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Amy K. Schmid

David M. Goodner Associate Professor
Biology
Box 90338, Durham, NC 27708-0338
125 Science Dr, French Family Science Center 4105, Durham, NC 27708

Selected Publications


TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.

Journal Article Molecular microbiology · April 2024 Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Halo ... Full text Cite

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.

Journal Article Nucleic acids research · January 2024 Maintaining the¬†intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repr ... Full text Cite

A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.

Journal Article PLoS genetics · January 2024 Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeo ... Full text Cite

Salactin, a dynamically unstable actin homolog in Haloarchaea.

Journal Article mBio · November 2023 ImportanceProtein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell p ... Full text Cite

The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria.

Journal Article mBio · April 2023 Histone proteins are found across diverse lineages of Archaea, many of which package DNA and form chromatin. However, previous research has led to the hypothesis that the histone-like proteins of high-salt-adapted archaea, or halophiles, function di ... Full text Cite

Hypochlorite Stress Assay for Phenotypic Analysis of the Halophilic Archaeon Haloferax volcanii Using an Improved Incubation Method and Growth Monitoring

Journal Article Bio-protocol · November 20, 2022 The study of haloarchaea provides an opportunity to expand understanding of the mechanisms used by extremophiles to thrive in and respond to harsh environments, including hypersaline and oxidative stress conditions. A common strategy used to investigate mo ... Full text Cite

TrmB Family Transcription Factor as a Thiol-Based Regulator of Oxidative Stress Response.

Journal Article mBio · August 2022 Oxidative stress causes cellular damage, including DNA mutations, protein dysfunction, and loss of membrane integrity. Here, we discovered that a TrmB (transcription regulator of mal operon) family protein (Pfam PF01978) composed of a single winged- ... Full text Cite

Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.

Journal Article Biomolecules · May 2022 Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The ... Full text Cite

An archaeal histone-like protein regulates gene expression in response to salt stress.

Journal Article Nucleic acids research · December 2021 Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone e ... Full text Cite

A Bayesian non-parametric mixed-effects model of microbial growth curves

Journal Article PLOS Computational Biology · October 26, 2020 Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety ... Full text Cite

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.

Journal Article mBio · August 2020 Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. ... Full text Cite

SnapShot: Microbial Extremophiles.

Journal Article Cell · February 2020 Extremophiles are remarkable examples of life's resilience, thriving in hot springs at boiling temperatures, in brine lakes saturated with salt, and in the driest deserts. We review the biogeography, currently known limits of life, and molecular adaptation ... Full text Cite

Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.

Journal Article Journal of molecular biology · September 2019 The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR ... Full text Cite

Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen.

Journal Article International journal of molecular sciences · September 2019 Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H ... Full text Cite

N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility.

Journal Article Frontiers in microbiology · January 2019 Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimmin ... Full text Cite

Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.

Journal Article Emerging topics in life sciences · December 2018 Gene regulation is intimately connected with metabolism, enabling the appropriate timing and tuning of biochemical pathways to substrate availability. In microorganisms, such as archaea and bacteria, transcription factors (TFs) often directly sense externa ... Full text Cite

GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii.

Journal Article Journal of bacteriology · September 2018 DeoR-type helix-turn-helix (HTH) domain proteins are transcriptional regulators of sugar and nucleoside metabolism in diverse bacteria and also occur in select archaea. In the model archaeon Haloferax volcanii, previous work implicated GlpR, a DeoR- ... Full text Cite

Copy number variation is associated with gene expression change in archaea.

Journal Article Microbial genomics · September 2018 Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness rema ... Full text Cite

Data and scripts from: Copy number variation is associated with gene expression change in archaea

Dataset · May 4, 2018 Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness rema ... Full text Cite

TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.

Journal Article Molecular microbiology · April 2024 Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Halo ... Full text Cite

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.

Journal Article Nucleic acids research · January 2024 Maintaining the¬†intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repr ... Full text Cite

A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.

Journal Article PLoS genetics · January 2024 Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeo ... Full text Cite

Salactin, a dynamically unstable actin homolog in Haloarchaea.

Journal Article mBio · November 2023 ImportanceProtein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell p ... Full text Cite

The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria.

