Publications
2024
Journal Article
Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems. Molecular Plant (2024)
Journal Article
The canalization in domesticated yeast: Metabolic traits develop robustness against Hsp90 stress during the evolutionary process. Green Carbon (2024)
Preprint
Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis in Myxococcus xanthus. bioRxiv: the preprint server for biology, 2024.11.26.625375 (2024)
Journal Article
15, 10235 (2024)
New-to-nature CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase. Nature Communications
Journal Article
Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes. The EMBO Journal, pp. 1 - 12 (2024)
Journal Article
15 (1), 9868 (2024)
The emergence of Sox and POU transcription factors predates the origins of animal stem cells. Nature Communications
Journal Article
9 (1), ysae016 (2024)
In- & Out-Cloning: plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. Synthetic Biology
Journal Article
15 (1), 9655 (2024)
Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast. Nature Communications
Journal Article
383 (6689), eadg4320 (2024)
Evolution-inspired engineering of nonribosomal peptide synthetases. Science
Journal Article
58 (24), pp. 211 - 215 (2024)
Metabolic state of bacterial cells: Deciphered through a simple mathematical model. IFAC-PapersOnLine
Journal Article
15 (1), 9306 (2024)
Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference. Nature Communications
Journal Article
15 (1), 9340 (2024)
Structure of the turnover-ready state of an ancestral respiratory complex I. Nature Communications
Journal Article
Evolution-assisted engineering of E. coli enables growth on formic acid at ambient CO2 via the Serine Threonine Cycle. Metabolic Engineering (2024)
Journal Article
Pyrrolizwilline, a unique bacterial alkaloid assembled by a nonribosomal peptide synthetase and non-enzymatic dimerization. Angewandte Chemie International Edition, e202411258 (2024)
Journal Article
Methylthio-alkane reductases use nitrogenase metalloclusters for carbon-sulfur bond cleavage. bioRxiv: the preprint server for biology, 2024.10.19.619033 (2024)
Preprint
Collective dynamics of Escherichia coli growth under near-lethal acid stress. bioRxiv: the preprint server for biology, 2024.10.17.618973 (2024)
Journal Article
22 (1), 500 (2024)
Cytosolic delivery of monobodies using the bacterial type III secretion system inhibits oncogenic BCR: ABL1 signaling. Cell Communication and Signaling
Journal Article
15 (1), 8898 (2024)
Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies. Nature Communications
Journal Article
12 (1), 201 (2024)
Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut. Microbiome
Journal Article
206 (11), e00108-24 (2024)
Combinatorial control of type IVa pili formation by the four polarized regulators MglA, SgmX, FrzS, and SopA. Journal of Bacteriology
Journal Article
96, 126121 (2024)
The mitochondrial citrate synthase from Tetrahymena thermophila does not form an intermediate filament. European Journal of Protistology
Journal Article
121 (43), e2308684121 (2024)
Unraveling abiotic organic synthesis pathways in the mafic crust of mid-ocean ridges. Proceedings of the National Academy of Sciences of the United States of America
Journal Article
52 (20), pp. 12592 - 12603 (2024)
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication. Nucleic Acids Research
Journal Article
58 (42), pp. 18777 - 18787 (2024)
Fulvic acid enhances nitrogen fixation and retention in paddy soils through microbial-coupled carbon and nitrogen cycling. Environmental Science & Technology
Review Article
9 (2024)
Synthetic biology education and pedagogy: a review of evolving practices in a growing discipline. Frontiers in Education
Journal Article
A cell-free system for functional studies of small membrane proteins. Journal of Biological Chemistry, 107850 (2024)
Review Article
7 (2024)
Mitochondria, peroxisomes and beyond—How dual targeting regulates organelle tethering. Contact
Journal Article
75 (18), pp. 5734 - 5749 (2024)
The role of chloroplast SRP54 domains and its C-terminal tail region in post- and co-translational protein transport in vivo. Journal of Experimental Botany
Preprint
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions. bioRxiv: the preprint server for biology, 2024.09.24.614802 (2024)
Preprint
Active segregation in binary mixtures under flow. bioRxiv: the preprint server for biology, 2024.09.20.614032 (2024)
Journal Article
in vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade. Synthetic Biology, ysae013 (2024)
Journal Article
A general substitution matrix for structural phylogenetics. bioRxiv: the preprint server for biology, 2024.09.19.613819 (2024)
Journal Article
9 (523) (2024)
Daily life in the Open Biologist's second job, as a Data Curator. Wellcome Open Research
Journal Article
20 (9), e1011384 (2024)
Temporal epigenome modulation enables efficient bacteriophage engineering and functional analysis of phage DNA modifications. PLOS Genetics
Journal Article
15 (1), 7616 (2024)
