scholarly journals Programmed Translational Frameshift in the Bacteriophage P2 FETUD Tail Gene Operon

2002 ◽  
Vol 184 (23) ◽  
pp. 6522-6531 ◽  
Author(s):  
Gail E. Christie ◽  
Louise M. Temple ◽  
Becky A. Bartlett ◽  
Tina S. Goodwin
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Initiation Site ◽  
Translation Initiation Site ◽  
Amino Acid Sequence Similarity ◽  
Reading Frame ◽  
Coding Regions ◽  
Translational Frameshift ◽  
Bacteriophage P2 ◽  
Contractile Tail

ABSTRACT The major structural components of the P2 contractile tail are encoded in the FETUD tail gene operon. The sequences of genes F I and F II, encoding the major tail sheath and tail tube proteins, have been reported previously (L. M. Temple, S. L. Forsburg, R. Calendar, and G. E. Christie, Virology 181:353-358, 1991). Sequence analysis of the remainder of this operon and the locations of amber mutations Eam30, Tam5, Tam64, Tam215, Uam25, Uam77, Uam92, and Dam6 and missense mutation Ets55 identified the coding regions for genes E, T, U, and D, completing the sequence determination of the P2 genome. Inspection of the DNA sequence revealed a new open reading frame overlapping the end of the essential tail gene E. Lack of an apparent translation initiation site and identification of a putative sequence for a programmed translational frameshift within the E gene suggested that this new reading frame (E′) might be translated as an extension of gene E, following a −1 translational frameshift. Complementation analysis demonstrated that E′ was essential for P2 lytic growth. Analysis of fusion polypeptides verified that this reading frame was translated as a −1 frameshift extension of gpE, with a frequency of approximately 10%. The arrangement of these two genes within the tail gene cluster of phage P2 and their coupling via a translational frameshift appears to be conserved among P2-related phages. This arrangement shows a striking parallel to the organization in the tail gene cluster of phage lambda, despite a lack of amino acid sequence similarity between the tail gene products of these phage families.

scholarly journals N-VEGF, a proteolytic product of the long isoform of VEGF-A, L-VEGF, shuttles to the nucleus to activate cellular stress survival circuits

2021 ◽  
Author(s):  
Marina Katsman ◽  
Aviva Azriel ◽  
Guy Horev ◽  
Ben-Zion Levi
Keyword(s):  
Initiation Site ◽  
Translation Initiation Site ◽  
Vascular Endothelial ◽  
Rna Seq ◽  
Coding Region ◽  
Nih3t3 Cells ◽  
Internal Ribosome Entry ◽  
Reading Frame ◽  
Endothelial Growth Factor

Vascular Endothelial Growth Factor A (VEGF-A) is a major angiogenesis stimulator in response to hypoxia. Its first exon possesses an elongated 5' Untranslated Region (5'UTR) and two Internal Ribosome Entry Sites (IRESs), enabling translation under hypoxia. It also encodes a 180 aa peptide that is in-frame with the classic coding region of VEGF-A. Upon hypoxia, Long VEGF-A (L-VEGF) is translated from this reading-frame concomitant with canonical VEGF-A isoforms. L-VEGF is proteolytically cleaved upstream to the VEGF-A translation initiation site to generate N-VEGF, which under hypoxia shuttles to cells nuclei. Here we show that hypoxia-independent nuclear mobilization of N-VEGF into NIH3T3 cells nuclei followed by RNA-seq leads to the identification of induced key genes associated with angiogenesis, cellular maintenance, and survival. Conversely, CRISPR-Cas9 mediated deletion of N-VEGF followed by RNA-Seq analysis underlined cells fragility under hypoxia supported by experimentations. This novel data highlights the role of this non-canonical VEGF-A isoform in potentiating the initial steps of angiogenesis along with cell survival circuits.

scholarly journals AdeR, a PucR-Type Transcription Factor, Activates Expression of l-Alanine Dehydrogenase and Is Required for Sporulation of Bacillus subtilis

