az34e  (DSMZ)

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: (a) Maximum likelihood phylogenetic tree based on the concatenation of 120 single‐copy genes. Different colours represent different families (GTDB r220). The tree scale bar represents 0.1 substitutions per site. The numbers in nodes represent bootstrap values, and accession numbers are given in parentheses. Thermoanaerobacter kivui was used as an outgroup and root of the tree. (b) Average nucleotide identity comparisons between publicly available Thermincola strains and strain AZ34E. (c) Average nucleotide identity comparisons between publicly available Carboxydocella strains and strain AZ29I.

Article Snippet: In addition, digital DNA–DNA hybridisation (dDDH) values (and confidence intervals) between the genomes of AZ29I, AZ34E, Thermincola carboxydiphila (DSM 17129 T ) and their closest relatives were calculated using the Type (Strain) Genome Server ( https://tygs.dsmz.de ) and the recommended settings of GGDC v4.0 (Meier‐Kolthoff et al. , ; Yoon et al. ).

Techniques:

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: Phylogenetic comparison of CODHs detected in the Themincola and Carboxydocella genomes. The tree was constructed with the LG + G4 model in IQ‐TREE v2.0.6 and visualised in iTOL v6.8.1. CODH sequences of Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ29I are depicted in bold. The CODHs of Carboxydothermus hydrogenoformans were used as reference points for functional predictions. The tree scale bar represents 1 substitution per site. The circles in nodes represent bootstrap values > 80. The genomic structure of cooS gene clusters encoding the different CODHs in Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ291 are shown in the boxes on the top right corner. Gene abbreviations: acsB, Acetyl‐CoA synthase; acsC, corrinoid iron–sulfur protein large subunit; acsD, corrinoid iron–sulfur protein small subunit; acsE, methyltransferase A; ATPase, AAA family ATPase; cooA, CO‐dependent transcriptional activator; cooC, CODH chaperone; cooF, ferredoxin‐like electron transfer Fe‐S protein; cooMKLXUH, sub‐units of the energy‐converting hydrogenase; cooS, CO‐dehydrogenase; FNOR, NAD/FAD oxidoreductase; hp, hypothetical protein; hypA, hydrogenase maturation protein; nqrF, Na(+)‐translocating NADH‐quinone reductase subunit F; TR, transcription regulator; YlmC, YlmC/YmxH family sporulation protein; YpiB, YpiB family protein.

Article Snippet: In addition, digital DNA–DNA hybridisation (dDDH) values (and confidence intervals) between the genomes of AZ29I, AZ34E, Thermincola carboxydiphila (DSM 17129 T ) and their closest relatives were calculated using the Type (Strain) Genome Server ( https://tygs.dsmz.de ) and the recommended settings of GGDC v4.0 (Meier‐Kolthoff et al. , ; Yoon et al. ).

Techniques: Comparison, Construct, Functional Assay

Journal: PLoS ONE

Article Title: SmSak, the Second Polo-Like Kinase of the Helminth Parasite Schistosoma mansoni: Conserved and Unexpected Roles in Meiosis

