic resistance, its genetic arrangement within this A. baumannii 8399 locus is different from that described in other bacteria. The product of om73 is a Fur- and iron-regulated surface-exposed outer-membrane protein. These characteristics together with the presence of a predicted TonB box and its high similarity to other siderophore receptors indicate that OM73 plays such a role in A. baumannii 8399. The 184 nt om73–p114 intergenic region contains promoter elements that could drive the expression of these divergently transcribed genes, all of which are in close proximity to almost perfect Fur boxes. This arrangement explains the iron- and Fur-regulated expression of om73, and provides strong evidence for a similar regulation for the expression of p114.
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Chan, J. Y., X. L. Han, and Y. W. Kan. "Isolation of cDNA encoding the human NF-E2 protein." Proceedings of the National Academy of Sciences 90, no. 23 (December 1, 1993): 11366–70. http://dx.doi.org/10.1073/pnas.90.23.11366.
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The human homolog of mouse NF-E2 was isolated from the K562 cell line and found to encode a member of the basic leucine-zipper family of DNA-binding regulatory proteins. The deduced amino acid sequence of the mouse and human proteins exhibited near identity. Comparison to the related protein, Nrf1, revealed significant homologies at isolated regions, particularly within the basic domain, suggesting that NF-E2 and Nrf1 are members of a distinct subfamily of basic leucine-zipper proteins that share similar DNA-binding properties. High levels of human NF-E2 mRNA were observed in human erythroleukemic cell lines examined. Extensive survey of human tissue samples found NF-E2 expression not limited to erythropoeitic organs. Expression in the colon and testis suggests that NF-E2 may participate in the regulation of genes other than globin.
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Kim, Kwi S., Timothy G. Lilburn, Michael J. Renner, and John A. Breznak. "arfI and arfII, Two Genes Encoding α-l-Arabinofuranosidases inCytophaga xylanolytica." Applied and Environmental Microbiology 64, no. 5 (May 1, 1998): 1919–23. http://dx.doi.org/10.1128/aem.64.5.1919-1923.1998.
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ABSTRACT arfI encoded the 57.7-kDa subunit of Cytophaga xylanolytica arabinofuranosidase I (ArfI). arfIIencoded a 59.2-kDa subunit of ArfII. Products of both cloned genes liberated arabinose from arabinan and arabinoxylan. The deduced amino acid sequences of ArfI and ArfII revealed numerous regions that were identical to each other and to regions of homologous proteins fromBacteroides ovatus, Bacillus subtilis, andClostridium stercorarium.
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Knudsen, Katrine, Anna Sofie Madsen, Per Mygind, Gunna Christiansen, and Svend Birkelund. "Identification of Two Novel Genes Encoding 97- to 99-Kilodalton Outer Membrane Proteins of Chlamydia pneumoniae." Infection and Immunity 67, no. 1 (January 1, 1999): 375–83. http://dx.doi.org/10.1128/iai.67.1.375-383.1999.
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ABSTRACT Two genes encoding 97- to 99-kDa Chlamydia pneumoniaeVR1310 outer membrane proteins (Omp4 and Omp5) with mutual similarity were cloned and sequenced. The proteins were shown to be constituents of the C. pneumoniae outer membrane complex, and the deduced amino acid sequences were similar to those of putative outer membrane proteins encoded by the Chlamydia psittaci andChlamydia trachomatis gene families. By use of a monospecific polyclonal antibody against purified recombinant Omp4, it was shown that without heating, the protein migrated at 65 to 75 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunoelectron microscopy showed that epitopes of Omp4 were exposed on the surface of C. pneumoniae elementary bodies, reticulate bodies, and outer membrane complex. Proteins encoded by the C. pneumoniae gene family seem to be dominant antigens in experimentally infected mice.
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Lang, Elza A. S., and Marilis V. Marques. "Identification and Transcriptional Control of Caulobacter crescentus Genes Encoding Proteins Containing a Cold Shock Domain." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5603–13. http://dx.doi.org/10.1128/jb.186.17.5603-5613.2004.
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ABSTRACT The cold shock proteins are small peptides that share a conserved domain, called the cold shock domain (CSD), that is important for nucleic acid binding. The Caulobacter crescentus genome has four csp genes that encode proteins containing CSDs. Three of these (cspA, cspB, and cspC) encode peptides of about 7 kDa and are very similar to the cold shock proteins of other bacteria. Analysis by reverse transcription-PCR of the fourth gene (cspD), which was previously annotated as encoding a 7-kDa protein, revealed that the mRNA is larger and probably encodes a putative 21-kDa protein, containing two CSDs. A search in protein sequences databases revealed that this new domain arrangement has thus far only been found among deduced peptides of α-proteobacteria. Expression of each Caulobacter csp gene was studied both in response to cold shock and to growth phase, and we have found that only cspA and cspB are induced by cold shock, whereas cspC and cspD are induced at stationary phase, with different induction rates. The transcription start sites were determined for each gene, and a deletion mapping of the cspD promoter region defined a sequence required for maximal levels of expression, indicating that regulation of this gene occurs at the transcriptional level. Deletion of cspA, but not cspD, caused a reduction in viability when cells were incubated at 10°C for prolonged times, suggesting that cspA is important for adaptation to a low temperature.
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Christensen, G. A., G. M. Zane, A. E. Kazakov, X. Li, D. A. Rodionov, P. S. Novichkov, I. Dubchak, A. P. Arkin, and J. D. Wall. "Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH." Journal of Bacteriology 197, no. 1 (October 13, 2014): 29–39. http://dx.doi.org/10.1128/jb.02083-14.
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Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbeDesulfovibrio vulgarisHildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction inD. vulgarisHildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putativerexgene was made inD. vulgarisHildenborough, and transcript expression studies ofsat, encoding sulfate adenylyl transferase, showed increased levels in theD. vulgarisHildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream ofsatwas identified, confirming RexDvHto be a repressor ofsat. We establishedin vitrothat the presence of elevated NADH disrupted the interaction between RexDvHand DNA. Examination of the 5′ transcriptional start site for thesatmRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvHas a transcription repressor forsatthat senses the redox status of the cell.
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Nagao, R. T., E. Czarnecka, W. B. Gurley, F. Schöffl, and J. L. Key. "Genes for low-molecular-weight heat shock proteins of soybeans: sequence analysis of a multigene family." Molecular and Cellular Biology 5, no. 12 (December 1985): 3417–28. http://dx.doi.org/10.1128/mcb.5.12.3417.
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Soybeans, Glycine max, synthesize a family of low-molecular-weight heat shock (HS) proteins in response to HS. The DNA sequences of two genes encoding 17.5- and 17.6-kilodalton HS proteins were determined. Nuclease S1 mapping of the corresponding mRNA indicated multiple start termini at the 5' end and multiple stop termini at the 3' end. These two genes were compared with two other soybean HS genes of similar size. A comparison among the 5' flanking regions encompassing the presumptive HS promoter of the soybean HS-protein genes demonstrated this region to be extremely homologous. Analysis of the DNA sequences in the 5' flanking regions of the soybean genes with the corresponding regions of Drosophila melanogaster HS-protein genes revealed striking similarity between plants and animals in the presumptive promoter structure of thermoinducible genes. Sequences related to the Drosophila HS consensus regulatory element were found 57 to 62 base pairs 5' to the start of transcription in addition to secondary HS consensus elements located further upstream. Comparative analysis of the deduced amino acid sequences of four soybean HS proteins illustrated that these proteins were greater than 90% homologous. Comparison of the amino acid sequence for soybean HS proteins with other organisms showed much lower homology (less than 20%). Hydropathy profiles for Drosophila, Xenopus, Caenorhabditis elegans, and G. max HS proteins showed a similarity of major hydrophilic and hydrophobic regions, which suggests conservation of functional domains for these proteins among widely dispersed organisms.
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Nagao, R. T., E. Czarnecka, W. B. Gurley, F. Schöffl, and J. L. Key. "Genes for low-molecular-weight heat shock proteins of soybeans: sequence analysis of a multigene family." Molecular and Cellular Biology 5, no. 12 (December 1985): 3417–28. http://dx.doi.org/10.1128/mcb.5.12.3417-3428.1985.