2012 ◽  
Vol 194 (18) ◽  
pp. 4995-5001 ◽  
Author(s):  
Ta-Hui Lin ◽  
Guei-Tsung Wei ◽  
Chien-Chen Su ◽  
Gwo-Chyuan Shaw
Keyword(s):  
Bacillus Subtilis ◽  
Inverted Repeat ◽  
Sequence Similarity ◽  
Initiation Site ◽  
Amino Acid Sequence Similarity ◽  
Mobility Shift ◽  
Transcriptional Initiation ◽  
Transcription Terminator ◽  
Content Type ◽  
Alanine Dehydrogenase

ABSTRACTTheBacillus subtilis aldgene encodesl-alanine dehydrogenase, which catalyzes the NAD+-dependent deamination ofl-alanine to pyruvate for the generation of energy and is required for normal sporulation. The transcription ofaldis induced by alanine, but the mechanism underlying alanine induction remains unknown. Here we report that a gene (formerlyyukFand now designatedadeR) located upstream ofaldis essential for the basal and alanine-inducible expression ofald. The disruption of theadeRgene caused a sporulation defect, whereas the complementation of anadeRmutation with an intactadeRgene restored the sporulation ability.adeRexpression was not subject to autoregulation and alanine induction. Deletion and mutation analyses revealed that an inverted repeat, centered at position −74.5 relative to the transcriptional initiation site ofald, was required foraldexpression and also likely served as a ρ-independent transcription terminator. Electrophoretic mobility shift assays showed that purified His-tagged AdeR was a specific DNA-binding protein and that this inverted repeat was required for AdeR binding. AdeR shows no significant amino acid sequence similarity to the known transcriptional activators ofaldgenes from other bacteria. AdeR appears to be a member of the PucR family of transcriptional regulators. Its orthologs of unknown function are present in some otherBacillusspecies. Collectively, these findings support the notion that AdeR is a transcriptional activator which mediatesaldexpression in response to alanine availability and is important for normal sporulation inB. subtilis.

scholarly journals SpCoel1: a sea urchin profilin gene expressed specifically in coelomocytes in response to injury.

1992 ◽  
Vol 3 (4) ◽  
pp. 403-414 ◽  
Author(s):  
L C Smith ◽  
R J Britten ◽  
E H Davidson
Keyword(s):  
Sea Urchin ◽  
Sequence Similarity ◽  
Single Copy ◽  
Untranslated Regions ◽  
Amino Acid Sequence Similarity ◽  
Signal Transduction System ◽  
Reading Frame ◽  
Purple Sea Urchin ◽  
Copy Gene ◽  
External Injury

SpCoel1 is a single copy gene that is specifically expressed in most of the coelomocytes of the adult purple sea urchin, Strongylocentrotus purpuratus. The 4-kb transcript from this gene has a relatively short (426 nucleotide) open reading frame (ORF) with long 3' and 5' untranslated regions. The ORF encodes a protein that has strong amino acid sequence similarity to profilins from yeast to mammals. Transcript titrations of SpCoel1 show significant increases per coelomocyte in animals that have been physiologically challenged. Increases in transcript levels are of similar magnitudes between animals receiving different treatments, such as injuries from needle punctures or from injections of foreign cells. The evidence presented here implies a molecular mechanism by which this lower deuterostome defense system responds to external insult, viz that an external "injury signal" activates a signal transduction system, which in turn mediates the alterations in cytoskeletal state that are required for coelomocyte activation.

Proline utilization in Saccharomyces cerevisiae: sequence, regulation, and mitochondrial localization of the PUT1 gene product

1987 ◽  
Vol 7 (12) ◽  
pp. 4431-4440
Author(s):  
S S Wang ◽  
M C Brandriss
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Translation Initiation Site ◽  
Lacz Gene ◽  
Oxygen Regulation ◽  
Reading Frame ◽  
Proline Utilization ◽  
Beta Galactosidase

