The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

Abstract

A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. Here, we selected~1,000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution , we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. Overall, patterns of gene gain and loss, including acquisition of accessory traits in independent transfer events, may have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories. INTRODUCTION :

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

“…The sparse and scattered distribution of the putative ETC gene homologs in Patescibacteria and DPANN ( Figure 8 ) suggest HGT origins rather than ancestral inheritance. This is consistent with the phylogenetic reconstructions of other energy transducing genes identified in Patescibacteria, which also suggest evolutionary origins from HGT ( Jaffe et al, 2020 ). Collectively, our observations indicate that the absence of complete electron transport chains in Patescibacteria and DPANN is an ancestral feature of the two superphyla, which we propose is more parsimonious than multiple gene loss events due to obligate symbiosis ( Brown et al, 2015 ; Hug et al, 2016 ; Castelle et al, 2018 ; Dombrowski et al, 2019 ; Méheust et al, 2019 ).…”

Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil

“…Given the unique challenges of the soil environment for microbes, we next assessed whether these soil CPR and DPANN exhibited similar traits to their counterparts in other environments. Recent studies show that CPR bacteria generally appear to have the capacity for glycolysis and fermentation (17), but often lack complete pathways to predictably de novo synthesize nucleotides and have many gaps in metabolism that suggest an obligate symbiotic lifestyle (8). We find that most of the genomes from this sampling effort encode the three central glycolysis enzymes reportedly found in nearly all CPR bacteria: triose phosphate isomerase (TIM), glyceraldehyde 3-phosphate (GAPDH), and phosphoglycerate kinase (PGK) (17).…”

“…Recent studies show that CPR bacteria generally appear to have the capacity for glycolysis and fermentation (17), but often lack complete pathways to predictably de novo synthesize nucleotides and have many gaps in metabolism that suggest an obligate symbiotic lifestyle (8). We find that most of the genomes from this sampling effort encode the three central glycolysis enzymes reportedly found in nearly all CPR bacteria: triose phosphate isomerase (TIM), glyceraldehyde 3-phosphate (GAPDH), and phosphoglycerate kinase (PGK) (17). As expected, based on prior studies of CPR bacteria and DPANN archaea (8), the genomes contain few if any TCA cycle genes and lack genes of the electron transport chain, and for synthesis of lipids and nucleotides (Fig 1d), suggesting they live anaerobic lifestyles with strong dependence on resources from other organisms.…”

MAPR origins reveal a new class of prokaryotic cytochrome b5 proteins and possible role in eukaryogenesis

“…Genomes containing genes clustering with the cytb5MY sequences were selected for further analysis, and annotated using InterProScan v5.48-83.0 (Jones et al, 2014). Taxonomic identification of these genomes was performed against the dereplicated genomes provided by Jaffe et al (2020) using fastANI (Jain et al, 2018) with default parameters or, if no results were found, by using a fragment length threshold of 1000 bp. Gene synteny analyses were performed using the genoPlotR package (Guy et al, 2010) and the Gene Neighborhood Viewer and Chromosomal Cassette Viewer tools (Mavromatis et al, 2009) of the Integrated Microbial Genomes (IMG) database (Chen et al, 2019).…”