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Zhang T, Yue G, Tian X, Xu Y, Li Z. LncSUMO1P3 exacerbates malignant behaviors of esophageal squamous cell carcinoma cells via miR-486-5p/PHF8/CD151. Heliyon 2023; 9:e19110. [PMID: 37809985 PMCID: PMC10558295 DOI: 10.1016/j.heliyon.2023.e19110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 10/10/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a malignancy usually associated with smoking or alcohol consumption. The involvement of long noncoding RNAs (lncRNAs) in the regulation of tumor development and metastasis through molecular mechanisms has been unveiled by accumulating evidence. However, the function of lncRNA SUMO1 Pseudogene 3 (lncSUMO1P3) essential to ESCC development remains obscure. Methods Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and Western blot (WB) analysis were done to measure RNA and protein levels. Functional assays were carried out to examine the changes in ESCC cell phenotype. Supported by bioinformatics analysis, mechanism assays were done for assessment of putative interactions among different genes. Results LlncSUMO1P3 was aberrantly up-regulated in ESCC cell lines, and lncSUMO1P3 deficiency could hamper cell proliferation, migration and invasion as well as epithelial-mesenchymaltransition (EMT) in ESCC while lncSUMO1P3 overexpression led to the opposite consequences. LncSUMO1P3 could competitively bind to microRNA-486-5p (miR-486-5p) or PHD finger protein 8 (PHF8) to modulate CD151 expression. CD151 was also verified to regulate ESCC cell biological behaviors. Conclusion Our study revealed that lncSUMO1P3, up-regulated in ESCC cells, could sponge miR-486-5p and recruit PHF8 to up-regulate CD151, thus influencing the malignant behaviors of ESCC cells.
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Affiliation(s)
- Tingyou Zhang
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Guojun Yue
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Xin Tian
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Ying Xu
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Zhongwen Li
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
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2
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Abstract
In general, the last step in the vegetative cycle of bacterial viruses, or bacteriophages, is lysis of the host. dsDNA phages require multiple lysis proteins, including at least one enzyme that degrades the cell wall (peptidoglycan (PG)). In contrast, the lytic ssDNA and ssRNA phages have a single lysis protein that achieves cell lysis without enzymatically degrading the PG. Here, we review four "single-gene lysis" or Sgl proteins. Three of the Sgls block bacterial cell wall synthesis by binding to and inhibiting several enzymes in the PG precursor pathway. The target of the fourth Sgl, L from bacteriophage MS2, is still unknown, but we review evidence indicating that it is likely a protein involved in maintaining cell wall integrity. Although only a few phage genomes are available to date, the ssRNA Leviviridae are a rich source of novel Sgls, which may facilitate further unraveling of bacterial cell wall biosynthesis and discovery of new antibacterial agents.
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Affiliation(s)
- Karthik Chamakura
- From the Department of Biochemistry and Biophysics and
- the Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas 77843-2128
| | - Ry Young
- From the Department of Biochemistry and Biophysics and
- the Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas 77843-2128
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3
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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Nishihara T, Fujisaki S, Nishimura Y, Minami Y, Yubisui T. Analysis of Six New Genes Encoding Lysis Proteins and Coat Proteins inEscherichia coliGroup A RNA Phages. Microbiol Immunol 2013; 50:61-6. [PMID: 16428875 DOI: 10.1111/j.1348-0421.2006.tb03772.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Group A RNA phages consist of four genes-maturation protein, coat protein, lysis protein and replicase genes. We analyzed six plasmids containing lysis protein genes and coat protein genes of Escherichia coli group A RNA phages and compared their amino acid sequences with the known proteins of E. coli(group A), Pseudomonas aeruginosa(PP7) RNA phages and Rg-lysis protein from Qbeta phage. The size of lysis proteins was different by the groups but the coat proteins were almost the same size among phages. The phylogenetic analysis shows that the sub-groups A-I and A-II of E. coli RNA phages were clearly dispersed into two clusters.
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Affiliation(s)
- Tohru Nishihara
- Department of Biochemistry, Kawasaki Medical School, Kurashiki, Okayama 701-0192, Japan.
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5
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Ackermann HW, Kropinski AM. Curated list of prokaryote viruses with fully sequenced genomes. Res Microbiol 2007; 158:555-66. [PMID: 17889511 DOI: 10.1016/j.resmic.2007.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2007] [Revised: 07/18/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
Genome sequencing is of enormous importance for classification of prokaryote viruses and for understanding the evolution of these viruses. This survey covers 284 sequenced viruses for which a full description has been published and for which the morphology is known. This corresponds to 219 (4%) of tailed and 75 (36%) of tailless viruses of prokaryotes. The number of sequenced tailless viruses almost doubles if viruses of unknown morphology are counted. The sequences are from representatives of 15 virus families and three groups without family status, including eight taxa of archaeal viruses. Tailed phages, especially those with large genomes and hosts other than enterobacteria or lactococci, mycobacteria and pseudomonads, are vastly under investigated.
