Matthew R. Johnson

Works (11)

Updated: July 5th, 2023 15:58

2009 article

Temperature, not LuxS, mediates AI-2 formation in hydrothermal habitats

Nichols, J. D., Johnson, M. R., Chou, C.-J., & Kelly, R. M. (2009, March 20). FEMS Microbiology Ecology, Vol. 68, pp. 173–181.

By: J. Nichols n, M. Johnson n, C. Chou n & R. Kelly n 

author keywords: autoinducer-2; AI-2; hyperthermophiles; hydrothermal environments; Thermotoga maritima; Pyrococcus furiosus
MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Carbon-Sulfur Lyases / genetics; Carbon-Sulfur Lyases / metabolism; Gas Chromatography-Mass Spectrometry; Gene Expression Regulation, Bacterial; Homoserine / analogs & derivatives; Homoserine / biosynthesis; Hot Temperature; Lactones; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Quorum Sensing; Thermotoga maritima / genetics; Thermotoga maritima / metabolism
topics (OpenAlex): Bacterial biofilms and quorum sensing; Microbial Community Ecology and Physiology; Genomics and Phylogenetic Studies
TL;DR: Autoinducer-2 (AI-2), a boronated furanone and proposed 'universal' interspecies mesophilic bacterial communication signal, could be formed by Thermotoga maritima and Pyrococcus furiosus through a combination of biotic and abiotic reaction steps, but did not induce any detectable quorum-sensing phenotypes in these organisms. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 article

Colocation of Genes Encoding a tRNA-mRNA Hybrid and a Putative Signaling Peptide on Complementary Strands in the Genome of the Hyperthermophilic BacteriumThermotoga maritima

Montero, C. I., Lewis, D. L., Johnson, M. R., Conners, S. B., Nance, E. A., Nichols, J. D., & Kelly, R. M. (2006, September 15). Journal of Bacteriology, Vol. 188, pp. 6802–6807.

By: C. Montero n, D. Lewis n, M. Johnson n, S. Conners n, E. Nance n, J. Nichols n, R. Kelly n 

MeSH headings : Amino Acid Sequence; Anti-Bacterial Agents / pharmacology; Chloramphenicol / pharmacology; Coculture Techniques; DNA, Bacterial / genetics; Gene Expression; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genome, Bacterial; Intracellular Signaling Peptides and Proteins / genetics; Methanococcus; RNA, Bacterial / analysis; RNA, Bacterial / genetics; RNA, Messenger / analysis; RNA, Messenger / genetics; Reverse Transcriptase Polymerase Chain Reaction; Sequence Alignment; Synteny; Thermotoga maritima / genetics; Transcription, Genetic
topics (OpenAlex): Bacterial Genetics and Biotechnology; Bacterial biofilms and quorum sensing; Probiotics and Fermented Foods
TL;DR: Specific DNA probes were designed and used in real-time PCR assays to follow the separate transcriptional responses of the colocated open reading frames (ORFs) during transition from exponential to stationary phase, chloramphenicol challenge, and syntrophic coculture with Methanococcus jannaschii. (via Semantic Scholar)
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14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 article

Microbial biochemistry, physiology, and biotechnology of hyperthermophilicThermotogaspecies

Conners, S. B., Mongodin, E. F., Johnson, M. R., Montero, C. I., Nelson, K. E., & Kelly, R. M. (2006, August 2). FEMS Microbiology Reviews, Vol. 30, pp. 872–905.

By: S. Conners n, E. Mongodin, M. Johnson n, C. Montero n, K. Nelson & R. Kelly n 

author keywords: Thermotoga; hyperthermophiles; functional genomics
MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Bacterial Proteins / physiology; Biotechnology; Carbohydrate Metabolism; Genetic Variation; Genome, Bacterial; Genomics; Gram-Negative Anaerobic Straight, Curved, and Helical Rods / genetics; Gram-Negative Anaerobic Straight, Curved, and Helical Rods / physiology; Hot Temperature; Iron / metabolism; Monosaccharides / biosynthesis; Phylogeny; Polysaccharides / biosynthesis; Signal Transduction; Sulfur / metabolism; Thermotoga maritima / genetics; Thermotoga maritima / isolation & purification; Thermotoga maritima / physiology
topics (OpenAlex): Enzyme Production and Characterization; Enzyme Structure and Function; Glycosylation and Glycoproteins Research
TL;DR: Structural genomics efforts aimed at the model hyperthermophile Thermotoga maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins, particularly for carbohydrate utilization and iron-sulfur cluster synthesis and repair. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 article

Role of the β1 Subunit in the Function and Stability of the 20S Proteasome in the Hyperthermophilic ArchaeonPyrococcus furiosus

Madding, L. S., Michel, J. K., Shockley, K. R., Conners, S. B., Epting, K. L., Johnson, M. R., & Kelly, R. M. (2006, November 18). Journal of Bacteriology, Vol. 189, pp. 583–590.

