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Phylogeny of Γ-Proteobacteria Inferred from Comparisons of 3' End Vol.2, No.6, 535-543 (2010) Natural Science http://dx.doi.org/10.4236/ns.2010.26067 Phylogeny of γ-proteobacteria inferred from comparisons of 3’ end 16S rRNA gene and 5’ end 16S-23S ITS nucleotide sequences Sabarimatou Yakoubou1,2, Jean-Charles Côté1* 1Agriculture and Agri-Food Canada, Research Centre, Gouin Blvd, St-Jean-sur-Richelieu, Québec, Canada; *Corresponding Author: [email protected] 2Département des Sciences Biologiques, Université du Québec à Montréal, CP 8888, Succ. “Centre-Ville” Montréal, Québec, Canada Received 27 January 2010; revised 25 March 2010; accepted 12 April 2010. ABSTRACT this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the The phylogeny of γ-proteobacteria was inferred entire 16S rRNA gene or the generation of exten- from nucleotide sequence comparisons of a sive phenotypic and genotypic data in phyloge- short 232 nucleotide sequence marker. A total of netic analyses. First, this marker is not allele-de- 64 γ-proteobacterial strains from 13 Orders, 22 pendant. Second, this 232 bp marker contains families, 40 genera and 59 species were analyz- 157 bp from the 3’ end of the 16S rRNA gene and ed. The short 232 nucleotide sequence marker 75 bp from the 5’ end of the 16S-23S ITS. The used here was a combination of a 157 nucleot- 157 bp allows discrimination among distantly ide sequence at the 3’ end of the 16S rRNA gene related species. Owing to its higher rate of nucl- and a 75 nucleotide sequence at the 5’ end of eotide substitutions, the 75 bp adds discrimina- the 16S-23S Internal Transcribed Spacer (ITS) ting power among closely related species from sequence. Comparative analyses of the 3’ end of same genus and closely related genera from the 16S rRNA gene nucleotide sequence sho- same family. Because of its higher percentage wed that the last 157 bp were conserved among of nucleotide sequence divergence than the 16S strains from same species and less conserved rRNA gene, the 232 bp marker can better discri- in more distantly related species. This 157 bp minate among closely related γ-proteobacterial sequence was selected as the first part in the species. Third, the method is simple, rapid, suit- construction of our nucleotide sequence marker. ed to large screening programs and easily acce- A bootstrapped neighbor-joining tree based on ssible to most laboratories. Fourth, this marker the alignment of this 157 bp was constructed. can also reveal γ-proteobacterial species which This 157 bp could distinguish γ-proteobacterial may appear misassigned and for which additi- species from different genera from same family. onal characterization appear warranted. Closely related species could not be distingu- ished. Next, an alignment of the 16S-23S ITS Keywords: γ-Proteobacteria; 16S rRNA; 16S-23S nucleotide sequences of alleles from same bac- ITS; Phylogeny terial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the 1. INTRODUCTION second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neigh- The phylum proteobacteria or ‘‘purple bacteria and their bor-joining tree based on the alignment of this relatives’’ encompasses bacteria with a wide variety of 232 bp sequence was constructed. Based on the phenotype and physiological attributes and habitats [1,2]. topology of the neighbour-joining tree, four maj- Proteobacteria have been classified based on the homo- or Groups, Group I to IV, were revealed with sev- logy of 16S ribosomal RNA or by hybridization of ribo- eral sub-groups and clusters. Our results, bas- somal DNA with 16S and 23S ribosomal RNA [3-6]. ed on the 232 bp sequence were, in general, in They have been subdivided in five major classes: α-, β-, agreement with the phylogeny of γ-proteobact- γ-, δ- and ε- [7-9]. eria based on the 16S rRNA gene. The use of Most γ-proteobacteria are Gram-negative. This class Copyright © 2010 SciRes. OPEN ACCESS 536 S. Yakoubou et al. / Natural Science 2 (2010) 535-543 comprises 14 Orders and more than 200 genera. The reconstruct the phylogeny of γ-proteobacteria. A total of γ-proteobacteria exhibit a wide range of metabolic diver- 64 γ-proteobacteria from 13 Orders, 22 families, 40 gen- sity. Most are chemo-organotrophs, some are phototro- era and 59 species was analyzed. phs or chemolitotrophs [1,2,10,11]. This class includes several medically and scientifically important bacteria. 