BØPosphere – May 2023 – Biowall Project

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Proceedings of the National Academy of Sciences of the United States of America

Metabolic homeostasis and growth in abiotic cells.

2023-05-01

PubMed:37126695; DOI:10.1073/pnas.2300687120

Amir Akbari¹, Bernhard O Palsson¹

Affiliations

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093

In life’s grand chemical array,
Metabolism’s dance holds sway,
From Earth’s dawn, a tale unknown,
Origins enshrouded, seeds were sown,
In the tapestry of beginnings, night and day.

CO2-fixing paths, geochemistry’s art,
Inorganic catalysts played their part,
Enzymes and genes yet to unfold,
Prebiotic echoes, secrets untold,
Carbon’s journey, a symphony to start.

Acetyl-CoA and tricarboxylic’s embrace,
Ancient pathways, time can’t erase,
Transition metals, guides of old,
Metabolic ballet, stories unfold,
A network’s whispers, time’s hidden face.

First principles guide, constraints align,
A carbon-fixing cycle, ambitions refine,
Steady states emerge, delicate and bright,
Homeostasis in the prebiotic night,
Essence of life, volume’s growth intertwine.

Expansion of volume, a key refrain,
In abiotic cells, where life took its first gain,
Metabolic rhythms, a dance so profound,
Life’s symphony echoes, in beginnings’ bound,
A story of growth, where life’s journey began.

Nature

Complete integration of carbene-transfer chemistry into biosynthesis.

2023-05-03

PubMed:37138074; DOI:10.1038/s41586-023-06027-2

Jing Huang¹, Andrew Quest², Pablo Cruz-Morales¹, Kai Deng³, Jose Henrique Pereira³, Devon Van Cura⁴, Ramu Kakumanu¹, Edward E K Baidoo¹, Qingyun Dan¹, Yan Chen¹, Christopher J Petzold¹, Trent R Northen³, Paul D Adams³, Douglas S Clark⁵, Emily P Balskus⁴, John F Hartwig⁶, Aindrila Mukhopadhyay⁷, Jay D Keasling⁸

Affiliations

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Department of Chemistry, University of California, Berkeley, CA, USA
Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, CA, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Making microbes do reactions that never existed in Nature! Wonderful and truly inspiring work @Nature .
Congratulations to @jaykeasling @Keasling_Lab @BalskusLab and all the authors.

2023-05-11

In biosynthesis’ gentle embrace,
Nature’s secrets we earnestly chase,
With carbene reactions, new art to be,
Yet cells lacked this chemistry spree,
Microbes now dance, a novel space.

Diazo ester, a precursor held tight,
Within Streptomyces metabolism, it took its flight,
Azaserine’s gift, a carbene in hand,
Intracellular symphony, a microbial band,
Creating compounds, a dazzling light.

Carbene-transfer reactions, once in need,
Now through cells’ dance, they succeed,
P450 mutants, a skilled guiding hand,
Diastereoselectivity grand,
A realm of products, where microbes lead.

bioRxiv

StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

2023-05-26

DOI:10.1101/2023.05.26.542519

J. Zhao, K. Chen, B. O. Palsson, L. Yang

Affiliations

Queen\\\’s University

Generalist microbes, skilled and bold,
In varied stress, their secrets hold,
Integrated systems, ingeniously employ,
Challenges they conquer, with tactics they deploy,
StressME’s tale, a saga to be told.

Thermal, oxidative, acid’s embrace,
In StressME’s realm, they interlace,
FoldME, OxidizeME, AcidifyME combine,
A symphony of responses, in genes they enshrine,
A unified dance, orchestrated with grace.

E. coli’s song, updated and refined,
StressME’s canvas, their stories defined,
Single-stress models find their place,
With tuned constants, predictions embrace,
Wild-type and stress-evolved, intricately intertwined.

Optimal strategies, proteomes align,
Cross-stress responses, a puzzle to design,
Trade-offs illuminate, in proteome’s array,
Metabolic versus protective, a balance they sway,
Stress-optimal proteomes, a dance so fine.

