Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria

Abstract

Genome sequences are enabling applications of different approaches to more clearly understand microbial phylogeny and systematics. Two of these approaches involve identification of conserved signature indels (CSIs) and conserved signature proteins (CSPs) that are specific for different lineages. These molecular markers provide novel and more definitive means for demarcation of prokaryotic taxa and for identification of species from these groups. Genome sequences are also enabling determination of phylogenetic relationships among species based upon sequences for multiple proteins. In this work, we have used all of these approaches for studying the phytopathogenic bacteria belonging to the genera Dickeya, Pectobacterium and Brenneria. Members of these genera, which cause numerous diseases in important food crops and ornamental plants, are presently distinguished mainly on the basis of their branching in phylogenetic trees. No biochemical or molecular characteristic is known that is uniquely shared by species from these genera. Hence, detailed studies using the above approaches were carried out on proteins from the genomes of these bacteria to identify molecular markers that are specific for them. In phylogenetic trees based upon concatenated sequences for 23 conserved proteins, members of the genera Dickeya, Pectobacterium and Brenneria formed a strongly supported clade within the other Enterobacteriales. Comparative analysis of protein sequences from the Dickeya, Pectobacterium and Brenneria genomes has identified 10 CSIs and five CSPs that are either uniquely or largely found in all genome-sequenced species from these genera, but not present in any other bacteria in the database. In addition, our analyses have identified 10 CSIs and 17 CSPs that are specifically present in either all or most sequenced Dickeya species/strains, and six CSIs and 19 CSPs that are uniquely found in the sequenced Pectobacterium genomes. Finally, our analysis also identified three CSIs and one CSP that are specifically shared by members of the genera Pectobacterium and Brenneria, but absent in species of the genus Dickeya, indicating that the former two genera shared a common ancestor exclusive of Dickeya. The identified CSIs and CSPs provide novel tools for identification of members of the genera Dickeya and Pectobacterium and for delimiting these taxa in molecular terms. Descriptions of the genera Dickeya and Pectobacterium have been revised to provide information for these molecular markers. Biochemical studies on these CSIs and CSPs, which are specific for these genera, may lead to discovery of novel properties that are unique to these bacteria and which could be targeted to develop antibacterial agents that are specific for these plant-pathogenic bacteria.

A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

“…The most parsimonious explanation for the shared presence of molecular characteristics such as CSIs and CSPs in evolutionarily related groups of organisms is the existence of a shared common ancestor in which the genetic changes leading to these markers first occurred and were then passed on to its various descendent species (Gupta 1998;Rokas and Holland 2000;Gogarten et al 2002;Gupta and Griffiths 2002;Gupta 2014). Thus, these CSIs also provide an important means of elucidating phylogeny and relationships that is independent of sequence based phylogenetic trees (Gao and Gupta Gupta et al 2014;Naushad et al 2014). In this work we have identified 17 CSIs and 98 CSPs which are specific to Clade 1 of the phylum Chlamydiae and 3 CSI variants and 15 CSPs which are specific to Clade 2 ( Fig.…”

“…The use of molecular characteristics in evolutionary and taxonomic research is increasingly prevalent (Belinky et al 2010;Luan et al 2013;Gupta 2014;Naushad et al 2014). The most parsimonious explanation for the shared presence of molecular characteristics such as CSIs and CSPs in evolutionarily related groups of organisms is the existence of a shared common ancestor in which the genetic changes leading to these markers first occurred and were then passed on to its various descendent species (Gupta 1998;Rokas and Holland 2000;Gogarten et al 2002;Gupta and Griffiths 2002;Gupta 2014).…”

“…These molecular signatures serve as analogs of the synapomorphic characters often used in eukaryotic cladistics and provide reliable evidence, independent of phylogenetic trees, for the existence of shared common ancestry. Two classes of molecular signatures have proven particularly useful in evolutionary studies: conserved signature insertions/deletions (CSIs), which are insertions or deletions (indels) uniquely present in the protein sequences of a related group of organisms, and conserved signature proteins (CSPs), which are lineage specific proteins found only in a related group of organisms Gupta 2014;Naushad et al 2014). CSIs and CSPs that are characteristic of the members of the phylum Chlamydiae or one of its subgroups have been previously identified (Griffiths et al 2005Gupta and Griffiths 2006).…”

Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies

“…Pasteurellales, Xanthomonadales, Enterobacteriales) Cutino-Jimenez et al, 2010;, 2013Naushad et al, 2014) and genus level (Bacillus, Clostridium and Borrelia) (Adeolu & Gupta, 2014;Bhandari & Gupta, 2014b;) that we have studied using this approach. In all of these cases, multiple highly specific CSIs have been identified for members of these groups at different phylogenetic levels, and the relationships inferred from them are strongly supported by different phylogenetic approaches.…”

“…For Gammaproteobacteria some CSIs have been identified at the class level, as well as many others that are specific for some of the orders (viz. Pasteurellales, Xanthomonadales and Enterobacteriales), and distinct subgroups within them (Cutino-Jimenez et al, 2010;Gao, Mohan, & Gupta, 2009;Gupta, 2000;, 2013Naushad, Lee, & Gupta, 2014).…”