scholarly journals Ancestral protein topologies draw the rooted bacterial tree of life

2021 ◽  
Author(s):  
Jorge-Uriel Dimas-Torres ◽  
Annia Rodriguez-Hernandez ◽  
Marco-Igor Valencia-Sanchez ◽  
Eduardo Campos-Chavez ◽  
Victoria Godinez-Lopez ◽  
...  
Keyword(s):  
Protein Evolution ◽  
Rna Binding ◽  
Current Trend ◽  
Trna Synthetase ◽  
Tree Of Life ◽  
Rrna Processing ◽  
Phylogenetic Data ◽  
Processing Enzyme ◽  
Binding Regions ◽  
Ancestral Protein

Many experimental and predicted observations remain unanswered in the current proposed trees of life (ToL). Also, the current trend in reporting phylogenetic data is based in mixing together the information of dozens of genomes or entire conserved proteins. In this work, we consider the modularity of protein evolution and, using only two domains with duplicated ancestral topologies from a single, universal primordial protein corresponding to the RNA binding regions of contemporary bacterial glycyl tRNA synthetase (bacGlyRS), archaeal CCA adding enzyme (arch-CCAadd) and eukaryotic rRNA processing enzyme (euk-rRNA), we propose a rooted bacterial ToL that agrees with several previous observations unaccounted by the available trees.

scholarly journals Chance, contingency, and necessity in the experimental evolution of ancestral proteins

2020 ◽  
Author(s):  
Victoria Cochran Xie ◽  
Jinyue Pu ◽  
Brian P.H. Metzger ◽  
Joseph W. Thornton ◽  
Bryan C. Dickinson
Keyword(s):  
Protein Evolution ◽  
Experimental Evolution ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Sequence Evolution ◽  
Protein Protein Interaction ◽  
Evolutionary Trajectories ◽  
Historical Moment ◽  
Related Proteins ◽  
Ancestral Protein

SUMMARYThe extent to which chance and contingency shaped the sequence outcomes of protein evolution is largely unknown. To directly characterize the causes and consequences of chance and contingency, we combined directed evolution with ancestral protein reconstruction. By repeatedly selecting a phylogenetic series of ancestral proteins in the B-cell lymphoma-2 family to evolve the same protein-protein interaction specificities that existed during history, we show that contingency and chance interact to make sequence evolution almost entirely unpredictable over the timescale of metazoan evolution. At any historical moment, multiple sets of mutations can alter or maintain specificity, and chance decides which ones occur. Contingency arises because historical sequence substitutions epistatically altered which mutations are compatible with new or ancestral functions. Evolutionary trajectories launched from different ancestors therefore lead to dramatically different outcomes over phylogenetic time, with virtually no mutations occurring repeatedly in distantly related proteins, even under identical selection conditions.

scholarly journals The 2.0 Å crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules

Structure ◽  
2000 ◽  
Vol 8 (2) ◽  
pp. 197-208 ◽  
Author(s):  
Ikuko Sugiura ◽  
Osamu Nureki ◽  
Yoshiko Ugaji-Yoshikawa ◽  
Sachiko Kuwabara ◽  
Atsushi Shimada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Thermus Thermophilus ◽  
Trna Synthetase ◽  
Methionyl Trna Synthetase

scholarly journals Imp3p and Imp4p, Two Specific Components of the U3 Small Nucleolar Ribonucleoprotein That Are Essential for Pre-18S rRNA Processing

1999 ◽  
Vol 19 (8) ◽  
pp. 5441-5452 ◽  
Author(s):  
Sarah J. Lee ◽  
Susan J. Baserga
Keyword(s):  
Ribosomal Proteins ◽  
18S Rrna ◽  
Rna Binding ◽  
Specific Protein ◽  
Rrna Processing ◽  
Binding Domains ◽  
U3 Snorna ◽  
Genes Encoding ◽  
Protein Components

ABSTRACT The function of the U3 small nucleolar ribonucleoprotein (snoRNP) is central to the events surrounding pre-rRNA processing, as evidenced by the severe defects in cleavage of pre-18S rRNA precursors observed upon depletion of the U3 RNA and its unique protein components. Although the precise function of each component remains unclear, since U3 snoRNA levels remain unchanged upon genetic depletion of these proteins, it is likely that the proteins themselves have significant roles in the cleavage reactions. Here we report the identification of two previously undescribed protein components of the U3 snoRNP, representing the first snoRNP components identified by using the two-hybrid methodology. By screening for proteins that physically associate with the U3 snoRNP-specific protein, Mpp10p, we have identified Imp3p (22 kDa) and Imp4p (34 kDa) (named for interacting with Mpp10p). The genes encoding both proteins are essential in yeast. Genetic depletion reveals that both proteins are critical for U3 snoRNP function in pre-18S rRNA processing at the A0, A1, and A2 sites in the pre-rRNA. Both Imp proteins associate with Mpp10p in vivo, and both are complexed only with the U3 snoRNA. Conservation of RNA binding domains between Imp3p and the S4 family of ribosomal proteins suggests that it might associate with RNA directly. However, as with other U3 snoRNP-specific proteins, neither Imp3p nor Imp4p is required for maintenance of U3 snoRNA integrity. Imp3p and Imp4p are therefore novel protein components specific to the U3 snoRNP with critical roles in pre-rRNA cleavage events.

