Biochemical and Genetic Characterization of Propionicin T1, a New Bacteriocin from Propionibacterium thoenii

ABSTRACT A collection of propionibacteria was screened for bacteriocin production. A new bacteriocin named propionicin T1 was isolated from two strains of Propionibacterium thoenii. This bacteriocin shows no sequence similarity to other bacteriocins. Propionicin T1 was active against all strains of Propionibacterium acidipropionici, Propionibacterium thoenii, andPropionibacterium jensenii tested and also againstLactobacillus sake NCDO 2714 but showed no activity againstPropionibacterium freudenreichii. The bacteriocin was purified, and the N-terminal part of the peptide was determined with amino acid sequencing. The corresponding gene pctA was sequenced, and this revealed that propionicin T1 is produced as a prebacteriocin of 96 amino acids with a typical sec leader, which is processed to give a mature bacteriocin of 65 amino acids. An open reading frame encoding a protein of 424 amino acids was found 68 nucleotides downstream the stop codon of pctA. The N-terminal part of this putative protein shows strong similarity with the ATP-binding cassette of prokaryotic and eukaryotic ABC transporters, and this protein may be involved in self-protection against propionicin T1. Propionicin T1 is the first bacteriocin from propionibacteria that has been isolated and further characterized at the molecular level.

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Cloning, Nucleotide Sequence, and Expression of the Gene Encoding the Bacteriocin Boticin B from Clostridium botulinum Strain 213B

Applied and Environmental Microbiology ◽

10.1128/aem.66.12.5480-5483.2000 ◽

2000 ◽

Vol 66 (12) ◽

pp. 5480-5483 ◽

Cited By ~ 16

Author(s):

Sean S. Dineen ◽

Marite Bradshaw ◽

Eric A. Johnson

Keyword(s):

Amino Acids ◽

Nucleotide Sequence ◽

Clostridium Botulinum ◽

Shuttle Vector ◽

Open Reading Frame ◽

Gene Encoding ◽

Reading Frame ◽

Heat Stable ◽

Group I

ABSTRACT Boticin B is a heat-stable bacteriocin produced byClostridium botulinum strain 213B that has inhibitory activity against various strains of C. botulinum and related clostridia. The gene encoding the bacteriocin was localized to a 3.0-kb HindIII fragment of an 18.8-kb plasmid, cloned, and sequenced. DNA sequencing revealed the boticin B structural gene,btcB, to be an open reading frame encoding 50 amino acids. A C. botulinum strain 62A transconjugant containing theHindIII fragment inserted into a clostridial shuttle vector expressed boticin B, although at much lower levels than those observed in C. botulinum 213B. To our knowledge, this is the first demonstration and characterization of a bacteriocin from toxigenic group I C. botulinum.

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Genomic Characterization of an Echovirus 7 Isolate of Southeast Asian Ancestry Recovered from a Child in Nigeria with Acute Flaccid Paralysis

Microbiology Resource Announcements ◽

10.1128/mra.00830-19 ◽

2019 ◽

Vol 8 (33) ◽

Author(s):

T. O. C. Faleye ◽

O. M. Adewumi ◽

J. A. Adeniji

Keyword(s):

Amino Acids ◽

Acute Flaccid Paralysis ◽

Southeast Asian ◽

Open Reading Frame ◽

Flaccid Paralysis ◽

Reading Frame ◽

Asian Ancestry ◽

Genomic Characterization

Here, we describe the genome of an echovirus 7 (E7) isolate of Southeast Asian ancestry recovered from a child in Nigeria with acute flaccid paralysis (AFP). The genome has 7,295 nucleotides (nt) and an open reading frame (ORF) with 2,195 amino acids.

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Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages

Journal of Virology ◽

10.1128/jvi.74.2.611-618.2000 ◽

2000 ◽

Vol 74 (2) ◽

pp. 611-618 ◽

Cited By ~ 57

Author(s):

Sophie Foley ◽

Anne Bruttin ◽

Harald Brüssow

Keyword(s):

Stop Codon ◽

Sequence Similarity ◽

Consensus Sequence ◽

Gc Content ◽

Streptococcus Thermophilus ◽

Variant Form ◽

Bacterial Genomes ◽

Stem Loop ◽

Reading Frame ◽

Group I

ABSTRACT Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilusbacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillusphage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns fromLactococcus, Lactobacillus, andBacillus phages.

