A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.


:The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. phiKZ encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit RNAPs. Polypeptides of one set are encoded by middle phage genes and are found in the phiKZ virions. Polypeptides of the second set are encoded by early phage genes and are absent from virions. Here, we report isolation of a five-subunit RNAP from phiKZ-infected cells. Four subunits of this enzyme are cellular RNAP subunits homologs of the non-virion set; the fifth subunit is a protein of unknown function. In vitro, this complex initiates transcription from late phiKZ promoters in rifampicin-resistant manner. Thus, this enzyme is a non-virion phiKZ RNAP responsible for transcription of late phage genes. The phiKZ RNAP lacks identifiable assembly and promoter specificity subunits/factors characteristic for eukaryal, archaeal and bacterial RNAPs and thus provides a unique model for comparative analysis of the mechanism, regulation and evolution of this important class of enzymes.


Nucleic Acids Res


Nucleic acids research


Yakunina M,Artamonova T,Borukhov S,Makarova KS,Severinov K,Minakhin L




Has Abstract


2015-12-02 00:00:00














  • Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae: the conserved zinc finger-like motif is functionally exchangeable in vivo.

    abstract::A cDNA encoding the 60 kDa subunit of mammalian splicing factor SF3a has been isolated. The deduced protein sequence reveals a 30% identity to the PRP9 splicing protein of the yeast S.cerevisiae. The highest homology is present in a zinc finger-like region in the C-terminal domain of both proteins. The PRP9 zinc finge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Krämer A,Legrain P,Mulhauser F,Gröning K,Brosi R,Bilbe G

    更新日期:1994-12-11 00:00:00

  • The transposable element Mdg3 in Drosophila melanogaster is flanked with the perfect direct and mismatched inverted repeats.

    abstract::MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bayev AA Jr,Krayev AS,Lyubomirskaya NV,Ilyin YV,Skryabin KG,Georgiev GP

    更新日期:1980-08-11 00:00:00

  • DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization.

    abstract::Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gilson E,Perrin D,Hofnung M

    更新日期:1990-07-11 00:00:00

  • Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution.

    abstract::Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of speci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saini V,Raghuvanshi S,Khurana JP,Ahmed N,Hasnain SE,Tyagi AK,Tyagi AK

    更新日期:2012-11-01 00:00:00

  • Distribution of 7-methylguanine and of replication sites in the different kinetic classes of DNA from rats treated with dimethylnitrosamine.

    abstract::The distribution of 7-methylguanine in the families of repetitive and unique sequences of rat liver chromatin DNA has been studied using the technique of DNA-DNA reassociation. Rats were injected with di[14C]methylnitrosamine and chromatin DNA was prepared 3 h later. The distribution of 7-methylguanine was found to be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Galbraith AI,Chapleo MR,Itzhaki RF

    更新日期:1978-09-01 00:00:00

  • Single-cell chromosomal imbalances detection by array CGH.

    abstract::Genomic imbalances are a major cause of constitutional and acquired disorders. Therefore, aneuploidy screening has become the cornerstone of preimplantation, prenatal and postnatal genetic diagnosis, as well as a routine aspect of the diagnostic workup of many acquired disorders. Recently, array comparative genomic hy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Le Caignec C,Spits C,Sermon K,De Rycke M,Thienpont B,Debrock S,Staessen C,Moreau Y,Fryns JP,Van Steirteghem A,Liebaers I,Vermeesch JR

    更新日期:2006-05-12 00:00:00

  • See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins.

    abstract::Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: van Mameren J,Peterman EJ,Wuite GJ

    更新日期:2008-08-01 00:00:00

  • The mitoribosome-specific protein mS38 is preferentially required for synthesis of cytochrome c oxidase subunits.

    abstract::Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS cata...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mays JN,Camacho-Villasana Y,Garcia-Villegas R,Perez-Martinez X,Barrientos A,Fontanesi F

    更新日期:2019-06-20 00:00:00

  • MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.

    abstract::MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 differ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RV

    更新日期:2011-01-01 00:00:00

  • Repeat 1 of TAL effectors affects target specificity for the base at position zero.

    abstract::AvrBs3, the founding member of the Xanthomonas transcription-activator-like effectors (TALEs), is translocated into the plant cell where it localizes to the nucleus and acts as transcription factor. The DNA-binding domain of AvrBs3 consists of 17.5 nearly-identical 34 amino acid-repeats. Each repeat specifies binding ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schreiber T,Bonas U

    更新日期:2014-06-01 00:00:00

  • A comparative study of G+C-rich satellite components of sheep and goat DNA.

    abstract::Restriction fragment patterns of G+C-rich satellites of sheep and goat DNA were compared. The 1,712 g/cm3 satellites of both species appear homologous, consisting of repeats 760 base pairs long and showing coincidence of position of primary+ EcoRI, BamHI and most BspRI restriction target sites. The EcoRI and BamHI end...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


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    更新日期:1979-01-01 00:00:00

  • N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity.