2. MATERIALS AND METHODS Some genera are human (Klebsiella, Shigella, Salmon- ella, Yersina, Vibrio), animal (Pasteurella) or plant path- 2.1. Bacterial Species and Strains ogens (Pseudomonas, Xanthomonas, Xylella). Others are obligate endosymbionts (Buchnera, Sodalis, Wiggleswo- A total of 64 γ-proteobacterial species and strains were rthia and Coxiella) [10-12]. Because of their biological analyzed. They were selected on the basis that their com- importance, γ-proteobacteria are extensively studied. plete genome sequences were freely available in Gen- The 16S ribosomal RNA (rRNA) gene has been est- Bank, at the National Center for Biotechnology Informa- ablished as the macromolecule of choice for phylogen- tion (NCBI) completed microbial genomes database etic analyses [5,13]. The current phylogeny of γ-proteo- (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Co bacteria is based on the homology of 16S rDNA nucleo- mplete.html). They encompassed 13 Orders, 22 families, tide sequences [3-6,11,14]. 40 genera and 59 species. These 13 γ-proteobacterial Or- The 16S-23S internal transcribed spacer (ITS) region ders included six Aeromonadales families, one Cardiob- is more variable than the 16S rRNA gene. It has been acteriales family, two Chromatiales families, one Enter- used, among others, in the study of specific γ-proteoba- obacteriales family, two Legionellales families, one Me- cterial diversity at the species level, including Escheri- thylococcales family, two Oceanospirillales families, chia, Haemophilus, Xanthomonas, Klebsiella and Pseud- one Pasteurellales family, two Pseudomonadales fami- omonas [15-19]. lies, two Thiotrichales families, one Vibrionales family Additional approaches, based on different genes, have and one Xanthomonadales family. All bacterial species been used for the study of γ-proteobacterial phylogeny and strains and the GenBank accession number for their [12,20-25]. Very recently, Gao et al., [26] have used a fully sequenced genome are listed in Table 1. combination of phylogenomic and comparative genomic 2.2. Sequences Analysis approaches to reconstruct the phylogeny of γ-proteob- acteria. The 16S rRNA gene nucleotide sequences were retriev- In an earlier work on the bacterial Gram-positive Ba- ed from GenBank (Table 1) for the 64 γ-proteobacteria cillus genus and related genera [27], a short 220 bp nu- species and strains under study. First, all 64 sequences cleotide sequence “marker” was used to reconstruct their were aligned using ClustalW [29] (data not shown). phylogeny. This 220 bp marker was a combination of a Next, the 3’ end of the 16S rRNA gene nucleotide sequ- 150 bp sequence at the 3’ end of the 16S rRNA gene and ences of alleles from same bacterial strain, of alleles a 70 bp sequence at the 5’ end of the 16S-23S ITS se- from different strains from same species, and of alleles quence. Owing to its higher rate of nucleotide substitu- from different species from same genus (data not shown) tion, the 70 bp sequence at the 5’ end of the 16S-23S ITS were aligned using ClustalW [29]. The length of the sequence added a greater discriminatory power among nucleotide sequence most conserved was determined at closely related species than 16S rRNA gene nucleotide 157 bp. Likewise, the 16S-23S Internal Transcribed sequences alone. They showed that the phylogeny in- Spacer (ITS) nucleotide sequences of alleles from same ferred from the 220 bp marker was in agreement with bacterial strain were also aligned using ClustalW. The then current classifications based on phenetic and mo- length of the nucleotide sequence most conserved was lecular data. The marker also indentified species which determined at 75 bp. appeared misassigned. It also created new clusters sug- These two most conserved nucleotide sequences, the gesting the creation of new taxa levels. In a very recent 157 bp at the 3’ end of 16S, and the 75 bp at the 5’ end study, we [28] have tested whether or not this marker of 16S-23S ITS were combined into a single 232 bp seq- could reconstruct the phylogeny of the bacterial Gram- uence for each bacterial species and strain under study. positive Order of the Bacillales. This 232 bp sequence will be used here as a phylogen- In the current study, we further assess the usefulness etic marker for the γ-proteobacteria under study. of a similar marker among 13 of the 14 γ-proteobacterial 2.3. Phylogenetic trees Orders. The last 157 bp at the 3’ end of the 16S rRNA gene was combined with the first 75 bp at the 5’ end of Two neighbor-joining trees were constructed [30], a first the 16S-23S Internal Transcribed Spacer (ITS) to yield a one based on the alignment of the last 157 bp at the 3’ single 232 bp DNA marker. This marker was used to end of the 16S rRNA gene described above, a second Copyright © 2010 SciRes. OPEN ACCESS S. Yakoubou et al. / Natural Science 2 (2010) 535-543 537 one based on the alignment of the 232 bp sequence also an (DDBJ) (http://clustalw.ddbj.nig.ac.jp/top-e.html), described above. Both trees were bootstrapped using with the Kimura’s parameter method [31]. The neighbor- 1,000 random samples of sites from the alignment, all joining tree was drawn using TreeView (version 1.6.6) using CLUSTAL W [29] at the DNA Data Bank of Jap- [32,33].
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