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Soybeans, Glycine max, synthesize a family of low-molecular-weight heat shock (HS) proteins in response to HS. The DNA sequences of two genes encoding 17.5- and 17.6-kilodalton HS proteins were determined. Nuclease S1 mapping of the corresponding mRNA indicated multiple start termini at the 5' end and multiple stop termini at the 3' end. These two genes were compared with two other soybean HS genes of similar size. A comparison among the 5' flanking regions encompassing the presumptive HS promoter of the soybean HS-protein genes demonstrated this region to be extremely homologous. Analysis of the DNA sequences in the 5' flanking regions of the soybean genes with the corresponding regions of Drosophila melanogaster HS-protein genes revealed striking similarity between plants and animals in the presumptive promoter structure of thermoinducible genes. Sequences related to the Drosophila HS consensus regulatory element were found 57 to 62 base pairs 5' to the start of transcription in addition to secondary HS consensus elements located further upstream. Comparative analysis of the deduced amino acid sequences of four soybean HS proteins illustrated that these proteins were greater than 90% homologous. Comparison of the amino acid sequence for soybean HS proteins with other organisms showed much lower homology (less than 20%). Hydropathy profiles for Drosophila, Xenopus, Caenorhabditis elegans, and G. max HS proteins showed a similarity of major hydrophilic and hydrophobic regions, which suggests conservation of functional domains for these proteins among widely dispersed organisms.
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Broderick, Kevin, Christopher Pittock, Tony Arioli, Ernest H. Creaser, Jeremy J. Weinman, and Barry G. Rolfe. "Pathogenesis-Related Proteins in Trifolium subterraneum: A General Survey and Subsequent Characterisation of a Protein Inducible by Ethephon and Redlegged Earth Mite Attack." Functional Plant Biology 24, no. 6 (1997): 819. http://dx.doi.org/10.1071/pp97022.
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One of the chief predators of subterranean clover (Trifolium subterraneum) pastures is redlegged earth mite (Halotydeus destructor; RLEM). Subterranean clover pathogenesis-related (PR) proteins induced by RLEM attack and ethephon treatment were surveyed, and PR proteins with peroxidase, β-1,3-glucanase and chitinase activities were detected. A protein co-migrating with a chitinase activity, induced by RLEM predation and treatment with ethephon, was isolated. It was purified and the N-terminal amino acid sequence determined. Using a degenerate oligonucleotide primer designed from this sequence, a corresponding cDNA fragment was amplified by reverse transcriptase-PCR, then cloned, and used as a probe to screen a subterranean clover cv. Karridale genomic library. The cDNA and a 97% homologous genomic clone were sequenced and the deduced amino acid sequence revealed an open reading frame of 157 amino acids capable of encoding a peptide of 16 478 Da. Significant homology (80%) was found between this protein and an abscisic acid (ABA)-responsive protein from Pisum sativum of unknown function which is an intracellular pathogenesis-related (IPR) protein. The gene encoding this protein also has homology to pea ‘disease response resistance genes’ and to proteins from other plant species in the PR-10 family. The induced protein was designated TsPR-10a due to its homology to other PR-10 proteins. Genomic Southern analysis indicates that the gene encoding this protein, designated Ypr10a, is a member of a multigene family with at least three members. Northern blot analysis indicates that the subterranean clover Ypr10a mRNA, or homologous transcript, level is strongly induced by ethephon treatment in both root and aerial tissues of 3 week old plants. The rapid induction kinetics of Ypr10a mRNA under ethephon treatment, its correlation with a putative chitinase activity, and homology to other PR-protein genes, suggests a pathogenesis-related role for TsPR-10a protein in subterranean clover.
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Boivin, Rodolphe, Diane Beauseigle, Chris L. Baszczynski, and Guy Bellemare. "Isolation of Lhcb3 sequences from Brassica napus: evidence for conserved genes encoding LHCII type III chlorophyll a/b binding proteins." Genome 36, no. 1 (February 1, 1993): 139–46. http://dx.doi.org/10.1139/g93-017.
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Three closely related sequences were isolated from Brassica napus genomic DNA and were identified as Lhcb3 (genes encoding type III chlorophyll a/b binding proteins of LHCII, the major light-harvesting complex of photosystem II). These genes, as was observed for a tomato Lhcb3, contain two introns and yield both divergent and conserved predicted amino acid segments as compared with type I and type II polypeptides. One of the B. napus genes, designated Lhcb3*1, is transcribed in vivo, since it is identical to corresponding sequences in a cDNA clone. The protein deduced from another sequence, Lhcb3*2, appears as the most divergent type III so far characterized. The partial sequence of a third gene, Lhcb3*3, was also recovered. The 5′ noncoding sequences of Lhcb3*1 and Lhcb3*2, in the far upstream region, are characterized by an extremely high AT content and extensive direct repeats. In the near upstream region, two long Lhcb3*2 segments are very similar to a segment proposed as containing regulatory signals in Lhcb3*1. Specific binding of nuclear proteins to Lhcb3*1 promoter fragments was detected by electrophoretic mobility-shift assays. The evolutionary relationship between genes for type III polypeptides and the other types present in LHCII is discussed.Key words: Brassica napus, chlorophyll a/b binding proteins, LHCII type III, promoter region, lhcb genes evolution.
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Ventura, Marco, Ivana Jankovic, D. Carey Walker, R. David Pridmore, and Ralf Zink. "Identification and Characterization of Novel Surface Proteins in Lactobacillus johnsonii and Lactobacillus gasseri." Applied and Environmental Microbiology 68, no. 12 (December 2002): 6172–81. http://dx.doi.org/10.1128/aem.68.12.6172-6181.2002.
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ABSTRACT We have identified and sequenced the genes encoding the aggregation-promoting factor (APF) protein from six different strains of Lactobacillus johnsonii and Lactobacillus gasseri. Both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. Multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. Northern blot analysis showed that both genes are transcribed, reaching their maximum expression during the exponential phase. Primer extension analysis revealed that apf1 and apf2 harbor a putative promoter sequence that is conserved in all of the genes. Western blot analysis of the LiCl cell extracts showed that APF proteins are located on the cell surface. Intact cells of L. johnsonii revealed the typical cell wall architecture of S-layer-carrying gram-positive eubacteria, which could be selectively removed with LiCl treatment. In addition, the amino acid composition, physical properties, and genetic organization were found to be quite similar to those of S-layer proteins. These results suggest that APF is a novel surface protein of the Lactobacillus acidophilus B-homology group which might belong to an S-layer-like family.
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Bai, Jing, Xiao-Na Liu, Ming-Xing Lu, and Yu-Zhou Du. "Characterization of genes encoding small heat shock proteins from Bemisia tabaci and expression under thermal stress." PeerJ 7 (June 5, 2019): e6992. http://dx.doi.org/10.7717/peerj.6992.
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Small heat shock proteins (sHSPs) are probably the most diverse in structure and function among the various super-families of stress proteins, and they play essential roles in various biological processes. The sweet potato whitefly, Bemisia tabaci (Gennadius), feeds in the phloem, transmits several plant viruses, and is an important pest on cotton, vegetables and ornamentals. In this research, we isolated and characterized three α-crystallin/sHSP family genes (Bthsp19.5, Bthsp19.2, and Bthsp21.3) from Bemisia tabaci. The three cDNAs encoded proteins of 171, 169, and 189 amino acids with calculated molecular weights of 19.5, 19.2, and 21.3 kDa and isoelectric points of 6.1, 6.2, and 6.0, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in Hemiptera and Thysanoptera insects species. All three sHSPs genes from Bemisia tabaci lacked introns. Quantitative real-time PCR analyses revealed that the three BtsHSPs genes were significantly up-regulated in Bemisia tabaci adults and pupae during high temperature stress (39, 41, 43, and 45 °C) but not in response to cold temperature stress (−6, −8, −10, and −12 °C). The expression levels of Bthsp19.2 and Bthsp21.3 in pupae was higher than adults in response to heat stress, while the expression level of Bthsp19.5 in adults was higher than pupae. In conclusion, this research results show that the sHSP genes of Bemisia tabaci had shown differential expression changes under thermal stress.
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Schipper, C., C. Hornung, P. Bijtenhoorn, M. Quitschau, S. Grond, and W. R. Streit. "Metagenome-Derived Clones Encoding Two Novel Lactonase Family Proteins Involved in Biofilm Inhibition in Pseudomonas aeruginosa." Applied and Environmental Microbiology 75, no. 1 (November 7, 2008): 224–33. http://dx.doi.org/10.1128/aem.01389-08.