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Affiliation(s)
- Hans-W Ackermann
- Felix d'Herelle Reference Center for Bacterial Viruses, Department of Medical Biology, Faculty of Medicine, Laval University, Québec, QC G1K 7P4, Canada.
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6
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Love DC, Sobsey MD. Simple and rapid F+ coliphage culture, latex agglutination, and typing assay to detect and source track fecal contamination. Appl Environ Microbiol 2007; 73:4110-8. [PMID: 17483282 PMCID: PMC1932791 DOI: 10.1128/aem.02546-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 04/27/2007] [Indexed: 11/20/2022] Open
Abstract
Simple, rapid, and reliable fecal indicator tests are needed to better monitor and manage ambient waters and treated waters and wastes. Antibody-coated polymeric bead agglutination assays can fulfill these needs and are inexpensive and portable for nonlaboratory settings, and their reagents can be stored at ambient temperatures for months. The goal of this study was to develop, optimize, and validate a rapid microbial water quality monitoring assay using F+ coliphage culture, latex agglutination, and typing (CLAT) to detect F+ coliphage groups with antibody-coated particles. Rapid (180 min) F+ coliphage culture gave comparable results to those with the 16- to 24-h culture time used in EPA method 1601 and was amenable to CLAT assay detection. CLAT was performed on a cardboard card by mixing a drop of coliphage enrichment culture with a drop of antibody-coated polymeric beads as the detection reagent. Visual agglutination or clumping of positive samples occurred in <60 seconds. The CLAT assay had sensitivities of 96.4% (185/192 samples) and 98.2% (161/164 samples) and specificities of 100% (34/34 samples) and 97.7% (129/132 samples) for F+ RNA and DNA coliphages, respectively. CLAT successfully classified F+ RNA coliphages into serogroups typically obtained from human (groups II and III) and animal (groups I and IV) fecal sources, in similar proportions to those obtained with a nucleic acid hybridization assay. This novel group-specific antibody-based particle agglutination technique for rapid and simple detection and grouping of F+ coliphages provides a new and improved tool for monitoring the microbiological quality of drinking, recreational, shellfishing, and other waters.
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Affiliation(s)
- David C Love
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
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7
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Nishihara T, Morisawa H, Ohta N, Atkins JF, Nishimura Y. A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame. Genes Cells 2005; 9:877-89. [PMID: 15461660 DOI: 10.1111/j.1365-2443.2004.00778.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The maturation/lysis (A2) protein encoded by the group B single-stranded RNA bacteriophage Qbeta mediates lysis of host Escherichia coli cells. We found a frameshift mutation in the replicase (beta-subunit) gene of Qbeta cDNA causes cell lysis. The mutant has a single base deletion 73 nucleotides (nt) 3' from the start of the replicase gene with consequent translation termination at a stop codon 129-131 nt further 3'. The 43-amino acid C-terminal part of the 67-amino acid product encoded by what in WT (wild-type) is the +1 frame, is rich in basic amino acids This 67-aa protein can mediate cell lysis whose characteristics indicate that the protein may cause lysis by a different mechanism and via a different target, than that caused by the A2 maturation/lysis protein. Synthesis of a counterpart of the newly discovered lysis product in wild-type phage infection would require a hypothetical ribosomal frameshifting event. The lysis gene of group A RNA phages is also short, 75 codons in MS2, and partially overlaps the first part of their equivalently located replicase gene, raising significant evolutionary implications for the present finding.
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Affiliation(s)
- Tohru Nishihara
- Department of Biochemistry, Kawasaki Medical School, Kurashiki City, Okayama, Japan.
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8
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Nishihara T. Various morphological aspects of Escherichia coli lysis by two distinct RNA bacteriophages. J Gen Virol 2002; 83:2601-2606. [PMID: 12237444 DOI: 10.1099/0022-1317-83-10-2601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transmission electron micrographs of Escherichia coli cells induced by cloned lysis genes from RNA bacteriophages GA (group A-II) and SP (group B-IV) revealed various morphological aspects of intermediates of lysing cells. Cells induced by the SP lysis gene became stretched and also tapered in shape and fragmentation of parts of the cells had also occurred. Cells induced by the GA lysis gene showed many ballooning structures on the cell surfaces and others leaked material through the cell wall. Some balloon-like structures also appeared on the surfaces of cells induced by the cloned lysis gene of RNA phage SP and material also appeared to be leaking through the cell wall in the photographs. The lysing cells observed by transmission electron microscopy showed various morphological aspects of intermediates of the lysing process.
