Genomewide comparison and novel ncRNAs of Aquificales

Lechner, Marcus; Nickel, Astrid I.; Wehner, Stefanie; Riege, Konstantin; Wieseke, Nicolas; Beckmann, Benedikt M.; Hartmann, Roland K.; Marz, Manja

doi:10.1186/1471-2164-15-522

Cited by 18 publications

(19 citation statements)

References 96 publications

(106 reference statements)

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“…The reconstructed species tree (see Fig. 3, support s = 0.61) is almost identical to the tree presented in [40]. All species are clustered correctly according to their taxonomic families.…”

Section: Resultssupporting

confidence: 59%

“…is misplaced next to Persephonella marina. This does not come as a surprise: Lechner et al [40] already suspected that the data from this species was contaminated with material from Hydrogenothermaceae.…”

Section: Resultsmentioning

confidence: 94%

“…As real-life applications we consider two sets of eubacterial genomes. The set of eleven Aquificales species studied in [40] covers the three families Aquificaceae, Hydrogenothermaceae, and Desulfurobacteriaceae.…”

Section: 3mentioning

confidence: 99%

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Phylogenomics with paralogs

Hellmuth

Wieseke

Lechner

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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115

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Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genomewide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer.orthology | paralogy | gene tree | species tree | cograph M olecular phylogenetics is primarily concerned with the reconstruction of evolutionary relationships between species based on sequence information. To this end, alignments of protein or DNA sequences are used, whose evolutionary history is believed to be congruent to that of the respective species. This property can be ensured most easily in the absence of gene duplications and horizontal gene transfer (HGT). Phylogenetic studies judiciously select families of genes that rarely exhibit duplications (such as rRNAs, most ribosomal proteins, and many of the housekeeping enzymes). In phylogenomics, elaborate automatic pipelines such as HaMStR (1), are used to filter genomewide data sets to at least deplete sequences with detectable paralogs (homologs in the same species).In the presence of gene duplications, however, it becomes necessary to distinguish between the evolutionary history of genes (gene trees) and the evolutionary history of the species (species trees) in which these genes reside. Leaves of a gene tree represent genes. Their inner nodes represent two kinds of evolutionary events, namely the duplication of genes within a genome-giving rise to paralogs-and speciations, in which the ancestral gene complement is transmitted to two daughter lineages. Two genes are (co)orthologous if their last common ancestor in the gene tree represents a speciation event, whereas they are paralogous if their last common ancestor is a duplication event; see refs. 2 and 3 for a more recent discussion on orthology and paralogy relationships. Speciation events, in turn, define the inner vertices of a species tree. However, they depend on both the gene and the species phylogeny, as well as the reconciliation between the two. The latter identifies speciation vertices in the gene tree with a particular speciation event in the species tree and places the gene duplication events on the edges of the species tree. Intriguingly, it is nevertheless possible in practice to distinguis...

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“…The reconstructed species tree (see Fig. 3, support s = 0.61) is almost identical to the tree presented in [40]. All species are clustered correctly according to their taxonomic families.…”

Section: Resultssupporting

confidence: 59%

Section: Resultsmentioning

confidence: 94%

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Phylogenomics with paralogs

Hellmuth

Wieseke

Lechner

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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115

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“…Legionella pneumophila also has been reported to express two 6S RNAs, Lp 6S RNA and Lp 6S-2 RNA, and two candidate 6S RNA encoding genes were identified in Hydrogenivirgia (29–32). The presence of two 6S RNAs in divergent bacteria raises interesting questions regarding how common it is to have multiple 6S RNAs, how they are independently regulated, if their activities are redundant or overlapping, and so forth.…”

Section: S Rnas Are Widespread Throughout the Bacterial Kingdommentioning

confidence: 99%

6S RNA, a Global Regulator of Transcription

Wassarman

2018

Microbiol Spectr

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6S RNA is a small RNA regulator of RNA polymerase that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNA polymerase resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity including: 1. Addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; 2. The nature of the 6S RNA-RNA polymerase interaction through examination of variant proteins and mutant RNAs, crosslinking approaches, and ultimately a cryo-EM structure; 3. The physiological consequences of 6S RNA function through identification of the 6S RNA-regulon and promoter features that determine 6S RNA sensitivity; 4. The mechanism and cellular impact of 6S RNA-directed synthesis of pRNAs (i.e. pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action and how it is regulated; yet, much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.

