Distribution and diversity of the Rap-Phr family in theBacillus genus
The Rap-Phr family of regulatory proteins is highly diversified and
widespread in the Bacillus genus. Rap homologs have been found in
the genomes of B. subtilis , Bacillus amyloliquefaciens,Bacillus pumilus, Bacillus anthracis, Bacillus cereus, Bacillus
halodurans , Bacillus stearothermophilus, and Bacillus
clausii . Also, one of these Rap-Phr cassettes has been studied
heterologously in another Bacillus species (RapQ-PhrQ), and was
found to be both functional and comparable to the native Rap
phosphatases of the host . These reports support the idea that the Rap
proteins and their Phr peptides play a common regulatory role in the
entire Bacillus genus.
Interestingly, Bacillus species that have at least one Rap-Phr
cassette normally possess multiple of these regulatory elements encoded
in their genomes. The first study to identify RapA as a Spo0F
phosphatase already established RapA and RapB as members of a
protein-aspartate phosphatase family with multiple members within the
same organism: B. subtilis strain JH642 . Subsequent studies have
identified further members of this phosphatase family in diverseB. subtilis strains (see Table 1). In 2016, Even-Tov et
al . compared over 400 Bacillus genomes, searching for Rap
homologs based on their conserved N-terminal 3-helix bundle and
C-terminal TPR domain structure. They found over 2500 raphomologs among the studied genomes, and that B. subtilis strains
have, on average, 11 rap genes per strain, while B. cereusstrains usually possess around 6 of these phosphatases .
How has the Rap-Phr family achieved such a widespread presence and
diversity among Bacilli ? There are two main factors that can be
considered when answering this question. First, bacteria commonly pass
on genes among sibling cells or cells from closely related species. This
ability, known as horizontal gene transfer (HGT), is an efficient
mechanism for individual organisms to acquire genes, regardless of
functionality . HGT of Rap-Phr cassettes is heightened due to the fact
that many rap-phr genes are encoded within mobile genetic
elements . In addition, the genes related to natural competence for the
uptake of DNA from the environment are widely conserved inBacilli . Even-Tov et al . recently estimated that up to
75% of Rap-Phr cassettes may be mobile, based on a GC-content
comparison with their host strain . Furthermore, some Rap-Phr cassettes
are able to regulate the mobility of the genetic element that contains
them, be them plasmids , or transposons . These features could then
favor a rapid expansion of Rap-Phr cassettes through HGT amongBacilli . Similarly, experimental selection for spores of B.
subtilis increases the copy number of a cryptic prophage, phi3T, that
carries Rap and Phr proteins . Interestingly, certain prophages, like
SPβ, that are similar to phi3T do not carry such rap gene, but
encode a biosynthetic gene cluster for a bacteriocin that presumably
benefit the fitness of the host bacterium . The Rap protein coded within
the phi3T prophage has been also hypothesized to contribute to phage
fitness . Further, genome analysis combined with targeted experimental
validation revealed that diversification of the autoinducer Phr peptides
might be driven by promiscuous duplication events followed by adjustment
of the Phr peptide in accordance with the respective evolutionary change
of its cognate Rap phosphatase .
A second factor that can help explain the diversity of the Rap-Phr
family is functional diversification through social selection.
Experimental analyses and modeling suggest that acquisition of
additional Rap-Phr system is facilitated by a facultative social
cheating mechanism in B. subtilis . At low frequency, a strain
harbouring an extra Rap-Phr system acts a cheater (i.e. exploiting the
public good produced by the wild type), while at high frequency it
returns to cooperation without fitness loss. Such social selection
processes in combination with HGT ensure the diversification and
maintainance of multiple copies of Rap-Phr systems in Bacilli .