Genomes and Genes
Experts and Doctors on bacterial genes in Ithaca, New York, United States
Locale: Ithaca, New York, United States
Topic: bacterial genes
- Buddha M, Keery K, Crane B. An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans. Proc Natl Acad Sci U S A. 2004;101:15881-6 pubmed publisher..Remarkably, TrpRS II also activates the NOS activity of deiNOS. These findings reveal a link between bacterial NOS and Trp metabolism in a second organism and may indicate yet another novel biological function for bacterial NOS...
- Stewart V, Parales J. Identification and expression of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12. J Bacteriol. 1988;170:1589-97 pubmed..Analysis of these operon fusions indicated that narL and narX are transcribed counterclockwise with respect to the E. coli genetic map and that narK is transcribed clockwise. ..
- Chien Y, Zinder S. Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol. 1996;178:143-8 pubmed..These results support a model in which the nitrogenase structural genes in M. barkeri are cotranscribed in a single NH4(+)-repressed operon...
- Charkowski A, Alfano J, Preston G, Yuan J, He S, Collmer A. The Pseudomonas syringae pv. tomato HrpW protein has domains similar to harpins and pectate lyases and can elicit the plant hypersensitive response and bind to pectate. J Bacteriol. 1998;180:5211-7 pubmed..These features of hrpW and its product suggest that P. syringae produces multiple harpins and that the target of these proteins is in the plant cell wall...
- Egan S, Stewart V. Mutational analysis of nitrate regulatory gene narL in Escherichia coli K-12. J Bacteriol. 1991;173:4424-32 pubmed..This finding suggests that narL505(V88A) did not confer molybdate-independent expression of fdnGHI. ..
- Lopez de Saro F, Yoshikawa N, Helmann J. Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. J Biol Chem. 1999;274:15953-8 pubmed..5 x 10(6) M-1, but we are unable to demonstrate the formation of a ternary complex containing core enzyme, delta, and sigmaA. ..
- Brahamsha B, Greenberg E. Cloning and sequence analysis of flaA, a gene encoding a Spirochaeta aurantia flagellar filament surface antigen. J Bacteriol. 1989;171:1692-7 pubmed..W. Charon, R. G. Cook, M. D. Fuentes, and R. J. Limberger, J. Bacteriol. 170:4072-4082, 1988). The region of identity in the deduced S. aurantia polypeptide was preceded by a possible signal sequence and signal peptidase cleavage site...
- Chien Y, Zinder S. Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum. J Bacteriol. 1994;176:6590-8 pubmed..It is not clear whether this similarity is due to horizontal gene transfer or to the resemblance of the M. barkeri and C. pasteurianum nitrogenase sequences to an ancestral nitrogenase...
- Chen C, Wang L, Winans S. Characterization of the supervirulent virG gene of the Agrobacterium tumefaciens plasmid pTiBo542. Mol Gen Genet. 1991;230:302-9 pubmed
- Cho H, Winans S. VirA and VirG activate the Ti plasmid repABC operon, elevating plasmid copy number in response to wound-released chemical signals. Proc Natl Acad Sci U S A. 2005;102:14843-8 pubmed..Mutating this sequence blocked the AS-induced copy number increase of a RepABC-dependent miniplasmid, indicating that phospho-VirG increases copy number solely by enhancing repABC expression. ..
- Willins D, Ryan C, Platko J, Calvo J. Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine. J Biol Chem. 1991;266:10768-74 pubmed..Lrp has some amino acid sequence similarity to AsnC, a protein that regulates asnA expression (Kolling, R., and Lother, H. (1985) J. Bacteriol. 164, 310-315). ..
- Elsinghorst E, Mortlock R. Molecular cloning of the Escherichia coli B L-fucose-D-arabinose gene cluster. J Bacteriol. 1994;176:7223-32 pubmed..D-Arabinose metabolism by E. coli B appears to be the result of acquisitive evolution, but the source of the darK gene has not been determined. ..
