When the pandemic opts for the lockdown: Secretion system evolution in the cholera bacterium

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic spread. In our recent study (Santoriello et al. (2020), Nat Commun, doi: 10.1038/s41467-020-20012-7), using genomic and molecular biology tools, we demonstrated that the T6SS island Auxiliary Cluster 3 (Aux3) is unique to pandemic strains of V. cholerae. We went on to show that Aux3 is related to a phage-like element circulating in environmental V. cholerae strains and that two genetic domestication events formed the pandemic Aux3 cluster during the evolution of the pandemic clone. Our findings support two main conclusions: (1) Aux3 evolution from phage-like element to T6SS cluster offers a snapshot of phage domestication in early T6SS evolution and (2) chromosomal maintenance of Aux3 was advantageous to the common ancestor of V. cholerae pandemic strains

Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism

Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily excised from and integrated into the genome via site-specific recombination, whereas pandemic Aux3 recombination is reduced. Our data suggest that environmental Aux3 acquisition conferred increased competitive fitness to pre-pandemic V. cholerae, leading to grounding of the element in the chromosome and propagation throughout the pandemic clade

Type VI secretion system mutations reduced competitive fitness of classical Vibrio cholerae biotype

The gram-negative bacterium Vibrio cholerae is the causative agent of the diarrhoeal disease cholera and is responsible for seven recorded pandemics. Several factors are postulated to have led to the decline of 6th pandemic classical strains and the rise of El Tor biotype V. cholerae, establishing the current 7th pandemic. We investigated the ability of classical V. cholerae of the 2nd and 6th pandemics to engage their type six secretion system (T6SS) in microbial competition against non-pandemic and 7th pandemic strains. We report that classical V. cholerae underwent sequential mutations in T6SS genetic determinants that initially exposed 2nd pandemic strains to microbial attack by non-pandemic strains and subsequently caused 6th pandemic strains to become vulnerable to El Tor biotype V. cholerae intraspecific competition. The chronology of these T6SS-debilitating mutations agrees with the decline of 6th pandemic classical strains and the emergence of 7th pandemic El Tor V. cholerae

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism–environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis and two transcriptomics datasets (including one with 38 separate experiments collected specifically for this study), we use a new combination of network component analysis and model selection to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. In total, we predict 2,258 novel regulatory interactions and recall 74% of the previously known interactions. We obtained experimental support for 391 (out of 635 evaluated) novel regulatory edges (62% accuracy), thus significantly increasing our understanding of various cell processes, such as spore formation

Pandemic Vibrio cholerae acquired competitive traits from an environmental Vibrio species

10.26508/lsa.202201437LIFE SCIENCE ALLIANCE6

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development

An increasing amount of evidence indicates that developmental programs are tightly regulated by the complex interplay between signaling pathways, as well as transcriptional and epigenetic processes. Here, we have uncovered coordination between transcriptional and morphogen cues to specify Merkel cells, poorly understood skin cells that mediate light touch sensations. In murine dorsal skin, Merkel cells are part of touch domes, which are skin structures consisting of specialized keratinocytes, Merkel cells, and afferent neurons, and are located exclusively around primary hair follicles. We show that the developing primary hair follicle functions as a niche required for Merkel cell specification. We find that intraepidermal Sonic hedgehog (Shh) signaling, initiated by the production of Shh ligand in the developing hair follicles, is required for Merkel cell specification. The importance of Shh for Merkel cell formation is further reinforced by the fact that Shh overexpression in embryonic epidermal progenitors leads to ectopic Merkel cells. Interestingly, Shh signaling is common to primary, secondary, and tertiary hair follicles, raising the possibility that there are restrictive mechanisms that regulate Merkel cell specification exclusively around primary hair follicles. Indeed, we find that loss of Polycomb repressive complex 2 (PRC2) in the epidermis results in the formation of ectopic Merkel cells that are associated with all hair types. We show that PRC2 loss expands the field of epidermal cells competent to differentiate into Merkel cells through the upregulation of key Merkel-differentiation genes, which are known PRC2 targets. Importantly, PRC2-mediated repression of the Merkel cell differentiation program requires inductive Shh signaling to form mature Merkel cells. Our study exemplifies how the interplay between epigenetic and morphogen cues regulates the complex patterning and formation of the mammalian skin structures

Shh signaling activity in the epidermis is required for Merkel cell formation.

