scholarly journals Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

2007 ◽  
Vol 74 (4) ◽  
pp. 1281-1283 ◽  
Author(s):  
Donald A. Comfort ◽  
Chung-Jung Chou ◽  
Shannon B. Conners ◽  
Amy L. VanFossen ◽  
Robert M. Kelly
Keyword(s):  
Glycoside Hydrolase ◽  
Bioinformatics Analysis ◽  
Pyrococcus Furiosus ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Processing Enzymes ◽  
Response Information ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

scholarly journals Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 57 ◽  
Author(s):  
Kadriye Çağlayan ◽  
Vahid Roumi ◽  
Mona Gazel ◽  
Eminur Elçi ◽  
Mehtap Acioğlu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Open Reading Frames ◽  
Cherry Tree ◽  
Coding Regions ◽  
Sweet Cherries ◽  
Identification And Characterization ◽  
Reading Frames

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

scholarly journals Identification and Characterization of a Gene Cluster for Synthesis of the Polyketide Antibiotic 2,4-Diacetylphloroglucinol from Pseudomonas fluorescens Q2-87

1999 ◽  
Vol 181 (10) ◽  
pp. 3155-3163 ◽  
Author(s):  
M. Gita Bangera ◽  
Linda S. Thomashow
Keyword(s):  
Genomic Dna ◽  
Plant Pathogens ◽  
Polyketide Synthase ◽  
Open Reading Frames ◽  
Fungal Plant Pathogens ◽  
Repressor Proteins ◽  
Flanking Regions ◽  
Identification And Characterization ◽  
Reading Frames

The polyketide metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) is produced by many strains of fluorescent Pseudomonas spp. with biocontrol activity against soilborne fungal plant pathogens. Genes required for 2,4-DAPG synthesis by P. fluorescensQ2-87 are encoded by a 6.5-kb fragment of genomic DNA that can transfer production of 2,4-DAPG to 2,4-DAPG-nonproducing recipientPseudomonas strains. In this study the nucleotide sequence was determined for the 6.5-kb fragment and flanking regions of genomic DNA from strain Q2-87. Six open reading frames were identified, four of which (phlACBD) comprise an operon that includes a set of three genes (phlACB) conserved between eubacteria and archaebacteria and a gene (phlD) encoding a polyketide synthase with homology to chalcone and stilbene synthases from plants. The biosynthetic operon is flanked on either side by phlEand phlF, which code respectively for putative efflux and regulatory (repressor) proteins. Expression in Escherichia coli of phlA, phlC, phlB, andphlD, individually or in combination, identified a novel polyketide biosynthetic pathway in which PhlD is responsible for the production of monoacetylphloroglucinol (MAPG). PhlA, PhlC, and PhlB are necessary to convert MAPG to 2,4-DAPG, and they also may function in the synthesis of MAPG.

scholarly journals Identification and Characterization of Phytoplasmal Genes, Employing a Novel Method of Isolating Phytoplasmal Genomic DNA

2003 ◽  
Vol 185 (22) ◽  
pp. 6513-6521 ◽  
Author(s):  
Sharon Melamed ◽  
Edna Tanne ◽  
Raz Ben-Haim ◽  
Orit Edelbaum ◽  
David Yogev ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Plant Pathogens ◽  
Open Reading Frames ◽  
Rrna Genes ◽  
Unique Method ◽  
Novel Method ◽  
Identification And Characterization ◽  
Reading Frames ◽  
Large Background

ABSTRACT Phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class Mollicutes. To be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. Because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal DNA from infected plants or insects has resulted in preparations with a large background of host DNA. Thus, studies of the phytoplasmal genome have been greatly hampered, and aside from the rRNA genes, only a few genes have hitherto been isolated and characterized. We developed a unique method to obtain host-free phytoplasmal genomic DNA from the insect vector's saliva, and we demonstrated the feasibility of this method by isolating and characterizing 78 new putative phytoplasmal open reading frames and their deduced proteins. Based on the newly accumulated information on phytoplasmal genes, preliminary characteristics of the phytoplasmal genome are discussed.

scholarly journals A Gene Encoding l-Methionine γ-Lyase Is Present in Enterobacteriaceae Family Genomes: Identification and Characterization of Citrobacter freundiil-Methionine γ-Lyase

