Genome Diversity of Spore-Forming Firmicutes

Abstract

Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes: Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in nutrient-rich environment. It argues that systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.

Giant viruses: spore‐like missing links between Rickettsia and mitochondria?

“…This scenario does not explain rRNA decay in Megavirales as compared with mitochondrial rRNA and the apparent independent origin of mitochondrial proteins. 68 The scenario suggests that similarities between giant viruses and bacterial endospores (these protein-coated forms enable bacteria to survive extreme conditions 70 and apparently evolved independently in different bacterial lineages [71][72][73] ), which are usually seen as analogies, 44,74 indicate common ancestry. Mitochondrial budding 54 also fits this hypothesis.…”

The RicAFT (YmcA‐YlbF‐YaaT) complex carries two [4Fe‐4S]2+ clusters and may respond to redox changes

“…The entire complex may then have been co-opted by the phosphorelay to regulate it in response to the redox state. As bacteria moved into more stable niches, with steady nutrient supplies and less changeable environments, sporulation was lost, along with most of the genes associated with sporulation (Galperin, 2013). Although the phosphorelay and Spo0A disappeared, the ric genes were not immediately lost, persisting in the non- rRNA sequences from the RDP database rooted to the outgroup Streptomyces fradiae as described in Experimental Procedures (Cole et al, 2009).…”

From root to tips: sporulation evolution and specialization inBacillus subtilisand the intestinal pathogenClostridioides difficile

“…For example, in nutrient-rich environments after 6,000 generations of B. subtilis, neutral processes but also selection were found to facilitate loss of sporulation (Maughan et al 2007), occurring by indels or single-nucleotide substitutions (Maughan et al 2009). In nature though, sporulation loss is mostly driven by consecutive gene losses as suggested earlier (Galperin et al 2012;Galperin 2013) and demonstrated in (Abecasis et al 2013) while Caldicellulosiruptor species have between 62.5 and 73%, so there is still some speculation as to whether the latter form spores or not (Abecasis et al 2013). The same question has persisted for sometime for Ruminococcus species (Galperin et al 2012;Abecasis et al 2013).…”

“…Still, they were recently shown to sporulate (Browne et al 2016;Mukhopadhya et al 2018), and are likely to spread as spore-like structures between hosts (Schloss et al 2014;Mukhopadhya et al 2018), which plays as a counter evolutionary force to the emergence of asporogenous phenotypes. In other cases, notably Epulopiscium and Candidatus Arthromitus, sporulation has evolved as a reproductive mechanism, involving some gene loss ( Figure 3B) and eventually the gain of new genes (Flint et al 2005;Galperin 2013), under distinct evolutionary forces.…”

“…A second layer of modified peptidoglycan essential for dormancy, the cortex, is surrounded by several proteinaceous layers (Henriques and Moran 2007). In Bacillus subtilis a multilayered protein coat forms the spore surface (Lai et al 2003;Kim et al 2006); in other species, such as Bacillus anthracis and often used as an indicator of sporulation ability (Galperin 2013;Filippidou et al 2016). The activity of Spo0A is required for the division that takes place at the onset of sporulation.…”