Selected Publications

Science. Mar 2023

Bacteria require phase separation for fitness in the mammalian gut

Emilia Krypotou 1 2, Guy E Townsend 1 2 3, Xiaohui Gao 1, Shoichi Tachiyama 1 2, Jun Liu 1 2, Nick D Pokorzynski 1, Andrew L Goodman 1 2, Eduardo A Groisman 1 2.

Nat Microbiol. Feb 2023

Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity

Yangqi Gu, Matthew J. Guberman-Pfeffer, Vishok Srikanth, Cong Shen, Fabian Giska, Kallol Gupta, Yuri Londer, Fadel A. Samatey, Victor S. Batista & Nikhil S. Malvankar.

EMBO J. Dec 2022

Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity.

Weiwei Han, Bee-Zen Peng, Chunyan Wang, Guy E Townsend II, Natasha A Barry, Frank Peske, Andrew L Goodman, Jun Liu, Marina V Rodnina, Eduardo A Groisman.

Nat Struct Mol Biol. Nov 2022

Cryo-EM structures of prefusion SIV envelope trimer.

Jason Gorman, Chunyan Wang…Jun Liu, Mario Roederer, Peter D Kwong, et al.

Cell. 2022 Nov

A microbial transporter of the dietary antioxidant ergothioneine.

Daniel G. Dumitrescu, Stavroula K. Hatzios, et al.

Proc Natl Acad Sci U S A . 2022 Oct. See also: Yale News “Some facts about foreign genes”. Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut.
Front. Microbiol. 2022 May. The Bacterial Flagellar Motor: Insights Into Torque Generation, Rotational Switching, and Mechanosensing.
Nat Commun. 2022 Apr. ZNF117 regulates glioblastoma stem cell differentiation towards oligodendroglial lineage.
Nat Chem Biol. 2022 Mar. An infection-induced oxidation site regulates legumain processing and tumor growth.
Proc Natl Acad Sci. 2022 Mar. FliL ring enhances the function of periplasmic flagella.
Nat Commun. 2022 Feb. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis.
Proc Natl Acad Sci. 2022 Feb. Top-down and bottom-up cohesiveness in microbial community coalescence.
Proc Natl Acad Sci. 2022 Jan. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation.
Annu Rev Microbiol. 2021 Oct. Cellular Adaptations to Cytoplasmic Mg 2+ Limitation.
Cell Syst. 2021 Oct. Functional attractors in microbial community assembly.
Nature. 2021 Sept. Structure of Geobacter pili reveals secretory rather than nanoqire behaviour.
Protein Sci. 2021 Aug. The regulation of DNA supercoiling across evolution.
Nat Ecol Evol. 2021 Jul. Engineering complex communities by directed evolution.
J Bacteriol. 2021 May. Low cytoplasmic magnesium increases the specificity of the Lon and ClpAP proteases.
Trends Microbiol. 2021 Apr. Structural basis of bacterial flagellar motor rotation and switching.
Elife. 2021 Apr. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments.
Nat Commun. 2021 Mar. Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentation.
Sci Signal. 2021 Jan. Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state.
Proc Natl Acad Sci USA. 2021 Jan. Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines.
PLoS Pathog. 2020 Dec. Chemical tools for decoding redox signaling at the host-microbe interface.
Biomolecules . 2020 Oct. Structural conservation and adaptation of the bacterial flagellar motor.
PLoS Genet. 2020 Oct. DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines.
Nucleic Acids Res. 2020 Oct. Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence.
Nat Struct Mol Biol. 2020 Sept. Molecular mechanism for rotational switching of the bacterial flagellar motor.
Proc Natl Acad Sci. 2020 Aug. Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter.
Nat Chem Biol. 2020 Aug. See also News and Views: Uncovering nature’s electronics and Live Science: Scientists find ‘secret molecule’ that allows bacteria to exhale electricity. Electric field stimulates production of highly conductive microbial OmcZ nanowires.
Nat Struct Mol Biol. 2020 Jun. Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles.
Proc Natl Acad Sci. 2020 Apr. Salmonella expresses foreign genes during infection by degrading their silencer.
Elife. 2020 Mar. An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete.
PLoS Biol. 2019 Dec. High-order interactions distort the functional landscape of microbial consortia.
Proteopedia 2019 - Curr Opin Biotechnol. 2014 Jun. Malvankar Lab OmcS nanowire structure named one of the highest impact structures of the century.
JBiol Chem. 2019 Jun. Functional characterization of a subtilisin-like serine protease from Vibrio cholerae.
Proc Natl Acad Sci U S A. 2019 Jun. Borrelia burgdorferi peptidoglycan is a persistent antigen in patients with Lyme arthritis.
Nature. 2019 Jun. Mapping human microbiome drug metabolism by gut bacteria and their genes.
Cell. 2019 May. Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria.
Cell. 2019 Apr. See also The New York Times: Wired Bacteria Form Nature’s Power Grid: ‘We Have an Electric Planet’. Structure of microbial nanowires reveals stacked hemes that transport electrons over micrometers.
Nat Microbiol. 2019 Mar. Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography.
PLoS Comput Biol. 2019 Feb. Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.
Curr Top Microbiol Immunol. 2019. Activity-Based Protein Profiling at the Host-Pathogen Interface.
Science. 2019 Feb. Separating host and microbiome contributions to drug pharmacokinetics and toxicity.
Proc Natl Acad Sci U S A. 2018 Dec. Dietary sugar silences a colonization factor in a mammalian gut symbiont.
PLoS Biol. 2018 Nov. Cryo-electron tomography of periplasmic flagella in Borrelia burgdorferi reveals a distinct cytoplasmic ATPase complex.
Science. 2018 Nov. De novo design of self-assembling helical protein filaments.
J Surg Res. 2018 Nov. Mucosal homeostasis is altered in the ileum of gnotobiotic mice.
Mol Microbiol. 2018 Nov. A tetratricopeptide repeat domain protein has profound effects on assembly of periplasmic flagella, morphology and motility of the lyme disease spirochete Borrelia burgdorferi.
Proc Natl Acad Sci U S A. 2018 Oct. On the deformability of an empirical fitness landscape by microbial evolution.
Elife. 2018 Oct. Visualization of the type III secretion mediated Salmonella-host cell interface using cryo-electron tomography.
Appl Environ Microbiol. 2018 Oct. Characterization of fluorescent proteins, promoters, and selectable markers for applications in the Lyme disease spirochete Borrelia burgdorferi.
Curr Top Microbiol Immunol. 2018 Sep. Activity-Based Protein Profiling at the Host-Pathogen Interface.
Elife. 2018 Sep. Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins.
Science. 2018 Aug. Emergent simplicity in microbial community assembly.
EMBO J. 2018 Jul. A protein that controls the onset of a Salmonella virulence program.
Cell Host Microbe. 2018 Jul. The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.
Mol Syst Biol. 2018 Jun. Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli.
Nat Microbiol. 2018 Jun. A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretionchannel.
Proc Natl Acad Sci U S A. 2018 May. Reduction in adaptor amounts establishes degradation hierarchy among protease substrates.
Biophys J. 2018 May. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells.
Nat Microbiol. 2018 May. Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner.
Cell. 2018 Mar. Subcellular Organization: A Critical Feature of Bacterial Cell Replication.
Ferroptosis: A Regulated Cell Death Nexus Linking Metabolism, Redox Biology, and Disease.
Molecular architecture of the sheathed polar flagellum in Vibrio alginolyticus.
Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.
Expressing the Geobacter metallireducens PilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity.
Engineering Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut.
An insider’s perspective: Bacteroides as a window into the microbiome.
Replication fork passage drives asymmetric dynamics of a critical nucleoid-associated protein in Caulobacter.
DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos.
Lyme disease and relapsing fever Borrelia elongate through zones of peptidoglycan synthesis that mark division sites of daughter cells.
Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress.
Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron.
Feedback Control of Two-Component Regulatory Systems
Learning from the Leaders: Gene Regulation by the Transcription Termination Factor Rho.
Acidic pH sensing in the bacterial cytoplasm is required for Salmonella virulence.
Human symbionts inject and neutralize antibacterial toxins to persist in the gut.
Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.