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ABSTRACT Here we report the isolation and characterization of three metagenome-derived clones that interfere with bacterial quorum sensing and degrade N-(3-oxooctanoyl)-l-homoserine lactone (3-oxo-C8-HSL). By using a traI-lacZ gene fusion, the metagenome-derived clones were identified from a soil DNA library and analyzed. The open reading frames linked to the 3-oxo-C8-HSL-degrading activities were designated bpiB01, bpiB04, and bpiB07. While the BpiB07 protein was similar to a known lactonase, no significant similarities were observed for the BpiB01 and BpiB04 proteins or the deduced amino acid sequences. High-performance liquid chromatography-mass spectrometry analyses confirmed that the identified genes encode novel lactone-hydrolyzing enzymes. The original metagenome-derived clones were expressed in Pseudomonas aeruginosa and employed in motility and biofilm assays. All clones were able to reproducibly inhibit motility in P. aeruginosa. Furthermore, these genes clearly inhibited biofilm formation in P. aeruginosa when expressed in P. aeruginosa PAO1. Thus, this is the first study in which metagenome-derived proteins have been expressed in P. aeruginosa to successfully inhibit biofilm formation.
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Yum, Do-Young, Bong-Yong Lee, and Jae-Gu Pan. "Identification of the yqhE andyafB Genes Encoding Two 2,5-Diketo-d-Gluconate Reductases inEscherichia coli." Applied and Environmental Microbiology 65, no. 8 (August 1, 1999): 3341–46. http://dx.doi.org/10.1128/aem.65.8.3341-3346.1999.
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ABSTRACT The identification of a gene (yiaE) encoding 2-ketoaldonate reductase (2KR) in our previous work led to the hypothesis that Escherichia coli has other ketogluconate reductases including 2,5-diketo-d-gluconate reductase (25DKGR) and to study of the related ketogluconate metabolism. By using the deduced amino acid sequences of 5-diketo-d-gluconate reductase (5KDGR) of Gluconobacter oxydans and 25DKGR ofCorynebacterium sp., protein databases were screened to detect homologous proteins. Among the proteins of E. coli, an oxidoreductase encoded by yjgU and having 56% similarity to 5KDGR of G. oxydans and two hypothetical oxidoreductases encoded by yqhE and yafB and having 49.8 and 42% similarity, respectively, to 25DKGR ofCorynebacterium sp. were detected. Recently, theyjgU gene was identified as encoding 5KDGR and renamedidnO (C. Bausch, N. Peekhaus, C. Utz, T. Blais, E. Murray, T. Lowary, and T. Conway, J. Bacteriol. 180:3704–3710, 1998). The pathways involved in the metabolism of ketogluconate by E. coli have been predicted by biochemical analysis of purified enzymes and chemical analysis of the pathway intermediates. The gene products of yqhE and yafB were identified as 25DKGR-A, and 25DKGR-B, respectively, catalyzing the reduction of 25KDG to 2-keto-l-gulonate (2KLG). The native 25DKGR-A, 25DKGR-B, and 5KDGR had apparent molecular weights of about 30,000, 30,000, and 54,000, respectively. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels, all three enzymes showed protein bands with a molecular weight of about 29,000, which indicated that 25DKGR-A, 25DKGR-B, and 5KDGR may exist as monomeric, monomeric, and dimeric proteins, respectively. The optimum pHs for reduction were 7.5, 7.0, and 8.0, respectively. The 5KDGR was active with NADH, whereas 25DKGR-A and 25DKGR-B were active with NADPH as a preferred electron donor. 25DKG can be converted to 5KDG by 2KR, which is then reduced tod-gluconate by 5KDGR. The pathways were compared with those of Erwinia sp. and Corynebacterium sp. A BLAST search of published and incomplete microbial genome sequences revealed that the ketogluconate reductases and their related metabolism may be widespread in many species.
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Molina, Antonio, Jörn Görlach, Sandra Volrath, and John Ryals. "Wheat Genes Encoding Two Types of PR-1 Proteins Are Pathogen Inducible, but Do Not Respond to Activators of Systemic Acquired Resistance." Molecular Plant-Microbe Interactions® 12, no. 1 (January 1999): 53–58. http://dx.doi.org/10.1094/mpmi.1999.12.1.53.
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Wheat cDNAs that encode proteins PR-1.1 and PR-1.2 were cloned. Deduced amino acid sequences were homologous to those of pathogen-induced, basic PR-1 proteins from plants. Although expression of PR1.1 and PR1.2 genes was induced upon infection with either compatible or incompatible isolates of the fungal pathogen Erysiphe graminis, these genes did not respond to activators of systemic acquired resistance (SAR), such as salicylic acid (SA), benzothiadiazole (BTH), or isonicotinic acid (INA)
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Teo, Jeanette W. P., Antonius Suwanto, and Chit Laa Poh. "Novel β-Lactamase Genes from Two Environmental Isolates of Vibrio harveyi." Antimicrobial Agents and Chemotherapy 44, no. 5 (May 1, 2000): 1309–14. http://dx.doi.org/10.1128/aac.44.5.1309-1314.2000.
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ABSTRACT Two ampicillin-resistant (Ampr) isolates ofVibrio harveyi, W3B and HB3, were obtained from the coastal waters of the Indonesian island of Java. Strain W3B was isolated from marine water near a shrimp farm in North Java while HB3 was from pristine seawater in South Java. In this study, novel β-lactamase genes from W3B (bla VHW-1) and HB3 (bla VHH-1) were cloned and their nucleotide sequences were determined. An open reading frame (ORF) of 870 bp encoding a deduced protein of 290 amino acids (VHW-1) was revealed for the bla gene of strain W3B while an ORF of 849 bp encoding a 283-amino-acid protein (VHH-1) was deduced forbla VHH-1. At the DNA level, genes for VHW-1 and VHH-1 have a 97% homology, while at the protein level they have a 91% homology of amino acid sequences. Neither gene sequence showed homology to any other β-lactamases in the databases. The deduced proteins were found to be class A β-lactamases bearing low levels of homology (<50%) to other β-lactamases of the same class. The highest level of identity was obtained with β-lactamases from Pseudomonas aeruginosa, i.e., PSE-1, PSE-4, and CARB-3, and Vibrio cholerae CARB-6. Our study showed that both strains W3B and HB3 possess an endogenous plasmid of approximately 60 kb in size. However, Southern hybridization analysis employingbla VHW-1 as a gene probe demonstrated that thebla gene was not located in the plasmid. A total of nine ampicillin-resistant V. harveyi strains, including W3B and HB3, were examined by pulsed-field gel electrophoresis ofNotI-digested genomic DNA. Despite a high level of intrastrain genetic diversity, thebla VHW-1 probe hybridized only to an 80- or 160-kb NotI genomic fragment in different isolates.
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Liszewska, Frantz, Dali Gaganidze, and Agnieszka Sirko. "Isolation of Nicotiana plumbaginifolia cDNAs encoding isoforms of serine acetyltransferase and O-acetylserine (thiol) lyase in a yeast two-hybrid system with Escherichia coli cysE and cysK genes as baits." Acta Biochimica Polonica 52, no. 1 (March 31, 2005): 117–28. http://dx.doi.org/10.18388/abp.2005_3496.
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We applied the yeast two-hybrid system for screening of a cDNA library of Nicotiana plumbaginifolia for clones encoding plant proteins interacting with two proteins of Escherichia coli: serine acetyltransferase (SAT, the product of cysE gene) and O-acetylserine (thiol)lyase A, also termed cysteine synthase (OASTL-A, the product of cysK gene). Two plant cDNA clones were identified when using the cysE gene as a bait. These clones encode a probable cytosolic isoform of OASTL and an organellar isoform of SAT, respectively, as indicated by evolutionary trees. The second clone, encoding SAT, was identified independently also as a "prey" when using cysK as a bait. Our results reveal the possibility of applying the two-hybrid system for cloning of plant cDNAs encoding enzymes of the cysteine synthase complex in the two-hybrid system. Additionally, using genome walking sequences located upstream of the sat1 cDNA were identified. Subsequently, in silico analyses were performed aiming towards identification of the potential signal peptide and possible location of the deduced mature protein encoded by sat1.
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Itoh, Kazuhito, Yoshiko Tashiro, Kazuko Uobe, Yoichi Kamagata, Kousuke Suyama, and Hiroki Yamamoto. "Root Nodule Bradyrhizobium spp. Harbor tfdAα and cadA, Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins." Applied and Environmental Microbiology 70, no. 4 (April 2004): 2110–18. http://dx.doi.org/10.1128/aem.70.4.2110-2118.2004.
