tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii.

Abstract:

:tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies.IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.

journal_name

J Bacteriol

journal_title

Journal of bacteriology

authors

Yu N,Jora M,Solivio B,Thakur P,Acevedo-Rocha CG,Randau L,de Crécy-Lagard V,Addepalli B,Limbach PA

doi

10.1128/JB.00690-18

subject

Has Abstract

pub_date

2019-04-09 00:00:00

issue

9

eissn

0021-9193

issn

1098-5530

pii

JB.00690-18

journal_volume

201

pub_type

杂志文章
  • The Rhizobium etli cyaC product: characterization of a novel adenylate cyclase class.

    abstract::Adenylate cyclases (ACs) catalyze the formation of 3',5'-cyclic AMP (cAMP) from ATP. A novel AC-encoding gene, cyaC, was isolated from Rhizobium etli by phenotypic complementation of an Escherichia coli cya mutant. The functionality of the cyaC gene was corroborated by its ability to restore cAMP accumulation in an E....

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.184.13.3560-3568.2002

    authors: Téllez-Sosa J,Soberón N,Vega-Segura A,Torres-Márquez ME,Cevallos MA

    更新日期:2002-07-01 00:00:00

  • Genomic comparison of Mycobacterium avium subsp. paratuberculosis sheep and cattle strains by microarray hybridization.

    abstract::Microarray-based comparisons of three Mycobacterium avium subsp. paratuberculosis isolates, including one sheep strain and two cattle strains, identified three large genomic deletions in the sheep strain, totaling 29,208 bp and involving 24 open reading frames. These deletions may help explain some of the differences ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.188.6.2290-2293.2006

    authors: Marsh IB,Bannantine JP,Paustian ML,Tizard ML,Kapur V,Whittington RJ

    更新日期:2006-03-01 00:00:00

  • Identification and characterization of a new ferric enterobactin receptor, CfrB, in Campylobacter.

    abstract::The ferric enterobactin (FeEnt) receptor CfrA is present in the majority of Campylobacter jejuni isolates and is responsible for high-affinity iron acquisition. Our recent work and that of others strongly suggested the existence of another FeEnt uptake system in Campylobacter. Here we have identified and characterized...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00478-10

    authors: Xu F,Zeng X,Haigh RD,Ketley JM,Lin J

    更新日期:2010-09-01 00:00:00

  • Homology among Escherichia coli K1 and K92 polysialytransferases.

    abstract::The neuS-encoded polysialytransferase (polyST) in Escherichia coli K1 catalyzes synthesis of polysialic acid homopolymers composed of unbranched sialyl alpha 2,8 linkages. Subcloning and complementation experiments showed that the K1 neuS was functionally interchangeable with the neuS from E. coli K92 (S. M. Steenberg...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.174.15.5127-5131.1992

    authors: Vimr ER,Bergstrom R,Steenbergen SM,Boulnois G,Roberts I

    更新日期:1992-08-01 00:00:00

  • (S)-3-hydroxy-3-methylglutaryl coenzyme A reductase, a product of the mva operon of Pseudomonas mevalonii, is regulated at the transcriptional level.

    abstract::We have cloned and sequenced a 505-base-pair (bp) segment of DNA situated upstream of mvaA, the structural gene for (S)-3-hydroxy-3-methylglutaryl coenzyme A reductase (EC 1.1.1.88) of Pseudomonas mevalonii. The DNA segment that we characterized includes the promoter region for the mva operon. Nuclease S1 mapping and ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.171.10.5567-5571.1989

    authors: Wang YL,Beach MJ,Rodwell VW

    更新日期:1989-10-01 00:00:00

  • Chemotaxis arrays in Vibrio species and their intracellular positioning by the ParC/ParP system.

    abstract::Most motile bacteria are able to bias their movement towards more favorable environments or to escape from obnoxious substances by a process called chemotaxis. Chemotaxis depends on a chemosensory system that is able to sense specific environmental signals and generate a behavioral response. Typically, the signal is t...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00793-17

    authors: Ringgaard S,Yang W,Alvarado A,Schirner K,Briegel A

    更新日期:2018-03-12 00:00:00

  • Bacteriocin (hemolysin) of Streptococcus zymogenes.