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Characterization of the mouse thyrotrophin-releasing hormone receptor gene: an exon corresponds to a deletion in the rat cDNA

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0110141 ◽

1993 ◽

Vol 11 (2) ◽

pp. 141-149 ◽

Cited By ~ 6

Author(s):

S M Duthie ◽

P L Taylor ◽

K A Eidne

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Stop Codon ◽

Amino Acid Sequences ◽

R Gene ◽

Coding Region ◽

Thyrotrophin Releasing Hormone ◽

Exon 2 ◽

Exon 4

ABSTRACT The cloning and characterization of the mouse TRH receptor (TRH-R) gene revealed an untranslated exon (exon 1), a single intron and an upstream dinucleotide repeat sequence (d(TG)16.d(AG)21) in the 5′ untranslated region (UTR). The coding region was contained almost entirely on a second exon (exon 2), with the final amino acid and stop codon at the COOH terminus of the gene encoded by a third exon (exon 3) flanked by two introns. The 3′ UTR was contained on the remainder of exon 3 and on the final exon (exon 4). Exon 3 (228 bp) corresponds exactly to a 228 bp deletion that exists in the rat TRH-R cDNA, but not in the mouse cDNA. The mouse TRH-R cDNA encodes a protein of 393 amino acids which is 96% homologous to the rat TRH-R protein of 412 amino acids, but is 19 amino acids shorter at its COOH terminus. The coding sequence for these 19 amino acids (plus 1 extra amino acid) does exist in the mouse TRH-R gene, but the sequence is encoded by exon 4, separated from the rest of the coding region by the stop codon and 223 bp of 3′ UTR on exon 3. Splicing of exon 3 in the mouse TRH-R gene would remove the last amino acid, the stop codon and the 223 bp of 3′ UTR, allowing transcription to continue into the 3′ UTR on exon 4, which encodes the 19 extra amino acids found in the rat cDNA. This would then result in an alternative 412 amino acid version of the mouse TRH-R protein, with 95% homology to the rat TRH-R. This study focused on the structural differences in the intracellular COOH-terminal tail of the receptor, which is known to be a functionally important domain in other members of the G protein-coupled receptor family. We have also recently characterized the human TRH-R cDNA, which revealed a third variant at the COOH terminus. Comparisons between mouse, rat and human TRH-Rs show that the amino acid sequences are virtually identical. However, significant differences between these species exist at the COOH terminus, with each TRH-R having a unique form of the COOH-terminal tail, beginning at exactly the same site and encoding 1, 20 and 6 amino acids in the mouse, rat and human respectively.

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Molecular cloning and characterization of CIDE-3, a novel member of the cell-death-inducing DNA-fragmentation-factor (DFF45)-like effector family

Biochemical Journal ◽

10.1042/bj20020656 ◽

2003 ◽

Vol 370 (1) ◽

pp. 195-203 ◽

Cited By ~ 79

Author(s):

Liang LIANG ◽

Mujun ZHAO ◽

Zhenhua XU ◽

Kazunari K. YOKOYAMA ◽

Tsaiping LI

Keyword(s):

