Results 11 - 20
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262
Gene identification in novel eukaryotic genomes by self-training algorithm
- NUCLEIC ACIDS RES
, 2005
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TyeA, a protein involved in control of Yop release and in translocation of Yersinia Yop effectors
- EMBO J
, 1998
"... Extracellular Yersinia spp. disarm the immune system by injecting the effector Yersinia outer proteins (Yops) into the target cell. Yop secretion is triggered by contact with eukaryotic cells or by Ca2 chelation. Two proteins, YopN and LcrG, are known to be involved in Yop-secretion control. Here w ..."
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Cited by 53 (5 self)
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Extracellular Yersinia spp. disarm the immune system by injecting the effector Yersinia outer proteins (Yops) into the target cell. Yop secretion is triggered by contact with eukaryotic cells or by Ca2 chelation. Two proteins, YopN and LcrG, are known to be involved in Yop-secretion control. Here we describe TyeA, a third protein involved in the control of Yop release. Like YopN, TyeA is localized at the bacterial surface. A tyeA knock-out mutant secreted Yops in the presence of Ca2 and in the absence of eukaryotic cells. Unlike a yopN null mutant, the tyeA mutant was defective for translocation of YopE and YopH, but not YopM, YopO and YopP, into eukaryotic cells. This is the first observation suggesting that Yop effectors can be divided into two sets for delivery into eukaryotic cells. TyeA was found to interact with the translocator YopD and with residues 242–293 of YopN. In contrast with a yopN null mutant, a yopNΔ248–272 mutant was also unable to translocate YopE and YopH. Our results suggest that TyeA forms part of the translocation-control apparatus together with YopD and YopN, and that the interaction of these proteins is required for selective translocation of Yops inside eukaryotic cells.
The Conserved Exon Method for Gene Finding
, 2000
"... A new approach to gene finding is introduced called the "Conserved Exon Method" (CEM). It is based on the idea of looking for conserved protein sequences by comparing pairs of DNA sequences, identifying putative exon pairs based on conserved regions and splice junction signals then chainin ..."
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Cited by 50 (0 self)
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A new approach to gene finding is introduced called the "Conserved Exon Method" (CEM). It is based on the idea of looking for conserved protein sequences by comparing pairs of DNA sequences, identifying putative exon pairs based on conserved regions and splice junction signals then chaining pairs of putative exons together. It simultaneously predicts gene structures in both human and mouse genomic sequences (or in other pairs of sequences at the appropriate evolutionary distance). Experimental results indicate the potential usefulness of this approach.
Identification of a putative alternate sigma factor and characterization of a multicomponent regulatory cascade controlling the expression of Pseudomonas syringae pv. syringae Pss61 hrp and hrmA
, 1994
"... The Pseudomonas syringae hrp and hrmA genes controlling pathogenicity and elicitation of the hypersensitive response and the avr genes controlling host range have been shown previously to be regulated by carbon, nitrogen, pH, osmolarity, and hypothetical plant factors. In P. syringae pv. syringae Ps ..."
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Cited by 48 (5 self)
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The Pseudomonas syringae hrp and hrmA genes controlling pathogenicity and elicitation of the hypersensitive response and the avr genes controlling host range have been shown previously to be regulated by carbon, nitrogen, pH, osmolarity, and hypothetical plant factors. In P. syringae pv. syringae Pss6l, inactivation of hrp complementation groups II and XIII reduced expression of a plasmid-borne hrmA'-lacZ fusion. The hrp regions II and XIII were cloned on separate plasmids and shown to enhance the activity of the hrmA promoter in Escherichia coli MC4100 transformants at least 100-fold. The nucleotide sequence of region XIII revealed two open reading frames (hrpR and hrpS) whose deduced products share homology with P. syringae pv. phaseolicola NPS3121 HrpS and are both related to the NtrC family of two-component signal transduction systems. HrpR and HrpS differ from most members of the protein family by lacking an amino-terminal domain which modulates the regulatory activity. A single open reading frame, hrpL, whose product shares homology with AlgU, a putative alternate sigma factor of P. aeruginosa, as well as with the related alternate sigma factors was identified. within region II. Key domains are partially conserved. Inactivation of hrpS in Pss6l repressed expression of a plasmid-borne hrpL'-lacZ fusion carried by pYXPLlR, and transformation of MC4100(pYXPL1R) with a plasmid carrying hrpRS increased hrpL promoter activity at least 200-fold. Neither hrpS nor hrpR, when cloned on separate plasmids, activated the hrpL promoter activity individually. The
Infection-Derived Enterococcus faecalis Strains Are Enriched in esp, a Gene Encoding a Novel Surface Protein
, 1998
"... These include: This article cites 47 articles, 26 of which can be accessed free at: ..."