An outer membrane porin-lipoprotein complex modulates elongasome movement to establish cell curvature in Rhodospirillum rubrum. Nature Communications
Journal Article
6 (5), e70022 (2024)
V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada. Environmental DNA
Journal Article
97 (4), pp. 2203 - 2215 (2024)
Effects of Xenorhabdus and Photorhabdus bacterial metabolites on the ovipositional activity of Aedes albopictus. Journal of Pest Science
Preprint
Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC. bioRxiv: the preprint server for biology, 2024.08.28.610035 (2024)
Journal Article
Isofunctional but structurally different methyltransferases for dithiolopyrrolone diversification. Angewandte Chemie International Edition, e202410799 (2024)
Review Article
1871 (8), 119826 (2024)
Bridging the gap: RNAylation conjugates RNAs to proteins. Biochimica et Biophysica Acta: BBA
Preprint
Expanding the biotechnological scope of metabolic sensors through computation-aided designs. bioRxiv: the preprint server for biology, 2024.08.23.609350 (2024)
Journal Article
15 (1), 7238 (2024)
Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community. Nature Communications
Preprint
A toolbox of FRET-based c-di-GMP biosensors and its FRET-To-Sort application for genome-wide mapping of the second messenger regulatory network. bioRxiv: the preprint server for biology, 2024.08.21.609041 (2024)
Journal Article
27 (9), 110774 (2024)
A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience
Journal Article
20 (8), e1012462 (2024)
MprF-mediated immune evasion is necessary for Lactiplantibacillus plantarum resilience in the Drosophila gut during inflammation. PLOS Pathogens
Journal Article
Bioengineering of syrbactin megasynthetases for immunoproteasome inhibitor production. Chem (2024)
Journal Article
10 (33), eado7729 (2024)
The iron nitrogenase reduces carbon dioxide to formate and methane under physiological conditions: A route to feedstock chemicals. Science Advances
Journal Article
15, 6829 (2024)
DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3'-end of genes and involved in the recycling of cleavage factors. Nature Communications
Journal Article
100 (9), fiae112 (2024)
Exploring modes of microbial interactions with implications for methane cycling. FEMS Microbiology Ecology
Journal Article
15 (1), 6725 (2024)
Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nature Communications
Journal Article
100 (9), fiae111 (2024)
Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus). FEMS Microbiology Ecology
Journal Article
12 (9), e00592-24 (2024)
Isolation and characterization of Septuagintavirus; a novel clade of Escherichia coli phages within the subfamily Vequintavirinae. Microbiology Spectrum
Preprint
Cytosolic delivery of monobodies using the bacterial type III secretion system inhibits oncogenic BCR::ABL1 signaling. Research Square, https://doi.org/10.21203/rs.3.rs-4705983/v1 (2024)
Journal Article
3 (8), pgae317 (2024)
The dynamics of the midgut microbiome in aedes aegypti during digestion reveal putative symbionts. PNAS Nexus
Journal Article
80, 102515 (2024)
Editorial overview: Rise of the bacterial nanomachines. Current Opinion in Microbiology
Journal Article
80, 102517 (2024)
Editorial overview: Systems and synthetic biology of microbial cells and communities. Current Opinion in Microbiology
Journal Article
34 (17), S0960-9822(24)00921-7, pp. 3855 - 3865.e7 (2024)
Characterization of the SUF FeS cluster synthesis machinery in the amitochondriate eukaryote Monocercomonoides exilis. Current Biology
Journal Article
17 (7), e14527 (2024)
Design, construction and optimization of formaldehyde growth biosensors with broad application in biotechnology. Microbial Biotechnology
Journal Article
7 (1) (2024)
Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Communications Chemistry
Journal Article
13 (8), pp. 2412 - 2424 (2024)
Chloroplast Cell-Free Systems from Different Plant Species as a Rapid Prototyping Platform. ACS Synthetic Biology
Journal Article
15 (1), 6014 (2024)
A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis. Nature Communications
Journal Article
385 (6705), pp. 174 - 178 (2024)
Integrated translation and metabolism in a partially self-synthesizing biochemical network. Science
Preprint
Membrane binding properties of the cytoskeletal protein bactofilin. bioRxiv: the preprint server for biology, 2024.06.14.599034 (2024)
Journal Article
The role of chloroplast SRP54 domains and its C-terminal tail region in post- and cotranslational protein transport in vivo. Journal of Experimental Botany, erae293 (2024)
Journal Article
15 (1), 5797 (2024)
Polar confinement of a macromolecular machine by an SRP-type GTPase. Nature Communications
Journal Article
108, 410 (2024)
A pH-dependent shift of redox cofactor specificity in a benzyl alcohol dehydrogenase of aromatoleum aromaticum EbN1. Applied Microbiology and Biotechnology
Journal Article
25, pp. 3182 - 3186 (2024)
A (metaphorical) moment for RNA-based biotechnology?: Current metaphors for RNA limit development of and public communication about RNA-based technologies. EMBO Reports