Selected Publications

Proc Natl Acad Sci U S A . 2022 Oct. See also: Yale News “Some facts about foreign genes”. Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut.

Front. Microbiol. 2022 May. The Bacterial Flagellar Motor: Insights Into Torque Generation, Rotational Switching, and Mechanosensing.

Nat Commun. 2022 Apr. ZNF117 regulates glioblastoma stem cell differentiation towards oligodendroglial lineage.

Nat Chem Biol. 2022 Mar. An infection-induced oxidation site regulates legumain processing and tumor growth.

Proc Natl Acad Sci. 2022 Mar. FliL ring enhances the function of periplasmic flagella.

Nat Commun. 2022 Feb. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis.

Proc Natl Acad Sci. 2022 Feb. Top-down and bottom-up cohesiveness in microbial community coalescence.

Proc Natl Acad Sci. 2022 Jan. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation.

Annu Rev Microbiol. 2021 Oct. Cellular Adaptations to Cytoplasmic Mg 2+ Limitation.

Cell Syst. 2021 Oct. Functional attractors in microbial community assembly.

Nature. 2021 Sept. Structure of Geobacter pili reveals secretory rather than nanoqire behaviour.

Protein Sci. 2021 Aug. The regulation of DNA supercoiling across evolution.

Nat Ecol Evol. 2021 Jul. Engineering complex communities by directed evolution.

J Bacteriol. 2021 May. Low cytoplasmic magnesium increases the specificity of the Lon and ClpAP proteases.

Trends Microbiol. 2021 Apr. Structural basis of bacterial flagellar motor rotation and switching.