Amino Acids ◽

Cell Death ◽

Small Intestine ◽

Dna Fragmentation ◽

Nuclear Dna ◽

Fluorescent Protein ◽

Reading Frame ◽

Reverse Transcription Pcr ◽

Green Fluorescent

DNA fragmentation is one of the critical steps in apoptosis, which is induced by DNA fragmentation factor (DFF). DFF is composed of two subunits, a 40kDa caspase-activated nuclease (DFF40) and a 45kDa inhibitor (DFF45). Recently a novel family of cell-death-inducing DFF45-like effectors (CIDEs) has been identified. Among CIDEs, two from human (CIDE-A and CIDE-B) and three from mouse (CIDE-A, CIDE-B and FSP27) have been reported. In this study human CIDE-3, a novel member of CIDEs, was identified upon sequence analysis of a previously unidentified cDNA that encoded a protein of 238 amino acids. It was shown to be a human homologue of mouse FSP27, and shared homology with the CIDE-N and CIDE-C domains of CIDEs. Apoptosis-inducing activity was clearly shown by DNA-fragmentation assay of the nuclear DNA of CIDE-3 transfected 293T cells. The expression pattern of CIDE-3 was different from that of CIDE-B. As shown by Northern-blot analysis, CIDE-3 was expressed mainly in human small intestine, heart, colon and stomach, while CIDE-B showed strong expression in liver and small intestine and at a lower level in colon, kidney and spleen. Green-fluorescent-protein-tagged CIDE-3 was revealed in some cytosolic corpuscles. Alternative splicing of the CIDE-3 gene was also identified by reverse transcription PCR, revealing that two transcripts, CIDE-3 and CIDE-3α, were present in HepG2 and A375 cells. CIDE-3 comprised a full-length open reading frame with 238 amino acids; in CIDE-3α exon 3 was deleted and it encoded a protein of 164 amino acids. Interestingly the CIDE-3α isoform still kept the apoptosis-inducing activity and showed the same pattern of subcellular localization as CIDE-3. Consistent with its chromosome localization at 3p25, a region associated with high frequency loss of heterozygosity in many tumours, CIDE-3 may play an important role in prevention of tumorigenesis.

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Molecular Cloning and Characterization of cgs, theBrucella abortus Cyclic β(1-2) Glucan Synthetase Gene: Genetic Complementation of Rhizobium meliloti ndvB andAgrobacterium tumefaciens chvB Mutants

Journal of Bacteriology ◽

10.1128/jb.180.17.4392-4400.1998 ◽

1998 ◽

Vol 180 (17) ◽

pp. 4392-4400 ◽

Cited By ~ 54

Author(s):

Nora Iñón de Iannino ◽

Gabriel Briones ◽

Marcelo Tolmasky ◽

Rodolfo A. Ugalde

Keyword(s):

Amino Acids ◽

Membrane Protein ◽

Rhizobium Meliloti ◽

Nodule Development ◽

Nucleotide Sequencing ◽

Insertion Mutant ◽

Reading Frame ◽

Glucan Synthesis ◽

Glucan Synthetase

ABSTRACT The animal pathogen Brucella abortus contains a gene,cgs, that complemented a Rhizobium melilotinodule development (ndvB) mutant and an Agrobacterium tumefaciens chromosomal virulence (chvB) mutant. The complemented strains recovered the synthesis of cyclic β(1-2) glucan, motility, virulence in A. tumefaciens, and nitrogen fixation in R. meliloti; all traits were strictly associated with the presence of an active cyclic β(1-2) glucan synthetase protein in the membranes. Nucleotide sequencing revealed the presence in B. abortus of an 8.49-kb open reading frame coding for a predicted membrane protein of 2,831 amino acids (316.2 kDa) and with 51% identity to R. meliloti NdvB. Four regions of the B. abortus protein spanning amino acids 520 to 800, 1025 to 1124, 1284 to 1526, and 2400 to 2660 displayed similarities of higher than 80% with R. meliloti NdvB. Tn3-HoHo1 mutagenesis showed that the C-terminal 825 amino acids of the Brucella protein, although highly conserved inRhizobium, are not necessary for cyclic β(1-2) glucan synthesis. Confirmation of the identity of this protein as B. abortus cyclic β(1-2) glucan synthetase was done by the construction of a B. abortus Tn3-HoHo1 insertion mutant that does not form cyclic β(1-2) glucan and lacks the 316.2-kDa membrane protein. The recovery of this mutant from the spleens of inoculated mice was decreased by 3 orders of magnitude compared with that of the parental strain; this result suggests that cyclic β(1-2) glucan may be a virulence factor inBrucella infection.