    abstract::The sensitivity of Streptococcus faecalis (ATTC 8043) to S. zymogenes X-14 bacteriocin depends greatly on its physiological age. Sensitivity decreases from the mid-log phase on and is completely lost in the stationary phase. The sensitivity of erythrocytes to the hemolytic capacity of the bacteriocin showed considerab...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.96.6.1895-1902.1968

    authors: Basinger SF,Jackson RW

    更新日期:1968-12-01 00:00:00

  • Identification of accessory genome regions in poultry Clostridium perfringens isolates carrying the netB plasmid.

    abstract::Necrotic enteritis (NE) is an economically important disease of poultry caused by certain Clostridium perfringens type A strains. NE pathogenesis involves the NetB toxin, which is encoded on a large conjugative plasmid within a 42-kb pathogenicity locus. Recent multilocus sequence type (MLST) studies have identified t...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.01032-12

    authors: Lepp D,Gong J,Songer JG,Boerlin P,Parreira VR,Prescott JF

    更新日期:2013-03-01 00:00:00

  • The RIB element in the goaG-pspF intergenic region of Escherichia coli.

    abstract::The sequence (2,700 bp) between the aldH and pspF genes of Escherichia coli was determined. The pspF gene encodes a sigma54 transcriptional activator of the phage shock protein (psp) operon (pspA to pspE). Downstream of the pspF transcribed region are two open reading frames (ORFs), ordL and goaG, convergently oriente...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.179.10.3095-3102.1997

    authors: Jovanovic G,Model P

    更新日期:1997-05-01 00:00:00

  • Salmonella typhimurium LT2 strains which are r- m+ for all three chromosomally located systems of DNA restriction and modification.

    abstract::We describe the derivation of two strains of Salmonella typhimurium LT2 which are r- m+ for all three of the known chromosomal genes for the restriction and modification of DNA, hsdLT, hsdSA, and hsdSB; the strains were designated LB5000 and LB5010. LB5000 is a smooth derivative sensitive to phage P22; LB5010 is a gal...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.156.1.471-474.1983

    authors: Bullas LR,Ryu JI

    更新日期:1983-10-01 00:00:00

  • Two homologous genes coding for spore-specific proteins are expressed at different times during development of Myxococcus xanthus.

    abstract::The ops and tps genes of Myxococcus xanthus have ca. 90% DNA and amino acid sequence homology and are in the same orientation separated by a spacer region of only 1.4 kilobases. The products of the two genes were found to cross-react immunologically, and both were capable of Ca2+-dependent self-assembly on the surface...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.163.1.121-125.1985

    authors: Teintze M,Thomas R,Furuichi T,Inouye M,Inouye S

    更新日期:1985-07-01 00:00:00

  • Ultrastructural studies of sporulation in Streptomyces.

    abstract::This is the first study of sporogenesis in Streptomyces carried out on a relatively high number of species (seven) which allows us, using also previously published results, to establish a general picture of this process. In the sporogenesis of Streptomyces two basic stages can be considered: the sporulation septum syn...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.127.3.1443-1454.1976

    authors: Hardisson C,Manzanal MB

    更新日期:1976-09-01 00:00:00

  • Absence of correlation between rates of cell wall turnover and autolysis shown by Bacillus subtilis mutants.

    abstract::Bacillus subtilis mutants with reduced rates of cell wall autolysis reached a constant rate of wall turnover after a longer lag than the standard strain but eventually showed the same turnover rate. In reverse, a turnover-deficient mutant autolysed at a slightly higher rate than the standard strain. Consequently, ther...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.157.1.318-320.1984

    authors: Vitković L,Cheung HY,Freese E

    更新日期:1984-01-01 00:00:00

  • Roles of DegP in prevention of protein misfolding in the periplasm upon overexpression of penicillin acylase in Escherichia coli.

    abstract::Enhancement of the production of soluble recombinant penicillin acylase in Escherichia coli via coexpression of a periplasmic protease/chaperone, DegP, was demonstrated. Coexpression of DegP resulted in a shift of in vivo penicillin acylase (PAC) synthesis flux from the nonproductive pathway to the productive one when...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.185.10.3020-3030.2003

    authors: Pan KL,Hsiao HC,Weng CL,Wu MS,Chou CP

    更新日期:2003-05-01 00:00:00

  • The groESL operon of Agrobacterium tumefaciens: evidence for heat shock-dependent mRNA cleavage.