Preprint
Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. bioRxiv: the preprint server for biology, 2024.07.05.602260 (2024)
Journal Article
15 (8), e0152424 (2024)
Multiple levels of transcriptional regulation control glycolate metabolism in Paracoccus denitrificans. mBio
Preprint
Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins. bioRxiv: the preprint server for biology, 2024.06.28.601168 (2024)
Preprint
Promiscuous NAD-dependent dehydrogenases enable efficient bacterial growth on the PET monomer ethylene glycol. bioRxiv: the preprint server for biology, 2024.06.28.601223 (2024)
Preprint
Yersinia actively downregulates type III secretion and adhesion at higher cell densities. bioRxiv, 2024.06.27.601021 (2024)
Preprint
A compact model of Escherichia coli core and biosynthetic metabolism. arXiv, arXiv:2406.16596 (2024)
Preprint
In- & Out-Cloning: Plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. bioRxiv: the preprint server for biology, 2024.06.22.600171 (2024)
Journal Article
135 (7), lxae149 (2024)
Enhanced production of trans-cinnamic acid in Photorhabdus luminescens with homolog expression and deletion strategies. Journal of Applied Microbiology
Journal Article
18 (1), wrae096 (2024)
Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water. The ISME Journal
Preprint
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication. bioRxiv: the preprint server for biology, 2024.06.12.598411 (2024)
Journal Article
33 (6), e5018 (2024)
Mutational and structural studies of (βα)8-barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism. Protein Science
Journal Article
Subtleties in clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast. bioRxiv, 2024.05.30.596561 (2024)
Journal Article
7 (5), pp. 472 - 474 (2024)
Bioproduction from methanol. Nature Catalysis
Journal Article
63 (33), e202406389 (2024)
Investigation of the Odilorhabdin biosynthetic gene cluster using NRPS engineering. Angewandte Chemie International Edition
Journal Article
25, pp. 2162 - 2167 (2024)
Cell consciousness: a dissenting opinion: The cellular basis of consciousness theory lacks empirical evidence for its claims that all cells have consciousness. EMBO Reports
Journal Article
13 (5), e12447 (2024)
Lipid A in outer membrane vesicles shields bacteria from polymyxins. Journal of extracellular vesicles
Journal Article
15 (6), e01039-24 (2024)
Framework for exploring the sensory repertoire of the human gut microbiota. mBio
Preprint
Structure of the turnover-ready state of an ancestral respiratory complex I. bioRxiv: the preprint server for biology, 2024.05.14.594153 (2024)
Journal Article
15 (6), e00826-24 (2024)
Genome reduction and horizontal gene transfer in the evolution of Endomicrobia—rise and fall of an intracellular symbiosis with termite gut flagellates. mBio
Journal Article
9, e00095-24 (2024)
Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities. mSystems
Preprint
Advancing chloroplast synthetic biology through high-throughput plastome engineering of Chlamydomonas reinhardtii. bioRxiv: the preprint server for biology, 2024.05.08.593163 (2024)
Journal Article
205, 108126 (2024)
A taste of a toxin paradise: Xenorhabdus and Photorhabdus bacterial secondary metabolites against Aedes aegypti larvae and eggs. Journal of Invertebrate Pathology
Journal Article
13 (5), pp. 1537 - 1548 (2024)
Modular low-copy-number plasmid vectors for Rhodobacterales with extended host range in Alphaproteobacteria. ACS Synthetic Biology
Journal Article
7 (1), 519 (2024)
Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Communications Biology
Preprint
The interplay between light, arsenic and H2O2 controls oxygenic photosynthesis in a Precambrian analog cyanobacterial mat. bioRxiv: the preprint server for biology, 2024.04.27.591451 (2024)
Preprint
In vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade. bioRxiv: the preprint server for biology, 2024.04.26.591264 (2024)
Preprint
A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. bioRxiv: the preprint server for biology, 2024.04.24.590872 (2024)
Preprint
The role of chloroplast SRP54 domains and its C-terminal tail region in post- and cotranslational protein transport in vivo. bioRxiv: the preprint server for biology, 2024.04.21.590438 (2024)
Preprint
The SPFH complex HflK-HflC regulates aerobic respiration in bacteria. bioRxiv: the preprint server for biology, 2024.04.21.590321 (2024)
Preprint
Atomic insights into the signaling landscape of E. coli PhoQ Histidine Kinase from Molecular Dynamics simulations. bioRxiv: the preprint server for biology, 2024.04.19.590235 (2024)
Preprint
A cell-free system for functional studies of small membrane proteins. bioRxiv: the preprint server for biology, 2023.12.22.573026 (2024)
Journal Article
121 (17), e2321989121 (2024)
Tight-packing of large pilin subunits provides distinct structural and mechanical properties for the Myxococcus xanthus type IVa pilus. Proceedings of the National Academy of Sciences of the United States of America