Abstract
The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.
Highlights
The phylum Proteobacteria is the most metabolically diverse bacterial phylum [1,2], constituting most of the known bacteria of medicinal, industrial, and agricultural significance [1,2]
Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed the presence of P450s only in 169 Gammaproteobacterial species, indicating that most of these species do not have P450s in their genomes (Figure 1 and Supplementary Dataset 1; Sheet 1)
Analysis of the Gammaproteobacteria genera disclosed that of the 161 genera, species belonging to 41 genera have P450s in their genomes m(SautpipolnemoenntPa4ry50Dsatiansetth1e;sSehegeetn1)e.rAa p(Souinpt ptolebme neontetdariys tDhaatttahseentu1m: bSehreoeftsp1e).ciHesogwe-ever, a significant nnuommebsearvaoiflasbpleeicniethseb1e2l0ognegnienragistovegreynloewra
Summary
The phylum Proteobacteria is the most metabolically diverse bacterial phylum [1,2], constituting most of the known bacteria of medicinal, industrial, and agricultural significance [1,2]. Based on the 16S rRNA gene sequence and multiprotein phylogenetic analysis, Proteobacteria are divided into seven classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, Zetaproteobacteria and Acidithiobacillia [3]. Proteobacteria members are well-known human pathogens; especially the class Gammaproteobacteria contain bacterial species that are medically, ecologically and scientifically important [1,2]. Gammaproteobacteria contain species with different physiology such as anaerobic, microaerophilic, and facultative aerobic, as well as different shapes such as rods, cocci or curve shapes [1]. Most of the bacterial species in this class are commensals with the ability to cause diseases and some of them are strictly pathogenic. We provide brief information on well-known pathogens of this class (Table 1)
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