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ABSTRACT The distribution of tfdAα and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine environments, was examined by PCR and Southern hybridization in several Bradyrhizobium strains including type strains of Bradyrhizobium japonicum USDA110 and Bradyrhizobium elkanii USDA94, in phylogenetically closely related Agromonas oligotrophica and Rhodopseudomonas palustris, and in 2,4-D-degrading Sphingomonas strains. All strains showed positive signals for tfdAα, and its phylogenetic tree was congruent with that of 16S rRNA genes in α-Proteobacteria, indicating evolution of tfdAα without horizontal gene transfer. The nucleotide sequence identities between tfdAα and canonical tfdA in β- and γ-Proteobacteria were 46 to 57%, and the deduced amino acid sequence of TfdAα revealed conserved residues characteristic of the active site of α-ketoglutarate-dependent dioxygenases. On the other hand, cadA showed limited distribution in 2,4-D-degrading Bradyrhizobium sp. and Sphingomonas sp. and some strains of non-2,4-D-degrading B. elkanii. The cadA genes were phylogenetically separated between 2,4-D-degrading and nondegrading strains, and the cadA genes of 2,4-D degrading strains were further separated between Bradyrhizobium sp. and Sphingomonas sp., indicating the incongruency of cadA with 16S rRNA genes. The nucleotide sequence identities between cadA and tftA of 2,4,5-trichlorophenoxyacetate-degrading Burkholderia cepacia AC1100 were 46 to 53%. Although all root nodule Bradyrhizobium strains were unable to degrade 2,4-D, three strains carrying cadA homologs degraded 4-chlorophenoxyacetate with the accumulation of 4-chlorophenol as an intermediate, suggesting the involvement of cadA homologs in the cleavage of the aryl ether linkage. Based on codon usage patterns and GC content, it was suggested that the cadA genes of 2,4-D-degrading and nondegrading Bradyrhizobium spp. have different origins and that the genes would be obtained in the former through horizontal gene transfer.
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Bintrim, Scott B., and Jerald C. Ensign. "Insertional Inactivation of Genes Encoding the Crystalline Inclusion Proteins of Photorhabdus luminescens Results in Mutants with Pleiotropic Phenotypes." Journal of Bacteriology 180, no. 5 (March 1, 1998): 1261–69. http://dx.doi.org/10.1128/jb.180.5.1261-1269.1998.
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ABSTRACT The entomopathogenic bacterium Photorhabdus luminescensexhibits phase variation when cultured in vitro. The variant forms ofP. luminescens are pleiotropic and are designated phase I and phase II variants. One of the characteristic phenotypes of phase I cells is the production of two types of intracellular protein inclusions. The genes encoding the protein monomers that form these inclusions, designated cipA and cipB, were cloned and characterized. cipA and cipB encode hydrophobic proteins of 11,648 and 11,308 Da, respectively. The deduced amino acid sequences of CipA and CipB have no significant amino acid sequence similarity to any other known protein but have 25% identity and 49% similarity to each other. Insertional inactivation ofcipA or cipB in phase I cells of P. luminescens produced mutants that differ from phase I cells in bioluminescence, the pattern and activities of extracellular products, biochemical traits, adsorption of dyes, and ability to support nematode growth and reproduction. In general, the cip mutants were phenotypically more similar to each other than to either phase I or phase II variants.
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Gao, Bingli, R. Allen, Tom Maier, Eric L. Davis, Thomas J. Baum, and Richard S. Hussey. "Identification of Putative Parasitism Genes Expressed in the Esophageal Gland Cells of the Soybean Cyst Nematode Heterodera glycines." Molecular Plant-Microbe Interactions® 14, no. 10 (October 2001): 1247–54. http://dx.doi.org/10.1094/mpmi.2001.14.10.1247.
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Cloning parasitism genes encoding secretory proteins expressed in the esophageal gland cells is the key to understanding the molecular basis of nematode parasitism of plants. Suppression subtractive hybridization (SSH) with the microaspirated contents from Heterodera glycines esophageal gland cells and intestinal region was used to isolate genes expressed preferentially in the gland cells of parasitic stages. Twenty-three unique cDNA sequences from a SSH cDNA library were identified and hybridized to the genomic DNA of H. glycines in Southern blots. Full-length cDNAs of 21 clones were obtained by screening a gland-cell long-distance polymerase chain reaction cDNA library. Deduced proteins of 10 clones were preceded by a signal peptide for secretion, and PSORT II computer analysis predicted eight proteins as extracellular, one as nuclear, and one as plasmalemma localized. In situ hybridization showed that four of the predicted extracellular clones were expressed specifically in the dorsal gland cell, one in the subventral gland cells, and three in the intestine in H. glycines. The predicted nuclear clone and the plasmalemma-localized clone were expressed in the subventral gland cells and the dorsal gland cell, respectively. SSH is an efficient method for cloning putative parasitism genes encoding esophageal gland cell secretory proteins that may have a role in H. glycines parasitism of soybean.
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Shen, Xi-Hui, Cheng-Ying Jiang, Yan Huang, Zhi-Pei Liu, and Shuang-Jiang Liu. "Functional Identification of Novel Genes Involved in the Glutathione-Independent Gentisate Pathway in Corynebacterium glutamicum." Applied and Environmental Microbiology 71, no. 7 (July 2005): 3442–52. http://dx.doi.org/10.1128/aem.71.7.3442-3452.2005.
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ABSTRACT Corynebacterium glutamicum used gentisate and 3-hydroxybenzoate as its sole carbon and energy source for growth. By genome-wide data mining, a gene cluster designated ncg12918-ncg12923 was proposed to encode putative proteins involved in gentisate/3-hydroxybenzoate pathway. Genes encoding gentisate 1,2-dioxygenase (ncg12920) and fumarylpyruvate hydrolase (ncg12919) were identified by cloning and expression of each gene in Escherichia coli. The gene of ncg12918 encoding a hypothetical protein (Ncg12918) was proved to be essential for gentisate-3-hydroxybenzoate assimilation. Mutant strain RES167Δncg12918 lost the ability to grow on gentisate or 3-hydroxybenzoate, but this ability could be restored in C. glutamicum upon the complementation with pXMJ19-ncg12918. Cloning and expression of this ncg12918 gene in E. coli showed that Ncg12918 is a glutathione-independent maleylpyruvate isomerase. Upstream of ncg12920, the genes ncg12921-ncg12923 were located, which were essential for gentisate and/or 3-hydroxybenzoate catabolism. The Ncg12921 was able to up-regulate gentisate 1,2-dioxygenase, maleylpyruvate isomerase, and fumarylpyruvate hydrolase activities. The genes ncg12922 and ncg12923 were deduced to encode a gentisate transporter protein and a 3-hydroxybenzoate hydroxylase, respectively, and were essential for gentisate or 3-hydroxybenzoate assimilation. Based on the results obtained in this study, a GSH-independent gentisate pathway was proposed, and genes involved in this pathway were identified.
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Jay, Z. J., D. B. Rusch, S. G. Tringe, C. Bailey, R. M. Jennings, and W. P. Inskeep. "Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities." Applied and Environmental Microbiology 80, no. 1 (October 25, 2013): 294–305. http://dx.doi.org/10.1128/aem.02860-13.
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ABSTRACTHigh-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions.Acidilobusspp. (orderDesulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of theThermoprotealesandSulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicatede novosequence assemblies ofAcidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populationsin situ. De novoassemblies of the highly similarAcidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription byAcidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis thatAcidilobusspp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.
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Abeliovich, H., Y. Tzfati, and J. Shlomai. "A trypanosomal CCHC-type zinc finger protein which binds the conserved universal sequence of kinetoplast DNA minicircles: isolation and analysis of the complete cDNA from Crithidia fasciculata." Molecular and Cellular Biology 13, no. 12 (December 1993): 7766–73. http://dx.doi.org/10.1128/mcb.13.12.7766.
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Replication of the kinetoplast DNA minicircle light strand initiates at a highly conserved 12-nucleotide sequence, termed the universal minicircle sequence. A Crithidia fasciculata single-stranded DNA-binding protein interacts specifically with the guanine-rich heavy strand of this origin-associated sequence (Y. Tzfati, H. Abeliovich, I. Kapeller, and J. Shlomai, Proc. Natl. Acad. Sci. USA 89:6891-6895, 1992). Using the universal minicircle sequence heavy-strand probe to screen a C. fasciculata cDNA expression library, we have isolated two overlapping cDNA clones encoding the trypanosomatid universal minicircle sequence-binding protein. The complete cDNA sequence defines an open reading frame encoding a 116-amino-acid polypeptide chain consisting of five repetitions of a CCHC zinc finger motif. A significant similarity is found between this universal minicircle sequence-binding protein and two other single-stranded DNA-binding proteins identified in humans and in Leishmania major. All three proteins bind specifically to single-stranded guanine-rich DNA ligands. Partial amino acid sequence of the endogenous protein, purified to homogeneity from C. fasciculata, was identical to that deduced from the cDNA nucleotide sequence. DNA-binding characteristics of the cDNA-encoded fusion protein expressed in bacteria were identical to those of the endogenous C. fasciculata protein. Hybridization analyses reveal that the gene encoding the minicircle origin-binding protein is nuclear and may occur in the C. fasciculata chromosome as a cluster of several structural genes.