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Affiliation(s)
- Tohru Nishihara
- Department of Biochemistry, Kawasaki Medical School, Kurashiki, Japan1
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9
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Cielens I, Ose V, Petrovskis I, Strelnikova A, Renhofa R, Kozlovska T, Pumpens P. Mutilation of RNA phage Qbeta virus-like particles: from icosahedrons to rods. FEBS Lett 2000; 482:261-4. [PMID: 11024472 DOI: 10.1016/s0014-5793(00)02061-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Icosahedral virus-like particles (VLPs) of RNA phage Qbeta are stabilized by four disulfide bonds of cysteine residues 74 and 80 within the loop between beta-strands F and G (FG loop) of the monomeric subunits, which determine the five-fold and quasi-six-fold symmetry contacts of the VLPs. In order to reduce the stability of Qbeta VLPs, we mutationally converted the amino acid stretch 76-ANGSCD-81 within the FG loop into the 76-VGGVEL-81 sequence. It led to production in Escherichia coli cells of aberrant rod-like Qbeta VLPs, along with normal icosahedral capsids. The length of the rod-like particles exceeded 4-30 times the diameter of icosahedral Qbeta VLPs.
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Affiliation(s)
- I Cielens
- Biomedical Research and Study Centre, University of Latvia, 1 Ratsupites Street, LV-1067, Riga, Latvia
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10
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Ni CZ, White CA, Mitchell RS, Wickersham J, Kodandapani R, Peabody DS, Ely KR. Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer. Protein Sci 1996; 5:2485-93. [PMID: 8976557 PMCID: PMC2143325 DOI: 10.1002/pro.5560051211] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.
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Affiliation(s)
- C Z Ni
- Structural Biology Program, La Jolla Cancer Research Center, Burnham Institute, California 92037, USA
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11
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Beekwilder J, Nieuwenhuizen R, Havelaar AH, van Duin J. An oligonucleotide hybridization assay for the identification and enumeration of F-specific RNA phages in surface water. THE JOURNAL OF APPLIED BACTERIOLOGY 1996; 80:179-86. [PMID: 8642014 DOI: 10.1111/j.1365-2672.1996.tb03207.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
F-specific RNA phages can be used as model organisms for enteric viruses to monitor the effectiveness of sewage treatment, and to assess the potential contamination of surface water with these viruses. In this paper a method is described which identifies RNA phages quantitatively by a plaque hybridization assay. Oligonucleotide probes were developed that can assign phages to their phylogenetic subgroups. Such a distinction is important, since some subgroups preferentially occur in sewage of human origin, while others tend to be associated with animal wastewater. The method has been tested on a large number of isolates and represents an improvement in time and reliability over the previously used serological classification.
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Affiliation(s)
- J Beekwilder
- Leiden Institute of Chemistry, Department of Biochemistry, Leiden University, The Netherlands
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12
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Hsu FC, Shieh YS, van Duin J, Beekwilder MJ, Sobsey MD. Genotyping male-specific RNA coliphages by hybridization with oligonucleotide probes. Appl Environ Microbiol 1995; 61:3960-6. [PMID: 8526509 PMCID: PMC167702 DOI: 10.1128/aem.61.11.3960-3966.1995] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
F-specific (F+) RNA coliphages are prevalent in sewage and other fecal wastes of humans and animals. There are four antigenically distinct serogroups of F+ RNA coliphages, and those predominating in humans (groups II and III) differ from those predominating in animals (groups I and IV). Hence, it may be possible to distinguish between human and animal wastes by serotyping F+ RNA coliphage isolates. Because serotyping is laborious and requires scarce antiserum reagents, we investigated genotyping using synthetic oligonucleotide probes as an alternative approach to distinguishing the four groups of F+ RNA coliphages. Oligoprobes I, II, III, IV, A, and B were selected to detect group I, II, III, IV, I plus II, and III plus IV phages, respectively. Methods for phage transfer from zones of lysis on a host cell lawn to candidate membrane filters and fixation of genomic nucleic acid on the membranes were optimized. The oligoprobes, which were end labeled with digoxigenin, were applied in DNA-RNA hybridization, and hybrids were observed by colorimetric, immunoenzymatic detection. Of 203 isolates of F+ RNA coliphages from environmental samples of water, wastes, and shellfish, 99.5 and 96.6% could be classified into each group by serotyping and genotyping, respectively. Probes A and B correctly identified 100% of the isolates. On the basis of these results, this method for genotyping F+ RNA coliphages appears to be practical and reliable for typing isolates in field samples.
