DisProt 2020_12 - first thematic release featuring a dataset of "unicellular toxins and antitoxins", revised and new entries
The DisProt curation team is proud to announce a new in-between-publication release featuring the first thematic DisProt dataset: "unicellular toxins and antitoxins", consisting of 23 new entries and 25 already existing entries that have been fully reannotated and updated. This is the first thematic release and the first fully reviewed dataset of DisProt, i.e. all the entries belonging to this dataset have been revised and validated by an independent curator to ensure a high level of reliability. All the entries included in this dataset have a tag attached - "unicellular toxins and antitoxins" - to help users easily identify them, as well as having the option to download them in a single file. We also revised previously published entries and added new entries annotated not only by our core team but also by new biocurators who joined the team after attending the first training session on DisProt curation in September 2020, along with newly added entries related to SARS-CoV-2. As a part of this effort, we have added a total of 137 new DisProt entries, 652 new pieces of evidence - 507 out of them reviewed and validated by an independent curator - that have now been made available to the community.
Written on Dec 22, 2020, by Bálint Mészáros, Lucía Beatriz Chemes, András Hatos, Tamás Lázár, Rita Pancsa and Federica Quaglia.DisProt first thematic dataset - “unicellular toxins and antitoxins”
What is a toxin?
Toxins are naturally produced molecules that are able to halt the growth, or cause disease or death to living cells and organisms. In general, toxins can be small molecules, peptides or proteins, which often exert their detrimental effect by targeting and disabling crucial enzymes and receptors, or by forming pores in the membrane of their targets.
Nature has devised an exceptionally wide range of toxins, which are of crucial importance in the realm of unicellular organisms. In lieu of claws, fangs, thorns or stings that animals and plants use to defend themselves from internal attacks, and immune systems used to combat infections, unicellular organisms have developed an array of toxins to sense signals from the external environment and protect themselves and their niche, necessary for survival.
I got the poison, I got the remedy
As the term toxin - together with other related terms, such as venom and poison - is used in everyday life, its exact meaning is often obscured. In general any material that has a detrimental effect on living organisms is called a poison. Toxins are defined by their natural origin, i.e. toxins are poisons that are produced by living organisms. In contrast, venoms are defined by their method of delivery: they are stored in dedicated glands of animals and are injected into the prey.
Poisons, toxins and venoms
A special class of toxins are parts of two component molecular systems called toxin-antitoxin systems. These systems are widespread in prokaryotes and are composed of two genes. One of these genes encodes a toxin protein, the other gene encodes an antitoxin or antidote that is able to counteract the effect of the toxin and prevent cell death. The antitoxin protein or RNA usually physically interacts with (i) the toxin protein to neutralize it; (ii) the toxin mRNA to block its translation; or (iii) the DNA encoding the toxin to inhibit its transcription. Toxin-antitoxin genes can be encoded on the chromosomal DNA, or extrachromosomally on plasmids in which case the system ensures the survival of the daughter cells that contain the plasmid.
Toxins and antitoxins in DisProt
In this thematic release, we curate toxins and antitoxins produced by unicellular organisms, including various bacteria and unicellular eukaryotes including important human pathogens such as E. coli, B. pertussis, V. cholerae, M. tuberculosis, C. botulinum and H. pylori, among others. These entries are marked with a dedicated tag named ‘unicellular toxins and antitoxins’. In the current release, 48 entries were assigned this tag, 23 of which were newly added and 25 which were included in earlier releases but have been extensively reannotated and updated with new regions of disorder, new experimental pieces of evidence and new functional annotations. The release covers a wide array of toxins that includes botulinum neurotoxin, hemolysins, enterotoxins and toxin-antitoxin systems. The current release highlights the extent to which unicellular organisms use disorder for both pathogenic and autoregulatory functions. Disorder functions range from toxin inactivation and targeting to allosteric regulation of enzymatic activity and transcriptional control.
Flagship release
This unicellular toxin and antitoxin dataset marks the beginning of the deployment of several new features of DisProt. It is the first thematic release with its own defining tag. This tag will be used in later curation work ensuring that new toxin or antitoxin entries will also be marked as such. In addition, this is the first sub-dataset of DisProt in which all annotations (and modifications of annotations) to entries were subsequently revised and validated by an independent curator to ensure a high level of reliability.
DisProt annotation round 2020-2022
A new annotation round of DisProt curation started in September 2020 and it introduced several improvements with respect to the previous DisProt annotation rounds. We set up a training session on IDP curation for the biocurators joining the DisProt team, moreover each biocurator is now assigned a reviewer who will provide support, revise and validate each new region annotated to ensure the quality of the new annotations provided.
In light of this, Federica and Bálint - instructors of the DisProt training sessions and reviewers of the new DisProt biocurators - are proud to announce that part of the new entries released now have been annotated by some of the biocurators who attended the first training session in September 2020: Jaime Santos Suárez, Samuel Peña Díaz, Martin Salas, Gabriele Pozzati, Matyas Pajkos, Aditi Shenoy, Tamas Szaniszlo, Zsófia Kálmán and Laszlo Dobson.