Elife. 2021 Apr. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments.

Nat Commun. 2021 Mar. Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentation.

Sci Signal. 2021 Jan. Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state.

Proc Natl Acad Sci USA. 2021 Jan. Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines.

PLoS Pathog. 2020 Dec. Chemical tools for decoding redox signaling at the host-microbe interface.

Biomolecules. 2020 Oct. Structural conservation and adaptation of the bacterial flagellar motor.

PLoS Genet. 2020 Oct. DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines.

Nucleic Acids Res. 2020 Oct. Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence.

Nat Struct Mol Biol. 2020 Sept. Molecular mechanism for rotational switching of the bacterial flagellar motor.

Proc Natl Acad Sci. 2020 Aug. Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter.

Nat Chem Biol. 2020 Aug. See also News and Views: Uncovering nature’s electronics and Live Science: Scientists find ‘secret molecule’ that allows bacteria to exhale electricity. Electric field stimulates production of highly conductive microbial OmcZ nanowires.

Nat Struct Mol Biol. 2020 Jun. Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles.

Proc Natl Acad Sci. 2020 Apr. Salmonella expresses foreign genes during infection by degrading their silencer.

Elife. 2020 Mar. An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete.

PLoS Biol. 2019 Dec. High-order interactions distort the functional landscape of microbial consortia.

Proteopedia 2019 - Curr Opin Biotechnol. 2014 Jun. Malvankar Lab OmcS nanowire structure named one of the highest impact structures of the century.

JBiol Chem. 2019 Jun. Functional characterization of a subtilisin-like serine protease from Vibrio cholerae.

Proc Natl Acad Sci U S A. 2019 Jun. Borrelia burgdorferi peptidoglycan is a persistent antigen in patients with Lyme arthritis.

Nature. 2019 Jun. Mapping human microbiome drug metabolism by gut bacteria and their genes.

Cell. 2019 May. Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria.

Cell. 2019 Apr. See also The New York Times: Wired Bacteria Form Nature’s Power Grid: ‘We Have an Electric Planet’. Structure of microbial nanowires reveals stacked hemes that transport electrons over micrometers.

Nat Microbiol. 2019 Mar. Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography.

PLoS Comput Biol. 2019 Feb. Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.

Curr Top Microbiol Immunol. 2019. Activity-Based Protein Profiling at the Host-Pathogen Interface.

Science. 2019 Feb. Separating host and microbiome contributions to drug pharmacokinetics and toxicity.

Proc Natl Acad Sci U S A. 2018 Dec. Dietary sugar silences a colonization factor in a mammalian gut symbiont.

PLoS Biol. 2018 Nov. Cryo-electron tomography of periplasmic flagella in Borrelia burgdorferi reveals a distinct cytoplasmic ATPase complex.

Science. 2018 Nov. De novo design of self-assembling helical protein filaments.

J Surg Res. 2018 Nov. Mucosal homeostasis is altered in the ileum of gnotobiotic mice.

Mol Microbiol. 2018 Nov. A tetratricopeptide repeat domain protein has profound effects on assembly of periplasmic flagella, morphology and motility of the lyme disease spirochete Borrelia burgdorferi.

Proc Natl Acad Sci U S A. 2018 Oct. On the deformability of an empirical fitness landscape by microbial evolution.

Elife. 2018 Oct. Visualization of the type III secretion mediated Salmonella-host cell interface using cryo-electron tomography.

Appl Environ Microbiol. 2018 Oct. Characterization of fluorescent proteins, promoters, and selectable markers for applications in the Lyme disease spirochete Borrelia burgdorferi.

Curr Top Microbiol Immunol. 2018 Sep. Activity-Based Protein Profiling at the Host-Pathogen Interface.

Elife. 2018 Sep. Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins.

Science. 2018 Aug. Emergent simplicity in microbial community assembly.

EMBO J. 2018 Jul. A protein that controls the onset of a Salmonella virulence program.

Cell Host Microbe. 2018 Jul. The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.

Mol Syst Biol. 2018 Jun. Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli.

Nat Microbiol. 2018 Jun. A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretionchannel.

Proc Natl Acad Sci U S A. 2018 May. Reduction in adaptor amounts establishes degradation hierarchy among protease substrates.

Biophys J. 2018 May. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells.

Nat Microbiol. 2018 May. Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner.

Cell. 2018 Mar. Subcellular Organization: A Critical Feature of Bacterial Cell Replication.

Replication fork passage drives asymmetric dynamics of a critical nucleoid-associated protein in Caulobacter.

DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos.

Lyme disease and relapsing fever Borrelia elongate through zones of peptidoglycan synthesis that mark division sites of daughter cells.

Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress.

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron.

Learning from the Leaders: Gene Regulation by the Transcription Termination Factor Rho.

Acidic pH sensing in the bacterial cytoplasm is required for Salmonella virulence.

Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.

Biomolecules . 2020 Oct. Structural conservation and adaptation of the bacterial flagellar motor.