- Pohlman R, Genetti H, Winans S. Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens. Mol Microbiol. 1994;14:655-68 pubmed
- Santos T, Caixeta L, Machado V, Rauf A, Gilbert R, Bicalho R. Antimicrobial resistance and presence of virulence factor genes in Arcanobacterium pyogenes isolated from the uterus of postpartum dairy cows. Vet Microbiol. 2010;145:84-9 pubmed publisher..All four virulence factor genes occurred in isolates from normal puerperium and clinical metritis; however, the fimA gene was present in significantly higher frequency in isolates from metritis cows...
- Chin N, Frey J, Chang C, Chang Y. Identification of a locus involved in the utilization of iron by Actinobacillus pleuropneumoniae. FEMS Microbiol Lett. 1996;143:1-6 pubmed..The afuABC operon is locating approximately 200 bp upstream of apxIC gene, but transcribed in opposite direction to the ApxI-toxin genes. ..
- Gaballa A, Cao M, Helmann J. Two MerR homologues that affect copper induction of the Bacillus subtilis copZA operon. Microbiology. 2003;149:3413-21 pubmed..The results demonstrate the direct regulation of the B. subtilis copper efflux system by CueR, and indirect regulation by a putative multidrug efflux system. ..
- Rojas C, Ham J, Schechter L, Kim J, Beer S, Collmer A. The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system. Mol Plant Microbe Interact. 2004;17:644-53 pubmed..chrysanthemi Hrp regulator genes hrpL and hrpS. Thus, the 44-kb region of the E. chrysanthemi EC16 genome that is centered on the hrplhrc cluster encodes a potpourri of virulence factors, but none of these appear to be a TTSS effector...
- Jeon C, Park M, Ro H, Park W, Madsen E. The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control. Appl Environ Microbiol. 2006;72:1086-95 pubmed..naphthalenivorans...
- Cho H, Winans S. TraA, TraC and TraD autorepress two divergent quorum-regulated promoters near the transfer origin of the Ti plasmid of Agrobacterium tumefaciens. Mol Microbiol. 2007;63:1769-82 pubmed..TraA preferentially acted in cis in repressing the traA and traC promoters and in the processing of oriT, which explains the very high activity of plasmid-borne traA-lacZ fusions reported in previous studies. ..
- Hao Z, Chen S, Wilson D. Cloning, expression, and characterization of cadmium and manganese uptake genes from Lactobacillus plantarum. Appl Environ Microbiol. 1999;65:4746-52 pubmed..The topology and potential Mn(2+)- and Cd(2+)-binding sites of MntA are discussed. A second clone containing a low-affinity Cd(2+) transport system was also isolated...
- Melnick J, Lis E, Park J, Kinsland C, Mori H, Baba T, et al. Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase. J Bacteriol. 2004;186:3660-2 pubmed..The genes encoding thiamine kinase in Escherichia coli (ycfN) and thiamine pyrophosphokinase in Bacillus subtilis (yloS) have been identified. This study completes the identification of the thiamine salvage enzymes in bacteria. ..
- Stewart V, Berg B. Influence of nar (nitrate reductase) genes on nitrate inhibition of formate-hydrogen lyase and fumarate reductase gene expression in Escherichia coli K-12. J Bacteriol. 1988;170:4437-44 pubmed..Insertions in narL had a lesser effect, and insertions in narX had no effect. We conclude that nitrate affects formate-hydrogen lyase synthesis by a pathway distinct from that for nitrate reductase and fumarate reductase. ..
- Chen L, James L, Helmann J. Metalloregulation in Bacillus subtilis: isolation and characterization of two genes differentially repressed by metal ions. J Bacteriol. 1993;175:5428-37 pubmed..Mutation of the putative iron box for gene mrgC leads to partial derepression in iron-replete medium. ..