Characterization of the RNA-binding regions in protein p36 of Heliothis armigera cypovirus 14

2007 ◽  
Vol 125 (2) ◽  
pp. 211-218 ◽  
Author(s):  
Wuguo Chen ◽  
Yuanyang Hu ◽  
Yang Li ◽  
Zheng Yu ◽  
Changjin Dong ◽  
...  
Keyword(s):  
Rna Binding ◽  
Heliothis Armigera ◽  
Binding Regions

Isolated RNA Binding Domain of a Class I tRNA Synthetase

Biochemistry ◽  
1995 ◽  
Vol 34 (27) ◽  
pp. 8896-8903 ◽  
Author(s):  
Andrew J. Gale ◽  
Paul Schimmel
Keyword(s):  
Rna Binding ◽  
Trna Synthetase ◽  
Binding Domain ◽  
Class I ◽  
Rna Binding Domain

Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution

1995 ◽  
Vol 73 (11-12) ◽  
pp. 979-986 ◽  
Author(s):  
V. Ramakrishnan ◽  
Sue Ellen Gerchman ◽  
Jadwiga H. Kycia ◽  
Christopher Davies ◽  
Barbara L. Golden ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
High Resolution ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Bacillus Stearothermophilus ◽  
Rna Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Regions

After along hiatus, the pace of determination of the structures of ribosomal proteins has accelerated dramatically. We discuss here the structures of five ribosomal proteins from Bacillus stearothermophilus: S5, S17, L6, L9, and L14. These structures represent several new motifs. Each of these structures has revealed new insights, and we have developed criteria for recognizing RNA-binding regions of each protein and correlating the structures with such properties as antibiotic resistance. The information here should also prove invaluable in an eventual high-resolution picture of the intact ribosome.Key words: ribosome, ribosomal proteins, ribosomal RNA, X-ray crystallography, NMR.

scholarly journals Role of protein dynamics in enthalpy-driven recognition of topologically distinct dsRNAs by dsRBDs

2019 ◽  
Author(s):  
H Paithankar ◽  
J Chugh
Keyword(s):  
Rna Binding ◽  
Conformational Exchange ◽  
Critical Feature ◽  
Binding Domains ◽  
Dsrna Binding ◽  
Study Results ◽  
Close Proximity ◽  
Binding Regions ◽  
Massive Number ◽  
Adaptive Nature

AbstractTaking leads from the fact that a handful of double-stranded RNA-binding domains (dsRBDs) interact with a massive number of topologically distinct double-stranded RNAs (dsRNAs) in crucial biological pathways, and to understand the adaptability required by dsRBDs to target the pool of dsRNA substrates, we employed two independent model dsRBDs in an ITC and NMR spectroscopy based study. Our previous study revealed the presence of microsecond timescale dynamics in RNA-binding regions in the two dsRBDs studied. In the current study, results from ITC-based titrations showed that the binding of dsRBD with topologically distinct dsRNAs is enthalpy-driven, with each dsRNA-dsRBD pair having distinct combination of enthalpy-entropy yielding a similar change in free energy upon RNA-binding. We also show that the each of the dsRNA, used in this study, binds to the dsRBD in a unique mode. Further, intrinsic conformational exchange present in the RNA-binding regions of the apo-dsRBD was shown to quench upon binding with a dsRNA, while conformational exchange got induced at the residues that are in close proximity to where exchange was present in the apo-protein. This apparent relay of conformational exchange from one site to the other site upon dsRNA-binding thus suggests the importance of intrinsic dynamics to adapt to target a variety of dsRNA-shapes.Statement of SignificanceThis study reports that the interaction between dsRBDs and dsRNAs is enthalpy-driven, is perturbed by subtle changes in dsRNA shapes, and exhibits a classic case of enthalpy-entropy compensation. Further, the intrinsic microsecond timescale conformational exchange present in the apo-dsRBD was observed to get quenched upon RNA-binding. An apparent relay of conformational exchange was also observed from quenched sites to spatially proximal sites upon RNA-binding, suggesting highly adaptive nature of the dsRBD, a critical feature required to target topologically distinct dsRNA.

Sign in / Sign up

Export Citation Format

Share Document