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proteomics

  • Open Access
    Alteration of Proteomes in First-Generation Cultures of <span class="named-content genus-species" id="named-content-1">Bacillus pumilus</span> Spores Exposed to Outer Space
    Editor's Pick Research Article | Molecular Biology and Physiology
    Alteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer Space

    Spore-forming bacteria are well known for their resistance to harsh environments and are of concern for spreading contamination to extraterrestrial bodies during future life detection missions. Bacillus pumilus has been regularly isolated from spacecraft-associated surfaces and exhibited unusual resistance to ultraviolet light and other sterilization techniques. A...

    Abby J. Chiang, Ganesh Babu Malli Mohan, Nitin K. Singh, Parag A. Vaishampayan, Markus Kalkum, Kasthuri Venkateswaran
  • Open Access
    Systems Analyses Reveal the Resilience of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
    Research Article | Synthetic Biology
    Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate

    Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the...

    Joseph Webb, Vicki Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony Larson, Kathryn Lilley, Graham Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
  • Open Access
    Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Editor's Pick Research Article | Applied and Environmental Science
    Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli

    A particular problem for the biotechnological production of many of the valuable chemicals that we are now able to manufacture in bacterial cells is that these products often poison the cells producing them. Solutions to improve product yields or alleviate such toxicity using the techniques of modern molecular biology first require a detailed understanding of the mechanisms of product toxicity. Here we have studied the economically...

    Calum A. Pattrick, Joseph P. Webb, Jeffrey Green, Roy R. Chaudhuri, Mark O. Collins, David J. Kelly
  • Open Access
    Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities
    Special Issue Perspective | Host-Microbe Biology
    Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

    Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.

    Manuel Kleiner
  • Open Access
    Systems-Level Analysis of Oxygen Exposure in <em>Zymomonas mobilis</em>: Implications for Isoprenoid Production
    Research Article | Molecular Biology and Physiology
    Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

    Microbially generated biofuels and bioproducts have the potential to provide a more environmentally sustainable alternative to fossil-fuel-derived products. In particular, isoprenoids, a diverse class of natural products, are chemically suitable for use as high-grade transport fuels and other commodity molecules. However, metabolic engineering for increased production of isoprenoids and other bioproducts is limited by an incomplete...

    Julia I. Martien, Alexander S. Hebert, David M. Stevenson, Matthew R. Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador-Noguez
  • Open Access
    Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease
    Research Article | Host-Microbe Biology
    Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

    A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a...

    Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
  • Open Access
    Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria

    Marine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine...

    Noelle A. Held, Matthew R. McIlvin, Dawn M. Moran, Michael T. Laub, Mak A. Saito
  • Open Access
    Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling <em>Bacteroidetes</em>
    Research Article | Applied and Environmental Science
    Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes

    Cellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to...

    Marcel Taillefer, Magnus Ø. Arntzen, Bernard Henrissat, Phillip B. Pope, Johan Larsbrink
  • Open Access
    Characterization of <span class="named-content genus-species" id="named-content-1">Aspergillus niger</span> Isolated from the International Space Station
    Research Article | Molecular Biology and Physiology
    Characterization of Aspergillus niger Isolated from the International Space Station

    A thorough understanding of how fungi respond and adapt to the various stimuli encountered during spaceflight presents many economic benefits and is imperative for the health of crew. As A. niger is a predominant ISS isolate frequently detected in built environments, studies of A. niger strains...

    Jillian Romsdahl, Adriana Blachowicz, Abby J. Chiang, Nitin Singh, Jason E. Stajich, Markus Kalkum, Kasthuri Venkateswaran, Clay C. C. Wang
  • Open Access
    Insect Transmission of Plant Pathogens: a Systems Biology Perspective
    Special Issue Perspective | Host-Microbe Biology
    Insect Transmission of Plant Pathogens: a Systems Biology Perspective

    Insect-vectored pathogens pose one of the greatest threats to plant and animal, including human, health on a global scale. Few effective control strategies have been developed to thwart the transmission of any insect-transmitted pathogen.

    Michelle Heck

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