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“…However, no rnpA and rnpB genes were identified in the genome of Aquifex aeolicus or other Aquificaceae (8)(9)(10)(11)(12). The genetic organization of A. aeolicus tRNAs in tandem clusters and as part of ribosomal operons and the detection of tRNAs with canonical mature 5′-ends in total RNA extracts from A. aeolicus implied the existence of a tRNA 5′-maturation activity (9) that was indeed subsequently detected in cell lysates of A. aeolicus (11,13).…”

mentioning

confidence: 99%

Minimal and RNA-free RNase P in Aquifex aeolicus

Nickel

Wäber

Gößringer

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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RNase P is an essential tRNA-processing enzyme in all domains of life. We identified an unknown type of protein-only RNase P in the hyperthermophilic bacterium Aquifex aeolicus: Without an RNA subunit and the smallest of its kind, the 23-kDa polypeptide comprises a metallonuclease domain only. The protein has RNase P activity in vitro and rescued the growth of Escherichia coli and Saccharomyces cerevisiae strains with inactivations of their more complex and larger endogenous ribonucleoprotein RNase P. Homologs of Aquifex RNase P (HARP) were identified in many Archaea and some Bacteria, of which all Archaea and most Bacteria also encode an RNA-based RNase P; activity of both RNase P forms from the same bacterium or archaeon could be verified in two selected cases. Bioinformatic analyses suggest that A. aeolicus and related Aquificaceae likely acquired HARP by horizontal gene transfer from an archaeon.protein-only RNase P | Aquifex aeolicus | tRNA processing | HARP T he architectural diversity of RNase P enzymes is unique: In Bacteria, Archaea, and in the nuclei and organelles of many Eukarya, RNase P is a complex consisting of a catalytic RNA subunit and a varying number of proteins (one in Bacteria, at least four in Archaea, and up to 10 in Eukarya) (1, 2). A different type of RNase P was discovered more recently in human mitochondria (3) and, subsequently, in land plants and some protists (4, 5). This form, termed proteinaceous or protein-only RNase P (PRORP), lacks any RNA subunit and consists of one or three (animal mitochondria) protein subunit(s); it is found in most branches of the eukaryotic phylogenetic tree (6).Bacterial RNase P enzymes identified so far are composed of a ∼400-nt-long catalytic RNA subunit (encoded by rnpB) and a small protein subunit of ∼14 kDa (encoded by rnpA) (7). However, no rnpA and rnpB genes were identified in the genome of Aquifex aeolicus or other Aquificaceae (8-12). The genetic organization of A. aeolicus tRNAs in tandem clusters and as part of ribosomal operons and the detection of tRNAs with canonical mature 5′-ends in total RNA extracts from A. aeolicus implied the existence of a tRNA 5′-maturation activity (9) that was indeed subsequently detected in cell lysates of A. aeolicus (11, 13). However, to date, the identity and biochemical composition of RNase P in A. aeolicus has remained enigmatic. Results and DiscussionHere, we pursued a classical biochemical approach to identify the RNase P of A. aeolicus. The purification procedure consisted of three consecutive chromatographic steps: anion exchange, hydrophobic interaction, and size exclusion chromatography (AEC, HIC, and SEC, respectively; Fig. 1A and SI Appendix, Figs. S1-S8). RNase P activity was assayed at all purification steps. To identify putative protein components of the enzyme, fractions with low and high RNase P activity from different purification steps were comparatively analyzed by step-gradient SDS/PAGE, and protein bands correlating with activity (Fig. 1B) were subjected to mass spectrometry. An example i...

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Genomewide comparison and novel ncRNAs of Aquificales

Cited by 18 publications

References 96 publications

Phylogenomics with paralogs

Phylogenomics with paralogs

6S RNA, a Global Regulator of Transcription

Minimal and RNA-free RNase P in Aquifex aeolicus

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