scholarly journals Experimental Determination of Evolutionary Barriers to Horizontal Gene Transfer

2019 ◽  
Author(s):  
Hande Acar Kirit ◽  
Mato Lagator ◽  
Jonathan P. Bollback
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Protein Interactions ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Protein Protein Interactions ◽  
Fitness Effects ◽  
Intrinsic Protein Disorder ◽  
Serovar Typhimurium

AbstractHorizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes. Several barriers have been suggested to impede the likelihood of horizontal transmission; however experimental evidence is scarce. We measured the fitness effects of genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli, and found that most result in strong fitness costs. Previously identified evolutionary barriers — gene function and the number of protein-protein interactions — did not predict the fitness effects of transferred genes. In contrast, dosage sensitivity, gene length, and the intrinsic protein disorder significantly impact the likelihood of a successful horizontal transfer. While computational approaches have been successful in describing long-term barriers to horizontal gene transfer, our experimental results identified previously underappreciated barriers that determine the fitness effects of newly transferred genes, and hence their short-term eco-evolutionary dynamics.

scholarly journals Experimental determination of evolutionary barriers to horizontal gene transfer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Hande Acar Kirit ◽  
Mato Lagator ◽  
Jonathan P. Bollback
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Protein Interactions ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Protein Protein Interactions ◽  
New Host ◽  
Transfer Event ◽  
Fitness Effects ◽  
Serovar Typhimurium

Abstract Background Horizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes that enables microbes to rapidly adapt to new environments. How the transferred gene alters the growth – fitness – of the new host affects the success of the horizontal gene transfer event and how rapidly the gene spreads in the population. Several selective barriers – factors that impact the fitness effect of the transferred gene – have been suggested to impede the likelihood of horizontal transmission, however experimental evidence is scarce. The objective of this study was to determine the fitness effects of orthologous genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli to identify the selective barriers using highly precise experimental measurements. Results We found that most gene transfers result in strong fitness costs. Previously identified evolutionary barriers — gene function and the number of protein-protein interactions — did not predict the fitness effects of transferred genes. In contrast, dosage sensitivity, gene length, and the intrinsic protein disorder significantly impact the likelihood of a successful horizontal transfer. Conclusion While computational approaches have been successful in describing long-term barriers to horizontal gene transfer, our experimental results identified previously underappreciated barriers that determine the fitness effects of newly transferred genes, and hence their short-term eco-evolutionary dynamics.

scholarly journals How environment shapes horizontal gene transfer

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Rama Bhatia ◽  
Hande Kirit ◽  
Jonathan Bollback
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Dosage ◽  
Recipient Cell ◽  
Endogenous Gene ◽  
Fitness Effects ◽  
Serovar Typhimurium ◽  
A Cell ◽  
Evolutionary Fate

The evolutionary fate of a horizontal gene transfer (HGT) event is determined by its fitness on the recipient cell, i.e., whether it is beneficial, neutral or deleterious. The distribution of fitness effects (DFE), thus is a fundamental predictor of the outcome of an HGT event. The environment plays a considerable role in determining the fitness cost of a horizontally transferred gene. We have studied the fitness effects of genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli in six environments, that potentially represent the conditions experienced by the two species. The data suggests high variability of genes in different environments. Genes, whose fitness varies substantially between environments, may be able to persist in populations while being deleterious in one environment, they may be neutral or even beneficial in another environment, suggesting that environmental fluctuations may increase the likelihood of HGT. In addition to the in vitro environments, we are also looking at, how changes in the intrinsic environment of a cell, after an HGT event, could affect fitness. An increase in protein dosage due to functional similarity of the horizontally transferred gene to the endogenous gene can cause an imbalance in the cell, thereby leading to a negative fitness effect. By comparing the growth rates of each ortholog gene with the wild type strain, we can elucidate when gene dosage acts as a barrier to HGT.

scholarly journals Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Avital Shushan ◽  
Mickey Kosloff
Keyword(s):  
Protein Interactions ◽  
Structural Elements ◽  
Protein Protein Interactions ◽  
Immunity Protein ◽  
Rational Engineering ◽  
High Affinity ◽  
Comparative Structure ◽  
Polar Interactions ◽  
Exquisite Specificity

AbstractThe interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.