- Chai Y, Winans S. RepB protein of an Agrobacterium tumefaciens Ti plasmid binds to two adjacent sites between repA and repB for plasmid partitioning and autorepression. Mol Microbiol. 2005;58:1114-29 pubmed publisher..We propose that RepA and RepB form complexes that bind both sites, possibly causing a loop that is important for repression of the repABC operon. Binding at one or both sites may also be required for accurate plasmid partitioning...
- Moser F, Irwin D, Chen S, Wilson D. Regulation and characterization of Thermobifida fusca carbohydrate-binding module proteins E7 and E8. Biotechnol Bioeng. 2008;100:1066-77 pubmed publisher..E8, and to a lesser extent E7, significantly enhanced the activity of Serratia marscescens Chitinase C on beta-chitin. ..
- Preston G, Deng W, Huang H, Collmer A. Negative regulation of hrp genes in Pseudomonas syringae by HrpV. J Bacteriol. 1998;180:4532-7 pubmed..These results suggest that HrpF, HrpG, and HrpT are all components of the type III protein secretion system whereas HrpV is a negative regulator of transcription of the Hrp regulon. ..
- Nightingale K, Milillo S, Ivy R, Ho A, Oliver H, Wiedmann M. Listeria monocytogenes F2365 carries several authentic mutations potentially leading to truncated gene products, including inlB, and demonstrates atypical phenotypic characteristics. J Food Prot. 2007;70:482-8 pubmed..Our results support that L. monocytogenes F2365 is characterized by genotypic and phenotypic properties that are atypical of other L. monocytogenes strains. ..
- Vander Horn P, Backstrom A, Stewart V, Begley T. Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12. J Bacteriol. 1993;175:982-92 pubmed..These mutants did not respond to 1-deoxy-D-threo-2-pentulose, indicating that they are blocked in the conversion of this precursor compound to the thiazole itself. ..
- Stewart V, Lin J, Berg B. Genetic evidence that genes fdhD and fdhE do not control synthesis of formate dehydrogenase-N in Escherichia coli K-12. J Bacteriol. 1991;173:4417-23 pubmed..Our complementation tests, with cloned E. coli fdhD and fdhE genes, indicate that the S. typhimurium fdnC and fdnB genes are functionally homologous to the E. coli fdhD and fdhE genes, respectively. ..
- Kalogeraki V, Winans S. The octopine-type Ti plasmid pTiA6 of Agrobacterium tumefaciens contains a gene homologous to the chromosomal virulence gene acvB. J Bacteriol. 1995;177:892-7 pubmed..Finally, mutations in these genes cannot be complemented extracellularly...
- Tosques I, Shi J, Shapleigh J. Cloning and characterization of nnrR, whose product is required for the expression of proteins involved in nitric oxide metabolism in Rhodobacter sphaeroides 2.4.3. J Bacteriol. 1996;178:4958-64 pubmed..sphaeroides 2.4.1. The likely effector of NnrR activity, as determined on the basis of work detailed in this paper and other studies, is discussed. ..
- Liao P, Choi Y, Lee K. FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots. Nucleic Acids Res. 2009;37:7302-11 pubmed publisher..coli. The results have implications for bioinformatic identification of novel frameshift proteins, ribosomal frameshifting, coding sequence detection and the application of mass spectrometry on studying frameshift proteins. ..
- Berg B, Li J, Heider J, Stewart V. Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine. J Biol Chem. 1991;266:22380-5 pubmed..Evidence from sequence and spectral analyses suggest that FdnI encodes cytochrome bFdn556. Implications for the membrane topology of formate dehydrogenase-N and its mechanism of proton translocation are discussed. ..
- Badel J, Shimizu R, Oh H, Collmer A. A Pseudomonas syringae pv. tomato avrE1/hopM1 mutant is severely reduced in growth and lesion formation in tomato. Mol Plant Microbe Interact. 2006;19:99-111 pubmed..These data suggest that AvrE1 acts within plant cells and promotes lesion formation and that the combined action of AvrE1 and HopM1 is particularly important in promoting bacterial growth in planta. ..