Chaperones, enzymes, a symphony grand,
Cytoplasmic whispers, periplasmic stand,
Stress-specific proteins, their tales unfold,
StressME’s insights, a treasure to behold,
E. coli’s world, in StressME’s hand.

bioRxiv

Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

2023-05-16

DOI:10.1101/2023.05.16.541042

A. Rajput, S. M. Chauhan, O. S. Mohite, J. C. Hyun, O. Ardalani, L. J. Jahn, M. O. Sommer, B. O. Palsson

Affiliations

Department of Bioengineering, University of California, San Diego, La Jolla, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of

In the realm of genomes, vast and grand,
Lactobacillaceae, a noble band,
Pangenomic analysis, a monumental quest,
Over three thousand genomes put to the test,
Pangenome’s secrets, we understand.

Transposons and mobilomes, players profound,
Shape the pangenome, patterns unwound,
Core, accessory, and rare genes align,
Phylogroups emerge, a complex design,
Genomic diversity, in knowledge we’re bound.

Biosynthetic gene clusters, diverse and profound,
Antimicrobials, probiotics unbound,
A world of functions, complex design,
Yet mysteries linger, awaiting the sign,
Lactobacillaceae’s secrets, to science, unwound.

FBA-classic

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Nucleic acids research

Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis.

2023-05-24

PubMed:37224536; DOI:10.1093/nar/gkad435

Heejo Choi¹, Markus W Covert¹

Affiliations

Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA

Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis
https://doi.org/10.1093/nar/gkad435…

2023-07-07

In E. coli’s realm, a mystery lies,
Aminoacylation’s intricate ties,
Whole-cell modeling, a method to trace,
The dance of proteins, in their rightful space,
Secrets of life, in genes’ intricate scheme.

From histidine’s realm, a challenge did brew,
Insufficient kcat, a puzzle to construe,
Protein synthesis, a delicate art,
In single cells’ world, they play their part,
Aminoacyl-tRNA synthetase’s role, in full view.

And then, arginine takes its cue,
N-acetylglutamate synthase’s plea,
Translation disrupted, biosynthesis askew,
E. coli’s secrets, a mystery to see,
Intricacies of cells, ever anew.

resources

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EcoSal Plus

The EcoCyc Database (2023).

2023-05-11

PubMed:37220074; DOI:None

Peter D Karp¹, Suzanne Paley¹, Ron Caspi¹, Anamika Kothari¹, Markus Krummenacker¹, Peter E Midford¹, Lisa R Moore¹, Pallavi Subhraveti¹, Socorro Gama-Castro², Victor H Tierrafria², Paloma Lara², Luis Muñiz-Rascado², César Bonavides-Martinez², Alberto Santos-Zavaleta², Amanda Mackie³, Gwanggyu Sun⁴, Travis A Ahn-Horst⁴, Heejo Choi⁴, Markus W Covert⁴, Julio Collado-Vides², Ian Paulsen⁵

Affiliations

Bioinformatics Research Group, SRI International, Menlo Park, California, USA
Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
Department of Bioengineering, Stanford University, Stanford, California, USA
School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia

NPJ systems biology and applications

An automated workflow for multi-omics screening of microbial model organisms.

2023-05-19

PubMed:37208327; DOI:10.1038/s41540-023-00277-6

Stefano Donati¹, Matthias Mattanovich¹, Pernille Hjort¹, Simo Abdessamad Baallal Jacobsen¹, Sarah Dina Blomquist¹, Drude Mangaard¹, Nicolas Gurdo¹, Felix Pacheco Pastor¹, Jérôme Maury¹, Rene Hanke¹, Markus J Herrgård², Tune Wulff¹, Tadas Jakočiūnas¹, Lars Keld Nielsen³, Douglas McCloskey⁴

Affiliations

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
BioInnovation Institute, Ole Maaløes Vej 3, 2200, København, Denmark
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.