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Cited by 44 (8 self)
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These include: This article cites 47 articles, 26 of which can be accessed free at:
Fur regulon of Salmonella typhimurium: identification of new iron-regulated genes
- J
, 1995
"... These include: Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Downloaded from ..."
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Cited by 41 (7 self)
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These include: Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Downloaded from
Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs
- Genome Res
, 2001
"... This is a copy of the free text from BioMed Centrals Repository (PMC) ..."
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Cited by 40 (7 self)
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This is a copy of the free text from BioMed Centrals Repository (PMC)
ExonHunter: a comprehensive approach to gene finding
- Bioinformatics
, 2005
"... We present ExonHunter, a new and comprehensive gene finder system that outperforms existing systems, featuring several new ideas and approaches. Our system combines numerous sources of information (genomic sequences, ESTs, and protein databases of related species) with a gene finder based on hidden ..."
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Cited by 40 (9 self)
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We present ExonHunter, a new and comprehensive gene finder system that outperforms existing systems, featuring several new ideas and approaches. Our system combines numerous sources of information (genomic sequences, ESTs, and protein databases of related species) with a gene finder based on hidden Markov model in a novel and systematic way. In our framework, various sources of information are expressed as partial probabilistic statements about positions in the sequence and their annotation. We then combine these into the final prediction with a quadratic programming method extending existing methods. Allowing only partial statements is key to our transparent handling of missing information and coping with the heterogeneous character of individual sources of information. As well, we give a new method for modeling length distribution of intergenic regions in hidden Markov models. On a commonly used test set, ExonHunter performs significantly better than ROSETTA, SLAM, or TWINSCAN, and more than two thirds of genes were predicted completely correctly.
The periplasmic, group III catalase of Vibrio fischeri is required for normal symbiotic competence and is induced both by oxidative stress and approach to stationary phase
- J
, 1998
"... The catalase gene, katA, of the sepiolid squid symbiont Vibrio fischeri has been cloned and sequenced. The predicted amino acid sequence of KatA has a high degree of similarity to the recently defined group III catalases, including those found in Haemophilus influenzae, Bacteroides fragilis, and Pro ..."
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Cited by 39 (21 self)
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The catalase gene, katA, of the sepiolid squid symbiont Vibrio fischeri has been cloned and sequenced. The predicted amino acid sequence of KatA has a high degree of similarity to the recently defined group III catalases, including those found in Haemophilus influenzae, Bacteroides fragilis, and Proteus mirabilis. Upstream of the predicted start codon of katA is a sequence that closely matches the consensus sequence for promoters regulated in Escherichia coli by the alternative sigma factor encoded by rpoS. Further, the level of expression of the cloned katA gene in an E. coli rpoS mutant is much lower than in wild-type E. coli. Catalase activity is induced three- to fourfold both as growing V. fischeri cells approach stationary phase and upon the addition of a small amount of hydrogen peroxide during logarithmic growth. The catalase activity was localized in the periplasm of wild-type V. fischeri cells, where its role could be to detoxify hydrogen peroxide coming from the external environment. No significant catalase activity could be detected in a katA null mutant strain, demonstrating that KatA is the predominately expressed catalase in V. fischeri and indicating that V. fischeri carries only a single catalase gene. The catalase mutant was defective in its ability to competitively colonize the light organs of juvenile squids in coinoculation experiments with the parent strain, suggesting that the catalase enzyme plays an important role in the symbiosis between V. fischeri and its squid host. The luminous marine bacterium Vibrio fischeri occupies a
Durbin R: Gene structure conservation aids similarity based gene prediction
- Nucleic Acids Research
"... One of the primary tasks in deciphering the functional contents of a newly sequenced genome is the identi®cation of its protein coding genes. Existing computational methods for gene prediction include ab initio methods which use the DNA sequence itself as the only source of information, comparative ..."
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Cited by 39 (3 self)
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One of the primary tasks in deciphering the functional contents of a newly sequenced genome is the identi®cation of its protein coding genes. Existing computational methods for gene prediction include ab initio methods which use the DNA sequence itself as the only source of information, comparative methods using multiple genomic sequences, and similarity based methods which employ the cDNA or protein sequences of related genes to aid the gene prediction. We present here an algorithm implemented in a computer program called Projector which combines comparative and similarity approaches. Projector employs similarity information at the genomic DNA level by directly using known genes annotated on one DNA sequence to predict the corresponding related genes on another DNA sequence. It therefore makes explicit use of the conservation of the exon±intron structure between two related genes in addition to the similarity of their encoded amino acid sequences. We evaluate the performance of Projector by comparing it with the program Genewise on a test set of 491 pairs of independently con®rmed mouse and human genes. It is more accurate than Genewise for genes whose proteins are <80 % identical, and is suitable for use in a combined gene prediction system where other methods identify well conserved and non-conserved genes, and pseudogenes.