2005 ◽  
Vol 187 (11) ◽  
pp. 3889-3893 ◽  
Author(s):  
Ilya V. Manukhov ◽  
Daria V. Mamaeva ◽  
Sergei M. Rastorguev ◽  
Nicolai G. Faleev ◽  
Elena A. Morozova ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
High Sequence Identity ◽  
E Coli ◽  
The Family ◽  
Serovar Typhimurium ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Citrobacter freundii cells produce l-methionine γ-lyase when grown on a medium containing l-methionine. The nucleotide sequence of the hybrid plasmid with a C. freundii EcoRI insert of about 3.0 kbp contained two open reading frames, consisting of 1,194 nucleotides and 1,296 nucleotides, respectively. The first one (denoted megL) encoded l-methionine γ-lyase. The enzyme was overexpressed in Escherichia coli and purified. The second frame encoded a protein belonging to the family of permeases. Regions of high sequence identity with the 3′-terminal part of the C. freundii megL gene located in the same regions of Salmonella enterica serovar Typhimurium, Shigella flexneri, E. coli, and Citrobacter rodentium genomes were found.

scholarly journals Molecular Characterization of a New Abortive Infection System (AbiU) from Lactococcus lactisLL51-1

2001 ◽  
Vol 67 (11) ◽  
pp. 5225-5232 ◽  
Author(s):  
Gang Dai ◽  
Ping Su ◽  
Gwen E. Allison ◽  
Bruce L. Geller ◽  
Ping Zhu ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Lactococcus Lactis ◽  
Open Reading Frames ◽  
Phage Resistance ◽  
Abortive Infection ◽  
Specific Phage ◽  
Type Phage ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis. AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10−1, 1.0 × 10−2, and 1.0 × 10−1, respectively. abiU involves two open reading frames,abiU1 (1,772 bp) and abiU2 (1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.

scholarly journals Identification and Characterization of Catabolic para-Nitrophenol 4-Monooxygenase and para-Benzoquinone Reductase from Pseudomonas sp. Strain WBC-3

2009 ◽  
Vol 191 (8) ◽  
pp. 2703-2710 ◽  
Author(s):  
Jun-Jie Zhang ◽  
Hong Liu ◽  
Yi Xiao ◽  
Xian-En Zhang ◽  
Ning-Yi Zhou
Keyword(s):  
Gene Cluster ◽  
Flavin Adenine Dinucleotide ◽  
Gel Filtration ◽  
Sole Source ◽  
Open Reading Frames ◽  
Flavin Mononucleotide ◽  
Large Component ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Pseudomonas sp. strain WBC-3 utilizes para-nitrophenol (PNP) as a sole source of carbon, nitrogen, and energy. In order to identify the genes involved in this utilization, we cloned and sequenced a 12.7-kb fragment containing a conserved region of NAD(P)H:quinone oxidoreductase genes. Of the products of the 13 open reading frames deduced from this fragment, PnpA shares 24% identity to the large component of a 3-hydroxyphenylacetate hydroxylase from Pseudomonas putida U and PnpB is 58% identical to an NAD(P)H:quinone oxidoreductase from Escherichia coli. Both PnpA and PnpB were purified to homogeneity as His-tagged proteins, and they were considered to be a monomer and a dimer, respectively, as determined by gel filtration. PnpA is a flavin adenine dinucleotide-dependent single-component PNP 4-monooxygenase that converts PNP to para-benzoquinone in the presence of NADPH. PnpB is a flavin mononucleotide-and NADPH-dependent p-benzoquinone reductase that catalyzes the reduction of p-benzoquinone to hydroquinone. PnpB could enhance PnpA activity, and genetic analyses indicated that both pnpA and pnpB play essential roles in PNP mineralization in strain WBC-3. Furthermore, the pnpCDEF gene cluster next to pnpAB shares significant similarities with and has the same organization as a gene cluster responsible for hydroquinone degradation (hapCDEF) in Pseudomonas fluorescens ACB (M. J. Moonen, N. M. Kamerbeek, A. H. Westphal, S. A. Boeren, D. B. Janssen, M. W. Fraaije, and W. J. van Berkel, J. Bacteriol. 190:5190-5198, 2008), suggesting that the genes involved in PNP degradation are physically linked.

scholarly journals Identification and Characterization of the Locus for Diffuse Adherence, Which Encodes a Novel Afimbrial Adhesin Found in Atypical Enteropathogenic Escherichia coli

