Identification of nodulation promoter (<i>nod</i>-box) regions of<i>Rhizobium galegae</i>

Suominen, Leena; Paulín, Lars; Saano, Aimo; Sarén, Ari-Matti; Tas, Éva; Lindström, Kristina

doi:10.1111/j.1574-6968.1999.tb13735.x

Cited by 13 publications

(3 citation statements)

References 33 publications

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“…The whole-genome sequence analysis confirmed previous work on the N. galegae symbiosis gene region [25, 26], and enabled an extended analysis of this region. As a result, a previously undiscovered putative nodulation gene, preceded by a nod-box sequence, was identified at the rightmost end (according to the arrangement in Figure 5).…”

Section: Resultssupporting

confidence: 77%

Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors

et al. 2014

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BackgroundThe species Neorhizobium galegae comprises two symbiovars that induce nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. The mechanism behind this strict host specificity is not yet known. In this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of N. galegae, with a special interest in genomic differences that may play a role in host specificity.ResultsThe genome sequences confirmed that the two representative strains are much alike at a whole-genome level. Analysis of orthologous genes showed that N. galegae has a higher number of orthologs shared with Rhizobium than with Agrobacterium. The symbiosis plasmid of strain HAMBI 1141 was shown to transfer by conjugation under optimal conditions. In addition, both sequenced strains have an acetyltransferase gene which was shown to modify the Nod factor on the residue adjacent to the non-reducing-terminal residue. The working hypothesis that this gene is of major importance in directing host specificity of N. galegae could not, however, be confirmed.ConclusionsStrains of N. galegae have many genes differentiating them from strains of Agrobacterium, Rhizobium and Sinorhizobium. However, the mechanism behind their ecological difference is not evident. Although the final determinant for the strict host specificity of N. galegae remains to be identified, the gene responsible for the species-specific acetylation of the Nod factors was identified in this study. We propose the name noeT for this gene to reflect its role in symbiosis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-500) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 77%

Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors

et al. 2014

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“…This is substantiated by the high similarity of the 47 basepair (bp) TFBS sequences of FdeR and NodD1 is observed (60%, see Figure b), in conjunction with the high amino acid similarity of the DBD of FdeR and NodD1 (61% DBD identity, 41% for the complete amino acid sequences, see Supplementary Figure S2). , In addition, both TFBSs share the common 25, 5, and 7 bp nod boxes and the pair of palindromic NodD consensus sequences, [AT-N 10 -GAT]-N 7 -[ATC-N 10 -AT] (see Figure b). ,, The chimeric biosensor variant, pChimNodD1-PfdeAR, was created by replacing the fdeR coding sequence in pSynFdeR with the nodD1 coding sequence, thus generating a chimeric TF-TFBS pair (see Figure a). No significant response was detected for any of three tested flavonoids (one-way ANOVA: F = 0.656, 0.067, and 0.163 with p -values = 0.773, 0.999, and 0.999 > 0.05 for naringenin, apigenin, and luteolin, respectively, see Supplementary Table S2).…”

Section: Resultsmentioning

confidence: 99%

Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids

et al. 2018

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Transcriptional biosensors enable key applications in both metabolic engineering and synthetic biology. Due to nature's immense variety of metabolites, these applications require biosensors with a ligand specificity profile customised to the researcher's needs. In this work, chimeric biosensors were created by introducing parts of a donor regulatory circuit from Sinorhizobium meliloti, delivering the desired luteolin-specific response, into a non-specific biosensor chassis from Herbaspirillum seropedicae. Two strategies were evaluated for the development of chimeric LysR-type biosensors with customised ligand specificity profiles towards three closely-related flavonoids, naringenin, apigenin and luteolin. In the first strategy, chimeric promoter regions were constructed at the biosensor effector module, while in the second strategy, chimeric transcription factors were created at the biosensor detector module. Via both strategies, the biosensor repertoire was expanded with luteolin-specific chimeric biosensors demonstrating a variety of 1 Page 1 of 42 ACS Paragon Plus Environment ACS Synthetic Biology response curves and ligand specificity profiles. Starting from the non-specific biosensor chassis, a shift from 27.5% to 95.3% luteolin specificity was achieved with the created chimeric biosensors. Both strategies provide a compelling, faster and more accessible route for the customisation of biosensor ligand specificity, compared to de novo design and construction of each biosensor circuit for every desired ligand specificity.

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“…The hrp box promoter is identified with the consensus pattern "GGAAC[CT]N(15,17)CCACNNA" [41][42][43] . The HMMER3 suite program nhmmer is used to search with custom HMM profiles that we have built for other elements from known sequences, including nod box and tts box regulatory elements, and chromosome dif sites 10,[44][45][46][47][48][49][50][51] . Bedtools is used to ensure that predicted regulatory sequences do not overlap with coding sequences 52 .…”

Section: Initial Annotation and Custom Gene Databasesmentioning

confidence: 99%

Beav: A bacterial genome and mobile element annotation pipeline

Jung,

Rahman,

Schiffer

et al. 2024

Preprint

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Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav.

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Identification of nodulation promoter (nod-box) regions ofRhizobium galegae

Cited by 13 publications

References 33 publications

Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors

Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors

Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids

Beav: A bacterial genome and mobile element annotation pipeline

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