Microbiology

Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology

1. Arthur Wickenhagen
2. Meaghan Flagg
3. Julia R. Port
4. Claude Kwe Yinda
5. Kerry Goldin
6. Shane Gallogly
7. Jonathan E. Schulz
8. Tessa Lutterman
9. Brandi N. Williamson
10. Franziska Kaiser
11. Reshma K. Mukesh
12. Sarah van Tol
13. Brian Smith
14. Neeltje van Doremalen
15. Colin A. Russell
16. Emmie de Wit
17. Vincent J. Munster

Reviewed by Rapid Reviews Infectious Diseases

The bat influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment

1. Maria Kaukab Osman
2. Jonathan Robert
3. Lukas Broich
4. Dennis Frank
5. Robert Grosse
6. Martin Schwemmle
7. Antoni G. Wrobel
8. Kevin Ciminski
9. Christian Sieben
10. Peter Reuther

Reviewed by preLights

The RND efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection

1. Hannah L. Pugh
2. Elizabeth M. Darby
3. Leah Burgess
4. Abigail L. Colclough
5. Asti-Rochelle Meosa John
6. Steven Dunn
7. Christopher Connor
8. Eoughin A. Perry
9. Alan McNally
10. Vassiliy N. Bavro
11. Jessica M. A. Blair

Reviewed by PREreview

The glycoprotein quality control factor Malectin promotes coronavirus replication and viral protein biogenesis

1. Jonathan P Davies
2. Lars Plate

• Curated by eLife

  eLife assessment

  This is a valuable study that utilizes proteomic and genetic approaches to identify the glycoprotein quality control factor malectin as a pro-viral host protein involved in the replication of coronavirus. The evidence supporting this conclusion is solid, although additional insight into the mechanistic basis of malectin-mediated viral replication would further strengthen this study. This work will be of interest to cell biologists studying the molecular mechanisms of glycoprotein quality control and virologists studying the host-pathogen interactions.

Reviewed by eLife

Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae

1. Yue Sun
2. Jingwei Li
3. Jiadai Huang
4. Shumin Li
5. Youyue Li
6. Beifang Lu
7. Xin Deng

• Curated by eLife

  eLife assessment

  This work advances our understanding of transcriptional regulation of virulence and metabolic pathways in plant pathogenic bacteria. Solid evidence for the claims is provided by computational analysis of newly generated data on the genome-wide binding of 170 transcription factors to their target genes, together with experimental validation of the biological functions of some of these transcription factors. The findings and resources from this study will be valuable to researchers in the fields of systems biology, bacteriology, and plant-microbe interactions.

Reviewed by eLife

Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and fluconazole resistance

1. Maruti Nandan Rai
2. Qing Lan
3. Chirag Parsania
4. Rikky Rai
5. Niranjan Shirgaonkar
6. Ruiwen Chen
7. Li Shen
8. Kaeling Tan
9. Koon Ho Wong

• Curated by eLife

  Evaluation Summary:

  The paper by Rai and colleagues examines the transcriptional response of Candida glabrata, a common human fungal pathogen, during interaction with macrophages. They use RNA PolII profiling to identify not just the total transcripts but instead focus on the actively transcribing genes. By examining the profile over time, they identify particular transcripts that are enriched at each time point, building a hierarchical model for how a transcription factor, CgXbp1, may regulate part of this response. While the authors have generated a large and potentially impactful dataset, along with several interesting observations, it is important to be cautious as the direct targets of CgXbp1 were characterized under one particular condition and the transcriptional analyses were obtained in another condition, one shown to be highly dynamic as during macrophage infection.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Hosts manipulate lifestyle switch and pathogenicity heterogeneity of opportunistic pathogens in the single-cell resolution

1. Ziguang Wang
2. Shuai Li
3. Sheng Zhang
4. Tianyu Zhang
5. Yujie Wu
6. Anqi Liu
7. Kui Wang
8. Xiaowen Ji
9. Haiqun Cao
10. Yinglao Zhang
11. Eng King Tan
12. Yongcheng Wang
13. Yirong Wang
14. Wei Liu

• Curated by eLife

  eLife assessment

  The fundamental findings of this work substantially advance our understanding of the impact of the host on its gut microbes. The authors provided compelling evidence at single-cell resolution that the host can drive heterogeneity in the populations of gut microbes with significant consequences for the host physiology.

Reviewed by eLife

A modified BPaL regimen for tuberculosis treatment replaces linezolid with inhaled spectinamides

1. Malik Zohaib Ali
2. Taru S Dutt
3. Amy MacNeill
4. Amanda Walz
5. Camron Pearce
6. Ha Lam
7. Jamie S Philp
8. Johnathan Patterson
9. Marcela Henao-Tamayo
10. Richard Lee
11. Jiuyu Liu
12. Gregory T Robertson
13. Anthony J Hickey
14. Bernd Meibohm
15. Mercedes Gonzalez Juarrero

• Curated by eLife

  eLife assessment

  In this useful study, the authors report the efficacy, hematological effects, and inflammatory response of the BPaL regimen (containing bedaquiline, pretomanid, and linezolid) compared to a variation in which Linezolid is replaced with the preclinical development candidate spectinamide 1599, administered by inhalation in tuberculosis-infected mice. The authors provide convincing evidence that supports the replacement of Linezolid in the current standard of care for drug-resistant tuberculosis. The work will be of interest to those studying tuberculosis treatment regimens.

Reviewed by eLife

Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action

1. Ritwik Maity
2. Xuepei Zhang
3. Francesca Romana Liberati
4. Chiara Scribani Rossi
5. Francesca Cutruzzolá
6. Serena Rinaldo
7. Massimiliano Gaetani
8. José Antonio Aínsa
9. Javier Sancho

• Curated by eLife

  eLife assessment

  This fundamental study provides insights into how pathogens respond, on a systemic level including several gene targets and clusters, to selected antimicrobial molecules. Compelling evidence is provided, through multi-omics and functional approaches, that very similar molecules originally designed to target the same bacterial protein act differently within the context of the whole set of cellular transcripts, expressed proteins, and pre-lethal metabolic changes. Given the rapid accumulation of omics data and the much slower capacity of extracting biologically relevant insights from big data, this work exemplifies how the development of sensitive data analysis is still a major necessity in modern research.

Reviewed by eLife

Growth consequences of the inhomogeneous organization of the bacterial cytoplasm

1. Johan H van Heerden
2. Alicia Berkvens
3. Daan H de Groot
4. Frank J Bruggeman

• Curated by eLife

  eLife assessment

  This important study examines E. coli growth and division, suggesting that inhomogeneous organization of ribosomes in the cytoplasm results in cell size-dependent growth rate perturbations. The work is conceptually appealing, but incomplete due to shortcomings in the experiments and modeling.

Reviewed by eLife