By: L. Madding n, J. Michel n, K. Shockley n, S. Conners n, K. Epting n, M. Johnson n, R. Kelly n 

MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Archaeal Proteins / physiology; Calorimetry, Differential Scanning; Genome, Archaeal; Hot Temperature; Molecular Chaperones / genetics; Molecular Chaperones / metabolism; Proteasome Endopeptidase Complex / genetics; Proteasome Endopeptidase Complex / metabolism; Proteasome Endopeptidase Complex / physiology; Protein Subunits / genetics; Protein Subunits / metabolism; Protein Subunits / physiology; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Temperature; Transcription, Genetic
topics (OpenAlex): Ubiquitin and proteasome pathways; Peptidase Inhibition and Analysis; Glycosylation and Glycoproteins Research
TL;DR: Results indicate that the β1 subunit in the P. furiosus 20S proteasome plays a thermostabilizing role and influences biocatalytic properties, suggesting that β subunit composition is a factor in archaeal proteasom function during thermal stress, when polypeptide turnover is essential to cell survival. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 article

Transcriptional and Biochemical Analysis of Starch Metabolism in the Hyperthermophilic Archaeon Pyrococcus furiosus

Lee, H.-S., Shockley, K. R., Schut, G. J., Conners, S. B., Montero, C. I., Johnson, M. R., … Adams, M. W. W. (2006, March 2). Journal of Bacteriology, Vol. 188, pp. 2115–2125.

By: H. Lee *, K. Shockley n, G. Schut *, S. Conners n, C. Montero n, M. Johnson n, C. Chou n, S. Bridger n ...

MeSH headings : Archaeal Proteins / genetics; Bacterial Proteins / genetics; DNA, Archaeal / chemistry; DNA, Archaeal / genetics; Gene Expression Profiling; Gene Expression Regulation, Archaeal; Glucose / metabolism; Glucosephosphates / metabolism; Glucosyltransferases / genetics; Glycogen Debranching Enzyme System / genetics; Glycoside Hydrolases / genetics; Monosaccharide Transport Proteins / genetics; Oligonucleotide Array Sequence Analysis; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Sequence Analysis, DNA; Starch / metabolism; Substrate Specificity
topics (OpenAlex): Enzyme Production and Characterization; Phytase and its Applications; Microbial Metabolites in Food Biotechnology
TL;DR: Starch metabolism in P. furiosus was examined by biochemical analyses in conjunction with global transcriptional response data for cells grown on a variety of glucans, and several hypothetical proteins encoded by three gene clusters are also involved in the transport and processing of alpha-glucan substrates by this organism. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2005 article

An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in theHyperthermophilic Bacterium Thermotoga maritima

Conners, S. B., Montero, C. I., Comfort, D. A., Shockley, K. R., Johnson, M. R., Chhabra, S. R., & Kelly, R. M. (2005, October 19). Journal of Bacteriology, Vol. 187, pp. 7267–7282.

By: S. Conners n, C. Montero n, D. Comfort n, K. Shockley n, M. Johnson n, S. Chhabra n, R. Kelly n 

MeSH headings : 5' Flanking Region / genetics; ATP-Binding Cassette Transporters / chemistry; ATP-Binding Cassette Transporters / genetics; Biological Evolution; Biological Transport / genetics; Carbohydrate Metabolism; Computational Biology; Gene Duplication; Gene Expression Profiling; Genes, Bacterial; Genes, Regulator; Genomics; Monosaccharide Transport Proteins / genetics; Nucleic Acid Conformation; Oligosaccharides / metabolism; Pentose Phosphate Pathway / genetics; Regulon / physiology; Rhamnose / metabolism; Thermotoga maritima / genetics; Thermotoga maritima / metabolism; Xylose / metabolism
topics (OpenAlex): Enzyme Production and Characterization; Genomics and Phylogenetic Studies; Microbial Community Ecology and Physiology
TL;DR: The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2005 article

Genome-Wide Transcriptional Variation within and between Steady States for Continuous Growth of the HyperthermophileThermotoga Maritima

Shockley, K. R., Scott, K. L., Pysz, M. A., Conners, S. B., Johnson, M. R., Montero, C. I., … Kelly, R. M. (2005, September 1). Applied and Environmental Microbiology, Vol. 71, pp. 5572–5576.

By: K. Shockley n, K. Scott *, M. Pysz n, S. Conners n, M. Johnson n, C. Montero n, R. Wolfinger*, R. Kelly n 

topics (OpenAlex): Algal biology and biofuel production; Aquaculture disease management and microbiota
TL;DR: Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to that between steady states, supporting the efficacy of chemostat-based approaches for functional genomics studies. (via Semantic Scholar)
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15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2004 article

Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms

Johnson, M. R., Montero, C. I., Conners, S. B., Shockley, K. R., Pysz, M. A., & Kelly, R. M. (2004, April 1). Biochemical Society Transactions, Vol. 32, pp. 188–192.

