Microbiology

Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance

1. Rauf Shiraliyev
2. Mehmet A Orman

• Curated by eLife

  eLife assessment

  The findings of this study are valuable as they challenge the dogma regarding the link between lowered bacterial metabolism and tolerance to aminoglycosides. The authors propose that the well-known tolerance to AG of mutants such as those of complexes I and II is not due to a decrease in the proton motive force and thus antibiotic uptake. The results presented here are convincing.

Reviewed by eLife

Widespread Horizontal Gene Transfer Among Animal Viruses

1. Christopher B. Buck
2. Nicole Welch
3. Anna K. Belford
4. Arvind Varsani
5. Diana V. Pastrana
6. Michael J. Tisza
7. Gabriel J. Starrett

• Curated by eLife

  eLife assessment

  This study is a computational analysis using publicly available deep sequencing datasets and the findings support the models that propose widespread gene transfer amongst DNA viruses. The evidence supporting the claims of the authors is solid, but reproducing the analysis based only on the information as presented in the Materials and Methods would be difficult as the data are currently presented. A Flow chart that details the process would help. This is an almost entirely computational study without experimental evidence but one that has the potential to become a fundamental resource for virus hunters - an activity of increasing importance.

Reviewed by eLife

Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification

1. Louna Fruchard
2. Anamaria Babosan
3. Andre Carvalho
4. Manon Lang
5. Blaise Li
6. Magalie Duchateau
7. Quentin Giai-Gianetto
8. Mariette Matondo
9. Frédéric Bonhomme
10. Isabelle Hatin
11. Hugo Arbes
12. Céline Fabret
13. Enora Corler
14. Guillaume Sanchez
15. Virginie Marchand
16. Yuri Motorin
17. Olivier Namy
18. Valérie de Crécy-Lagard
19. Didier Mazel
20. Zeynep Baharoglu

• Curated by eLife

  eLife assessment

  This study investigates the role of queuosine (Q) tRNA modification in aminoglycoside tolerance in Vibrio cholerae and presents convincing evidence to conclude that Q is essential for the efficient translation of TAT codons, although this depends on the context. The absence of Q reduces aminoglycoside tolerance potentially by reprogramming the translation of an oxidative stress response gene, rxsA. Overall, the findings point to an important mechanism whereby changes in Q modification levels control the decoding of mRNAs enriched in TAT codons under antibiotic stress.

Reviewed by eLife

Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

1. Ruihan Dong
2. Rongrong Liu
3. Ziyu Liu
4. Yangang Liu
5. Gaomei Zhao
6. Honglei Li
7. Shiyuan Hou
8. Xiaohan Ma
9. Huarui Kang
10. Jing Liu
11. Fei Guo
12. Ping Zhao
13. Junping Wang
14. Cheng Wang
15. Xingan Wu
16. Sheng Ye
17. Cheng Zhu

• Curated by eLife

  eLife assessment

  This study presents a useful pipeline for de novo design of antimicrobial peptides active both against bacteria and viruses. The method is based on deep learning, using a GAN generator and a regression tasked to predict antimicrobial activity. The evidence supporting the conclusions is promising but incomplete: three generated peptides are studied experimentally in vitro, and one is then tested in vivo in mice; the comparisons to other design methods could also be strengthened. This work will be of interest to the community working on machine learning for biomedical applications and specifically on antimicrobial peptides.

Reviewed by eLife

Rapid bacterial evaluation beyond the colony forming unit in osteomyelitis

1. Qi Sun
2. Kimberley Huynh
3. Dzenita Muratovic
4. Nicholas J Gunn
5. Anja R Zelmer
6. Lucian Bogdan Solomon
7. Gerald J Atkins
8. Dongqing Yang

• Curated by eLife

  eLife assessment

  This fundamental study addresses discrepancies in determining bacterial burden in osteomyelitis as determined by culture and enumeration using DNA. The authors present compelling data demonstrating the emergence of discrepancies between CFU counts and genome copy numbers detected by PCR in Staphylococcus aureus strains infecting osteocyte-like cells. The observations represent a substantial addition to the field of musculoskeletal infection, with possible broad applicability and clinical benefit to other infectious diseases.

Reviewed by eLife

Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses

1. Cody J. Warren
2. Arturo Barbachano-Guerrero
3. Vanessa L. Bauer
4. Alex C. Stabell
5. Obaiah Dirasantha
6. Qing Yang
7. Sara L. Sawyer

• Curated by eLife

  eLife assessment

  This study presents an important finding on how lentiviral infection has driven the diversification of the HIV/SIV entry receptor CD4. Using a combination of molecular evolution approaches coupled with functional testing of extant and ancestral reconstructions of great ape CD4, the authors provide solid evidence to support the idea that endemic simian immunodeficiency virus infection in gorillas have selected for gorilla CD4 alleles that are more resistant to SIV infection. Expanding the study to interrogate the evolution and function of additional primate CD4 sequences could yield more convincing evidence.

Reviewed by eLife

2-oxoglutarate triggers assembly of active dodecameric Methanosarcina mazei glutamine synthetase

1. Eva Herdering
2. Tristan Reif-Trauttmansdorff
3. Anuj Kumar
4. Tim Habenicht
5. Georg Hochberg
6. Stefan Bohn
7. Jan Schuller
8. Ruth A. Schmitz

• Curated by eLife

  eLife assessment

  This manuscript reports a valuable new mechanism of regulation of the glutamine synthetase in the archaeon Methanosarcina mazei and clarifies the direct activation of glutamine synthetase activity by 2-oxoglutarate, thus introducing a novel understanding of how 2-oxoglutarate serves as a central indicator of carbon and nitrogen sensing. The authors provide solid evidence using mass photometry, specific activity measurements, and single particle cryo-EM data. This study is of interest to biologists working on the regulation of metabolism.

Reviewed by eLife

Characterization of natural product inhibitors of quorum sensing in Pseudomonas aeruginosa reveals competitive inhibition of RhlR by ortho -vanillin

1. Kathryn E. Woods
2. Sana Akhter
3. Blanca Rodriguez
4. Kade A. Townsend
5. Nathan Smith
6. Ben Smith
7. Alice Wambua
8. Vaughn Craddock
9. Rhea G. Abisado-Duque
10. Emma E. Santa
11. Daniel E. Manson
12. Berl R. Oakley
13. Lynn E. Hancock
14. Yinglong Miao
15. Helen E. Blackwell
16. Josephine R. Chandler

Reviewed by preLights

Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines

1. Paula F. Zamora
2. Thomas G. Reidy
3. Catherine R. Armbruster
4. Ming Sun
5. Daria Van Tyne
6. Paul E. Turner
7. Jonathan L. Koff
8. Jennifer M. Bomberger

Reviewed by preLights

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

1. Caleb R. Carr
2. Katharine H. D. Crawford
3. Michael Murphy
4. Jared G. Galloway
5. Hugh K. Haddox
6. Frederick A. Matsen
7. Kristian G. Andersen
8. Neil P. King
9. Jesse D. Bloom

Reviewed by PREreview