<p>(A-C) IF stainings for Merkel cell markers Krt8 (K8) (A,C), Krt20 (K20) (B), Sox2 (B), and Isl1 (C) show a highly significant reduction in the number of Merkel cells in P0 Smoothened epidermis-conditional knockout (Smo cKO) (K14-Cre; Smo^flox/flox) mice when compared to control (ctrl). Quantification of Krt8(+) and Krt20(+) Merkel cells in control and Smo cKO P0 skin (right panel of B) (both p<0.0001). (D) TUNEL staining shows no increase in apoptosis in the skin of P0 Smo cKO mice. Note that cells undergoing cornification are TUNEL(+) as previously reported [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006151#pgen.1006151.ref033" target="_blank">33</a>]. (E) At E15, specification of hair follicles is not affected in P0 Smo cKO mice when compared with control. The number of hair follicles is quantified in the right panel (p = 0.3140). IF staining for Krt14 (K14) labels the epidermis (epi) and Sox2 labels the dermal condensate (dc) of the developing hair follicles in E15 WT and Smo cKO mice. (F) IF staining for Merkel cell markers Krt8 and Sox2 shows a complete absence of Merkel cells in E15 Smo cKO compared to control. The number of Krt8(+) Merkel cells is quantified in the right panel (p = 0.0018). (G) IF stainings for Merkel cell markers Krt8 and <i>in situ</i> hybridization for <i>Gli1</i> RNA in E16 WT skin indicates that <i>Gli1</i> is expressed in about 45% of the Krt14(+) (K14) cells (yellow arrowheads) surrounding the Merkel cells and in about 13% of early Merkel cells present in the skin at this time point, quantified in the right panel (p = 0.0022). (H) <i>In situ</i> hybridization for <i>Gli1</i> RNA in E16 WT back skin indicates that <i>Gli1</i> is not expressed in most Krt14(+) cells of the interfollicular epidermis (IFE). (I,J) IF stainings for Merkel cell markers Krt8 (I,J), Krt20 (I), and Sox2 (J) show that significantly fewer Merkel cells are present in the glabrous paw skin of Smo cKO mice compared to control paws. Quantification of Krt8(+) Merkel cells in paws (right panel of J) (p<0.0001). (K,L) IF stainings for Merkel cell markers Krt8 (K,L), Krt20 (K), and Sox2 (L) show that significantly fewer Merkel cells are present in the glabrous paw skin of Shh cKO mice compared to control paws. Quantification of Krt8(+) Merkel cells in paws (right panel of L) (p<0.0001). Unless otherwise indicated, all epidermis represented is dorsal skin. Scale bars: (A,E): 100μm; (B-D,F-L): 25 μm.</p

Loss of PRC2 results in ectopic formation of Merkel cells around all hair follicle types.

