Finding prokaryotic genes by the ‘frame-by-frame’
  algorithm: targeting gene starts and overlapping genes

Shmatkov, A. M.; Melikyan, Arik; L.Chernousko, Felix; Borodovsky, Mark

doi:10.1093/bioinformatics/15.11.874

Cited by 40 publications

(16 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The insert of pBK129 was sequenced, and analysis of the DNA sequence (GenBank accession no. DQ195264) showed that it contained about 26 kb of nucleotides, including 24 intact genes ranging from traD to mclB as well as a part of traG (27). These genes were positioned in the same order as their counterparts of pTiR10, a wild-type Ti plasmid of octopine strain R10 (40).…”

Section: Resultsmentioning

confidence: 99%

Dual Control of Quorum Sensing by Two TraM-Type Antiactivators in Agrobacterium tumefaciens Octopine Strain A6

2006

View full text Add to dashboard Cite

Agrobacterium tumefaciens wild-type strains have a unique quorum-sensing (QS)-dependent Ti plasmid conjugative transfer phenotype in which QS signaling is activated by corresponding conjugative opine inducers. Strain K588, with a nopaline-type chromosomal background harboring an octopine-type Ti plasmid, however, is a spontaneous mutant displaying a constitutive phenotype in QS. In this study, we show that a single amino acid mutation (L54P) in the QS antiactivator TraM encoded by the traM gene of Ti plasmid is responsible for the constitutive phenotype of strain K588. Introduction of the L54P point mutation to the TraM of wild-type strain A6 by allelic replacement, however, failed to generate the expected constitutive phenotype in this octopine-type strain. Intriguingly, the QS-constitutive phenotype appeared when the pTiA6 carrying the mutated traM was placed in the chromosomal background of the nopaline-type strain C58C1RS, suggesting an unknown inhibitory factor(s) encoded by the chromosomal background of strain A6 but not by C58C1RS. Low-stringency Southern blotting analysis showed that strain A6, but not strain C58 and its derivatives, contains a second traM homologue. The homologue, designated traM2, has 64% and 65% identities with traM at the DNA and peptide levels, respectively. Similar to TraM, TraM2 is a potent antiactivator that functions by blocking TraR, the QS activator, from specific binding to the tra gene promoters. Deletion of traM2 in strain A6 harboring the mutated traM confers a constitutive QS phenotype. The results demonstrate that the QS system in strain A6 is subjected to the dual control of TraM and TraM2.

show abstract

Section: Resultsmentioning

confidence: 99%

Dual Control of Quorum Sensing by Two TraM-Type Antiactivators in Agrobacterium tumefaciens Octopine Strain A6

2006

View full text Add to dashboard Cite

show abstract

“…Open reading frames (ORFs) were identified with GeneMark (39), heuristic GeneMark (7), and frame-by-frame GeneMark (48) in combination with ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). If multiple translation initiation sites for an ORF were suggested, manual inspection for the presence of a convincing Shine-Dalgarno sequence and/or close packing with the nearest upstream ORF was used to select the most probable start codon.…”

Section: Methodsmentioning

confidence: 99%

Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages

Cornelissen

Hardies

Shaburova

et al. 2012

J Virol

View full text Add to dashboard Cite

The 283,757-bp double-stranded DNA genome of Pseudomonas fluorescens phage OBP shares a general genomic organization with Pseudomonas aeruginosa phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the KZ-related phages, supports the proposed division in the "EL-like viruses," and the "phiKZ-like viruses" within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the KZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3=-5= exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the KZ-related phages. P seudomonas fluorescens phage OBP (vB_PflM_OBP) (30, 47) is member of a growing group of giant phages, isolated, to date, only from Pseudomonas species and represented by the completely sequenced and well-studied Pseudomonas aeruginosa myovirus KZ (9,18,19,[31][32][33]36,42). Three other phages encoding many proteins with similarity to KZ proteins have been completely sequenced: EL (23), 2012-1 (52), and PA3 (43). Krylov et al. (33) assigned 19 unsequenced Pseudomonas phages to this group. We refer to the group as KZ-related phages. Lavigne et al. (35) have argued that EL should be classified as a genus separate from KZ and 2012-1 based on its less extensive levels of similarity. By that criterion, PA3 belongs to the "phiKZ-like viruses" and the results reported here classify OBP as the second member of the possible genus EL-like viruses.OBP shares a number of definitive properties with the other KZ-related phages. Typically, KZ-related phages have a very large icosahedral head, ϳ122 nm in diameter, and a long (ϳ190-nm) contractile tail surrounded by fibers. A KZ-related phage head contains a proteinic inner body, which has been speculated to organize the packaged DNA (18, 32). The exceptionally large genomes of the KZ-related phages (between 211 and 317 kb of nonredundant sequence) are composed of circularly permuted and terminally redundant linear double-stranded DNAs as determined for KZ and 2012-1 (42, 52). The KZ-related genomes display a pronounced difference in GϩC content (between 36.8 and 48%) and all have markedly lower GϩC content than the chromosomes of their GC-rich Pseudomonas hosts (60 to 66% GϩC).This group of phages has numerous genes involved in nucleotide metabolism (e.g., thymidylate synthase, thymidylate kinase, ribonucleoside diphosphate reductase, subunit beta [NrdB], and dihydrofolate reductase) and at least six genes enco...

show abstract

“…The next submodel is the RBS model which models the RBS as well as the nucleotides between the RBS and the start codon. After the start codon we model 3 bases explicitly since it appears that the codon usage immediately downstream of start codons differs from the rest of the gene [13]. Similarly we model the last codon before the stop codon explicitly and 6 bases after the stop in order to capture information present around the stop codon.…”

Section: Methodsmentioning

confidence: 99%

“…Due to their modular structure, HMMs are a suitable frame work for gene finding, and they are now used in GeneMark.hmm [10], GeneMarkS [11,12] and Frame-by-Frame [13]. GeneMarkS uses a mixture of Markov chains of order 0, 1 and 2 in combination with features of already annotated genomes to bootstrap an initial estimation of coding statistics, which is then iteratively improved by the GeneMark.hmm2.1 algorithm.…”

Section: Introductionmentioning

confidence: 99%

EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance

Larsen

Krogh²

2003

BMC Bioinformatics

137

View full text Add to dashboard Cite

show abstract

Finding prokaryotic genes by the ‘frame-by-frame’ algorithm: targeting gene starts and overlapping genes

Abstract: mark@amber.gatech.edu.

Cited by 40 publications

References 29 publications

Dual Control of Quorum Sensing by Two TraM-Type Antiactivators in Agrobacterium tumefaciens Octopine Strain A6

Dual Control of Quorum Sensing by Two TraM-Type Antiactivators in Agrobacterium tumefaciens Octopine Strain A6

Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages

EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance

Contact Info

Product

Resources

About