Genomics of<i>Actinobacteria</i>: Tracing the Evolutionary History of an Ancient Phylum

Ventura, Marco; Canchaya, Carlos; Tauch, Andreas; Chandra, Govind; Fitzgerald, Gerald F.; Chater, Keith F.; Sinderen, Douwe van

doi:10.1128/mmbr.00005-07

Cited by 903 publications

(667 citation statements)

References 513 publications

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“…Therefore, it cannot be stated with certainty that these partial sequences also conserve both acidic amino acids, although each of them conserves the E108 position. Further analysis of ActRs sequence characteristics reveals that genes of the LG1-A and LG-B type exhibit a much lower GC content (B40-50%, Supplementary Figure S2) than commonly perceived for organisms belonging to the phylum Actinobacteria, who are commonly referred to as 'High GC Gram-positive bacteria' (Ventura et al, 2007).…”

Section: Isolate Mwh-uga1 Encodes An Lg1-actrmentioning

confidence: 99%

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

et al. 2009

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Microbial rhodopsins are membrane proteins that utilize a retinal chromophore to harvest sunlight for energetic and photosensory functions. Recently, a group of novel rhodopsin sequences named 'actinorhodopsins' (ActRs) was hypothesized to exist among uncultured planktonic Actinobacteria. ActRs were discovered by mining metagenomic data obtained during the Venter Institute's Global Ocean Sampling expedition, from a hypersaline lagoon, two estuaries and a freshwater lake. On the basis of these findings, and many studies that show Actinobacteria are common inhabitants of lakes, we predicted that ActR genes would likely be present in other freshwater habitats and among the genomes of cultivated Actinobacteria. Using degenerate polymerase chain reaction primers, we discovered an ActR gene present in an actinobacterial isolate of the family Microbacteriaceae. Isolate MWH-Uga1 was cultivated prior to this study from a freshwater pond in Uganda and belongs to a group of Actinobacteria previously identified in freshwater ecosystems. ActR genes were also discovered present in numerous mixed cultures containing freshwater Actinobacteria and among environmental DNA samples obtained from three freshwater sources; a small woodland pond and the Laurentian Great Lakes Superior and Erie. An analysis of small subunit ribosomal RNA genes from metagenomic DNA samples harboring ActR genes suggests that organisms belonging to the acI lineage, an uncultured group of Actinobacteria commonly present in fresh waters, may utilize rhodopsins. The co-occurrence of an acI organism with a specific ActR variant in a mixed culture supports our hypothesis. The ISME Journal (2009) 3, 726-737; doi:10.1038/ismej.2009 published online 26 February 2009 Subject Category: microbial ecology and functional diversity of natural habitats

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Section: Isolate Mwh-uga1 Encodes An Lg1-actrmentioning

confidence: 99%

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

et al. 2009

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“…Bifidobacteria are high G þ C Gram-positive bacteria belonging to the Bifidobacteriaceae family and the Actinobacteria class (Ventura et al, 2007). Traditionally, estimates of microbial diversity were based solely on culturable microorganisms.…”

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Microbiomic analysis of the bifidobacterial population in the human distal gut

et al. 2009

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One of the most complex microbial ecosystems is represented by the microbiota of the human gastrointestinal tract (GIT). Although this microbial consortium has been recognized to have a crucial effect on human health, its precise composition is still not fully established. Among the GIT bacteria, bifidobacteria represent an important commensal group whose presence is often associated with health-promoting effects. In this work, we assessed the complexity of the human intestinal bifidobacterial population by analysing the diversity of several 16S rRNA gene-based libraries. These analyses showed the presence of novel bifidobacterial phylotypes, which had not been found earlier and may thus represent novel taxa within the genus Bifidobacterium.

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“…In addition, the DNA sequences has allowed for selection of appropriate probes for diagnosis, strain typing, and reconstruction of evolutionary schemes. During the preparation of this article, a comprehensive review of actinobacteria from a genomics perspective has been published [175]. The basis of pathogenicity of mycobacteria is thought to depend completely or in part on members of expanded gene families such as esx, PE-PPE, pks, mce etc.…”

Section: Discussionmentioning

confidence: 99%

Defining mycobacteria: Shared and specific genome features for different lifestyles

Vissa

Sakamuri

et al. 2009

Indian J Microbiol

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During the last decade, the combination of rapid whole genome sequencing capabilities, application of genetic and computational tools, and establishment of model systems for the study of a range of species for a spectrum of biological questions has enhanced our cumulative knowledge of mycobacteria in terms of their growth properties and requirements. The adaption of the corynebacterial surrogate system has simplifi ed the study of cell wall biosynthetic machinery common to actinobacteria. Comparative genomics supported by experimentation reveals that superimposed on a common core of 'mycobacterial' gene set, pathogenic mycobacteria are endowed with multiple copies of several protein families that encode novel secretion and transport systems such as mce and esx; immunomodulators named PE/PPE proteins, and polyketide synthases for synthesis of complex lipids. The precise timing of expression, engagement and interactions involving one or more of these redundant proteins in their host environments likely play a role in the defi nition and differentiation of species and their disease phenotypes. Besides these, only a few species specifi c 'virulence' factors i.e., macromolecules have been discovered. Other subtleties may also arise from modifi cations of shared macromolecules. In contrast, to cope with the broad and changing growth conditions, their saprophytic relatives have larger genomes, in which the excess coding capacity is dedicated to transcriptional regulators, transporters for nutrients and toxic metabolites, biosynthesis of secondary metabolites and catabolic pathways. In this review, we present a sampling of the tools and techniques that are being implemented to tease apart aspects of physiology, phylogeny, ecology and pathology and illustrate the dominant genomic characteristics of representative species. The investigation of clinical isolates, natural disease states and discovery of new diagnostics, vaccines and drugs for existing and emerging mycobacterial diseases, particularly for multidrug resistant strains are the challenges in the coming decades.

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Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Cited by 903 publications

References 513 publications

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria

Microbiomic analysis of the bifidobacterial population in the human distal gut

Defining mycobacteria: Shared and specific genome features for different lifestyles

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