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Abeliovich, H., Y. Tzfati, and J. Shlomai. "A trypanosomal CCHC-type zinc finger protein which binds the conserved universal sequence of kinetoplast DNA minicircles: isolation and analysis of the complete cDNA from Crithidia fasciculata." Molecular and Cellular Biology 13, no. 12 (December 1993): 7766–73. http://dx.doi.org/10.1128/mcb.13.12.7766-7773.1993.
Full textAbstract:
Replication of the kinetoplast DNA minicircle light strand initiates at a highly conserved 12-nucleotide sequence, termed the universal minicircle sequence. A Crithidia fasciculata single-stranded DNA-binding protein interacts specifically with the guanine-rich heavy strand of this origin-associated sequence (Y. Tzfati, H. Abeliovich, I. Kapeller, and J. Shlomai, Proc. Natl. Acad. Sci. USA 89:6891-6895, 1992). Using the universal minicircle sequence heavy-strand probe to screen a C. fasciculata cDNA expression library, we have isolated two overlapping cDNA clones encoding the trypanosomatid universal minicircle sequence-binding protein. The complete cDNA sequence defines an open reading frame encoding a 116-amino-acid polypeptide chain consisting of five repetitions of a CCHC zinc finger motif. A significant similarity is found between this universal minicircle sequence-binding protein and two other single-stranded DNA-binding proteins identified in humans and in Leishmania major. All three proteins bind specifically to single-stranded guanine-rich DNA ligands. Partial amino acid sequence of the endogenous protein, purified to homogeneity from C. fasciculata, was identical to that deduced from the cDNA nucleotide sequence. DNA-binding characteristics of the cDNA-encoded fusion protein expressed in bacteria were identical to those of the endogenous C. fasciculata protein. Hybridization analyses reveal that the gene encoding the minicircle origin-binding protein is nuclear and may occur in the C. fasciculata chromosome as a cluster of several structural genes.
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Reenan, R. A., and R. D. Kolodner. "Isolation and characterization of two Saccharomyces cerevisiae genes encoding homologs of the bacterial HexA and MutS mismatch repair proteins." Genetics 132, no. 4 (December 1, 1992): 963–73. http://dx.doi.org/10.1093/genetics/132.4.963.
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Abstract Homologs of the Escherichia coli (mutL, S and uvrD) and Streptococcus pneumoniae (hexA, B) genes involved in mismatch repair are known in several distantly related organisms. Degenerate oligonucleotide primers based on conserved regions of E. coli MutS protein and its homologs from Salmonella typhimurium, S. pneumoniae and human were used in the polymerase chain reaction (PCR) to amplify and clone mutS/hexA homologs from Saccharomyces cerevisiae. Two DNA sequences were amplified whose deduced amino acid sequences both shared a high degree of homology with MutS. These sequences were then used to clone the full-length genes from a yeast genomic library. Sequence analysis of the two MSH genes (MSH = mutS homolog), MSH1 and MSH2, revealed open reading frames of 2877 bp and 2898 bp. The deduced amino acid sequences predict polypeptides of 109.3 kD and 109.1 kD, respectively. The overall amino acid sequence identity with the E. coli MutS protein is 28.6% for MSH1 and 25.2% for MSH2. Features previously found to be shared by MutS homologs, such as the nucleotide binding site and the helix-turn-helix DNA binding motif as well as other highly conserved regions whose function remain unknown, were also found in the two yeast homologs. Evidence presented in this and a companion study suggest that MSH1 is involved in repair of mitochondrial DNA and that MSH2 is involved in nuclear DNA repair.
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Fan, Jing, Chunxian Chen, Qibin Yu, Zheng-Guo Li, and Frederick G. Gmitter. "Characterization of three terpenoid glycosyltransferase genes in ‘Valencia’ sweet orange (Citrus sinensis L. Osbeck)." Genome 53, no. 10 (October 2010): 816–23. http://dx.doi.org/10.1139/g10-068.
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Three putative terpenoid UDP-glycosyltransferase (UGT) genes, designated CsUGT1, CsUGT2, and CsUGT3, were isolated and characterized in ‘Valencia’ sweet orange ( Citrus sinensis L. Osbeck). CsUGT1 consisted of 1493 nucleotides with an open reading frame encoding 492 amino acids, CsUGT2 consisted of 1727 nucleotides encoding 504 amino acids, and CsUGT3 consisted of 1705 nucleotides encoding 468 amino acids. CsUGT3 had a 145 bp intron at 730–874, whereas CsUGT1 and CsUGT2 had none. The three deduced glycosyltransferase proteins had a highly conserved plant secondary product glycosyltransferase motif in the C terminus. Phylogenetic analysis showed that CsUGT1 and CsUGT3 were classified into group L of glycosyltransferase family 1, and CsUGT2 was classified into group D. Through Southern blotting analysis, CsUGT1 was found to have two copies in the sweet orange genome, whereas CsUGT2 and CsUGT3 had at least seven and nine copies, respectively. CsUGT1, CsUGT2, and CsUGT3 were constitutively expressed in leaf, flower, and fruit tissues. The results facilitate further investigation of the function of terpenoid glycosyltransferases in citrus and the biosynthesis of terpenoid glycosides in vitro.
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Sasaki, Hiraku, Eiichi Kawamoto, Yoshikazu Tanaka, Takuo Sawada, Satoshi Kunita, and Ken-ichi Yagami. "Identification and Characterization of Hemolysin-Like Proteins Similar to RTX Toxin in Pasteurella pneumotropica." Journal of Bacteriology 191, no. 11 (April 10, 2009): 3698–705. http://dx.doi.org/10.1128/jb.01527-08.
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ABSTRACT Pasteurella pneumotropica is an opportunistic pathogen that causes lethal pneumonia in immunodeficient rodents. The virulence factors of this bacterium remain unknown. In this study, we identified the genes encoding two RTX toxins, designated as pnxI and pnxII, from the genomic DNA of P. pneumotropica ATCC 35149 and characterized with respect to hemolysis. The pnxI operon was organized according to the manner in which the genes encoded the structural RTX toxin (pnxIA), the type I secretion systems (pnxIB and pnxID), and the unknown orf. The pnxII gene was involved only with the pnxIIA that coded for a structural RTX toxin. Both the structural RTX toxins of deduced PnxIA and PnxIIA were involved in seven of the RTX repeat and repeat-like sequences. By quantitative PCR analysis of the structural RTX toxin-encoding genes in P. pneumotropica ATCC 35149, the gene expression of pnxIA was found to have increased from the early log phase, while that of pnxIIA increased from the late log to the early stationary phase. As expressed in Escherichia coli, both the recombinant proteins of PnxIA and PnxIIA showed weak hemolytic activity in both sheep and murine erythrocytes. On the basis of the results of the Southern blotting analysis, the pnxIA gene was detected in 82% of the isolates, while the pnxIIA gene was detected in 39%. These results indicate that the products of both pnxIA and pnxIIA were putative associations of virulence factors in the rodent pathogen P. pneumotropica.
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O’Keeffe, Triona, Colin Hill, and R. Paul Ross. "Characterization and Heterologous Expression of the Genes Encoding Enterocin A Production, Immunity, and Regulation inEnterococcus faecium DPC1146." Applied and Environmental Microbiology 65, no. 4 (April 1, 1999): 1506–15. http://dx.doi.org/10.1128/aem.65.4.1506-1515.1999.
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ABSTRACT Enterocin A is a small, heat-stable, antilisterial bacteriocin produced by Enterococcus faecium DPC1146. The sequence of a 10,879-bp chromosomal region containing at least 12 open reading frames (ORFs), 7 of which are predicted to play a role in enterocin biosynthesis, is presented. The genes entA,entI, and entF encode the enterocin A prepeptide, the putative immunity protein, and the induction factor prepeptide, respectively. The deduced proteins EntK and EntR resemble the histidine kinase and response regulator proteins of two-component signal transducing systems of the AgrC-AgrA type. The predicted proteins EntT and EntD are homologous to ABC (ATP-binding cassette) transporters and accessory factors, respectively, of several other bacteriocin systems and to proteins implicated in the signal-sequence-independent export of Escherichia colihemolysin A. Immediately downstream of the entT andentD genes are two ORFs, the product of one of which, ORF4, is very similar to the product of the yteI gene ofBacillus subtilis and to E. coli protease IV, a signal peptide peptidase known to be involved in outer membrane lipoprotein export. Another potential bacteriocin is encoded in the opposite direction to the other genes in the enterocin cluster. This putative bacteriocin-like peptide is similar to LafX, one of the components of the lactacin F complex. A deletion which included one of two direct repeats upstream of the entA gene abolished enterocin A activity, immunity, and ability to induce bacteriocin production. Transposon insertion upstream of the entF gene also had the same effect, but this mutant could be complemented by exogenously supplied induction factor. The putative EntI peptide was shown to be involved in the immunity to enterocin A. Cloning of a 10.5-kb amplicon comprising all predicted ORFs and regulatory regions resulted in heterologous production of enterocin A and induction factor in Enterococcus faecalis, while a four-gene construct (entAITD) under the control of a constitutive promoter resulted in heterologous enterocin A production in both E. faecalis and Lactococcus lactis.