Journal Article mBio · April 2023 Histone proteins are found across diverse lineages of Archaea, many of which package DNA and form chromatin. However, previous research has led to the hypothesis that the histone-like proteins of high-salt-adapted archaea, or halophiles, function di ... Full text Cite

Hypochlorite Stress Assay for Phenotypic Analysis of the Halophilic Archaeon Haloferax volcanii Using an Improved Incubation Method and Growth Monitoring

Journal Article Bio-protocol · November 20, 2022 The study of haloarchaea provides an opportunity to expand understanding of the mechanisms used by extremophiles to thrive in and respond to harsh environments, including hypersaline and oxidative stress conditions. A common strategy used to investigate mo ... Full text Cite

TrmB Family Transcription Factor as a Thiol-Based Regulator of Oxidative Stress Response.

Journal Article mBio · August 2022 Oxidative stress causes cellular damage, including DNA mutations, protein dysfunction, and loss of membrane integrity. Here, we discovered that a TrmB (transcription regulator of mal operon) family protein (Pfam PF01978) composed of a single winged- ... Full text Cite

Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.

Journal Article Biomolecules · May 2022 Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The ... Full text Cite

An archaeal histone-like protein regulates gene expression in response to salt stress.

Journal Article Nucleic acids research · December 2021 Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone e ... Full text Cite

A Bayesian non-parametric mixed-effects model of microbial growth curves

Journal Article PLOS Computational Biology · October 26, 2020 Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety ... Full text Cite

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.

Journal Article mBio · August 2020 Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. ... Full text Cite

SnapShot: Microbial Extremophiles.

Journal Article Cell · February 2020 Extremophiles are remarkable examples of life's resilience, thriving in hot springs at boiling temperatures, in brine lakes saturated with salt, and in the driest deserts. We review the biogeography, currently known limits of life, and molecular adaptation ... Full text Cite

Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.

Journal Article Journal of molecular biology · September 2019 The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR ... Full text Cite

Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen.

Journal Article International journal of molecular sciences · September 2019 Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H ... Full text Cite

N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility.

Journal Article Frontiers in microbiology · January 2019 Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimmin ... Full text Cite

Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.

Journal Article Emerging topics in life sciences · December 2018 Gene regulation is intimately connected with metabolism, enabling the appropriate timing and tuning of biochemical pathways to substrate availability. In microorganisms, such as archaea and bacteria, transcription factors (TFs) often directly sense externa ... Full text Cite

GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii.

Journal Article Journal of bacteriology · September 2018 DeoR-type helix-turn-helix (HTH) domain proteins are transcriptional regulators of sugar and nucleoside metabolism in diverse bacteria and also occur in select archaea. In the model archaeon Haloferax volcanii, previous work implicated GlpR, a DeoR- ... Full text Cite

Copy number variation is associated with gene expression change in archaea.

Journal Article Microbial genomics · September 2018 Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness rema ... Full text Cite

Data and scripts from: Copy number variation is associated with gene expression change in archaea

Dataset · May 4, 2018 Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness rema ... Full text Cite

Archaeal cells share common size control with bacteria despite noisier growth and division.

Journal Article Nature microbiology · February 2018 In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent stud ... Full text Cite

Clustering gene expression time series data using an infinite Gaussian process mixture model.

Journal Article PLoS Comput Biol · January 2018 Transcriptome-wide time series expression profiling is used to characterize the cellular response to environmental perturbations. The first step to analyzing transcriptional response data is often to cluster genes with similar responses. Here, we present a ... Full text Link to item Cite

Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth.

Journal Article Frontiers in microbiology · January 2018 Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These acids have long been used as bacteriostatic compounds in the food industry, and ... Full text Cite

Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks.

Journal Article Annual review of genetics · November 2017 Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of tr ... Full text Cite

Systematic discovery of Archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis

Journal Article mSystems · October 31, 2017 To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, sali ... Full text Cite

A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.

Journal Article Nucleic acids research · September 2017 Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subj ... Full text Cite

Detecting differential growth of microbial populations with Gaussian process regression.

Journal Article Genome research · February 2017 Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are desi ... Full text Cite

Systems biology approaches to defining transcription regulatory networks in halophilic archaea.