<p>(A) Whole-mount immunofluorescence staining showing Merkel cell-specific marker Krt8 (K8) in P0 Ezh1/2 2KO (K14-Cre; Ezh1^del/del;Ezh2^flox/flox) and EED cKO (K14-Cre; EED^flox/flox) epidermis compared to control (ctrl). Clusters of Merkel cells (≥3 Krt8(+) cells) are quantified, and the number of clusters of Merkel cells per mm² is presented to the right (Kruskal-Wallis test p<0.0001; ctrl vs. Ezh1/2 2KO, *** p<0.0001; ctrl vs. EED cKO, *** p<0.0001). (B-B’) All hair types can have adjacent Merkel cells in EED cKO (B’), while only first wave hair follicles have adjacent Merkel cells in WT (B) epidermis. IF stainings for Sox2 and integrin α8 (α8) are used to label the dermal papillae (dp) or dermal condensate (dc) of different hair follicle types. The dermal papillae of first (left) and second (middle) wave hair follicles are Sox2(+), and the two types of hair follicles can be discriminated by size. The dermal papillae of the third (right) wave hair follicles are Sox2(-)/α8(+), and these hair follicles are very short at P0. IF staining for Sox2 identifies early-specified Merkel Cells (MC) and Krt20 (K20) identifies mature Merkel cells in the epidermis, which is labeled with E-Cadherin (ECad). (C-D”) Early immature Krt8(+) Merkel cells are found around the WT first wave (C) of developing hair follicles, but not the second wave (D) (control: 0% of placodes, 0.81% of hair germs, 19.65% of hair pegs, and 63.89% of bulbous pegs harbor Merkel cells around them; 148 hair follicles analyzed). (C’,C”,D’,D”) Krt8(+) Merkel cells are found around second wave and first wave developing hair follicles in Ezh1/2 2KO (C’,D’) and EED cKO (C”,D”) E16 embryos (Ezh1/2 2KO: 11.26% of placodes, 23.64% of hair germs, 58.33% of hair pegs, and 100% of bulbous pegs harbor Merkel cells around them; 160 hair follicles analyzed. EED cKO: 12.04% of placodes, 25.76% of hair germs, 70.37% of hair pegs, and 100% of bulbous pegs harbor Merkel cells around them; 213 hair follicles analyzed). Krt14 (K14) labels the developing hair follicles, and integrin α8 labels the dermal condensate in the first stages of hair follicle development; this becomes the dermal papilla in the bulbous peg stage. At E16, the first wave hair follicles are in the hair peg or bulbous peg stages (C-C”), while the second wave hair follicles are in the placode and hair germ stages (D-D”). Scale bars (A): 200 μm; (B-D”) 25 μm.</p

Shh overexpression results in increased formation of cells expressing Merkel markers.

<p>(A) Schematic diagram showing transgenic mouse and lentiviral constructs for the Shh overexpression experiment. CD1 female mice were mated with male Rosa26-rtTA mice and <i>in utero</i> lentiviral injections were performed in pregnant females E9. Doxycycline treatment was initiated by gavage at E12, and females were continuously fed Doxycycline until embryo collection at E17. In the presence of Doxycycline, lentivirus-injected mouse embryos express both H2B-RFP and Shh proteins. (B-E) IF stainings showing the altered morphology of epidermis infected with Shh+H2B-RFP (C,C’) and the significant increase in the numbers of Krt8(+) (K8) cells in the infected epidermis (C,C’,E) compared to control, un-infected epidermis (E17 control) (B,B’,D). Quantification of Krt8(+) cells per mm of back skin in E17 control and Shh overexpression (right panel) (p<0.0001). (F,F’) IF staining for Phospho-Histone H3 (PH3) showing a significant increase in proliferation in E17 Shh o/exp epidermis (F’) compared to control (F). Quantification of number of PH3(+) per mm² of Krt14(+) epidermal cells is represented on the right (p<0.0001). (G,G’) TUNEL staining showing no increase in apoptosis in E17 Shh o/exp epidermis (G’) compared to control (G). Note that cells undergoing cornification are TUNEL(+), as previously reported [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006151#pgen.1006151.ref033" target="_blank">33</a>]. (H-I’) IF staining showing an increase in the number of Sox2(+)/Krt8(+) cells in E17 Shh o/exp epidermis (I,I’) compared to control (H,H’). (J-K’) IF stainings showing an increase in the number of Isl1(+)/Krt8(+) cells in E17 Shh o/exp epidermis (K,K’) compared to control (J,J’). Scale bars: (B-C’): 100μm; (D-K’): 25 μm.</p

Loss of EED does not affect the hair follicle microenvironment, but leads to upregulation of Merkel cell differentiation genes.