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Shisheva, A., T. C. Südhof, and M. P. Czech. "Cloning, characterization, and expression of a novel GDP dissociation inhibitor isoform from skeletal muscle." Molecular and Cellular Biology 14, no. 5 (May 1994): 3459–68. http://dx.doi.org/10.1128/mcb.14.5.3459.
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Cellular mechanisms for controlling membrane trafficking appear to involve small GTP-binding proteins such as the Rab proteins. Rab function is regulated by GDP dissociation inhibitor (GDI), which releases Rab proteins from membranes and inhibits GDP dissociation. Here we report the isolation of a full-length cDNA encoding a novel GDI isoform of 445 amino acids (GDI-2) with a deduced molecular weight of 50,649 from mouse skeletal muscle. Full-length and partial cDNA clones encoding a previously reported GDI protein (GDI-1) were also isolated from cDNA libraries prepared from rat brain and mouse skeletal muscle, respectively. The degree of deduced amino acid sequence identity between mouse GDI-2 and our mouse GDI-1 cDNA clone is 86%. Northern (RNA blot) analysis revealed that in human tissues, both GDI-1 and GDI-2 transcripts were abundant in brain, skeletal muscle, and pancreas but were weakly expressed in heart and liver. GDI-1 mRNA was expressed in kidney, whereas GDI-2 was almost absent, while in lung the relative amounts of these mRNA species were reversed. Specific antibodies against mouse GDI-1 and GDI-2 based on unique peptide sequences in the proteins were raised. Differentiation of 3T3-L1 fibroblasts into highly insulin-responsive adipocytes was accompanied by large increases in both mRNA and protein levels of GDI-1 and GDI-2. GDI-1 and GDI-2 expressed as glutathione S-transferase fusion proteins were both able to solubilize the membrane-bound forms of Rab4 and Rab5 in a GDP/GTP-dependent manner. Taken together, these data demonstrate that the protein products of at least two genes regulate the membrane dynamics of Rab proteins in mice.
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Shisheva, A., T. C. Südhof, and M. P. Czech. "Cloning, characterization, and expression of a novel GDP dissociation inhibitor isoform from skeletal muscle." Molecular and Cellular Biology 14, no. 5 (May 1994): 3459–68. http://dx.doi.org/10.1128/mcb.14.5.3459-3468.1994.
Full textAbstract:
Cellular mechanisms for controlling membrane trafficking appear to involve small GTP-binding proteins such as the Rab proteins. Rab function is regulated by GDP dissociation inhibitor (GDI), which releases Rab proteins from membranes and inhibits GDP dissociation. Here we report the isolation of a full-length cDNA encoding a novel GDI isoform of 445 amino acids (GDI-2) with a deduced molecular weight of 50,649 from mouse skeletal muscle. Full-length and partial cDNA clones encoding a previously reported GDI protein (GDI-1) were also isolated from cDNA libraries prepared from rat brain and mouse skeletal muscle, respectively. The degree of deduced amino acid sequence identity between mouse GDI-2 and our mouse GDI-1 cDNA clone is 86%. Northern (RNA blot) analysis revealed that in human tissues, both GDI-1 and GDI-2 transcripts were abundant in brain, skeletal muscle, and pancreas but were weakly expressed in heart and liver. GDI-1 mRNA was expressed in kidney, whereas GDI-2 was almost absent, while in lung the relative amounts of these mRNA species were reversed. Specific antibodies against mouse GDI-1 and GDI-2 based on unique peptide sequences in the proteins were raised. Differentiation of 3T3-L1 fibroblasts into highly insulin-responsive adipocytes was accompanied by large increases in both mRNA and protein levels of GDI-1 and GDI-2. GDI-1 and GDI-2 expressed as glutathione S-transferase fusion proteins were both able to solubilize the membrane-bound forms of Rab4 and Rab5 in a GDP/GTP-dependent manner. Taken together, these data demonstrate that the protein products of at least two genes regulate the membrane dynamics of Rab proteins in mice.
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Cao, Bang Phi. "Genome-wide analysis of NIN-like protein (NLP) family in maize (Zea mays L.) by using bioinformatic methods." Science and Technology Development Journal - Natural Sciences 1, T2 (June 30, 2017): 39–47. http://dx.doi.org/10.32508/stdjns.v1it2.450.
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The NIN-like proteins (NLP) belong to RWP-RK transcription factor family and possess the similarity characteristics of NIN (Nodules INception). The NLPs regulate the expression of genes which are involved in nitrate signaling in plants. In this work, we have performed a genome-wide analysis of the NLP gene family in maize (Zea mays L.) through the bioinformatic methods. We identified a total of nine NLP encoding genes in whole genome of maize. The genomic sequences of these genes were from 2855 to 8092 nucleotides in length and contained three or four introns. Their predicted protein sizes ranged in size from 786 to 945 amino acids. The theoretical isoelectric point values of most deduced protein were less than 7. The maize NLP proteins possessed conserved regions of plant NLP at N-terminal as well as at C-terminal including the RWP-RK and PB1 domains. Based on the phylogenic analysis, we detected three current whole-genome gene duplication events which occurred in maize genome apter speciation point. All of NLP genes expressed in tissues at different development stages, from germinating seed to maturation seed were examined. The ZmNLP5, ZmNLP6 and ZmNLP7 were weakly expressed in comparison to others genes in most examined tissues.
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Buck, Teresa M., Rick Jordan, James Lyons-Weiler, Joshua L. Adelman, Patrick G. Needham, Thomas R. Kleyman, and Jeffrey L. Brodsky. "Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeastSaccharomyces cerevisiae." Physiological Genomics 47, no. 6 (June 2015): 198–214. http://dx.doi.org/10.1152/physiolgenomics.00101.2014.
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Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to ER-associated degradation, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α-subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR was expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and compared with previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses.
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Müller, C., S. Nolden, P. Gebhardt, E. Heinzelmann, C. Lange, O. Puk, K. Welzel, W. Wohlleben, and D. Schwartz. "Sequencing and Analysis of the Biosynthetic Gene Cluster of the Lipopeptide Antibiotic Friulimicin in Actinoplanes friuliensis." Antimicrobial Agents and Chemotherapy 51, no. 3 (January 12, 2007): 1028–37. http://dx.doi.org/10.1128/aac.00942-06.
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ABSTRACT Actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin, which is a cyclic peptide with one exocyclic amino acid linked to a branched-chain fatty acid acyl residue. The structural relationship to daptomycin and the excellent antibacterial performance of friulimicin make the antibiotic an attractive drug candidate. The complete friulimicin biosynthetic gene cluster of 24 open reading frames from A. friuliensis was sequenced and analyzed. In addition to genes for regulation, self-resistance, and transport, the cluster contains genes encoding peptide synthetases, proteins involved in the synthesis and linkage of the fatty acid component of the antibiotic, and proteins involved in the synthesis of the nonproteinogenic amino acids pipecolinic acid, methylaspartic acid, and 2,3-diaminobutyric acid. By using heterologous gene expression in Escherichia coli, we provide biochemical evidence for the stereoselective synthesis of l-pipecolinic acid by the deduced protein of the lysine cyclodeaminase gene pip. Furthermore, we show the involvement of the dabA and dabB genes in the biosynthesis of 2,3-diaminobutyric acid by gene inactivation and subsequent feeding experiments.
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Das, Amaresh, Eric D. Coulter, Donald M. Kurtz, and Lars G. Ljungdahl. "Five-Gene Cluster in Clostridium thermoaceticumConsisting of Two Divergent Operons Encoding Rubredoxin Oxidoreductase- Rubredoxin and Rubrerythrin–Type A Flavoprotein– High-Molecular-Weight Rubredoxin." Journal of Bacteriology 183, no. 5 (March 1, 2001): 1560–67. http://dx.doi.org/10.1128/jb.183.5.1560-1567.2001.