The PUT1 gene of Saccharomyces cerevisiae, believed to encode proline oxidase, has been completely sequenced and contains an open reading frame capable of encoding a polypeptide of 476 amino acids in length. The amino terminus of the protein deduced from the DNA sequence has a characteristic mitochondrial import signal; two PUT1-lacZ gene fusions were constructed that produced mitochondrially localized beta-galactosidase in vivo. The transcription initiation and termination sites of the PUT1 mRNA were determined. By using a PUT1-lacZ gene fusion that makes a cytoplasmic beta-galactosidase, the regulation of the PUT1 gene was studied. PUT1 is inducible by proline, responds only slightly to carbon catabolite repression, and is not regulated by the cytochrome activator proteins HAP1 and HAP2. The PUT1 gene is under oxygen regulation; expression in anaerobically grown cells is 10-fold lower than in aerobically grown cells. Oxygen regulation is abolished when cells are respiratory deficient. PUT1 expression in a [rho-] strain grown either aerobically or anaerobically is as high as that seen in a [rho+] strain grown aerobically. Studies on PUT1 promoter deletions define a region between positions -458 and -293 from the translation initiation site that is important for full expression of the PUT1 gene and required for oxygen regulation.

scholarly journals Novel Aeromonas hydrophila PPD134/91 Genes Involved in O-Antigen and Capsule Biosynthesis

2002 ◽  
Vol 70 (5) ◽  
pp. 2326-2335 ◽  
Author(s):  
Y. L. Zhang ◽  
E. Arakawa ◽  
K. Y. Leung
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Aeromonas Hydrophila ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Inhibitory Effect ◽  
Amino Acid Sequence Similarity ◽  
O Antigen ◽  
Serotype O ◽  
Surface Polysaccharides

ABSTRACT The sequences of the O-antigen and capsule gene clusters of the virulent Aeromonas hydrophila strain PPD134/91 were determined. The O-antigen gene cluster is 17,296 bp long and comprises 17 genes. Seven pathway genes for the synthesis of rhamnose and mannose, six transferase genes, one O unit flippase gene, and one O-antigen chain length determinant gene were identified by amino acid sequence similarity. PCR and Southern blot analysis were performed to survey the distribution of these 17 genes among 11 A. hydrophila strains of different serotypes. A. hydrophila PPD134/91 might belong to serotype O:18, as represented by JCM3980; it contained all the same O-antigen genes as JCM3980 (97 to 100% similarity at the DNA and amino acid levels). The capsule gene cluster of A. hydrophila PPD134/91 is 17,562 bp long and includes 13 genes, which were assembled into three distinct regions similar to those of the group II capsule gene cluster of Escherichia coli and other bacteria. Regions I and III contained four and two capsule transport genes, respectively. Region II had five genes which were highly similar to capsule synthesis pathway genes found in other bacteria. Both the purified O-antigen and capsular polysaccharides increased the ability of the avirulent A. hydrophila strain PPD35/85 to survive in naïve tilapia serum. However, the purified surface polysaccharides had no inhibitory effect on the adhesion of A. hydrophila PPD134/91 to carp epithelial cells.

A comparative study of odorant binding protein genes: differential expression of the PBP1-GOBP2 gene cluster inManduca sexta(Lepidoptera) and the organization of OBP genes inDrosophila melanogaster(Diptera)

2002 ◽  
Vol 205 (6) ◽  
pp. 719-744 ◽  
Author(s):  
Richard G. Vogt ◽  
Matthew E. Rogers ◽  
Marie-dominique Franco ◽  
Ming Sun
Keyword(s):  
Gene Family ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Cell Communication ◽  
Gene Families ◽  
Cell Types ◽  
Amino Acid Sequence Similarity ◽  
Olfactory Sensilla ◽  
Wide Range ◽  
Odorant Binding