doi: 10.1371/journal.pone.0040045

Figure Lengend Snippet: A. Constitutively active SmSak induces germinal vesicle breakdown (GVBD) and meiosis progression in Xenopus oocytes. Different samples of oocytes (n = 15) were microinjected with cRNA encoding SmSak, SmSak DK , SmSakT 175 D, SmSakT 175 D DK or SmSakT 175 A. Percentages of oocytes exhibiting GVBD 18 h after microinjection of cRNA are indicated. Non-injected oocytes were used as control. Western blot analysis of oocyte extracts was performed as described in to detect the gel-shift of endogenous phosphorylated Plx1 and Cdc25C proteins (indicated by arrows). The expression of the different forms of V5-tagged recombinant SmSak was confirmed by the use of anti-V5 antibodies. B. SmSak mutants do not alter the GVBD induced by progesterone. The experiment was performed as in A , except that PG was added to the different oocyte groups two hours after microinjection of cRNA preparations. Gel-shifts of Plx1 and Cdc25C are observed in all oocyte groups associated with high levels of GVBD. C. Endogenous Plx1 is required for the induction of GVBD by SmSakT 175 D. Oocytes were injected or not with 5 ng anti-Plx1 antibodies one hour before the injection of 10 or 60 ng SmSak 175 D cRNA. Meiosis resumption was monitored as in A and B . SmSakT 175 D induces GVBD (as already shown in A ) following the injection of 60 ng cRNA but has no more effect in Plx1-depleted oocytes. In control oocytes, it was confirmed that anti-Plk1 antibodies blocked completely the GVBD induced by PG. D. Comparative analysis of the capacity of SmSak and SmPlk1 to induce GVBD in different conditions. Normal versus Plx1-depleted oocytes were incubated with or without (w/o) PG following the expression of SmPlk1, SmPlkT 182 D, SmSak or SmSakT 175 D. PG stimulates GVBD in the oocytes expressing each of the parasite kinases, provided that Plx1 is functional in oocytes. In Plx1-depleted oocytes, only SmPlk1 proteins are efficient. In the absence of PG, only constitutively active kinases are efficient, provided that Plx1 is functional. In Plx1-depleted oocytes, only SmPlkT 182 D can induce GVBD. These results were correlated with our previous data and those presented in A , B and C . All percentages of GVBD represent the mean of three independent experiments. In A , B and C , blots are representative for the three experiments.

Article Snippet: Blocking of endogenous Plx1 activity was performed by injecting 5 ng (in 25 nl) of anti- Xenopus Plk antibodies (AZ34, Santa Cruz Biotechnology, Inc., USA) one hour before the injection of cRNA encoding schistosome Plks or before the addition of the natural inducer of GVBD, progesterone (PG, 2 μg/ml).

Techniques: Microinjection, Injection, Control, Western Blot, Gel Shift, Expressing, Recombinant, Incubation, Functional Assay

Journal: PLoS ONE

Article Title: SmSak, the Second Polo-Like Kinase of the Helminth Parasite Schistosoma mansoni: Conserved and Unexpected Roles in Meiosis

doi: 10.1371/journal.pone.0040045

Figure Lengend Snippet: A. Co-immunoprecipitation of SmPlk1 and SmSak expressed in Xenopus oocytes. Oocytes were injected with V5 tagged-SmPlk1, Myc tagged-SmSak or with both kinases simultaneously. Non-injected oocytes were used as controls. Following 18 h, GVBD was monitored. Oocyte lysates were prepared and parasite kinases were immunoprecipitated with anti-V5 or anti-Myc antibodies, then analyzed by western blotting. Results show that immunoprecipitates contained both SmPlk1 and SmSak when the proteins were co-expressed. B. Co-activation of SmPlk1 and SmSak induces GVBD. In normal or Plx1-depleted oocytes, SmSak was expressed with SmPlk1 or with SmPlk1T 182 V and reciproqually SmPlk1 was expressed with SmSak or with SmSak T 175 A. SmPlk1T 182 V and SmSakT 175 A were also expressed together. Only the co-expression of SmSak and SmPlk1 induced GVBD in normal as well as in Plx1-depleted oocytes. All the other combinations were inefficient, except the co-expression of SmSak with SmPlk1T 182 V, that allowed GVBD but only in normal oocytes (containing a functional Plx1).

Article Snippet: Blocking of endogenous Plx1 activity was performed by injecting 5 ng (in 25 nl) of anti- Xenopus Plk antibodies (AZ34, Santa Cruz Biotechnology, Inc., USA) one hour before the injection of cRNA encoding schistosome Plks or before the addition of the natural inducer of GVBD, progesterone (PG, 2 μg/ml).

Techniques: Immunoprecipitation, Injection, Western Blot, Activation Assay, Expressing, Functional Assay