Comparative Genomic Analysis Reveals 2-Oxoacid Dehydrogenase Complex Lipoylation Correlation with Aerobiosis in Archaea

et al. (2014) Comparative Genomic Analysis Reveals 2-Oxoacid Dehydrogenase Complex Lipoylation Correlation with Aerobiosis in Archaea. PLoS ONE 9(1): e87063. doi:10.1371/journal.pone.0087063 Comparative Genomic Analysis Reveals 2-Oxoacid Dehydrogenase Complex Lipoylation Correlation with Aerobiosis in Archaea Steve Dorus 0 Kirill Borziak 0 Mareike G. Posner 0 Abhishek Upadhyay 0 Michael J. Danson 0 Stefan Bagby 0 Paul Jaak Janssen, Belgian Nuclear Research Centre SCK/CEN, Belgium 0 1 Department of Biology, Syracuse University , Syracuse , New York, United States of America, 2 Department of Biology & Biochemistry, University of Bath , Claverton Down , United Kingdom , 3 Centre for Extremophile Research, University of Bath , Claverton Down , United Kingdom Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/ LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments. - Culture-independent, metagenomic analyses have been particularly successful in advancing our knowledge of microbial abundance across diverse ecological niches (reviewed by [1]). Nonetheless, few studies have leveraged the wealth of genomic data across diverse archaeal taxa to explore adaptation to extreme archaeal environments although this must have a functional basis in genomic diversification [2,3,4,5]. Recent experimental studies have begun to utilize metagenomic data to decipher evolutionary processes [6] but substantial obstacles remain in applying such approaches to the complex biotic and abiotic interactions of natural populations (reviewed by [7]). To what extent can comparative genomic approaches inform our understanding of the evolution and functional capacity of organisms that cannot be cultured or studied in the laboratory? Further, can abiotic characteristics of extremophile habitats be inferred directly from the analysis of metagenomic data? Archaeal evolution has been dominated by reductions in genome complexity and the retention of highly variable genetic architectures across lineages ( [8] and reviewed by [9]). Recent analyses reveal two distinct phases of archaeal genome evolution. The first, the innovation phase, is associated with an increase in genome complexity and an associated increase in gene families to an average of approximately 2500 gene families. The second, the reductive phase, is characterized by genome streamlining and the retention of a more minimal, and potentially heterogeneous, gene repertoire (14001800 gene families) [10]. This persistent genomic streamlining has radically altered the repertoires of even the most highly conserved gene classes, including those involved in translation, replication, cell division and DNA repair, and is thus central to functional diversity across the domain [11]. In addition to the diversifying impact of differential gene loss across taxa, archaeal genome analyses have revealed notable exceptions where horizontal gene transfer (HGT) has been a prevalent force. For example, gene flow from eubacteria to Halobacteriales has contributed to the absence of reductive genome evolution in this archaeal order [10]. We therefore propose that gene repertoire heterogeneity, particularly associated with metabolism and homeostasis, may reflect archaeal adaptation to, and exploitation of, a remarkable diversity of environments. We assess this possibility by considering aerobiosis within archaea because (i) archaea display tremendous diversity in their utilization and tolerance of aerobic environments and (ii) aerobiosis pathways have been well characterized biochemically. Lipoylation, the covalent attachment of lipoic acid to the dihydrolipoyl acyltransferase (E2) subunit of 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya (reviewed by [12,13]). Specifically, OADHC lipoylation is required for channeling substrates between the active sites of the three protein subunits of OADHCs: 2-oxoacid decarboxylase (E1), E2 and dihydrolipoamide dehydrogenase (E3). The lipoyl domain of E2 (E2lipD) is the post-translational modification target. The mechanisms of lipoylation have been studied to varying extents in all domains of life [14,15,16,17]. In Escherichia coli, lipoylation is catalyzed by two routes: lipoic acid synthetase (LipA) and lipoyl(octanoyl) transferase (LipB), or lipoate protein ligase (LplA) [18]. LipB and LipA work in tandem: LipB catalyzes the covalent attachment of octanoic acid to the E2 lipoyl domain, and then LipA introduces sulphur atoms at the C6 and C8 positions. Alternatively, LplA can catalyse both conversion of lipoic acid to lipoyl-AMP and subsequent covalent attachment of the lipoyl moiety to E2lipD [19,20]. It is noteworthy that greater diversity in lipoyl biosynthesis has been observed in other eubacteria, including an alternative octanoyl transferease, LipM, and a lipoyl-scavenging protein, LipL (...truncated)