Journal Article Methods (San Diego, Calif.) · September 2015 To survive complex and changing environmental conditions, microorganisms use gene regulatory networks (GRNs) composed of interacting regulatory transcription factors (TFs) to control the timing and magnitude of gene expression. Genome-wide datasets; such a ... Full text Cite

Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein.

Journal Article mBio · September 2015 UnlabelledIn all three domains of life, organisms use nonspecific DNA-binding proteins to compact and organize the genome as well as to regulate transcription on a global scale. Histone is the primary eukaryotic nucleoprotein, and its evolutionary ... Full text Cite

A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.

Journal Article PLoS genetics · January 2015 Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress. Although the architecture of many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in ... Full text Cite

Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.

Journal Article PLoS One · 2015 Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in th ... Full text Link to item Cite

Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli.

Journal Article PLoS One · 2015 The production of outer membrane vesicles by Gram-negative bacteria has been well documented; however, the mechanism behind the biogenesis of these vesicles remains unclear. Here a high-throughput experimental method and systems-scale analysis was conducte ... Full text Open Access Link to item Cite

How archaeal cells generate their cell shape

Conference MOLECULAR BIOLOGY OF THE CELL · January 1, 2015 Link to item Cite

A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon Halobacterium salinarum.

Journal Article Mol Microbiol · September 2014 Co-ordinating metabolism and growth is a key challenge for all organisms. Despite fluctuating environments, cells must produce the same metabolic outputs to thrive. The mechanisms underlying this 'growth homeostasis' are known in bacteria and eukaryotes, b ... Full text Link to item Cite

Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.

Journal Article Nucleic acids research · October 2013 Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challe ... Full text Cite

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon.

Journal Article BMC genomics · July 2012 BackgroundPrevious work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV, and gamma radiation. Dynamic alteration of the gene regula ... Full text Cite

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.

Journal Article Nucleic acids research · April 2011 Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well unders ... Full text Cite

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.

Journal Article Molecular systems biology · January 2009 During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to ac ... Full text Cite

Prevalence of transcription promoters within archaeal operons and coding sequences.

Journal Article Molecular systems biology · January 2009 Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory l ... Full text Cite

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Journal Article Journal of proteome research · September 2008 The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the pre ... Full text Cite

A predictive model for transcriptional control of physiology in a free living cell.

Journal Article Cell · December 2007 The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through t ... Full text Cite

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

Journal Article BMC bioinformatics · November 2007 BackgroundInformation resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoi ... Full text Cite

The anatomy of microbial cell state transitions in response to oxygen.

Journal Article Genome research · October 2007 Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. However, the chronology of events and the regulatory processes that determine how and when changes in environmental oxygen tension result ... Full text Cite

Prokaryotic Systems Biology

Chapter · December 7, 2006 Prokaryotic systems biology is a holistic biological approach that enables comprehensive understanding of an organism. However, two opposing strategies have been proposed to attain such understanding: the top-down and bottom-up approaches. Here we present ... Link to item Cite

Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1.

Journal Article Microbiology (Reading, England) · September 2006 The potential functions have been investigated of two proteins in Deinococcus radiodurans R1 predicted to be involved in the maintenance and integrity of the S layer: the hexagonally packed intermediate (Hpi) protein, and SlpA (DR2577), a homologue of an S ... Cite

Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans.

Journal Article Journal of bacteriology · May 2005 The sig1 gene, predicted to encode an extracytoplasmic function-type heat shock sigma factor of Deinococcus radiodurans, has been shown to play a central role in the positive regulation of the heat shock operons groESL and dnaKJ. To determine if Sig1 is re ... Full text Cite

Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans.

Journal Article Journal of proteome research · May 2005 The results of previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groESL and dnaKJ operons and proteases such as clpB a ... Full text Cite

HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans.

Journal Article Molecular microbiology · March 2005 The HspR protein functions as a negative regulator of chaperone and protease gene expression in a diversity of bacteria. Here we have identified, cloned and deleted the Deinococcus radiodurans HspR homologue, DR0934. Delta hspR mutants exhibit moderate gro ... Full text Cite

Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans.

Journal Article Journal of bacteriology · November 2002 Two genes bearing similarity to alternative sigma factors were identified in the Deinococcus radiodurans genome sequence and designated sig1 and sig2. These genes were cloned and inactivated, and both were found to be important for survival during heat and ... Full text Cite