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ABSTRACT A five-gene cluster encoding four nonheme iron proteins and a flavoprotein from the thermophilic anaerobic bacteriumClostridium thermoaceticum (Moorella thermoacetica) was cloned and sequenced. Based on analysis of deduced amino acid sequences, the genes were identified asrub (rubredoxin), rbo (rubredoxin oxidoreductase), rbr (rubrerythrin), fprA (type A flavoprotein), and a gene referred to as hrb(high-molecular-weight rubredoxin). Northern blot analysis demonstrated that the five-gene cluster is organized as two subclusters, consisting of two divergently transcribed operons,rbr-fprA-hrb and rbo-rub. The rbr, fprA, and rub genes were expressed inEscherichia coli, and their encoded recombinant proteins were purified. The molecular masses, UV-visible absorption spectra, and cofactor contents of the recombinant rubrerythrin, rubredoxin, and type A flavoprotein were similar to those of respective homologs from other microorganisms. Antibodies raised againstDesulfovibrio vulgaris Rbr reacted with both native and recombinant Rbr from C. thermoaceticum, indicating that this protein was expressed in the native organism. Since Rbr and Rbo have been recently implicated in oxidative stress protection in several anaerobic bacteria and archaea, we suggest a similar function of these proteins in oxygen tolerance of C. thermoaceticum.
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Radoux, V., P. P. Chen, J. A. Sorge, and D. A. Carson. "A conserved human germline V kappa gene directly encodes rheumatoid factor light chains." Journal of Experimental Medicine 164, no. 6 (December 1, 1986): 2119–24. http://dx.doi.org/10.1084/jem.164.6.2119.
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The full-length gene that encodes the light chain variable regions of an idiotypically related group of human IgM kappa rheumatoid factors (RFs) has been cloned and sequenced. The deduced amino acid sequence is identical to four separate RF proteins. These results prove that genes capable of encoding human anti-IgG autoantibody light chains without any somatic mutation are present in the kappa gene repertoire of normal people.
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Neumann, Anke, Gert Wohlfarth, and Gabriele Diekert. "Tetrachloroethene Dehalogenase from Dehalospirillum multivorans: Cloning, Sequencing of the Encoding Genes, and Expression of the pceA Gene in Escherichia coli." Journal of Bacteriology 180, no. 16 (August 15, 1998): 4140–45. http://dx.doi.org/10.1128/jb.180.16.4140-4145.1998.
Full textAbstract:
ABSTRACT The genes encoding tetrachloroethene reductive dehalogenase, a corrinoid-Fe/S protein, of Dehalospirillum multivorans were cloned and sequenced. The pceA gene is upstream ofpceB and overlaps it by 4 bp. The presence of a ς70-like promoter sequence upstream of pceA and of a ρ-independent terminator downstream of pceB indicated that both genes are cotranscribed. This assumption is supported by reverse transcriptase PCR data. The pceA and pceB genes encode putative 501- and 74-amino-acid proteins, respectively, with calculated molecular masses of 55,887 and 8,354 Da, respectively. Four peptides obtained after trypsin treatment of tetrachloroethene (PCE) dehalogenase were found in the deduced amino acid sequence of pceA. The N-terminal amino acid sequence of the PCE dehalogenase isolated from D. multivorans was found 30 amino acids downstream of the N terminus of the deduced pceA product. The pceAgene contained a nucleotide stretch highly similar to binding motifs for two Fe4S4 clusters or for one Fe4S4 cluster and one Fe3S4 cluster. A consensus sequence for the binding of a corrinoid was not found in pceA. No significant similarities to genes in the databases were detected in sequence comparisons. The pceB gene contained two membrane-spanning helices as indicated by two hydrophobic stretches in the hydropathic plot. Sequence comparisons of pceBrevealed no sequence similarities to genes present in the databases. Only in the presence of pUBS 520 supplying the recombinant bacteria with high levels of the rare Escherichia colitRNA4 Arg was pceA expressed, albeit nonfunctionally, in recombinant E. coli BL21 (DE3).
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Bergmann, David J., Alan B. Hooper, and Martin G. Klotz. "Structure and Sequence Conservation of hao Cluster Genes of Autotrophic Ammonia-Oxidizing Bacteria: Evidence for Their Evolutionary History." Applied and Environmental Microbiology 71, no. 9 (September 2005): 5371–82. http://dx.doi.org/10.1128/aem.71.9.5371-5382.2005.
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ABSTRACT Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c 554; and cycB, cytochrome c m 552. The deduced protein sequences of HAO, c 554, and c m 552 were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c m 552, NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c 554 gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c 554 gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.
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Mabuchi, Naoto, and Yoshio Araki. "Cloning and sequencing of two genes encoding chitinases A and B from Bacillus cereus CH." Canadian Journal of Microbiology 47, no. 10 (October 1, 2001): 895–902. http://dx.doi.org/10.1139/w01-093.
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Two genes encoding chitinases A and B (chiA and chiB) from Bacillus cereus CH were cloned into Escherichia coli XL1-Blue MRF' by using pBluescript II SK+, and their nucleotide sequences were determined. Open reading frames of the chiA and chiB genes encoded distinct polypeptide chains consisting of 360 and 674 amino acid residues, respectively, with calculated molecular sizes of 39 470 and 74 261 Da, respectively. Comparison of the deduced amino acid sequences with those of other bacterial chitinases revealed that chitinase A consisted of a catalytic domain, while chitinase B consisted of three functional domains, a catalytic domain, a fibronectin type III-like domain, and a cellulose-binding domain. The primary structures of these two proteins were not similar to each other.Key words: Bacillus cereus, chitinase, cloning.
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Takeda, Yasuo, Kazuma Takase, Ichiro Yamato, and Keietsu Abe. "Sequencing and Characterization of the xyl Operon of a Gram-Positive Bacterium, Tetragenococcus halophila." Applied and Environmental Microbiology 64, no. 7 (July 1, 1998): 2513–19. http://dx.doi.org/10.1128/aem.64.7.2513-2519.1998.
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ABSTRACT The xyl operon of a gram-positive bacterium,Tetragenococcus halophila (previously calledPediococcus halophilus), was cloned and sequenced. The DNA was about 7.7 kb long and contained genes for a ribose binding protein and part of a ribose transporter, xylR (a putative regulatory gene), and the xyl operon, along with its regulatory region and transcription termination signal, in this order. The DNA was AT rich, the GC content being 35.8%, consistent with the GC content of this gram-positive bacterium. The xyl operon consisted of three genes, xylA, encoding a xylose isomerase, xylB, encoding a xylulose kinase, andxylE, encoding a xylose transporter, with predicted molecular weights of 49,400, 56,400, and 51,600, respectively. The deduced amino acid sequences of the XylR, XylA, XylB, and XylE proteins were similar to those of the corresponding proteins in other gram-positive and -negative bacteria, the similarities being 37 to 64%. Each polypeptide of XylB and XylE was expressed functionally inEscherichia coli. XylE transported d-xylose in a sodium ion-dependent manner, suggesting that it is the first described xylose/Na+ symporter. The XylR protein contained a consensus sequence for binding catabolites of glucose, such as glucose-6-phosphate, which has been discovered in glucose and fructose kinases in bacteria. Correspondingly, the regulatory region of this operon contained a putative binding site of XylR with a palindromic structure. Furthermore, it contained a consensus sequence, CRE (catabolite-responsive element), for binding CcpA (catabolite control protein A). We speculate that the transcriptional regulation of this operon resembles the regulation of catabolite-repressible operons such as the amy, lev, xyl, andgnt operons in various gram-positive bacteria. We discuss the significance of the regulation of gene expression of this operon inT. halophila.
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Nizan, Roni, Isaac Barash, Lea Valinsky, Amnon Lichter, and Shulamit Manulis. "The Presence of hrp Genes on the Pathogenicity-Associated Plasmid of the Tumorigenic Bacterium Erwinia herbicola pv. gypsophilae." Molecular Plant-Microbe Interactions® 10, no. 5 (July 1997): 677–82. http://dx.doi.org/10.1094/mpmi.1997.10.5.677.