- Chen L, Helmann J. Bacillus subtilis MrgA is a Dps(PexB) homologue: evidence for metalloregulation of an oxidative-stress gene. Mol Microbiol. 1995;18:295-300 pubmed..These results indicate a complex interplay between metal ions and the expression of the B. subtilis oxidative stress response. ..
- Cho K, Fuqua C, Martin B, Winans S. Identification of Agrobacterium tumefaciens genes that direct the complete catabolism of octopine. J Bacteriol. 1996;178:1872-80 pubmed..Insertions of the third group was localized to a gene whose product is required for degradation of proline. We therefore have identified all steps required for the catabolism of octopine to glutamate. ..
- Rabin R, Stewart V. Either of two functionally redundant sensor proteins, NarX and NarQ, is sufficient for nitrate regulation in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1992;89:8419-23 pubmed..Analysis of narX* and narL missense alleles in narQ+ versus narQ::Tn10 backgrounds suggests that NarQ and NarX may have subtle functional differences. ..
- Raengpradub S, Wiedmann M, Boor K. Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions. Appl Environ Microbiol. 2008;74:158-71 pubmed..monocytogenes and L. innocua sigma(B) regulons show considerable conservation, with a common set of at least 49 genes that are sigma(B) dependent in both species...
- Parales R, Harwood C. Nucleotide sequence of the gyrB gene of Pseudomonas putida. Nucleic Acids Res. 1990;18:5880 pubmed
- Palaniappan R, Chang Y, Chang C, Pan M, Yang C, Harpending P, et al. Evaluation of lig-based conventional and real time PCR for the detection of pathogenic leptospires. Mol Cell Probes. 2005;19:111-7 pubmed..Hence, conventional and real time PCR with lig primers would be a sensitive and rapid tool for early diagnosis of leptospirosis...
- den Bakker H, Didelot X, Fortes E, Nightingale K, Wiedmann M. Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evol Biol. 2008;8:277 pubmed publisher..While lineage I and lineage II should be considered separate species from an evolutionary viewpoint, maintaining single species name may be warranted since both lineages cause the same type of human disease. ..
- Bignell D, Seipke R, Huguet Tapia J, Chambers A, Parry R, Loria R. Streptomyces scabies 87-22 contains a coronafacic acid-like biosynthetic cluster that contributes to plant-microbe interactions. Mol Plant Microbe Interact. 2010;23:161-75 pubmed publisher..Thus, the cfa-like biosynthetic cluster is a newly discovered locus in S. scabies that contributes to host-pathogen interactions. ..
- Rodriguez E, Han Y, Lei X. Cloning, sequencing, and expression of an Escherichia coli acid phosphatase/phytase gene (appA2) isolated from pig colon. Biochem Biophys Res Commun. 1999;257:117-23 pubmed..In conclusion, the DNA fragment isolated from E. coli in pig colon seems to encode for a new acid phosphatase/phytase and is designated as E. coli appA2. ..
- Stewart V. Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli. Mol Microbiol. 1993;9:425-34 pubmed..An additional challenge is to determine how or if the FNR and NARL proteins interact to mediate dual positive control of transcription initiation. ..
- Bartnikas T, Tosques I, Laratta W, Shi J, Shapleigh J. Characterization of the nitric oxide reductase-encoding region in Rhodobacter sphaeroides 2.4.3. J Bacteriol. 1997;179:3534-40 pubmed..Regulatory studies demonstrated that the first four genes, norCBQD, are expressed only when the oxygen concentration is low and nitrate is present but that the two distal genes, nnrTU, are expressed constitutively...