2005 ◽  
Vol 73 (8) ◽  
pp. 4753-4765 ◽  
Author(s):  
Isabel C. A. Scaletsky ◽  
Jane Michalski ◽  
Alfredo G. Torres ◽  
Michelle V. Dulguer ◽  
James B. Kaper
Keyword(s):  
Escherichia Coli ◽  
Genomic Region ◽  
Open Reading Frames ◽  
E Coli ◽  
Atypical Epec ◽  
Structural Subunit ◽  
K 12 ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT The O26 serogroup of enteropathogenic Escherichia coli (EPEC) is one of the serogroups most frequently implicated in infant diarrhea and is also common among enterohemorrhagic E. coli (EHEC) strains. The most common O26 strains belong to EPEC/EHEC serotype O26:H11 and are generally Shiga toxin (Stx) positive. Stx-negative E. coli strains that are negative for the EPEC EAF plasmid and bundle-forming pilus (Bfp) are classified as atypical EPEC. Here, we report a novel adhesin present in an stx-negative bfpA-negative atypical EPEC O26:H11 strain isolated from an infant with diarrhea. A cloned 15-kb genomic region from this strain, designated the locus for diffuse adherence (lda), confers diffuse adherence on HEp-2 cells when expressed in E. coli K-12. Sequence analysis of lda revealed a G+C content of 46.8% and 15 open reading frames sharing homology with the E. coli K88 fae and CS31A clp fimbrial operons. The lda region is part of a putative 26-kb genomic island inserted into the proP gene of the E. coli chromosome. Hybridization studies have demonstrated the prevalence of the minor structural subunit gene, ldaH, across E. coli serogroups O5, O26, O111, and O145. A second plasmid-encoded factor that contributed to the Hep-2 adherence of this strain was also identified but was not characterized. Null mutations that abolish adherence to HEp-2 cells can be restored by plasmid complementation. Antiserum raised against the major structural subunit, LdaG, recognizes a 25-kDa protein from crude heat-extracted protein preparations and inhibits the adherence of the E. coli DH5α lda + clone to HEp-2 cells. Electron microscopy revealed a nonfimbrial structure surrounding the bacterial cell.

scholarly journals Identification and Characterization of a Novel Family of Pneumococcal Proteins That Are Protective against Sepsis

2001 ◽  
Vol 69 (2) ◽  
pp. 949-958 ◽  
Author(s):  
John E. Adamou ◽  
Jon H. Heinrichs ◽  
Alice L. Erwin ◽  
William Walsh ◽  
Tony Gayle ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Systemic Disease ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Gene Products ◽  
Homologous Proteins ◽  
Potential Vaccine ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Four pneumococcal genes (phtA, phtB, phtD, andphtE) encoding a novel family of homologous proteins (32 to 87% identity) were identified from the Streptococcus pneumoniae genomic sequence. These open reading frames were selected as potential vaccine candidates based upon their possession of hydrophobic leader sequences which presumably target these proteins to the bacterial cell surface. Analysis of the deduced amino acid sequences of these gene products revealed the presence of a histidine triad motif (HxxHxH), termed Pht (pneumococcal histidine triad) that is conserved and repeated several times in each of the four proteins. The four pht genes (phtA, phtB, phtD, and a truncated version of phtE) were expressed inEscherichia coli. A flow cytometry-based assay confirmed that PhtA, PhtB, PhtD and, to a lesser extent, PhtE were detectable on the surface of intact bacteria. Recombinant PhtA, PhtB, and PhtD elicited protection against certain pneumococcal capsular types in a mouse model of systemic disease. These novel pneumococcal antigens may serve as effective vaccines against the most prevalent pneumococcal serotypes.

scholarly journals Identification and Characterization of an Active Plasmid Partition Mechanism for the Novel Lactococcus lactisPlasmid pCI2000

2000 ◽  
Vol 182 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Karen Kearney ◽  
Gerald F. Fitzgerald ◽  
Jos F. M. L. Seegers
Keyword(s):  
Open Reading Frames ◽  
Gram Negative Bacteria ◽  
The Novel ◽  
Replication Proteins ◽  
Gram Positive Bacteria ◽  
Plasmid Partition ◽  
Replication Region ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT The replication region of the lactococcal plasmid pCI2000 was subcloned and analyzed. The nucleotide sequence of one 5.6-kbEcoRI fragment which was capable of supporting replication when cloned on a replication probe vector revealed the presence of seven putative open reading frames (ORFs). One ORF exhibited significant homology to several replication proteins from plasmids considered to replicate via a theta mode. Deletion analysis showed that this ORF, designated repA, is indeed required for replication. The results also suggest that the origin of replication is located outside repA. Upstream and divergently transcribed from repA, an ORF that showed significant (48 to 64%) homology to a number of proteins that are required for faithful segregation of chromosomal or plasmid DNA of gram-negative bacteria was identified. Gene interruption and transcomplementation experiments showed that this ORF, designated parA, is required for stable inheritance of pCI2000 and is active in trans. This is the first example of such a partitioning mechanism for plasmids in gram-positive bacteria.

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