scholarly journals attI1-Located Small Open Reading Frames ORF-17 and ORF-11 in a Class 1 Integron Affect Expression of a Gene Cassette Possessing a Canonical Shine-Dalgarno Sequence

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Costas C. Papagiannitsis ◽  
Leonidas S. Tzouvelekis ◽  
Eva Tzelepi ◽  
Vivi Miriagou
Keyword(s):  
Single Gene ◽  
Gene Cassette ◽  
Open Reading Frames ◽  
Translation Initiation Region ◽  
Class 1 Integron ◽  
Reading Frame ◽  
Class 1 ◽  
Shine Dalgarno Sequence ◽  
Reading Frames ◽  
Small Open Reading Frames

ABSTRACT By searching the Integrall integron and GenBank databases, a novel open reading frame (ORF) of 51 nucleotides (nts) (ORF-17) overlapping the previously described ORF-11 was identified within the attI1 site in virtually all class 1 integrons. Using a set of isogenic plasmid constructs carrying a single gene cassette (bla GES-1) and possessing a canonical translation initiation region, we found that ORF-17 contributes to GES-1 expression.

scholarly journals Genetic and Enzymatic Properties of Metallo-β-Lactamase VIM-5 from a Clinical Isolate of Enterobacter cloacae

2005 ◽  
Vol 49 (10) ◽  
pp. 4400-4403 ◽  
Author(s):  
Gulcin G. Gacar ◽  
Kenan Midilli ◽  
Fetiye Kolayli ◽  
Kivanc Ergen ◽  
Sibel Gundes ◽  
...  
Keyword(s):  
Clinical Isolate ◽  
Single Gene ◽  
Enterobacter Cloacae ◽  
Gene Cassette ◽  
Enzymatic Properties ◽  
Class 1 Integron ◽  
Hindiii Fragment ◽  
Clinical Strains ◽  
Class 1

ABSTRACT A VIM-5-producing Enterobacter cloacae isolate (EDV/1) was identified in a collection of clinical strains stored before 2002. The gene, bla VIM-5, was located on a 2,712-bp BamHI-HindIII fragment of a 23-kbp (approximately) nonconjugative plasmid (pEDV5) in a class 1 integron as a single gene cassette.

scholarly journals The product of the H19 gene may function as an RNA.

1990 ◽  
Vol 10 (1) ◽  
pp. 28-36 ◽  
Author(s):  
C I Brannan ◽  
E C Dees ◽  
R S Ingram ◽  
S M Tilghman
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Translation Termination ◽  
Sedimentation Coefficient ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Translational Machinery ◽  
H19 Gene ◽  
Reading Frames ◽  
Small Open Reading Frames

The mouse H19 gene was identified as an abundant hepatic fetal-specific mRNA under the transcriptional control of a trans-acting locus termed raf. The protein this gene encoded was not apparent from an analysis of its nucleotide sequence, since the mRNA contained multiple translation termination signals in all three reading frames. As a means of assessing which of the 35 small open reading frames might be important to the function of the gene, the human H19 gene was cloned and sequenced. Comparison of the two homologs revealed no conserved open reading frame. Cellular fractionation showed that H19 RNA is cytoplasmic but not associated with the translational machinery. Instead, it is located in a particle with a sedimentation coefficient of approximately 28S. Despite the fact that it is transcribed by RNA polymerase II and is spliced and polyadenylated, we suggest that the H19 RNA is not a classical mRNA. Instead, the product of this unusual gene may be an RNA molecule.

scholarly journals GES-13, a β-Lactamase Variant Possessing Lys-104 and Asn-170 in Pseudomonas aeruginosa

2010 ◽  
Vol 54 (3) ◽  
pp. 1331-1333 ◽  
Author(s):  
S. D. Kotsakis ◽  
C. C. Papagiannitsis ◽  
E. Tzelepi ◽  
N. J. Legakis ◽  
V. Miriagou ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Broad Spectrum ◽  
Potent Inhibitor ◽  
Single Gene ◽  
Gene Cassette ◽  
Class 1 Integron ◽  
Class 1

ABSTRACT GES-13 β-lactamase, a novel GES variant possessing Lys-104 and Asn-170, was identified in Pseudomonas aeruginosa. bla GES-13 was the single gene cassette of a class 1 integron probably located in the chromosome. GES-13 efficiently hydrolyzed broad-spectrum cephalosporins and aztreonam. Imipenem was a potent inhibitor of GES-13 but was not hydrolyzed at measurable rates.