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Three new dominant C1 suppressor alleles in Zea mays

Genetics Research ◽

10.1017/s0016672398003218 ◽

1998 ◽

Vol 71 (2) ◽

pp. 127-132 ◽

Cited By ~ 5

Author(s):

TATJANA SINGER ◽

ALFONS GIERL ◽

PETER A. PETERSON

Keyword(s):

Amino Acids ◽

Transcriptional Activation ◽

Stop Codon ◽

Suppressive Effect ◽

Wild Type ◽

Activation Domain ◽

Reading Frame ◽

Transcriptional Activation Domain ◽

Imprecise Excision ◽

Carboxy Terminal

Three new dominant suppressor mutations of the C1 transcription regulator gene in maize – C1-IΔ1, C1-IΔ2 and C1-IΔ3 – are described that suppress anthocyanin colouration in kernels similar to the function of the C1-I standard inhibitor. The C1-IΔ mutations were induced by imprecise excision of an En/Spm transposon in the third exon of the C1 gene. These transposon footprints cause a frameshift in the C1 open reading frame that leads to truncated proteins due to an early stop codon 30 amino acids upstream of the wild-type C1 protein. Therefore, the C1-IΔ gene products lack the carboxy-terminal transcriptional activation domain of C1. The C1-I standard allele also lacks this domain and in addition differs in 17 amino acids from the wild-type C1 allele. The new C1-IΔ alleles provide evidence that deletion of the carboxy-terminal activation domain alone is sufficient to generate a dominant suppressive effect on the function of wild-type C1.

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Characterization of a human colonic cDNA encoding a structurally novel urea transporter, hUT-A6

AJP Cell Physiology ◽

10.1152/ajpcell.00363.2003 ◽

2004 ◽

Vol 287 (4) ◽

pp. C1087-C1093 ◽

Cited By ~ 54

Author(s):

Craig P. Smith ◽

Elizabeth A. Potter ◽

Robert A. Fenton ◽

Gavin S. Stewart

Keyword(s):

Amino Acids ◽

Alternative Splicing ◽

Protein Kinase ◽

Protein Kinase A ◽

Colonic Mucosa ◽

Stop Codon ◽

Hydrophobic Core ◽

Urea Transporter ◽

Kinase A

Two closely related genes, UT-A ( Slc14a2) and UT-B ( Slc14a1), encode specialized transporter proteins that modulate the movement of urea across cell membranes. In this article, we report the characterization of a cDNA isolated from human colonic mucosa encoding a novel UT-A urea transporter, hUT-A6. The encoded protein is 235 amino acids (aa) in length, making it the smallest UT-A member characterized. On the basis of previous structural predictions, hUT-A6 is structurally unique in that it consists of a single hydrophobic core flanked by hydrophilic NH2- and COOH-terminal domains. The transcript encoding hUT-A6 contains a novel 129-bp exon, exon 5a, which, as a result of alternative splicing, introduces a unique 19-aa segment and a stop codon. Functionally, the protein transports urea, and this activity is inhibited by phloretin. Interestingly, despite the lack of a protein kinase A (PKA) consensus site {[RK]( 2 )-X-[ST]}, transport of urea by hUT-A6 is stimulated by PKA agonists. Deletion of the two PKA consensus sites from murine UT-A3 (mUT-A3) did not affect the stimulatory response of PKA agonists, which, together with the lack of PKA consensus sites in hUT-A6, indicates that regulation of hUT-A6 and mUT-A3 is not mediated through a classic PKA phosphorylation consensus.

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Novel Numerical Characterization of Protein Sequences Based on Individual Amino Acid and Its Application

BioMed Research International ◽

10.1155/2015/909567 ◽

2015 ◽

Vol 2015 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Yan-ping Zhang ◽

Ya-jun Sheng ◽

Wei Zheng ◽

Ping-an He ◽

Ji-shuo Ruan

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Catalytic Mechanism ◽

Graphical Representation ◽

Sequence Similarity ◽

Protein Sequences ◽

Numerical Characteristic ◽

Individual Amino Acid ◽

Numerical Characterization

The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.

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Characterization of three terpenoid glycosyltransferase genes in ‘Valencia’ sweet orange (Citrus sinensis L. Osbeck)

Genome ◽

10.1139/g10-068 ◽

2010 ◽

Vol 53 (10) ◽

pp. 816-823 ◽

Cited By ~ 3

Author(s):

Jing Fan ◽

Chunxian Chen ◽

Qibin Yu ◽

Zheng-Guo Li ◽

Frederick G. Gmitter

Keyword(s):

Amino Acids ◽

Citrus Sinensis ◽

Southern Blotting ◽

Sweet Orange ◽

Secondary Product ◽

Reading Frame ◽

C Terminus ◽

Group D

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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