Nsion of pterin cofactorsnitrogen, and sulfur metabolism. Recently, genes related to molybdenum cofactor protein synthesis have been shown to be upregulated under conditions of stress in Mtb [52]. Molybdenum cofactor biosynthesis has been previously linked to pathogenesis. The regulator of the moa1 locus, MoaR1, was identified as having a SNP in M. bovis BCG, but not in virulent M. bovis or Mtb [53]. In addition, moa3 is present with varying frequency in the RD1 region, which is absent in M. bovis BCG, of pathogenic strains [54]. In agreement with previous observations of expansions of molybdopterin biosynthesis genes, we observe five protein domains related to pterin cofactor biosynthesis among the top protein domains expanded in the Mtb complex compared to the non-pathogenic Mycobacteria (Table 2, -“d”). Among the top GO terms expanded in the Mtb clade relative to the soil dwellers (Table 3), there are also several groups involved in pterin and molybdopterin biosynthesis. Some of these gene copies (the moa1 locus) are believed to have been acquired by lateral gene transfer on the branch leading to the Mtb complex [10,50]. We also observe evidence for selection on molybdenumrelated genes in our dN/dS data. On the branch leading to the pathogenic Mycobacteria, several orthogroups with high log likelihood scores when testing for selection are related to molybdenum (see Supplementary Information website). The orthogroup containing BisC (biotin sulfoxide reductase, a molybdoenzyme), as well as the orthogroup containing ModA (an ABC-family molybdate transporter), are among those with the highest d N /d S values on the branch leading to the pathogens. MoaB2 is one of the highest-scoring genes on all three branches tested.Expansions of genes of unknown function in Mtb cladeThere are also many categories of unknown function that are greatly expanded in the Mtb clade relative to the nonpathogenic Mycobacteria (Tables 2 and 3, red). For example, Rv0918 (in the Pfam group of unknown function PF08681) was found in a genetic screen that facilitates isolation of mutants defective in arresting the maturation of phagosomes [55], helping Mtb to survive within host cells. PF07161 contains four lipoproteins (LprF, LprG, LprA, LppX). LprG and LppX were found to be in vivo essential genes by TraSH analysis [56].Detection of conserved noncoding sequencesGenes involved in the first steps of pterin cofactor (a component of the molybdenum cofactor) biosynthesis are known to be expanded in the Mtb complex [50]. Molybdenum cofactor-requiring enzymes (such as xanthine oxidase and aldehyde oxidase) could have physiological functions in the metabolism of reactive oxygen species during stress response [51]. Molybdenum cofactor is an efficient catalyst in oxygen-transfer reactions, can be used in anaerobic respiration, and can catalyze redox reactions in carbon,Sequence conservation – or phylogenetic footprinting provides a powerful approach for PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27527552 identifying potential functional noncoding sequences, and has been used in a variety of eukaryotic and prokaryotic organisms to identify protein coding genes, noncoding RNAs, and regulatory elements [57,58]. For optimal power, the organisms being RDX5791 structure analyzed must be sufficiently distant such that non-functional elements have diverged, but not so distant such thatMcGuire et al. BMC Genomics 2012, 13:120 http://www.biomedcentral.com/1471-2164/13/Page 14 offunctional elements have evolved or re-arranged. Organisms within the Mtb co.