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The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway.

Cecagno R, Fritsch TE, Schrank IS - Biomed Res Int (2015)

Bottom Line: We performed an in silico comparative genomic analysis to understand the genomic plasticity of A. amazonense.Moreover, the presence of the coding sequence for nitrilase indicates the presence of the alternative route that uses IAN as an intermediate for auxin synthesis, but it remains to be established whether the IAN pathway is the Trp-independent route.Future investigations are necessary to support the hypothesis that its genomic structure has evolved to meet the requirement for adaptation to the rhizosphere and interaction with host plants.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biotecnologia, Laboratório de Microrganismos Diazotróficos, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.

ABSTRACT
The rhizosphere bacterium Azospirillum amazonense associates with plant roots to promote plant growth. Variation in replicon numbers and rearrangements is common among Azospirillum strains, and characterization of these naturally occurring differences can improve our understanding of genome evolution. We performed an in silico comparative genomic analysis to understand the genomic plasticity of A. amazonense. The number of A. amazonense-specific coding sequences was similar when compared with the six closely related bacteria regarding belonging or not to the Azospirillum genus. Our results suggest that the versatile gene repertoire found in A. amazonense genome could have been acquired from distantly related bacteria from horizontal transfer. Furthermore, the identification of coding sequence related to phytohormone production, such as flavin-monooxygenase and aldehyde oxidase, is likely to represent the tryptophan-dependent TAM pathway for auxin production in this bacterium. Moreover, the presence of the coding sequence for nitrilase indicates the presence of the alternative route that uses IAN as an intermediate for auxin synthesis, but it remains to be established whether the IAN pathway is the Trp-independent route. Future investigations are necessary to support the hypothesis that its genomic structure has evolved to meet the requirement for adaptation to the rhizosphere and interaction with host plants.

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Histogram distribution of predicted proteins in A. amazonense compared with six closely related genomes using BLASTP-based homology value (H value). The H-value reflects the degree of similarity in terms of length of match and the degree of identity at amino acid level between the matching CDS in the subject genome and the query CDS examined with E value > 10−8.
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fig1: Histogram distribution of predicted proteins in A. amazonense compared with six closely related genomes using BLASTP-based homology value (H value). The H-value reflects the degree of similarity in terms of length of match and the degree of identity at amino acid level between the matching CDS in the subject genome and the query CDS examined with E value > 10−8.

Mentions: Comparative genomic analysis using in silico subtractive hybridization allowed searching for specific proteins of the A. amazonense genome against multiple closely related bacterial genomes. Therefore, to determine the possible differences between the A. amazonense genome and each of the selected six closely related genomes, an in silico subtractive hybridization technique was applied. The histogram of H-values (Figure 1) was used to set the cutoff to discriminate between A. amazonense-specific and conserved coding sequences. Proteins with homology (H) values of less than 0.42 and more than 0.64 were arbitrarily defined as specific and conserved coding sequences, respectively [12]. This cutoff value was proposed by Shao et al. [12] and has been used in comparative genomic analyses to differentiate strains of pseudomonads [12, 15] or to compare genomes of species from the genus Erwinia [16].


The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway.

Cecagno R, Fritsch TE, Schrank IS - Biomed Res Int (2015)

Histogram distribution of predicted proteins in A. amazonense compared with six closely related genomes using BLASTP-based homology value (H value). The H-value reflects the degree of similarity in terms of length of match and the degree of identity at amino acid level between the matching CDS in the subject genome and the query CDS examined with E value > 10−8.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383252&req=5

fig1: Histogram distribution of predicted proteins in A. amazonense compared with six closely related genomes using BLASTP-based homology value (H value). The H-value reflects the degree of similarity in terms of length of match and the degree of identity at amino acid level between the matching CDS in the subject genome and the query CDS examined with E value > 10−8.
Mentions: Comparative genomic analysis using in silico subtractive hybridization allowed searching for specific proteins of the A. amazonense genome against multiple closely related bacterial genomes. Therefore, to determine the possible differences between the A. amazonense genome and each of the selected six closely related genomes, an in silico subtractive hybridization technique was applied. The histogram of H-values (Figure 1) was used to set the cutoff to discriminate between A. amazonense-specific and conserved coding sequences. Proteins with homology (H) values of less than 0.42 and more than 0.64 were arbitrarily defined as specific and conserved coding sequences, respectively [12]. This cutoff value was proposed by Shao et al. [12] and has been used in comparative genomic analyses to differentiate strains of pseudomonads [12, 15] or to compare genomes of species from the genus Erwinia [16].

Bottom Line: We performed an in silico comparative genomic analysis to understand the genomic plasticity of A. amazonense.Moreover, the presence of the coding sequence for nitrilase indicates the presence of the alternative route that uses IAN as an intermediate for auxin synthesis, but it remains to be established whether the IAN pathway is the Trp-independent route.Future investigations are necessary to support the hypothesis that its genomic structure has evolved to meet the requirement for adaptation to the rhizosphere and interaction with host plants.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biotecnologia, Laboratório de Microrganismos Diazotróficos, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.

ABSTRACT
The rhizosphere bacterium Azospirillum amazonense associates with plant roots to promote plant growth. Variation in replicon numbers and rearrangements is common among Azospirillum strains, and characterization of these naturally occurring differences can improve our understanding of genome evolution. We performed an in silico comparative genomic analysis to understand the genomic plasticity of A. amazonense. The number of A. amazonense-specific coding sequences was similar when compared with the six closely related bacteria regarding belonging or not to the Azospirillum genus. Our results suggest that the versatile gene repertoire found in A. amazonense genome could have been acquired from distantly related bacteria from horizontal transfer. Furthermore, the identification of coding sequence related to phytohormone production, such as flavin-monooxygenase and aldehyde oxidase, is likely to represent the tryptophan-dependent TAM pathway for auxin production in this bacterium. Moreover, the presence of the coding sequence for nitrilase indicates the presence of the alternative route that uses IAN as an intermediate for auxin synthesis, but it remains to be established whether the IAN pathway is the Trp-independent route. Future investigations are necessary to support the hypothesis that its genomic structure has evolved to meet the requirement for adaptation to the rhizosphere and interaction with host plants.

Show MeSH