Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Ramulu, Hemalatha Golaconda; Groussin, Mathieu; Talla, Emmanuel; Planel, Rémi; Daubin, Vincent; Brochier-Armanet, Céline

doi:10.1016/j.ympev.2014.02.013

Cited by 32 publications

(33 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fact, using a concatenated sequence based on a full set of ribosomal proteins has become a common approach to resolve Fournier and Gogarten, 2010;Lasek-Nesselquist and Gogarten, 2013). The major advantage of using these proteins as phylogenomic markers for prokaryotic organisms is that these genes are rarely subject to horizontal gene transfer (Ciccarelli et al, 2006;Ramulu et al, 2014), which has been generally accepted as the prevalent source of error in prokaryotic systematics (Bapteste and Boucher, 2008). Results from the current study showing different branching patterns depending on which ribosomal proteins are used caution against their indiscriminate use for systematics of Proteobacteria and perhaps other prokaryotic groups.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary origin of a streamlined marine bacterioplankton lineage

Luo

2014

The ISME Journal

View full text Add to dashboard Cite

Planktonic bacterial lineages with streamlined genomes are prevalent in the ocean. The base composition of their DNA is often highly biased towards low G þ C content, a possible source of systematic error in phylogenetic reconstruction. A total of 228 orthologous protein families were sampled that are shared among major lineages of Alphaproteobacteria, including the marine freeliving SAR11 clade and the obligate endosymbiotic Rickettsiales. These two ecologically distinct lineages share genome sizes of o1.5 Mbp and genomic G þ C content of o30%. Statistical analyses showed that only 28 protein families are composition-homogeneous, whereas the other 200 families significantly violate the composition-homogeneous assumption included in most phylogenetic methods. RAxML analysis based on the concatenation of 24 ribosomal proteins that fall into the heterogeneous protein category clustered the SAR11 and Rickettsiales lineages at the base of the Alphaproteobacteria tree, whereas that based on the concatenation of 28 homogeneous proteins (including 19 ribosomal proteins) disassociated the lineages and placed SAR11 at the base of the non-endosymbiotic lineages. When the two data sets were concatenated, only a model that accounted for compositional bias yielded a tree identical to the tree built with compositionhomogeneous proteins. Ancestral genome analysis suggests that the first evolved SAR11 cell had a small genome streamlined from its ancestor by a factor of two and coinciding with an ecological transition, followed by further gradual streamlining towards the extant SAR11 populations.

show abstract

Section: Discussionmentioning

confidence: 99%

Evolutionary origin of a streamlined marine bacterioplankton lineage

Luo

2014

The ISME Journal

View full text Add to dashboard Cite

show abstract

“…In standard microbial phylogenomic analyses, however, proteins are often selected based on their functional conservation instead of compositional homogeneity in order to minimize the impact of lateral gene transfer on the resulting phylogeny [83,84]. Therefore, a second approach is to employ an appropriate model to account for the compositional bias contained in a gene family data set that is composition-blind.…”

Section: Microscale Heterogeneity and Ecological Strategies Of Marinementioning

confidence: 99%

How do divergent ecological strategies emerge among marine bacterioplankton lineages?

Luo

Moran

2015

Trends in Microbiology

View full text Add to dashboard Cite

“…Reference phylogenies of Firmicutes, Cyanobacteria, Proteobacteria, and Enterobacteriaceae strains contained in our local database were inferred using ribosomal proteins as suggested elsewhere (Ramulu et al, 2014). The reference tree of Firmicutes has been rooted according to a recent study (Antunes et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Reference phylogenies of species containing Ldc, Adc or Odc homologues were inferred using ribosomal proteins as suggested elsewhere (Ramulu et al ., 2014). Ribosomal protein sequences from the complete proteomes of these species were identified using the RiboDB database engine (Jauffrit et al ., 2016) and aligned with MAFFT using the L-INS-i option.…”

Section: Methodsmentioning

confidence: 99%

Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative:Pseudomonas aeruginosaLdcA

Carriel-Lopez¹,

Garcia²,

Castelli³

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

SummaryPolyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by PLP-dependent amino acid decarboxylases referred to as LAOdcs (Lysine-Arginine-Ornithine decarboxylases). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancestral nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomortadaceae {Gammaproteobacteria). We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines - cadaverine, putrescine and spermidine - in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of putrescine and spermidine to complement the growth phenotype of the IdcA mutant.

show abstract

Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Cited by 32 publications

References 86 publications

Evolutionary origin of a streamlined marine bacterioplankton lineage

Evolutionary origin of a streamlined marine bacterioplankton lineage

How do divergent ecological strategies emerge among marine bacterioplankton lineages?

Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative:Pseudomonas aeruginosaLdcA

Contact Info

Product

Resources

About