- Taylor S, Kelleher N, Kinsland C, Chiu H, Costello C, Backstrom A, et al. Thiamin biosynthesis in Escherichia coli. Identification of ThiS thiocarboxylate as the immediate sulfur donor in the thiazole formation. J Biol Chem. 1998;273:16555-60 pubmed..ThiF catalyzes the adenylation by ATP of the carboxyl-terminal glycine of ThiS. This reaction is likely to be involved in the activation of ThiS for sulfur transfer from cysteine or from a cysteine-derived sulfur donor. ..
- Cao M, Wang T, Ye R, Helmann J. Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons. Mol Microbiol. 2002;45:1267-76 pubmed..Our findings are consistent with the idea that one function of ECF sigma factors is to coordinate antibiosis stress responses and cell envelope homeostasis. ..
- Chen L, Keramati L, Helmann J. Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions. Proc Natl Acad Sci U S A. 1995;92:8190-4 pubmed..These data indicate that the peroxide stress response of B. subtilis is regulated by a repressor that senses both metal ion levels and H2O2. ..
- Huang H, He S, Bauer D, Collmer A. The Pseudomonas syringae pv. syringae 61 hrpH product, an envelope protein required for elicitation of the hypersensitive response in plants. J Bacteriol. 1992;174:6878-85 pubmed..These results suggest that the P. syringae pv. syringae HrpH protein is involved in the secretion of a proteinaceous HR elicitor...
- Deng W, Rehm A, Charkowski A, Rojas C, Collmer A. Pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in P. syringae pv. syringae B728a. J Bacteriol. 2003;185:2592-602 pubmed
- Barril J, Kim S, Batt C. Cloning and sequencing of the Lactococcus lactis subsp. lactis dnaK gene using a PCR-based approach. Gene. 1994;142:91-6 pubmed..Alignment of the deduced aa sequence with those of other bacterial DnaK showed a high degree of homology and is most similar to the Bacillus megaterium DnaK. ..
- Renna M, Najimudin N, Winik L, Zahler S. Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin. J Bacteriol. 1993;175:3863-75 pubmed..Two mutations that cause increased expression of the alsSD operon have been isolated, cloned, and sequenced. They each change an amino acid in the AlsR protein. ..
- Culman S, Bukowski R, Gauch H, Cadillo Quiroz H, Buckley D. T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinformatics. 2009;10:171 pubmed publisher..T-REX provides a free, platform-independent tool to the research community that allows for an integrated, rapid, and more robust analysis of T-RFLP data. ..
- Chang Y, Ma D, Wang Y, Chin N, Chengappa M, Shin S, et al. Sequence analysis of leukotoxin secretion determinants from a Pasteurella haemolytica-like organism. DNA Seq. 1995;5:291-7 pubmed..Infect. Immun. 61:2089-2095), which encodes a 105-kda polypeptide with cytotoxic activity. DNA sequence analysis of the pHLBD genes shows 83.93% and 86.05% homologous to that of P. haemolytica IktBD genes, respectively...
- Stewart V, Parales J, Merkel S. Structure of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12. J Bacteriol. 1989;171:2229-34 pubmed..We report here the nucleotide sequences of narL and narX. The deduced protein sequences aid in defining distinct subclasses of regulators and sensors in the family of two-component regulatory proteins. ..
- Rahm B, Richardson R. Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. Environ Sci Technol. 2008;42:416-21 pubmed..2 micromol/L/hr did not necessarily lead to corresponding increases in transcript levels...
- Vander Horn P, Zahler S. Cloning and nucleotide sequence of the leucyl-tRNA synthetase gene of Bacillus subtilis. J Bacteriol. 1992;174:3928-35 pubmed..subtilis ilv-leu operon. The DNA of the B. subtilis leuS open reading frame is 48% identical to the leuS gene of Escherichia coli and is predicted to encode a polypeptide with 46% identity to the leucyl-tRNA synthetase of E. coli. ..
- Berg B, Stewart V. Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12. Genetics. 1990;125:691-702 pubmed..We conclude that regulation of fdnGHI and narGHJI expression is mediated through common pathways. ..