<p>(A-E) Shh and Wnt pathways do not appear to be majorly altered in PRC-null developing skin. (A) RT-qPCR analysis of Shh pathway genes shows no significant difference in their expression in P0 EED cKO (K14-Cre; EED^flox/flox) compared to control epidermis, while <i>Shh</i> expression is slightly reduced in EED-null compared to control epidermis (Gli1, p = 0.2000; Gli2, p = 0.1143; Gli3, p = 0.3429; Ptch1, p = 0.1143; Shh, p = 0.0286). RT-qPCR analysis of Wnt pathway genes shows no significant difference in expression of most genes in P0 EED cKO compared to control epidermis (Wnt3, p = 0.4857; Wnt4, p = 0.1143; Wnt7a, p = 0.3429; Wnt7b, p = 0.4857; Wnt10a, p = 0.2000; Wnt10b, p = 0.0286; Tcf3, p = 0.6857; Tcf4, p = 0.4857; Dkkl1, p = 0.6857; Axin2, p = 0.2000; Sp5, p = 0.0286). (B,C) Immunohistochemistry staining for β-catenin does not show major differences in expression or nuclear staining in first wave (B) or second wave (C) hair follicles in EED cKO skin compared to control at E16. Note that, as has been previously described, the stratum corneum is prematurely acquired in the PRC2-null E16 embryo [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006151#pgen.1006151.ref051" target="_blank">51</a>]. (D,E) <i>In situ</i> hybridization for <i>Gli1</i> RNA (D) and <i>Shh</i> RNA (E) shows no major changes in expression in Ezh1/2 2KO (K14-Cre; Ezh1^del/del;Ezh2^flox/flox) skin compared to control at E16. (F) FACS scheme for Merkel cell (MC) sorting. After gating on singlets and live cells, EpCAM-APC staining was used to gate on all epidermal cells and Atoh1-GFP labels Merkel cells. EpCAM-APC(+) Atoh1-GFP(-) cells were sorted as epidermal controls. (G) ChIP-qPCR showing significantly lower levels of H3K27me3 at Merkel genes, <i>Isl1</i>, <i>Sox2</i>, and <i>Atoh1</i>, in FACS-sorted Merkel cells compared to FACS-sorted epidermal cells. (Neuro, p = 0.0411; Olig1, p = 0.0200; Isl1, p = 0.0022; Sox2, p = 0.0194; Atoh1, p = 0.0050). (H) RT-qPCR showing specific expression of MC signature genes <i>Isl1</i>, <i>Sox2</i>, and <i>Atoh1</i> in FACS-sorted Merkel cells compared to FACS-sorted epidermal cells (<i>Isl1</i>, p = 0.0004; <i>Sox2</i>, p = 0.0004; <i>Atoh1</i>, p = 0.0004) (I) IF staining showing that Krt8(+) (K8) MCs have the H3K27me3 mark in P0 control Krt14(+) (K14) epidermis. Krt14(+) cells serve as a positive control for H3K27me3 staining. Quantification of H3K27me3 staining intensity (below) (Kruskal-Wallis test p<0.0001; MC vs. K14(+), n.s. p>0.05). (J) RT-qPCR in skin epidermal samples showing upregulation of Merkel cell genes <i>Isl1</i>, <i>Atoh1</i> and <i>Sox2</i> in EED cKO animals compared to control. The average of at least three animals is presented compared to Cre(-) siblings (WT) <i>(Isl1</i>, p = 0.0286; <i>Atoh1</i>, p = 0.0286; <i>Sox2</i>, p = 0.0286). (K) ChIP-qPCR analysis in skin epidermal samples from WT and EED cKO animals showing specific H3K27me3 signal at the <i>Isl1</i>, <i>Sox2</i>, and <i>Atoh1</i> promoters. <i>Actin</i> is used as a negative control, and <i>Neuro</i> and <i>Olig3</i> are used as positive controls. Dotted line shows the level of the negative region (all p<0.0001). Scale bars: (B,C,I): 25 μm; (D,E): 100μm.</p