    abstract::The heat shock response of the groESL operon of Agrobacterium tumefaciens was studied at the RNA level. The operon was found to be activated under heat shock conditions and transcribed as a polycistronic mRNA that contains the groES and groEL genes. After activation, the polycistronic mRNA appeared to be cleaved betwe...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.177.3.750-757.1995

    authors: Segal G,Ron EZ

    更新日期:1995-02-01 00:00:00

  • Homology between Escherichia coli plasmids ColE1 and p15A.

    abstract::The location and extent of the homology between plasmids ColE1 and p15A were determined by analysis of heteroduplexes formed between them as well as with a related plasmid, pBR322, and by hybridization of radioactive deoxyribonucleic acids to restriction fragments of p15A and ColE1. The homology between the plasmids c...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.145.3.1305-1309.1981

    authors: Bird RE

    更新日期:1981-03-01 00:00:00

  • Role of RsbU in controlling SigB activity in Staphylococcus aureus following alkaline stress.

    abstract::SigB is an alternative sigma factor that controls a large regulon in Staphylococcus aureus. Activation of SigB requires RsbU, a protein phosphatase 2C (PP2C)-type phosphatase. In a closely related organism, Bacillus subtilis, RsbU activity is stimulated upon interaction with RsbT, a kinase, which following an activati...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.01514-08

    authors: Pané-Farré J,Jonas B,Hardwick SW,Gronau K,Lewis RJ,Hecker M,Engelmann S

    更新日期:2009-04-01 00:00:00

  • Role of the catabolite activator protein in the maltose regulon of Escherichia coli.

    abstract::The maltose regulon consists of three operons controlled by a positive regulatory gene, malT. Deletions of the gene crp were introduced into strains which carried a malT-lacZ hybrid gene. From the observed reduction in beta-galactosidase activity it was concluded that the expression of malT-lacZ, and therefore of malT...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.150.2.722-729.1982

    authors: Chapon C

    更新日期:1982-05-01 00:00:00

  • Uptake of the glucose analogue 2-deoxyglucose by germinating mitospores of Allomyces macrogynus.

    abstract::Mitospores or cysts of Allomyces macrogynus do not take up the glucose analogue 2-deoxyglucose. Uptake of 2-deoxyglucose by germlings begins at 25 min into germination, the start of the rhizoid stage, and increases in rate by approximately 50-fold until 100 min into germination. The rate remains constant from 100 to 2...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.124.2.843-848.1975

    authors: Burke DD

    更新日期:1975-11-01 00:00:00

  • Purification, properties, and regulation of glutamic dehydrogenase of Bacillus licheniformis.

    abstract::Cell-free extracts of Bacillus licheniformis and B. cereus were found to contain high specific activities of nicotinamide adenine dinucleotide phosphate (NADP)-dependent-l-glutamate dehydrogenase [EC 1.4.1.4; l-glutamate: NADP oxidoreductase (deaminating)]. Maximum specific activities were found in extracts of cells d...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.106.2.375-385.1971

    authors: Phibbs PV Jr,Bernlohr RW

    更新日期:1971-05-01 00:00:00

  • Complementation of the lytD1 mutation of Escherichia coli by either the cI or cro gene of bacteriophage lambda.

    abstract::The lytD1 mutant of Escherichia coli exhibits temperature-sensitive growth which is attributed to cellular autolysis at the restrictive temperature. Either of two cloned phage lambda genes, identified as cI and cro, suppressed the lytD1(Ts) lysis phenotype, suggesting that lytD encodes a DNA-binding protein with a DNA...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.173.2.893-895.1991

    authors: Dai DX,Ishiguro EE

    更新日期:1991-01-01 00:00:00

  • Structure and immunochemistry of the cell wall mannans from Saccharomyces chevalieri, Saccharomyces italicus, Saccharomyces diastaticus, and Saccharomyces carlsbergensis.

    abstract::The mannans of Saccharomyces chevalieri, S. italicus, S. diastaticus, and S. carlsbergensis, were acetolyzed, and the fragments were separated by gel filtration. All gave similar acetolysis fingerprints, which were distinguished from S. cerevisiae by the presence of a pentasaccharide component in addition to the mono-...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.117.2.461-467.1974

    authors: Ballou CE,Lipke PN,Raschke WC

    更新日期:1974-02-01 00:00:00

  • Glycerol-induced unraveling of the tight helical conformation of Escherichia coli type 1 fimbriae.