SUMMARYInsects discriminate odors using sensory organs called olfactory sensilla, which display a wide range of phenotypes. Sensilla express ensembles of proteins, including odorant binding proteins (OBPs), olfactory receptors (ORs) and odor degrading enzymes (ODEs); odors are thought to be transported to ORs by OBPs and subsequently degraded by ODEs. These proteins belong to multigene families. The unique combinatorial expression of specific members of each of these gene families determines, in part, the phenotype of a sensillum and what odors it can detect. Furthermore, OBPs, ORs and ODEs are expressed in different cell types, suggesting the need for cell–cell communication to coordinate their expression. This report examines the OBP gene family. In Manduca sexta, the genes encoding PBP1Msex and GOBP2Msex are sequenced, shown to be adjacent to one another, and characterized together with OBP gene structures of other lepidoptera and Drosophila melanogaster. Expression of PBP1Msex, GOBP1Msex and GOBP2Msex is characterized in adult male and female antenna and in larval antenna and maxilla. The genomic organization of 25 D. melanogaster OBPs are characterized with respect to gene locus, gene cluster, amino acid sequence similarity, exon conservation and proximity to OR loci, and their sequences are compared with 14 M. sexta OBPs. Sensilla serve as portals of important behavioral information, and genes supporting sensilla function are presumably under significant evolutionary selective pressures. This study provides a basis for studying the evolution of the OBP gene family, the regulatory mechanisms governing the coordinated expression of OBPs, ORs and ODEs, and the processes that determine specific sensillum phenotypes.

scholarly journals Characterization of a Eukaryotic-Like Tyrosine Protein Kinase Expressed by the Shiga Toxin-Encoding Bacteriophage 933W

2004 ◽  
Vol 186 (11) ◽  
pp. 3472-3479 ◽  
Author(s):  
Jessica S. Tyler ◽  
David I. Friedman
Keyword(s):  
Shiga Toxin ◽  
Pathogenic Bacteria ◽  
Kinase Activity ◽  
Catalytic Domain ◽  
Selective Pressure ◽  
Sequence Similarity ◽  
Amino Acid Sequence Similarity ◽  
Reading Frame ◽  
Tyrosine Protein Kinase

ABSTRACT The Shiga toxin (Stx)-encoding bacteriophage 933W contains an open reading frame, stk, with amino acid sequence similarity to the catalytic domain of eukaryotic serine/threonine (Ser/Thr) protein kinases (PKs). Eukaryotic PKs are related by a common catalytic domain, consisting of invariant and nearly invariant residues necessary for ATP binding and phosphotransfer. We demonstrate that rather than a Ser/Thr kinase, stk encodes a eukaryotic-like tyrosine (Tyr) kinase. An affinity-purified recombinant Stk (rStk) autophosphorylates and catalyzes the phosphorylation of an artificial substrate on Tyr residues and not on Ser or Thr residues. A change of an invariant lysine within the putative catalytic domain abolishes this kinase activity, indicating that Stk uses a phosphotransfer mechanism similar to the mechanism used by eukaryotic PKs. We provide evidence suggesting that stk is cotranscribed with cI from the phage promoter responsible for maintaining CI expression during lysogeny. The stk gene was identified in prophages obtained from independently isolated Stx-producing Escherichia coli clinical isolates, suggesting that selective pressure has maintained the stk gene in these pathogenic bacteria.

Isolation, Characterization, and Heterologous Expression of the Novel Lantibiotic Epicidin 280 and Analysis of Its Biosynthetic Gene Cluster

1998 ◽  
Vol 64 (9) ◽  
pp. 3140-3146 ◽  
Author(s):  
Christoph Heidrich ◽  
Ulrike Pag ◽  
Michaele Josten ◽  
Jörg Metzger ◽  
Ralph W. Jack ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Staphylococcus Epidermidis ◽  
High Performance ◽  
Sequence Similarity ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Reverse Phase ◽  
Reading Frame ◽  
Reading Frames

ABSTRACT Epicidin 280 is a novel type A lantibiotic produced byStaphylococcus epidermidis BN 280. During C18reverse-phase high-performance liquid chromatography two epicidin 280 peaks were obtained; the two compounds had molecular masses of 3,133 ± 1.5 and 3,136 ± 1.5 Da, comparable antibiotic activities, and identical amino acid compositions. Amino acid sequence analysis revealed that epicidin 280 exhibits 75% similarity to Pep5. The strains that produce epicidin 280 and Pep5 exhibit cross-immunity, indicating that the immunity peptides cross-function in antagonization of both lantibiotics. The complete epicidin 280 gene cluster was cloned and was found to comprise at least five open reading frames (eciI, eciA, eciP,eciB, and eciC, in that order). The proteins encoded by these open reading frames exhibit significant sequence similarity to the biosynthetic proteins of the Pep5 operon ofStaphylococcus epidermidis 5. A gene for an ABC transporter, which is present in the Pep5 gene cluster but is necessary only for high yields (G. Bierbaum, M. Reis, C. Szekat, and H.-G. Sahl, Appl. Environ. Microbiol. 60:4332–4338, 1994), was not detected. Instead, upstream of the immunity gene eciI we found an open reading frame, eciO, which could code for a novel lantibiotic modification enzyme involved in reduction of an N-terminally located oxopropionyl residue. Epicidin 280 produced by the heterologous host Staphylococcus carnosus TM 300 after introduction of eciIAPBC (i.e., no eciO was present) behaved homogeneously during reverse-phase chromatography.