    abstract::Heterochromatin protein 1 (HP1) is an evolutionarily conserved chromosomal protein that binds to lysine 9-methylated histone H3 (H3K9me), a hallmark of heterochromatin. Although HP1 phosphorylation has been described in several organisms, the biological implications of this modification remain largely elusive. Here we...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nishibuchi G,Machida S,Osakabe A,Murakoshi H,Hiragami-Hamada K,Nakagawa R,Fischle W,Nishimura Y,Kurumizaka H,Tagami H,Nakayama J

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  • Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung-/-Msh2-/- mice.

    abstract::Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kemmerich K,Dingler FA,Rada C,Neuberger MS

    更新日期:2012-07-01 00:00:00

  • SIRT1 is regulated by a PPAR{γ}-SIRT1 negative feedback loop associated with senescence.

    abstract::Human Silent Information Regulator Type 1 (SIRT1) is an NAD(+)-dependent deacetylase protein which is an intermediary of cellular metabolism in gene silencing and aging. SIRT1 has been extensively investigated and shown to delay senescence; however, less is known about the regulation of SIRT1 during aging. In this stu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Han L,Zhou R,Niu J,McNutt MA,Wang P,Tong T

    更新日期:2010-11-01 00:00:00

  • Cloning of Drosophila GCN5: conserved features among metazoan GCN5 family members.

    abstract::PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Smith ER,Belote JM,Schiltz RL,Yang XJ,Moore PA,Berger SL,Nakatani Y,Allis CD

    更新日期:1998-06-15 00:00:00

  • DNA nicking favors PCR recombination.

    abstract::We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Marton A,Delbecchi L,Bourgaux P

    更新日期:1991-05-11 00:00:00

  • DBTGR: a database of tunicate promoters and their regulatory elements.

    abstract::The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sierro N,Kusakabe T,Park KJ,Yamashita R,Kinoshita K,Nakai K

    更新日期:2006-01-01 00:00:00

  • A processed chicken pseudogene (CPS1) related to the ras oncogene superfamily.

    abstract::We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Alsip GR,Konkel DA

    更新日期:1986-03-11 00:00:00

  • Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    abstract::In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang G,Lukoszek R,Mueller-Roeber B,Ignatova Z

    更新日期:2011-04-01 00:00:00

  • Crystal structure of a tick-borne flavivirus RNA-dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses.

    abstract::The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yang J,Jing X,Yi W,Li XD,Yao C,Zhang B,Zheng Z,Wang H,Gong P

    更新日期:2021-01-06 00:00:00

  • Molecular dissection of the domain architecture and catalytic activities of human PrimPol.

    abstract::PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Keen BA,Jozwiakowski SK,Bailey LJ,Bianchi J,Doherty AJ

    更新日期:2014-05-01 00:00:00

  • Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter.

    abstract::Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sengar A,Vandana JJ,Chambers VS,Di Antonio M,Winnerdy FR,Balasubramanian S,Phan AT

    更新日期:2019-02-20 00:00:00

  • Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

    abstract::Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the huma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vitezic M,Lassmann T,Forrest AR,Suzuki M,Tomaru Y,Kawai J,Carninci P,Suzuki H,Hayashizaki Y,Daub CO

    更新日期:2010-12-01 00:00:00

  • Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae.

    abstract::Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lopes JM,Henry SA

    更新日期:1991-07-25 00:00:00

  • Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.

    abstract::Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

    更新日期:2017-12-15 00:00:00

  • A comprehensive catalog of predicted functional upstream open reading frames in humans.

    abstract::Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: McGillivray P,Ault R,Pawashe M,Kitchen R,Balasubramanian S,Gerstein M

    更新日期:2018-04-20 00:00:00

  • Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator.

    abstract::The mode of action of regulated promoters is largely determined by kinetic parameters which govern the interaction between promoters and proteins involved in induction and repression of transcription. To gain insight into the interplay between positively and negatively acting transcriptional regulators, in this case A...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lutz R,Lozinski T,Ellinger T,Bujard H

    更新日期:2001-09-15 00:00:00

  • Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III.

    abstract::RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Iben JR,Mazeika JK,Hasson S,Rijal K,Arimbasseri AG,Russo AN,Maraia RJ

    更新日期:2011-08-01 00:00:00

  • A fiber optic biosensor for fluorimetric detection of triple-helical DNA.

    abstract::A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Uddin AH,Piunno PA,Hudson RH,Damha MJ,Krull UJ

    更新日期:1997-10-15 00:00:00

  • Functional RNA polymerase II promoters in solitary retroviral long terminal repeats (LTR-IS elements).

    abstract::LTR-IS elements are middle repetitive sequences in the mouse genome with structural features of solitary retroviral LTRs. In order to get some insight in the possible functional role of these sequences the promotor activity of two LTR-IS representatives differing by 105 bp in their U3 region was investigated. Gene fus...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Köhrer K,Grummt I,Horak I

    更新日期:1985-04-11 00:00:00