    abstract::Glycerol was found to unravel the helical conformation of Escherichia coli type 1 fimbriae without appreciable depolymerization. The linearized fimbrial polymers have a diameter of 2 nm, react strongly with a monoclonal antibody directed at an inaccessible epitope on native fimbriae, and display greater mannose-bindin...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.174.15.5145-5148.1992

    authors: Abraham SN,Land M,Ponniah S,Endres R,Hasty DL,Babu JP

    更新日期:1992-08-01 00:00:00

  • Genes involved in cell wall localization and side chain formation of rhamnose-glucose polysaccharide in Streptococcus mutans.

    abstract::We identified in Streptococcus mutans six new genes (rgpA through rgpF), whose disruption results in a loss of serotype-specific antigenicity, specified by the glucose side chains of rhamnose-glucose polysaccharide from the cell wall. Rhamnose and glucose content of the cell wall decreased drastically in all these dis...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.180.21.5803-5807.1998

    authors: Yamashita Y,Tsukioka Y,Tomihisa K,Nakano Y,Koga T

    更新日期:1998-11-01 00:00:00

  • Observations on replication and cell division in synchronous cultures of the blue-green alga Anacystis nidulans.

    abstract::A second synchrony induction treatment, half-way through the deoxyribonucleic acid replication process of an already synchronized culture, resulted in defective subsequent cell growth. This supports a previous explanation for the partial loss of viability after synchrony induction. ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.107.2.583-584.1971

    authors: Herdman M,Carr NG

    更新日期:1971-08-01 00:00:00

  • Analysis of Halobacterium halobium gas vesicles.

    abstract::Gas vesicles, isolated from lysed Halobacterium halobium cells, gave an amino acid analysis which accounted for 78% of the weight, and the balance was mainly salt and water. One percent of tightly bound d-galactose was found, as well as 2% of phosphate that was not released by treatment which promotes beta-elimination...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.114.3.1058-1067.1973

    authors: Krantz MJ,Ballou CE

    更新日期:1973-06-01 00:00:00

  • Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D.

    abstract::Production of Bacillus subtilis exoproteases is positively regulated by the DegS-DegU two-component regulatory system and other regulatory factors including DegR and ProB. It was shown that the expression of degR was virtually abolished in a sigD mutant and that the transcriptional initiation site in vivo is preceded ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.178.1.216-222.1996

    authors: Ogura M,Tanaka T

    更新日期:1996-01-01 00:00:00

  • The herpes simplex virus thymidine kinase gene is not transcribed in Saccharomyces cerevisiae.

    abstract::The herpes simplex virus thymidine kinase gene has been cloned into a chimeric yeast plasmid cloning vehicle and transformed into appropriate yeast strains. Plasmids carrying the herpes simplex virus thymidine kinase gene can be propagated as autonomously replicating plasmids, but no RNA specific to the thymidine kina...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.149.2.542-547.1982

    authors: Kiss GB,Pearlman RE,Cornish KV,Friesen JD,Chan VL

    更新日期:1982-02-01 00:00:00

  • RmpA regulation of capsular polysaccharide biosynthesis in Klebsiella pneumoniae CG43.

    abstract::Sequence analysis of the large virulence plasmid pLVPK in Klebsiella pneumoniae CG43 revealed the presence of another mucoid factor encoding gene rmpA besides rmpA2. Promoter activity measurement indicated that the deletion of rmpA reduced K2 capsular polysaccharide (CPS) biosynthesis, resulting in decreased colony mu...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00031-10

    authors: Cheng HY,Chen YS,Wu CY,Chang HY,Lai YC,Peng HL

    更新日期:2010-06-01 00:00:00

  • A Ti plasmid-encoded enzyme required for degradation of mannopine is functionally homologous to the T-region-encoded enzyme required for synthesis of this opine in crown gall tumors.

    abstract::The mocC gene encoded by the octopine/mannityl opine-type Ti plasmid pTi15955 is related at the nucleotide sequence level to mas1' encoded by the T region of this plasmid. While Mas1 is required for the synthesis of mannopine (MOP) by crown gall tumor cells, MocC is essential for the utilization of MOP by Agrobacteriu...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.178.11.3285-3292.1996

    authors: Kim KS,Chilton WS,Farrand SK

    更新日期:1996-06-01 00:00:00