Back

Ancestral protein topologies draw the rooted bacterial tree of life

Dimas-Torres, J.-U.; Rodriguez-Hernandez, A.; Valencia-Sanchez, M.-I.; Campos-Chavez, E.; Godinez-Lopez, V.; Rodriguez-Chamorro, D.-E.; Hernandez-Gonzalez, A.; Arciniega, M.; Torres-Larios, A.

2021-08-20 evolutionary biology
10.1101/2021.08.20.456953 bioRxiv
Show abstract

Aminoacyl tRNA synthetases (aaRSs) are among the proposed proteins present in the Last Universal Common Ancestor (LUCA). There are two types of glycyl tRNA synthetases (GlyRSs), from which the archaeal-eukaryal type is the one suggested to be present in LUCA. Here we solved the crystal structure of a complete bacterial glycyl tRNA synthetase (bacGlyRS) and show that indeed, bacGlyRS carries several structural signals that point it at the origin of all aaRSs. Furthermore, if bacGlyRS is ancestral, it should help to build a reliable Tree of Life (ToL). Given the modular nature of protein evolution, we used only two sub-domain segments with duplicated ancestral topologies, no detected orthologs and an assumed limited horizontal gene transfer (HGT). These motifs correspond to the non-specific RNA binding regions of contemporary bacGlyRS, archaeal CCA-adding enzyme (arch-CCAadd), and eukaryotic rRNA processing enzyme (euk-rRNA). The calculated, rooted bacterial ToL agrees with several phyla relationships unaccounted by the available trees.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
eLife
● 5828 papers in training set
Top 2%
22.1%
Similar papers in this journal
2
Genome Biology and Evolution
◐ 338 papers in training set
Top 0.2%
18.6%
Similar papers in this journal
3
Molecular Biology and Evolution
◐ 542 papers in training set
Top 0.4%
15.2%
Similar papers in this journal
50% of probability mass above
4
Protein Science
○ 246 papers in training set
Top 0.7%
5.5%
Similar papers in this journal
5
International Journal of Molecular Sciences
○ 494 papers in training set
Top 4%
3.2%
Similar papers in this journal
6
Frontiers in Microbiology
○ 427 papers in training set
Top 3%
3.1%
7
Nucleic Acids Research
◐ 1281 papers in training set
Top 7%
2.4%
8
Communications Biology
○ 993 papers in training set
Top 12%
1.9%
9
PeerJ
◐ 308 papers in training set
Top 5%
1.7%
10
Journal of Molecular Evolution
○ 22 papers in training set
Top 0.2%
1.5%
11
Nature Communications
○ 5641 papers in training set
Top 48%
1.3%
12
Scientific Reports
○ 3612 papers in training set
Top 62%
1.1%
13
iScience
○ 1154 papers in training set
Top 29%
1.1%
14
Proteins: Structure, Function, and Bioinformatics
○ 88 papers in training set
Top 1%
1.1%
15
Journal of Molecular Biology
○ 232 papers in training set
Top 3%
1.1%
16
BMC Biology
○ 265 papers in training set
Top 4%
1.1%
17
Journal of Cellular Biochemistry
○ 11 papers in training set
Top 0.2%
0.9%
18
PLOS Biology
● 486 papers in training set
Top 11%
0.9%
19
Biology Direct
○ 11 papers in training set
Top 0.1%
0.6%
20
RNA
● 189 papers in training set
Top 1%
0.6%
21
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 44%
0.6%
22
Life Science Alliance
● 285 papers in training set
Top 9%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.