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The pathogenicity-associated plasmid (pPATH) of Erwinia herbicola pv. gypsophilae (Ehg), which is present only in pathogenic strains, contains a gene cluster encoding indole-3-acetic acid and cytokinin biosynthesis. The transposon-reporter Tn3-Spice was used to generate nonpathogenic mutants on two overlapping cosmids, pLA150 and pLA352, of the pPATH. A cluster of such mutations, which spanned 16 kb, mapped approximately 15 kb from the gene cluster involved in phytohormone biosynthesis. Non-pathogenic mutants also failed to elicit the hypersensitive reaction (HR) on tobacco. Pathogenicity and HR were restored concomitantly to these mutants by in trans complementation with wild-type Ehg DNA. A 3.8-kb HindIII DNA fragment that complemented the hrp mutants was sequenced and six complete and two partial open reading frames (ORFs) were identified. Comparison of the deduced amino acid sequences of the eight ORFs showed striking homology and co-linearity with hrp genes of E. amylovora as well as with other plant and mammalian pathogenic bacterial genes encoding proteins of the type III secretion system. Limited DNA sequencing at various sites on the remaining 11-kb region of pLA352 also showed high identity to Hrp proteins of E. amylovora, E. stewartii, and Pseudomonas syringae. These results suggest that hrp genes are mandatory for gall formation by E. herbicola pv. gypsophilae.
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Tal, Rony, Hing C. Wong, Roger Calhoon, David Gelfand, Anna Lisa Fear, Gail Volman, Raphael Mayer, et al. "Three cdg Operons Control Cellular Turnover of Cyclic Di-GMP in Acetobacter xylinum: Genetic Organization and Occurrence of Conserved Domains in Isoenzymes." Journal of Bacteriology 180, no. 17 (September 1, 1998): 4416–25. http://dx.doi.org/10.1128/jb.180.17.4416-4425.1998.
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ABSTRACT Cyclic di-GMP (c-di-GMP) is the specific nucleotide regulator of β-1,4-glucan (cellulose) synthase in Acetobacter xylinum. The enzymes controlling turnover of c-di-GMP are diguanylate cyclase (DGC), which catalyzes its formation, and phosphodiesterase A (PDEA), which catalyzes its degradation. Following biochemical purification of DGC and PDEA, genes encoding isoforms of these enzymes have been isolated and found to be located on three distinct yet highly homologous operons for cyclic diguanylate, cdg1, cdg2, andcdg3. Within each cdg operon, apdeA gene lies upstream of a dgc gene.cdg1 contains two additional flanking genes,cdg1a and cdg1d. cdg1a encodes a putative transcriptional activator, similar to AadR of Rhodopseudomonas palustris and FixK proteins of rhizobia. The deduced DGC and PDEA proteins have an identical motif structure of two lengthy domains in their C-terminal regions. These domains are also present in numerous bacterial proteins of undefined function. The N termini of the DGC and PDEA deduced proteins contain putative oxygen-sensing domains, based on similarity to domains on bacterial NifL and FixL proteins, respectively. Genetic disruption analyses demonstrated a physiological hierarchy among the cdg operons, such that cdg1contributes 80% of cellular DGC and PDEA activities andcdg2 and cdg3 contribute 15 and 5%, respectively. Disruption of dgc genes markedly reduced in vivo cellulose production, demonstrating that c-di-GMP controls this process.
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Turroni, Francesca, Elena Foroni, Mary O'Connell Motherway, Francesca Bottacini, Vanessa Giubellini, Aldert Zomer, Alberto Ferrarini, et al. "Characterization of the Serpin-Encoding Gene of Bifidobacterium breve 210B." Applied and Environmental Microbiology 76, no. 10 (March 26, 2010): 3206–19. http://dx.doi.org/10.1128/aem.02938-09.
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ABSTRACT Members of the serpin (serine protease inhibitor) superfamily have been identified in higher multicellular eukaryotes, as well as in bacteria, although examination of available genome sequences has indicated that homologs of the bacterial serpin-encoding gene (ser) are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least 5, and perhaps up to 9, of the 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria produce serpins that form a separate clade. We characterized the ser 210B locus of Bifidobacterium breve 210B, which encompasses a number of genes whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, microarray, reverse transcription-PCR (RT-PCR), and quantitative real-time PCR (qRT-PCR) analyses revealed that a 3.5-kb polycistronic mRNA encompassing the ser 210B operon with a single transcriptional start site is strongly induced following treatment of B. breve 210B cultures with some proteases. Interestingly, transcription of other bifidobacterial ser homologs appears to be triggered by different proteases.
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Gielkens, Marco M. C., Ester Dekkers, Jaap Visser, and Leo H. de Graaff. "Two Cellobiohydrolase-Encoding Genes from Aspergillus niger Require d-Xylose and the Xylanolytic Transcriptional Activator XlnR for Their Expression." Applied and Environmental Microbiology 65, no. 10 (October 1, 1999): 4340–45. http://dx.doi.org/10.1128/aem.65.10.4340-4345.1999.
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ABSTRACT Two cellobiohydrolase-encoding genes, cbhA andcbhB, have been isolated from the filamentous fungusAspergillus niger. The deduced amino acid sequence shows that CbhB has a modular structure consisting of a fungus-type cellulose-binding domain (CBD) and a catalytic domain separated by a Pro/Ser/Thr-rich linker peptide. CbhA consists only of a catalytic domain and lacks a CBD and linker peptide. Both proteins are homologous to fungal cellobiohydrolases in family 7 of the glycosyl hydrolases. Northern blot analysis showed that the transcription of thecbhA and cbhB genes is induced byd-xylose but not by sophorose and, in addition, requires the xylanolytic transcriptional activator XlnR.
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Contzen, Matthias, and Andreas Stolz. "Characterization of the Genes for Two Protocatechuate 3,4-Dioxygenases from the 4-Sulfocatechol-Degrading Bacterium Agrobacterium radiobacter Strain S2." Journal of Bacteriology 182, no. 21 (November 1, 2000): 6123–29. http://dx.doi.org/10.1128/jb.182.21.6123-6129.2000.
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ABSTRACT The genes for two different protocatechuate 3,4-dioxygenases (P34Os) were cloned from the 4-sulfocatechol-degrading bacteriumAgrobacterium radiobacter strain S2 (DSMZ 5681). ThepcaH1G1 genes encoded a P34O (P34O-I) which oxidized protocatechuate but not 4-sulfocatechol. These genes were part of a protocatechuate-degradative operon which strongly resembled the isofunctional operon from the protocatechuate-degrading strainAgrobacterium tumefaciens A348 described previously by D. Parke (FEMS Microbiol. Lett. 146:3–12, 1997). The second P34O (P34O-II), encoded by the pcaH2G2 genes, was functionally expressed and shown to convert protocatechuate and 4-sulfocatechol. A comparison of the deduced amino acid sequences of PcaH-I and PcaH-II, and of PcaG-I and PcaG-II, with each other and with the corresponding sequences from the P34Os, from other bacterial genera suggested that the genes for the P34O-II were obtained by strain S2 by lateral gene transfer. The genes encoding the P34O-II were found in a putative operon together with two genes which, according to sequence alignments, encoded transport proteins. Further downstream from this putative operon, two open reading frames which code for a putative regulator protein of the IclR family and a putative 3-carboxymuconate cycloisomerase were identified.
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Toyoshima, Hiroki, Ami Miyata, Risako Yoshida, Taichiro Ishige, Shinichi Takaichi, and Shinji Kawasaki. "Distribution of the Water-Soluble Astaxanthin Binding Carotenoprotein (AstaP) in Scenedesmaceae." Marine Drugs 19, no. 6 (June 20, 2021): 349. http://dx.doi.org/10.3390/md19060349.
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Photooxidative stress-inducible water-soluble astaxanthin-binding proteins, designated as AstaP, were identified in two Scenedesmaceae strains, Coelastrella astaxanthina Ki-4 and Scenedesmus obtusus Oki-4N; both strains were isolated under high light conditions. These AstaPs are classified as a novel family of carotenoprotein and are useful for providing valuable astaxanthin in water-soluble form; however, the distribution of AstaP orthologs in other microalgae remains unknown. Here, we examined the distribution of AstaP orthologs in the family Scenedesmaceae with two model microalgae, Chlamydomonas reinhardtii and Chlorella variabilis. The expression of AstaP orthologs under photooxidative stress conditions was detected in cell extracts of Scenedesmaceae strains, but not in model algal strains. Aqueous orange proteins produced by Scenedesmaceae strains were shown to bind astaxanthin. The protein from Scenedesmus costatus SAG 46.88 was purified. It was named ScosAstaP and found to bind astaxanthin. The deduced amino acid sequence from a gene encoding ScosAstaP showed 62% identity to Ki-4 AstaP. The expression of the genes encoding AstaP orthologs was shown to be inducible under photooxidative stress conditions; however, the production amounts of AstaP orthologs were estimated to be approximately 5 to 10 times lower than that of Ki-4 and Oki-4N.