In silico specificity determination of neoantigen-reactive T-lymphocytes

2021 ◽  
Vol 67 (3) ◽  
pp. 251-258
Author(s):  
A.E. Kniga ◽  
I.V. Polyakov ◽  
A.V. Nemukhin
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Molecular Docking ◽  
Protein Interactions ◽  
Structural Features ◽  
Immune Recognition ◽  
Protein Protein Interactions ◽  
Binary Classifiers

Effective personalized immunotherapies of the future will need to capture not only the peculiarities of the patient’s tumor but also of his immune response to it. In this study, using results of in vitro high-throughput specificity assays, and combining comparative models of pMHCs and TCRs using molecular docking, we have constructed all-atom models for the putative complexes of all their possible pairwise TCR-pMHC combinations. For the models obtained we have calculated a dataset of physics-based scores and have trained binary classifiers that perform better compared to their solely sequence-based counterparts. These structure-based classifiers pinpoint the most prominent energetic terms and structural features characterizing the type of protein-protein interactions that underlies the immune recognition of tumors by T cells.

Determination of Protein–Protein Interactions in a Mixture of Two Monoclonal Antibodies

2019 ◽  
Vol 16 (12) ◽  
pp. 4775-4786 ◽  
Author(s):  
Priyanka Singh ◽  
Aisling Roche ◽  
Christopher F. van der Walle ◽  
Shahid Uddin ◽  
Jiali Du ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Protein Interactions ◽  
Protein Protein Interactions

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

Address of the President Lord Todd at the anniversary meeting, 30 November 1976

1977 ◽  
Vol 352 (1671) ◽  
pp. 451-462
Keyword(s):  
Protein Interactions ◽  
Complex Analysis ◽  
Organic Molecules ◽  
Heavy Atom ◽  
Vitamin B ◽  
Protein Protein Interactions ◽  
X Ray Crystallography ◽  
Polypeptide Chains ◽  
Complex Organic

The Copley Medal is awarded to Professor Dorothy M. C. Hodgkin, O. M., F. R. S. Professor Dorothy Hodgkin is distinguished for her research on the structure of complex organic molecules by the method of X-ray crystallography. She was among the first to appreciate the importance of heavy-atom phase-determining methods and these she used to effect the first complete determination of the stereochemistry of a sterol derivative in her analysis of cholesteryl iodide. The same powerful method of analysis and in particular her extraordinary gift of being able to interpret correctly the complex, partially resolved and often misleading electron density patterns that are first obtained, have been responsible for her success in elucidating the structures of many other important natural products, especially penicillin and vitamin B 12 . This last is by far the most beautiful and complex analysis which has yet been completed in this field and it is of fundamental importance to chemical science. In recent years Professor Hodgkin’s main interest has been devoted to the structure of insulin, on which she has been working on and off since 1935. Carried out with characteristic precision, this work has become a mine of stereochemical information relating to contacts between polypeptide chains and is of great significance for our interpretation of protein-protein interactions.

NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges

1998 ◽  
Vol 76 (2-3) ◽  
pp. 177-188 ◽  
Author(s):  
Jianxing Song ◽  
Feng Ni
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Experimental Approach ◽  
Structural Information ◽  
Peptide Ligands ◽  
Protein Protein Interactions ◽  
Binding Residues ◽  
Related Proteins ◽  
Binding Inhibitors

Using the design of bivalent and bridge-binding inhibitors of thrombin as an example, we review an NMR-based experimental approach for the design of functional mimetics of protein-protein interactions. The strategy includes: (i) identification of binding residues in peptide ligands by differential resonance perturbation, (ii) determination of protein-bound structures of peptide ligands by use of transferred NOEs, (iii) minimization of larger protein and peptide ligands on the basis of NMR structural information, and (iv) linkage of two weakly binding mimetics to produce an inhibitor with enhanced affinity and specificity. This approach can be especially effective for the design of potent and selective functional mimetics of protein-protein interactions because it is less likely that the surfaces of two related proteins or enzymes share two identical binding sites or regions.Key words: NMR, protein-protein interactions, functional mimetics, bridge-binding inhibitors, thrombin.

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