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Abstract Background In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: http://www.megx.net/tetra Results TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C)-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. Conclusions Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand-alone program, the method is now accessible in an easy to use manner for a broad audience. This will hopefully facilitate the interrelation of genomic fragments from metagenome libraries, ultimately leading to new insights into the genetic potentials of yet uncultured microorganisms.

Abstract: Rhodopirellula baltica (strain SH 1T) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum Planctomycetes. Little is known about the regulatory strategies of free-living bacteria with large (7.15 Mb) genomes. Therefore, a consistent, quantitative and qualitative description was produced by comparing R. baltica’s transcriptional regulator pool with that of 123 publicly available bacterial genomes. The overall results are congruous with earlier observations that in Bacteria, the proportion of genes encoding transcriptional regulators generally increases with genome size. However, R. baltica distinctly stands out from this trend with only 2.4% (174) of all genes predicted to encode transcriptional regulators. The qualitative investigation of R. baltica’s transcriptional regulators revealed a clear shift towards high numbers of two-component systems (66) as well as high numbers of sigma factors (49), with more than 76% (37) belonging to the extra-cytoplasmic function subfamily of sigma-70. Only one predicted sigma factor showed a relatively close phylogenetic relationship to that of another bacterium, the sigma factor SigZ of Bacillus subtilis. In summary, analysis of the R. baltica genome revealed disparate regulatory mechanisms and a clear bias towards direct environmental sensing. This strategy might provide a selective advantage for organisms living in habitats with frequently changing environmental conditions. [Copyright &y& Elsevier]

The unexpected presence of archaea-like genes for tetrahydromethanopterin (H4MPT)-dependent enzymes in the completely sequenced genome of the aerobic marine planctomycetePirellulasp. strain 1 (“Rhodopirellula baltica”) and in the currently sequenced genome of the aerobic freshwater planctomyceteGemmata obscuriglobusstrain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes inPlanctomycetesand methylotrophic proteobacteria and performed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor ofBacteriaandArchaeaor were transferred laterally from the archaeal to the bacterial domain and therein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and bacterial H4MPT-dependent C1-transfer may be proposed: (i) lateral gene transfer (LGT) fromArchaeato a common ancestor ofProteobacteriaandPlanctomycetesseems more likely than the presence of the genes in the common ancestor ofBacteriaandArchaea; (ii) a single event of interdomain LGT can be favored over two independent events; and (iii) the archaeal donor of the genes might have been a representative of theMethanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages. [ABSTRACT FROM AUTHOR]

Background: In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: http://www.megx.net/tetra Results: TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C)-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. Conclusions: Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand-alone program, the method is now accessible in an easy to use manner for a broad audience. This will hopefully facilitate the interrelation of genomic fragments from metagenome libraries, ultimately leading to new insights into the genetic potentials of yet uncultured microorganisms. [ABSTRACT FROM AUTHOR]