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Affiliation(s)
- F C Hsu
- University of North Carolina, Chapel Hill 27599, USA
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13
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Abstract
Bacteriophage lysis involves at least two fundamentally different strategies. Most phages elaborate at least two proteins, one of which is a murein hydrolase, or lysin, and the other is a membrane protein, which is given the designation holin in this review. The function of the holin is to create a lesion in the cytoplasmic membrane through which the murein hydrolase passes to gain access to the murein layer. This is necessary because phage-encoded lysins never have secretory signal sequences and are thus incapable of unassisted escape from the cytoplasm. The holins, whose prototype is the lambda S protein, share a common organization in terms of the arrangement of charged and hydrophobic residues, and they may all contain at least two transmembrane helical domains. The available evidence suggests that holins oligomerize to form nonspecific holes and that this hole-forming step is the regulated step in phage lysis. The correct scheduling of the lysis event is as much an essential feature of holin function as is the hole formation itself. In the second strategy of lysis, used by the small single-stranded DNA phage phi X174 and the single-stranded RNA phage MS2, no murein hydrolase activity is synthesized. Instead, there is a single species of small membrane protein, unlike the holins in primary structure, which somehow causes disruption of the envelope. These lysis proteins function by activation of cellular autolysins. A host locus is required for the lytic function of the phi X174 lysis gene E.
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Affiliation(s)
- R Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843
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14
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Witherell GW, Gott JM, Uhlenbeck OC. Specific interaction between RNA phage coat proteins and RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1991; 40:185-220. [PMID: 2031083 DOI: 10.1016/s0079-6603(08)60842-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- G W Witherell
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309
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15
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Abstract
Premature termination of translation in eubacteria, like Escherichia coli, often leads to reinitiation at nearby start codons. Restarts also occur in response to termination at the end of natural coding regions, where they serve to enforce translational coupling between adjacent cistrons. Here, we present a model in which the terminated but not released ribosome reaches neighboring initiation codons by lateral diffusion along the mRNA. The model is based on the finding that introduction of an additional start codon between the termination and the reinitiation site consistently obstructs ribosomes to reach the authentic restart site. Instead, the ribosome now begins protein synthesis at this newly introduced AUG codon. This ribosomal scanning-like movement is bidirectional, has a radius of action of more than 40 nucleotides in the model system used, and activates the first encountered restart site. The ribosomal reach in the upstream direction is less than in the downstream one, probably due to dislodging by elongating ribosomes. The proposed model has parallels with the scanning mechanism postulated for eukaryotic translational initiation and reinitiation.
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Affiliation(s)
- M R Adhin
- Department of Biochemistry, Leiden University, The Netherlands
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16
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Skripkin EA, Adhin MR, de Smit MH, van Duin J. Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. J Mol Biol 1990; 211:447-63. [PMID: 2407856 DOI: 10.1016/0022-2836(90)90364-r] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The RNA of the Escherichia coli RNA phages is highly structured with 75% of the nucleotides estimated to take part in base-pairing. We have used enzymatic and chemical sensitivity of nucleotides, phylogenetic sequence comparison and the phenotypes of constructed mutants to develop a secondary structure model for the central region (900 nucleotides) of the group I phage MS2. The RNA folds into a number of, mostly irregular, helices and is further condensed by several long-distance interactions. There is substantial conservation of helices between the related groups I and II, attesting to the relevance of discrete RNA folding. In general, the secondary structure is thought to be needed to prevent annealing of plus and minus strand and to confer protection against RNase. Superimposed, however, are features required to regulate translation and replication. The MS2 RNA section studied here contains three translational start sites, as well as the binding sites for the coat protein and the replicase enzyme. Considering the density of helices along the RNA, it is not unexpected to find that all these sites lie in helical regions. This fact, however, does not mean that these sites are recognized as secondary structure elements by their interaction partners. This holds true only for the coat protein binding site. The other four sites function in the unfolded state and the stability of the helix in which they are contained serves to negatively control their accessibility. Mutations that stabilize helices containing ribosomal binding sites reduce their efficiency and vice versa. Comparison of homologous helices in different phage RNAs indicates that base substitutions have occurred in such a way that the thermodynamic stability of the helix is maintained. The evolution of individual helices shows several distinct size-reduction patterns. We have observed codon deletions from loop areas and shortening of hairpins by base-pair deletions from either the bottom, the middle or the top of stem structures. Evidence for the coaxial stacking of some helical segments is discussed.
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Affiliation(s)
- E A Skripkin
- Department of Biochemistry, Gorlaeus Laboratories, Leiden University, The Netherlands
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