By: M. Johnson n, C. Montero n, S. Conners n, K. Shockley n, M. Pysz n & R. Kelly n 

author keywords: ecology; functional qenomics; hyperthermophile; microarray; mixed culture
MeSH headings : Biofilms; DNA, Complementary / metabolism; Ecology; Gene Transfer Techniques; Genes, Archaeal; Genome; Genome, Archaeal; Microscopy, Fluorescence; Oligonucleotide Array Sequence Analysis; Phylogeny; RNA, Ribosomal, 16S / genetics; Temperature
topics (OpenAlex): Microbial Community Ecology and Physiology; Genomics and Phylogenetic Studies; Bacteriophages and microbial interactions
TL;DR: Functional genomics-based approaches are described, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality. (via Semantic Scholar)
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15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
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2004 article

Population density‐dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima

Johnson, M. R., Montero, C. I., Conners, S. B., Shockley, K. R., Bridger, S. L., & Kelly, R. M. (2004, November 25). Molecular Microbiology, Vol. 55, pp. 664–674.

By: M. Johnson n, C. Montero n, S. Conners n, K. Shockley n, S. Bridger n & R. Kelly n 

MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Culture Media; Ecosystem; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Archaeal; Genome, Bacterial; Methanococcus / genetics; Methanococcus / growth & development; Methanococcus / metabolism; Oligonucleotide Array Sequence Analysis; Polysaccharides, Bacterial / metabolism; Signal Transduction; Temperature; Thermotoga maritima / growth & development; Thermotoga maritima / metabolism; Transcription, Genetic
topics (OpenAlex): Bacterial biofilms and quorum sensing; Oral microbiology and periodontitis research; Bacterial Genetics and Biotechnology
TL;DR: Results point to the existence of peptide‐based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats. (via Semantic Scholar)
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14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
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2004 article

Transcriptional Analysis of Biofilm Formation Processes in the Anaerobic, Hyperthermophilic Bacterium Thermotoga maritima

Pysz, M. A., Conners, S. B., Montero, C. I., Shockley, K. R., Johnson, M. R., Ward, D. E., & Kelly, R. M. (2004, October 1). Applied and Environmental Microbiology, Vol. 70, pp. 6098–6112.

By: M. Pysz n, S. Conners n, C. Montero n, K. Shockley n, M. Johnson n, D. Ward n, R. Kelly n 

MeSH headings : ATP-Binding Cassette Transporters / genetics; ATP-Binding Cassette Transporters / metabolism; Base Sequence; Biofilms / growth & development; Bioreactors; DNA, Bacterial / genetics; Gene Expression Profiling; Genes, Bacterial; Iron / metabolism; Models, Biological; Oligonucleotide Array Sequence Analysis; Oxidative Stress; Polysaccharides, Bacterial / genetics; Polysaccharides, Bacterial / metabolism; Sulfur / metabolism; Temperature; Thermotoga maritima / genetics; Thermotoga maritima / physiology; Thermotoga maritima / ultrastructure; Transcription, Genetic
topics (OpenAlex): Microbial Community Ecology and Physiology; Bacterial biofilms and quorum sensing; Oral microbiology and periodontitis research
TL;DR: In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments. (via Semantic Scholar)
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14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2004 article

Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima

Pysz, M. A., Shockley, K. R., Montero, C. I., Conners, S. B., Johnson, M. R., Kelly, R. M., & Ward, D. E. (2004, June 1). Extremophiles, Vol. 8, pp. 209–217.

By: M. Pysz n, K. Shockley n, C. Montero n, S. Conners n, M. Johnson n, R. Kelly n , D. Ward n

author keywords: cDNA microarray; groESL; heat shock; hrcA; hyperthermophile; Thermotoga
MeSH headings : Base Sequence; DNA, Bacterial / genetics; Endopeptidases / genetics; Gene Expression; Genome, Bacterial; Heat-Shock Response / genetics; Hot Temperature; Oligonucleotide Array Sequence Analysis; SOS Response, Genetics; Sigma Factor / genetics; Thermotoga maritima / genetics; Thermotoga maritima / metabolism; Transcription, Genetic
topics (OpenAlex): Enzyme Structure and Function; Heat shock proteins research; Protein Structure and Dynamics
TL;DR: The results reported here indicate that, while T. maritima shares core elements of the bacterial heat-shock response with mesophiles, the thermal stress regulatory strategies of this organism differ significantly, and it remains to be elucidated whether these differences are related to thermophilicity or phylogenetic placement. (via Semantic Scholar)
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14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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