Link to this post | posted 22 Dec, 2017 07:04

jparker

Paola (K5) may have a novel toxin/antitoxin system Gp86 (57,020-57,295) and Gp87 (57,297-57,725) – Structural models have led student team Sick Virions to believe that gp85 and gp86 belongs to a putative Toxin-Antitoxin system (TA system). Even though the two components resemble defined proteins from different TA systems, it has been suggested through structural analysis that the two different systems pose enough similarity between them so that the components are interchangeable while still being functional. Paola gp86 was reported as a type II BrnT toxin by the tool HHpred, which indicating that gp86 shares structural similarity with BrnT toxin from brucella abortus. Top two hits both call for this function with probability 99.7, good E-value and high coverage above 85%. 3D crystal structure of gp86 constructed by Phyre and Pymol suggests gp86 conserved the important beta-sheet domains as BrnT toxin has, which can interact with BrnA antitoxin. However, the sequence of gp86 does not align with that of BrnT toxin BlastX was used for the alignment. Gp86 has a length of 276bp, about the same length as BrnT toxin. In addition, gp87 shows structural similarity to RelB antitoxin, even though the coverage of this HHpred hit is low, Heaton et al (2012) indicates that BrnT has secondary structure highly resembles to RelE structure, the toxin paired with RelB, and BrnT and RelB may interact. This adds to the evidence of gp85 should be called for BrnT toxin. >Paola gp86 MARWADDRAEHLWERHEKTIEQAEEALNDPARVTLDPDPASKSGGGVRVVGYSPTAGCVLCVIVVPYEGELWGATAFPANKTYQRIYKEGAZ >Paola gp87 MSKKPNEELTRVLNNAALMAETDAEIMGDHVDLTDVKITRGGPRTRVLQIRLNDDELAELERQADDRDLPASTVAREILLRALFPRPAADPVAFSREGVAEALLRYVDAVVDRQLAARVEEVYRKGAEAFMVPGPAGYGSPMZ DNAM file for Paola is attached. Edited 22 Dec, 2017 07:04 32Kb

Link to this post | posted 30 Dec, 2017 11:19
welkin	Hi Jordan, So what exactly are you proposing? 86 is BrnT rather than RelE, and and 87 is RelB? Does BrnT have its own anti-toxin we should be looking for?

Link to this post | posted 27 Jan, 2018 00:54
jparker	Sorry, it looks like I got my gene numbers muddled. I am proposing this, for lack of a better idea: gp85: BrnT-like toxin gp86: RelB-like antitoxin

Link to this post | posted 31 May, 2018 17:57

delesall

Where are we with this? We would like to call BrnT-like toxin for gene 38 in GEazy Gordonia phage GEazy gene 38 (30023- 29697, based on the HHpred database, has been identified as having great similarities with Ribonuclease toxin BrnT from Brucella abortus (3U97_A Ribonuclease toxin BrnT). This hit had a probability of 99.19%, and an E-value of 1.1E-12. Gene 38 is 327bp long, which is characteristic of other documented BrnT proteins. However, no antitoxin could be identified, although there were many flanking genes with no identified functions both before gene 38 and after. A two gene operon of toxin and antitoxin genes is characteristic of this toxin system. BrnT toxins have a RelE-like fold that is essential for interacting with the antitoxin. GEazy gene 38: MQYTYLMRIEIKANAQEHGIEGSEIRTVVSYPALEIPIAARRPGAELVLYIGPASDNEPYIEVIADLADAGMAIVFHAMMLRRQLVANLGLTDLLPTNIYGPQRPQRKZ Citations: Heaton, Brook E., et al. "Molecular structure and function of the novel BrnT/BrnA toxin-antitoxin system of Brucella abortus." Journal of Biological Chemistry 287.15 (2012): 12098-12110. HHpred data: https://toolkit.tuebingen.mpg.de/#/jobs/7676101 https://www.rcsb.org/structure/3U97

Link to this post | posted 05 Jun, 2018 16:26
welkin	I guess my questions here is what is the difference between BrnT and RelE, and can HHPred actually distinguish the difference between the two?

Link to this post | posted 05 Jun, 2018 16:45
delesall	Based on what I can find http://pfam.xfam.org/family/PF14384 BrnT/BrnA belongs to type I toxin-antitoxin while RelE/RelB is a type II. The HHPred match to BrnT is quite nice (99%, low E, covering 80%,. The HHpred match to RelE is quite poor (48% prob, E value greater that 40, covering 50%)

Link to this post | posted 18 Mar, 2019 19:51

kbutela

I have encountered this same pattern of HHPred hits for PhrostedPhlake gp39; no matches to RelE are showing up in this HHPred search. gp38 (reverse, so the "downstream" gene) has no hits to BrnA but does contain a ribbon-helix-helix DNA binding domain similar to BrnA (antitoxin). Clustal Omega alignments to other BrnT toxins are poor (found in some Mycobacterium and Rhodococcus sp, along with numerous gram negatives), and the conserved residues present in the gram-negatives tested in the Heaton et al paper that Veronique posted are also not present in the PhrostedPhlake gp39 and other BrnT genes annotated in some Actinobacteria. Should we just call this as NKF since no consensus was reached on the call of BrnT?

Link to this post | posted 19 Mar, 2019 00:16
delesall	I ended up calling ribonuclease toxin for my gene - somewhat generic but also informative…

Link to this post | posted 19 Mar, 2019 13:20
welkin	It sound to me like we can add ribonuclease toxin BrnT to the list. Thanks!

Link to this post | posted 19 Mar, 2019 14:46
kbutela	Thanks Welkin and Veronique!