Haloferax volcanii Immersed Liquid Biofilms Develop Independently of Known Biofilm Machineries and Exhibit Rapid Honeycomb Pattern Formation

Schiller, Heather; Schulze, Stefan; Mutan, Zuha; Vaulx, Charlotte de; Runcie, Catalina; Schwartz, J.S.; Rados, Theopi; Bisson‐Filho, Alexandre W.; Pohlschröder, Mechthild

doi:10.1128/msphere.00976-20

Cited by 8 publications

(3 citation statements)

References 70 publications

(95 reference statements)

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“…Among the significantly differentially expressed proteins, numerous proteins associated with carbohydrate metabolism, such as aglB, glgB, pckA, aceF, pykA, fbaB, deoB, and fbaB, highlight their underlying roles in K. pneumoniae . A former study reveals that mutants of the haloarchaeon that interfere with the biosynthesis of type IV pili, as well as aglB deletion mutants, lack obvious defects in biofilms formed in liquid cultures ( 41 ). In addition, chaperone proteins were also significantly differentially expressed under antibiotic stress and were involved in protein folding ( 42 , 43 ).…”

Section: Discussionmentioning

confidence: 99%

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

Fan,

Chen,

Deng

et al. 2024

Microbiol Spectr

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Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important multidrug resistance (MDR) pathogen that threatens human health and is the main source of hospital-acquired infection. Outer membrane vesicles (OMVs) are extracellular vesicles derived from Gram-negative bacteria and contain materials involved in bacterial survival and pathogenesis. They also contribute to cellular communication to nearby or distant recipient cells and influence their functions and phenotypes. In this study, we sought to understand the mechanism of bacterial response to meropenem pressure and explore the relationship between pathogenic proteins and the high pathogenicity of bacteria. We performed whole-genome PacBio sequencing on a clinical CRKP strain, and its OMVs were characterized using nanoparticle tracking analysis, transmission electron microscopy, and proteomic analysis. Thousands of vesicle proteins have been identified in mass spectrometry-based high-throughput proteomics analyses of K. pneumoniae OMVs. Protein functionality analysis showed that the OMVs were predominantly involved in metabolic, intracellular compartments, nucleic acid binding, survival, defense, and antibiotic resistance, such as Chromosome partition protein MukB, 3-methyl-2-oxobutanoate hydroxymethyltransferase, methionine—tRNA ligase, Heat shock protein 60 family chaperone GroEL, and Gamma-glutamyl phosphate reductase. Additionally, a protein-protein interaction network demonstrated that OMVs from meropenem-treated K. pneumoniae showed the highest connectivity in DNA polymerase I, phenylalanine–tRNA ligase beta subunit, DNA-directed RNA polymerase subunit beta, methionine–tRNA ligase, DNA-directed RNA polymerase subunit beta, and DNA-directed RNA polymerase subunit alpha. The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-treated K. pneumoniae , which provides clues for revealing the biogenesis and pathophysiological functions of Gram-negative bacteria OMVs. The significant differentially expressed proteins identified in this study are of great significance for exploring effective control strategies for CRKP infection. IMPORTANCE Meropenem is one of the main antibiotics used in the clinical treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP). This study demonstrated that some important metabolic changes occurred in meropenem-induced CRKP-outer membrane vesicles (OMVs), The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-induced Klebsiella pneumoniae . Furthermore, this is the ﬁrst study to discuss the protein-protein interaction network of the OMVs released by CRKP, especially under antibiotic stress.

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Section: Discussionmentioning

confidence: 99%

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

Fan,

Chen,

Deng

et al. 2024

Microbiol Spectr

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“…Then, we directed the students toward the best screen to use, discussed how the screen works, and pointed out things to consider when setting up the screen. Schiller et al describes honeycomb formation of Haloferax volcanii liquid biofilms upon reduction of humidity ( 11 ), so we had the students construct a screen to search for mutants unable to form honeycombs, as well as carotenoid-forming mutants and mutants defective in biofilm formation. Time in this 0.5-credit course was limited, since the students only met synchronously for 1.5 h per week.…”

Section: Methodsmentioning

confidence: 99%

The Best of Both Worlds: Discovery-Driven Learning through a Lab-Seminar Approach

Egan

Hogan

Maupin-Furlow

et al. 2022

J Microbiol Biol Educ.

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“…Its genome has been sequenced and carefully annotated [ 1 , 10 , 11 ]. A plethora of biological aspects have been successfully tackled in this species, with examples including DNA replication [ 4 ]; cell division and cell shape [ 12 , 13 , 14 , 15 , 16 ]; metabolism [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]; protein secretion [ 26 , 27 , 28 , 29 ]; motility and biofilms [ 30 , 31 , 32 , 33 , 34 , 35 ]; mating [ 36 ]; signaling [ 37 ]; virus defense [ 38 ]; proteolysis [ 39 , 40 , 41 , 42 , 43 , 44 ]; posttranslational modification (N-glycosylation; SAMPylation) [ 45 , 46 , 47 , 48 , 49 , 50 ]; gene regulation [ 21 , 25 , 51 , 52 , 53 , 54 , 55 ]; microproteins [ 56 , 57 , 58 ] and small noncoding RNAs (sRNAs) […”

Section: Introductionmentioning

confidence: 99%

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Pfeiffer

Dyall‐Smith

2021

Genes

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Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

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Haloferax volcanii Immersed Liquid Biofilms Develop Independently of Known Biofilm Machineries and Exhibit Rapid Honeycomb Pattern Formation

Cited by 8 publications

References 70 publications

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

The Best of Both Worlds: Discovery-Driven Learning through a Lab-Seminar Approach

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

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