Large-scale computational discovery and analysis of virus-derived microbial nanocompartments

An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know?

(2021) Chalita Chomkatekaew et al.   Frontiers in Microbiology

Exploring targeting peptide-shell interactions in encapsulin nanocompartments

(2021) Wiggert J. Altenburg et al.   Scientific Reports

Drug Resistance in Nontuberculous Mycobacteria: Mechanisms and Models

(2021) Saloni Saxena et al.   Biology-Basel

Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery

(2021) Renuga Devi Kanabalan et al.   MICROBIOLOGICAL RESEARCH

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

(2021) Yanting Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism

(2021) Robert J Nichols et al.   eLife

Antimicrobial Resistance in ESKAPE Pathogens

(2020) David M. P. De Oliveira et al.   CLINICAL MICROBIOLOGY REVIEWS

Formation and function of bacterial organelles

(2020) Chris Greening et al.   NATURE REVIEWS MICROBIOLOGY

Advances in encapsulin nanocompartment biology and engineering

(2020) Jesse A. Jones et al.   BIOTECHNOLOGY AND BIOENGINEERING

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea

(2019) Didi He et al.   BIOCHEMICAL JOURNAL

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

(2019) Frédéric Lemoine et al.   NUCLEIC ACIDS RESEARCH

The amazing HK97 fold: versatile results of modest differences

(2019) Robert L Duda et al.   Current Opinion in Virology

Large protein organelles form a new iron sequestration system with high storage capacity

(2019) Tobias W Giessen et al.   eLife

Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding

(2019) Philip A. Ash et al.   ACCOUNTS OF CHEMICAL RESEARCH

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

(2019) Rémi Zallot et al.   BIOCHEMISTRY

In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites

(2019) Chantal D. Bader et al.   BIOTECHNOLOGY ADVANCES

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

(2019) Wei Zheng et al.   Future Generation Computer Systems-The International Journal of eScience

Evolving Strategies to Manage Clostridium difficile Colitis

(2019) Jessica A. Bowman et al.   JOURNAL OF GASTROINTESTINAL SURGERY

DALI and the persistence of protein shape

(2019) Liisa Holm   PROTEIN SCIENCE

The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria

(2019) John C. Tracey et al.   Scientific Reports

The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer

(2018) Elissa D. Pastuzyn et al.   CELL

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacterial microcompartments

(2018) Cheryl A. Kerfeld et al.   NATURE REVIEWS MICROBIOLOGY

Structure, function and evolution of the hemerythrin-like domain superfamily

(2018) Claudia Alvarez-Carreño et al.   PROTEIN SCIENCE

Structure, Total Synthesis and Biosynthesis of Chloromyxamides - Myxobacterial Tetrapeptides Featuring an Uncommon 6-Chloromethyl-5-methoxypipecolic Acid Building Block

(2018) Jan Gorges et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

‘Democratized’ genomic enzymology web tools for functional assignment

(2018) Rémi Zallot et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple origins of viral capsid proteins from cellular ancestors

(2017) Mart Krupovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Widespread distribution of encapsulin nanocompartments reveals functional diversity

(2017) Tobias W. Giessen et al.   Nature Microbiology

Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science

(2016) Tobias W Giessen   CURRENT OPINION IN CHEMICAL BIOLOGY

Bacterial terpene cyclases

(2016) Jeroen S. Dickschat   NATURAL PRODUCT REPORTS

Ohr plays a central role in bacterial responses against fatty acid hydroperoxides and peroxynitrite

(2016) Thiago G. P. Alegria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

(2016) Didi He et al.   eLife

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

(2015) John A. Gerlt et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes

(2015) Toni Gabaldón et al.   BIOCHIMIE

Nature׳s favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold

(2015) Margaret M. Suhanovsky et al.   VIROLOGY

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

(2015) Yuji Sekiguchi et al.   PeerJ

DERA is the human deoxyribose phosphate aldolase and is involved in stress response

(2014) Lisa Salleron et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin

(2014) Yasunori Okamoto et al.   CHEMICAL COMMUNICATIONS

Compartmentalization and organelle formation in bacteria

(2014) Elias Cornejo et al.   CURRENT OPINION IN CELL BIOLOGY

A virus capsid‐like nanocompartment that stores iron and protects bacteria from oxidative stress

(2014) Colleen A McHugh et al.   EMBO JOURNAL

Characterization of aMycobacterium tuberculosisNanocompartment and Its Potential Cargo Proteins

(2014) Heidi Contreras et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

(2014) C. Brasen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Molecular chaperones and proteostasis regulation during redox imbalance

(2014) Katerina Niforou et al.   Redox Biology

Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics

(2013) Christina Ferousi et al.   BMC MICROBIOLOGY

Assemblyin vitroofRhodococcus jostii RHA1 encapsulin and peroxidase DypB to form a nanocompartment

(2013) Rahman Rahmanpour et al.   FEBS Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus

(2013) Takuya Ouchi et al.   Nature Chemical Biology

Evolution of intracellular compartmentalization

(2012) Yoan Diekmann et al.   BIOCHEMICAL JOURNAL

The Structure of the BfrB–Bfd Complex Reveals Protein–Protein Interactions Enabling Iron Release from Bacterioferritin

(2012) Huili Yao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Insight into the Clostridium difficile Ethanolamine Utilisation Microcompartment

(2012) Alison C. Pitts et al.   PLoS One

Bacterial cysteine desulfurases: versatile key players in biosynthetic pathways of sulfur-containing biofactors

(2011) Ryota Hidese et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Identification of DypB fromRhodococcus jostiiRHA1 as a Lignin Peroxidase

(2011) Mark Ahmad et al.   BIOCHEMISTRY

Salmonella enterica Serovar Typhimurium Colonizing the Lumen of the Chicken Intestine Grows Slowly and Upregulates a Unique Set of Virulence and Metabolism Genes

(2011) P. C. Harvey et al.   INFECTION AND IMMUNITY

Engineering Hyperthermophilic ArchaeonPyrococcus furiosusto Overproduce Its Cytoplasmic [NiFe]-Hydrogenase

(2011) Sanjeev K. Chandrayan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Biochemical and genetic characterization of the three metabolic routes in Thermococcus kodakarensis linking glyceraldehyde 3-phosphate and 3-phosphoglycerate

(2011) Kohei Matsubara et al.   MOLECULAR MICROBIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota

(2011) P. Thiennimitr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fossil record of an archaeal HK97-like provirus

(2011) Joshua Heinemann et al.   VIROLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Ethanolamine Utilization Contributes to Proliferation ofSalmonella entericaSerovar Typhimurium in Food and in Nematodes

(2010) Shabarinath Srikumar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

(2010) Marnix H. Medema et al.   BMC GENOMICS

Ohr (Organic Hydroperoxide Resistance Protein) Possesses a Previously Undescribed Activity, Lipoyl-dependent Peroxidase

(2010) José R. R. Cussiol et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Heterologous Expression and Maturation of an NADP-Dependent [NiFe]-Hydrogenase: A Key Enzyme in Biofuel Production

(2010) Junsong Sun et al.   PLoS One

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

(2009) Aditi Kanhere et al.   BMC EVOLUTIONARY BIOLOGY

Medium- and short-chain dehydrogenase/reductase gene and protein families

(2008) K. L. Kavanagh et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Novel Multiprotein Complexes Identified in the Hyperthermophilic ArchaeonPyrococcus furiosusby Non-denaturing Fractionation of the Native Proteome

(2008) Angeli Lal Menon et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural basis of enzyme encapsulation into a bacterial nanocompartment

(2008) Markus Sutter et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY