NAR: PhaSepDB, a new phase protein separation database

Phase separation refers to the process
by which biological macromolecules (proteins, DNA, RNAs, etc.
) in a solution form a concentrated phase (or heterogeneous) at the appropriate temperature, pH and salt concentrations after reaching a certain concentration.
Recent studies have shown that phase separation is one of the important mechanisms driving the formation of membraneless organelles in cells, and is involved in regulating important biological processes
such as gene transcription, signaling, chromatin assembly, and protein degradation.
Protein is one of the main components of intracellular phase isolation droplets, in recent years, more and more proteins have been shown to be able to occur phase separation, and the properties and regulation of the phase separation process have also been deeply studied
.

Recently, Li Tingting's research group in the Department of Medical Bioinformatics of Peking University School of Basic Medicine published an article online in the journal Nucleic Acids Research "PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners, and other.
" experimental information", released a new version of phase isolate protein data PhaSepDB (http://db.
phasep.
pro/).

The new database includes phase-isolated protein studies as of 2022/04/01, providing annotated information
on phase-separated droplet status and phase-separation regulation.
Li Tingting's research group is committed to studying the phase separation process through bioinformatics, and has built a phase separation protein database PhaSepDB, a phase separation protein prediction tool PhaSePred, etc
.
The website (http://lab.
phasep.
pro/) has more than 40,000 users worldwide and an average of more than 2,000 daily visits, and PhaSepDB has also authorized Dewpoint therapeutics, a leading pharmaceutical company in the field of phase separation, to support the research and development of phase separation-related drugs, to promote the application of phase separation in the field of health, and to serve global health
.

In this work, the authors first review the data in the first edition of the database [1] and add new comments
.
Subsequently, the authors searched at PuBMed 1812 phase-isolated protein-related papers published between 2019/07/01 (first edition indexing deadline) and 2022/04/01, from which new phase-isolated proteins were manually collected and annotated
.
At present, PhaSepDB contains a total of 1419 phase isolation experimental entries (a total of 868 proteins).

The authors divide phase separation entries into two categories, PS-self: proteins can occur phase separation alone in vitro; PS-other: Proteins rely on mutual partners for in vitro phase isolation and/or only in vivo phase isolation experimental basis
.

Table 1 Overview of datasets in PhaSepDB v1.
0, v2.
0 (released in 2021), and v2.
1

The new database provides detailed annotations (Table 1) on phase isolate protein experiment entries, including:

1. The state of matter in which phase isolate proteins form condensates: liquid, glue-solid;

2. The diagram describing whether the protein undergoes phase separation under different experimental conditions in the original text;

3. Protein phase isolation verification experiment: in vivo and in vivo droplet formation experiment and FRAP experiment;

4. Fragments of protein phase separation, and the key domains in them;

5. Partners that regulate protein phase separation behavior: including proteins, RNA, DNA, etc.
   ;

6. Mutations affecting protein phase separation, post-translational modifications, oligomerization, repetition, variable shearing
   .
   

In addition to experimentally validated phase isolate proteins, the database contains a large number of membraneless organelle-localized proteins
.
Although the phase-separation capabilities of membraneless organelle-localized proteins have not been experimentally validated, they constitute a collection of proteins where phase separation can occur for further exploration
by phase-separation researchers.
The database currently contains 770 low-throughput membraneless organelle-associated protein entries and 7303 high-throughput entries
.

Figure 1: PhaSepDB2.
1 database interface introduction

Through the updated phase separation database (Figure 1), users can search for currently known phase isolation proteins as well as membraneless organelle proteins
where phase separation may occur.
Based on these data, researchers can further investigate the properties of phase isolate proteins, such as the properties of phase isolate proteins that can occur alone in vitro[2], the formation of differences in liquid and colloid solid condensate proteins, mutations or post-translational modifications that affect protein phase separation capabilities, and the key segments and domains
that mediate protein phase separation.

Li Tingting, a researcher in the Department of Medical Bioinformatics of Peking University School of Basic Medicine, is the corresponding author of this paper, and Hou Chao, a doctoral student of Peking University School of Basic Medicine, Wang Xinxin, an undergraduate student, and Xie Haotai, a doctoral student of Peking University First Hospital, are the first authors
of this paper.

Original link: https://academic.
oup.
com/nar/advance-article/doi/10.
1093/nar/gkac783/6702591

1.
You, K.
, et al.
, PhaSepDB: a database of liquid-liquid phase separation related proteins.
Nucleic Acids Res, 2020.
48(D1): p.
D354-D359.

2.
Chen, Z.
, et al.
, Screening membraneless organelle participants with machine-learning models that integrate multimodal features.
Proc Natl Acad Sci U S A, 2022.
119(24): p.
e2115369119.

(School of Basic Medicine, Peking University)