scholarly journals Identification of Human Astrovirus Genome-Linked Protein (VPg) Essential for Virus Infectivity

2012 ◽  
Vol 86 (18) ◽  
pp. 10070-10078 ◽  
Author(s):  
Cristina Fuentes ◽  
Albert Bosch ◽  
Rosa M. Pintó ◽  
Susana Guix
Keyword(s):  
Rna Virus ◽  
Sequence Similarity ◽  
Amino Acid Sequence Similarity ◽  
Virus Infectivity ◽  
Coding Region ◽  
Content Type ◽  
Reading Frame ◽  
High Amino Acid ◽  
Human Astrovirus ◽  
Experimental Findings

Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The presence of such protein in the familyAstroviridaehas not been fully elucidated, although a putative VPg coding region in open reading frame 1a (ORF1a) of astrovirus with high amino acid sequence similarity to the VPg coding region ofCaliciviridaehas been previously identified. In this work we present several experimental findings that show that human astrovirus (HAstV) RNA encodes a VPg essential for viral infectivity: (i) RNase treatment of RNA purified from astrovirus-infected cells results in a single protein of 13 to 15 kDa, compatible with the predicted astrovirus VPg size; (ii) the antibody used to detect this 13- to 15-kDa protein is specifically directed against a region that includes the putative VPg coding region; (iii) the 13- to 15-kDa protein detected has been partially sequenced and the sequence obtained is contained in the computationally predicted VPg; (iv) the protein resulting from this putative VPg coding region is a highly disordered protein, resembling the VPg of sobemo-, calici- and potyviruses; (v) proteolytic treatment of the genomic RNA leads to loss of infectivity; and (vi) mutagenesis of Tyr-693 included in the putative VPg protein is lethal for HAstV replication, which strongly supports its functional role in the covalent link with the viral RNA.

scholarly journals The engL Gene Cluster ofClostridium cellulovorans Contains a Gene for Cellulosomal ManA

2000 ◽  
Vol 182 (1) ◽  
pp. 244-247 ◽  
Author(s):  
Yutaka Tamaru ◽  
Roy H. Doi
Keyword(s):  
Gene Cluster ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Sequence Similarity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Glycosyl Hydrolases ◽  
High Sequence Similarity ◽  
Reading Frame ◽  
Plant Cell Wall Degradation

ABSTRACT A five-gene cluster around the gene in Clostridium cellulovorans that encodes endoglucanase EngL, which is involved in plant cell wall degradation, has been cloned and sequenced. As a result, a mannanase gene, manA, has been found downstream of engL. The manA gene consists of an open reading frame with 1,275 nucleotides encoding a protein with 425 amino acids and a molecular weight of 47,156. ManA has a signal peptide followed by a duplicated sequence (DS, or dockerin) at its N terminus and a catalytic domain which belongs to family 5 of the glycosyl hydrolases and shows high sequence similarity with fungal mannanases, such as Agaricus bisporus Cel4 (17.3% identity),Aspergillus aculeatus Man1 (23.7% identity), andTrichoderma reesei Man1 (22.7% identity). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and N-terminal amino acid sequence analyses of the purified recombinant ManA (rManA) indicated that the N-terminal region of the rManA contained a DS and was truncated in Escherichia coli cells. Furthermore, Western blot analysis indicated that ManA is one of the cellulosomal subunits. ManA production is repressed by cellobiose.

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