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A novel taxonomic marker that discriminates between morphologically complex actinomycetes.

Girard G, Traag BA, Sangal V, Mascini N, Hoskisson PA, Goodfellow M, van Wezel GP - Open Biol (2013)

Bottom Line: The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes.Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora, Salinispora and Verrucosispora may represent different clades of the same genus.It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands.

ABSTRACT
In the era when large whole genome bacterial datasets are generated routinely, rapid and accurate molecular systematics is becoming increasingly important. However, 16S ribosomal RNA sequencing does not always offer sufficient resolution to discriminate between closely related genera. The SsgA-like proteins are developmental regulatory proteins in sporulating actinomycetes, whereby SsgB actively recruits FtsZ during sporulation-specific cell division. Here, we present a novel method to classify actinomycetes, based on the extraordinary way the SsgA and SsgB proteins are conserved. The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes. Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora, Salinispora and Verrucosispora may represent different clades of the same genus. It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches. A new phylogenetic tree of industrially relevant actinomycetes is presented and compared with that based on 16S rRNA sequences.

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Maximum-likelihood tree based on the alignment of RpoB proteins from a range of morphologically complex actinomycetes. For input sequences and their accession numbers, see the electronic supplementary material, data file S2.
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RSOB130073F2: Maximum-likelihood tree based on the alignment of RpoB proteins from a range of morphologically complex actinomycetes. For input sequences and their accession numbers, see the electronic supplementary material, data file S2.

Mentions: Comparison of maximum-likelihood trees of two standard taxonomic indicators, namely 16S rRNA (figure 1) and RpoB (the β-subunit of RNA polymerase [35]; figure 2), with that of SsgB (figure 3) indicates that the clades consistently group together (terminal branches) within the accepted taxonomic framework [11] as operational taxonomic units (OTUs). The congruence analysis using CONCATERPILLAR [36] revealed a phylogenetic congruence between RpoB and SsgB protein sequences (p = 0.2771); however, 16S rRNA nucleotide sequences were topologically incongruent with them (p = 0.0015). Interestingly, the groupings of the OTUs are consistent between all the trees, yet the branches indicate the overall phylogenetic history of the genes is likely to be different. The reasons for this can be attributed to gene duplication and gene loss, and to lateral gene transfer, where genes are exchanged between lineages [37,38]. Indeed, expansion of developmental gene families in actinomycetes through duplication has been studied previously [39].Figure 1.


A novel taxonomic marker that discriminates between morphologically complex actinomycetes.

Girard G, Traag BA, Sangal V, Mascini N, Hoskisson PA, Goodfellow M, van Wezel GP - Open Biol (2013)

Maximum-likelihood tree based on the alignment of RpoB proteins from a range of morphologically complex actinomycetes. For input sequences and their accession numbers, see the electronic supplementary material, data file S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814722&req=5

RSOB130073F2: Maximum-likelihood tree based on the alignment of RpoB proteins from a range of morphologically complex actinomycetes. For input sequences and their accession numbers, see the electronic supplementary material, data file S2.
Mentions: Comparison of maximum-likelihood trees of two standard taxonomic indicators, namely 16S rRNA (figure 1) and RpoB (the β-subunit of RNA polymerase [35]; figure 2), with that of SsgB (figure 3) indicates that the clades consistently group together (terminal branches) within the accepted taxonomic framework [11] as operational taxonomic units (OTUs). The congruence analysis using CONCATERPILLAR [36] revealed a phylogenetic congruence between RpoB and SsgB protein sequences (p = 0.2771); however, 16S rRNA nucleotide sequences were topologically incongruent with them (p = 0.0015). Interestingly, the groupings of the OTUs are consistent between all the trees, yet the branches indicate the overall phylogenetic history of the genes is likely to be different. The reasons for this can be attributed to gene duplication and gene loss, and to lateral gene transfer, where genes are exchanged between lineages [37,38]. Indeed, expansion of developmental gene families in actinomycetes through duplication has been studied previously [39].Figure 1.

Bottom Line: The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes.Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora, Salinispora and Verrucosispora may represent different clades of the same genus.It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands.

ABSTRACT
In the era when large whole genome bacterial datasets are generated routinely, rapid and accurate molecular systematics is becoming increasingly important. However, 16S ribosomal RNA sequencing does not always offer sufficient resolution to discriminate between closely related genera. The SsgA-like proteins are developmental regulatory proteins in sporulating actinomycetes, whereby SsgB actively recruits FtsZ during sporulation-specific cell division. Here, we present a novel method to classify actinomycetes, based on the extraordinary way the SsgA and SsgB proteins are conserved. The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes. Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora, Salinispora and Verrucosispora may represent different clades of the same genus. It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches. A new phylogenetic tree of industrially relevant actinomycetes is presented and compared with that based on 16S rRNA sequences.

Show MeSH
Related in: MedlinePlus