scholarly journals Small open reading frames and cellular stress responses

2019 ◽  
Vol 15 (2) ◽  
pp. 108-116 ◽  
Author(s):  
Alexandra Khitun ◽  
Travis J. Ness ◽  
Sarah A. Slavoff
Keyword(s):  
Stress Responses ◽  
Cellular Stress ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Cellular Stress Responses ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Increasing evidence suggests that some small open reading frame-encoded polypeptides (SEPs) function in prokaryotic and eukaryotic cellular stress responses.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

scholarly journals Complete Nucleotide Sequence of Klebsiella pneumoniae Multiresistance Plasmid pJHCMW1

2002 ◽  
Vol 46 (11) ◽  
pp. 3422-3427 ◽  
Author(s):  
Renee Sarno ◽  
Glen McGillivary ◽  
David J. Sherratt ◽  
Luis A. Actis ◽  
Marcelo E. Tolmasky
Keyword(s):  
Klebsiella Pneumoniae ◽  
Single Gene ◽  
Antibiotic Resistance Genes ◽  
Gene Cassette ◽  
Open Reading Frames ◽  
The Other ◽  
Gene Encoding ◽  
The Subject ◽  
Plasmid Stabilization ◽  
Reading Frames

ABSTRACT The multiresistance plasmid pJHCMW1, harbored by a clinical Klebsiella pneumoniae strain isolated from a neonate with meningitis, was sequenced. A circular sequence of 11,354 bp was generated, of which 7,993 bp make up Tn1331, a transposon including the antibiotic resistance genes aac(6′)-Ib, aadA1, bla OXA-9, and bla TEM-1. The gene aac(6′)-Ib is included in a gene cassette, and both aadA1 and bla OXA-9 are included in a single-gene cassette that may have arisen as a consequence of a recombination event involving two integrons. The pJHCMW1 plasmid replicates through a ColE1-like RNA-regulated mechanism, includes a functional oriT, and two loci with similarity to XerCD site-specific recombination target sites involved in plasmid stabilization by the resolution of multimers. One of these two loci, mwr, is active and has been the subject of previous studies, and the other, dxs, is not functional but binds the recombinase XerD with low affinity. Two additional open reading frames were identified, one with low similarity to two hypothetical membrane proteins from Mycobacterium tuberculosis and Mycobacterium leprae and the other with low similarity to psiB, a gene encoding a function that facilitates the establishment of the transferring plasmid in the recipient bacterial cell during the process of conjugation.

scholarly journals smORFunction: a tool for predicting functions of small open reading frames and microproteins

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at https://www.cuilab.cn/smorfunction.

The product of the H19 gene may function as an RNA

1990 ◽  
Vol 10 (1) ◽  
pp. 28-36
Author(s):  
C I Brannan ◽  
E C Dees ◽  
R S Ingram ◽  
S M Tilghman
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Translation Termination ◽  
Sedimentation Coefficient ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Translational Machinery ◽  
H19 Gene ◽  
Reading Frames ◽  
Small Open Reading Frames

The mouse H19 gene was identified as an abundant hepatic fetal-specific mRNA under the transcriptional control of a trans-acting locus termed raf. The protein this gene encoded was not apparent from an analysis of its nucleotide sequence, since the mRNA contained multiple translation termination signals in all three reading frames. As a means of assessing which of the 35 small open reading frames might be important to the function of the gene, the human H19 gene was cloned and sequenced. Comparison of the two homologs revealed no conserved open reading frame. Cellular fractionation showed that H19 RNA is cytoplasmic but not associated with the translational machinery. Instead, it is located in a particle with a sedimentation coefficient of approximately 28S. Despite the fact that it is transcribed by RNA polymerase II and is spliced and polyadenylated, we suggest that the H19 RNA is not a classical mRNA. Instead, the product of this unusual gene may be an RNA molecule.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

scholarly journals smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

2020 ◽  
Author(s):  
Xiangwen Ji ◽  
Chunmei Cui ◽  
Qinghua Cui
Keyword(s):  
Open Reading Frames ◽  
Open Reading Frame ◽  
Biological Processes ◽  
Reading Frame ◽  
Functional Annotations ◽  
Uniprot Database ◽  
Muscle Formation ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Abstract Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

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