Microbiology

Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections

1. Gabriel Innocenti
2. Maureen Obara
3. Bibiana Costa
4. Henning Jacobsen
5. Maeva Katzmarzyk
6. Luka Cicin-Sain
7. Ulrich Kalinke
8. Marco Galardini

Reviewed by Review Commons

Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level

1. Hina Khan
2. Partha Paul
3. Harsh Goar
4. Bhanwar Bamniya
5. Navin Baid
6. Dibyendu Sarkar

• Curated by eLife

  eLife assessment

  This important study describes how PhoP regulates cyclic-AMP production in the human pathogen Mycobacterium tuberculosis. The authors provide convincing evidence that PhoP acts as a repressor of the cyclic-AMP-specific phosphodiesterase, Rv0805, which can degrade cyclic-AMP. The revised manuscript has addressed all outstanding comments and the work will be of interest to bacteriologists.

Reviewed by eLife

Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning

1. Carolin Gerke
2. Liane Bauersfeld
3. Ivo Schirmeister
4. Chiara Noemi-Marie Mireisz
5. Valerie Oberhardt
6. Lea Mery
7. Di Wu
8. Christopher Sebastian Jürges
9. Robbert M Spaapen
10. Claudio Mussolino
11. Vu Thuy Khanh Le-Trilling
12. Mirko Trilling
13. Lars Dölken
14. Wolfgang Paster
15. Florian Erhard
16. Maike Hofmann
17. Andreas Schlosser
18. Hartmut Hengel
19. Frank Momburg
20. Anne Halenius

• Curated by eLife

  eLife assessment

  This study presents a useful finding on a virally encoded immune-evasin which differentially inhibits antigen presentation by cellular protein complexes called Major histocompatibility complex (MHC) class I, thereby diminishing the activation of cytotoxic T cells. The evidence supporting the claims of the authors is solid, although the addition of more mechanistic insights would strengthen the study. The work will be of interest to virologists and immunologists working on the adaptive immune response to herpesviral infection. Some conclusions would require additional experimental support.

Reviewed by eLife

Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum

1. Jessica Gray
2. Von Vergel L Torres
3. Emily Goodall
4. Samantha A McKeand
5. Danielle Scales
6. Christy Collins
7. Laura Wetherall
8. Zheng Jie Lian
9. Jack A Bryant
10. Matthew T Milner
11. Karl A Dunne
12. Christopher Icke
13. Jessica L Rooke
14. Thamarai Schneiders
15. Peter A Lund
16. Adam F Cunningham
17. Jeff A Cole
18. Ian R Henderson

• Curated by eLife

  eLife assessment

  This valuable study is of relevance for those interested in the mechanism required for infections of humans by Klebsiella pneumoniae. The authors apply TraDIS (high-density TnSeq) to K. pneumoniae with the goal of identifying genes required for survival under various infection-relevant conditions and the gene sets identified, together with the raw sequence data, will be resources for the Klebsiella research community. The evidence to support the lists of essential and conditionally-essential genes is convincing. The study provides strong evidence that some genes are conditionally essential in urine because of iron limitation, but there is less mechanistic insight for genes that are conditionally essential in serum.

Reviewed by eLife

Secreted antigen A peptidoglycan hydrolase is essential for Enterococcus faecium cell separation and priming of immune checkpoint inhibitor therapy

1. Steven Klupt
2. Kyong Tkhe Fam
3. Xing Zhang
4. Pavan Kumar Chodisetti
5. Abeera Mehmood
6. Tumara Boyd
7. Danielle Grotjahn
8. Donghyun Park
9. Howard C Hang

• Curated by eLife

  eLife assessment

  The authors build upon prior data implicating the secreted peptidoglycan hydrolase SagA produced by Enterococcus faecium in immunotherapy. Leveraging new strains with sagA deletion/complementation constructs, the investigators reveal that sagA is non-essential, with sagA deletion leading to a marked growth defect due to impaired cell division, and sagA being necessary for the immunogenic and anti-tumor effects of E. faecium. In aggregate, the study utilizes compelling methods to provide both fundamental new insights into E. faecium biology and host interactions and a proof-of-concept for identifying the bacterial effectors of immunotherapy response.

Reviewed by eLife

Modular small RNA drives pathogen emergence

1. Deepak Balasubramanian
2. Salvador Almagro-Moreno

Reviewed by PREreview

CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

1. Ryan T Bell
2. Harutyun Sahakyan
3. Kira S Makarova
4. Yuri I Wolf
5. Eugene V Koonin

• Curated by eLife

  eLife assessment

  This paper marks a fundamental advance in our understanding of prokaryotic Type IV restriction systems. The authors provide an encyclopedic overview of a hitherto uncharacterized branch of these systems, which they name CoCoNuTs, for coiled-coil nuclease tandems. They provide compelling evidence that these nucleases target RNA and are part of an echeloned defense response following viral infection. This article will be of great interest to scientists studying prokaryotic immunity mechanisms, as well as broadly to protein scientists engaged in the analysis, classification, and functional annotation of the proteome of life.

Reviewed by eLife

A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria

1. Talia Backman
2. Sergio M. Latorre
3. Efthymia Symeonidi
4. Artur Muszyński
5. Ella Bleak
6. Lauren Eads
7. Paulina I. Martinez-Koury
8. Sarita Som
9. Aubrey Hawks
10. Andrew D. Gloss
11. David M. Belnap
12. Allison M. Manuel
13. Adam M. Deutschbauer
14. Joy Bergelson
15. Parastoo Azadi
16. Hernán A. Burbano
17. Talia L. Karasov

Reviewed by Rapid Reviews Infectious Diseases

Reducing the Bacterial Lag Phase Through Methylated Compounds: Insights from Algal-Bacterial Interactions

1. Martin Sperfeld
2. Delia A. Narváez-Barragán
3. Sergey Malitsky
4. Veronica Frydman
5. Lilach Yuda
6. Jorge Rocha
7. Einat Segev

Reviewed by Arcadia Science

Bacterial vampirism mediated through taxis to serum

1. Siena J Glenn
2. Zealon Gentry-Lear
3. Michael Shavlik
4. Michael J Harms
5. Thomas J Asaki
6. Arden Baylink

• Curated by eLife

  eLife assessment

  This work uses an interdisciplinary approach combining microfluidics, structural biology, and genetic analyses to provide important findings that show that pathogenic enteric bacteria exhibit taxis toward human serum. The data are compelling and show that the behavior utilizes the bacterial chemotaxis system and the chemoreceptor Tsr, which senses the amino acid L-serine. The work provides an ecological context for the role of serine as a bacterial chemoattractant and could have clinical implications for bacterial bloodstream invasion during episodes of gastrointestinal bleeding.

Reviewed by eLife