Interested in automating workflows for the generation of big multi-omics datasets of microbes? In this manuscript we share our experience at @DTUBiosustain discussing possibilities and limitations

2023-05-19

bioRxiv

Foldy: a web application for interactive protein structure analysis

2023-05-14

DOI:10.1101/2023.05.11.540333

J. B. Roberts, A. A. Nava, A. N. Pearson, M. R. Incha, L. E. Valencia, M. Ma, A. Rao, J. D. Keasling

Affiliations

UC Berkeley: University of California Berkeley

New preprint! Foldy is an open-source web app for interactive structure analysis. Research groups can set up their own Foldy instance so any member can easily predict structures with AlphaFold, dock ligands with DiffDock or Vina, and more!

Preprint:

2023-05-16

physiology

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Nucleic acids research

The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.

2023-04-07

PubMed:37026477; DOI:10.1093/nar/gkad253

Ye Gao¹, Ina Bang², Yara Seif³, Donghyuk Kim², Bernhard O Palsson³

Affiliations

Department of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA

Ever wondered about how different regulons are between strains of a species? The tantalizing answer for FUR is now available. https://bit.ly/3oepXkd @DTUBiosustain @UCSDJacobs

2023-04-17

Scientific reports

E. coli allantoinase is activated by the downstream metabolic enzyme, glycerate kinase, and stabilizes the putative allantoin transporter by direct binding.

2023-05-05

PubMed:37147430; DOI:10.1038/s41598-023-31812-4

Irina A Rodionova¹, Ali Hosseinnia², Sunyoung Kim², Norman Goodacre³, Li Zhang⁴, Zhongge Zhang⁴, Bernhard Palsson⁵, Peter Uetz³, Mohan Babu², Milton H Saier⁶

Affiliations

Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.
Department of Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA, 92093-0116, USA
Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093, USA.

bioRxiv

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

2023-05-16

DOI:10.1101/2023.05.16.541025

I. A. Rodionova, H. Lim, D. A. Rodionov, Y. Hutchison, C. Dalldorf, Y. Gao, J. Monk, B. O. Palsson

Affiliations

University of California, San Diego

metabolic-engineering

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Metabolic engineering communications

Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller’s dried grains with solubles (DDGS).

2023-05-01

PubMed:37234932; DOI:10.1016/j.mec.2023.e00223

Jasper L S P Driessen¹, Josefin Johnsen¹, Ivan Pogrebnyakov¹, Elsayed T T Mohamed¹, Solange I Mussatto², Adam M Feist¹, Sheila I Jensen¹, Alex T Nielsen¹

Affiliations

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800, Kongens Lyngby, Denmark

non-microbe-hosts

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Biotechnology and bioengineering

Reconstructing the cell-cell interaction network among mouse immune cells.

2023-05-25

PubMed:37227044; DOI:10.1002/bit.28431

Somayeh Azadian¹, Alireza Doustmohammadi², Mohadeseh Naseri³, Masoud Khodarahmi⁴, Seyed Shahriar Arab⁵, Mahboubeh Yazdanifar⁶, Javad Zahiri⁷, Nathan E Lewis⁸

Affiliations

Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
Bahar Medical Centre, Karaj, Iran
Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
Department of Pediatrics, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California, USA
Department of Neuroscience, University of California San Diego, San Diego, California, USA
Department of Pediatrics, La Jolla, California, USA

bioRxiv

Inferring secretory and metabolic pathway activity from omic data with secCellFie

2023-05-07

DOI:10.1101/2023.05.04.539316

H. O. Masson, M. Samoudi, C. M. Robinson, C.-C. Kuo, L. Weiss, K. Shams Ud Doha, A. Campos, V. Tejwani, H. Dahodwala, P. Menard, B. G. Voldborg, S. Sharfstein, N. Lewis

Affiliations

UCSD

human-health

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PLoS biology

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta.

2023-05-19

PubMed:37205710; DOI:10.1371/journal.pbio.3002125

Cecilia Noecker¹, Juan Sanchez², Jordan E Bisanz¹, Veronica Escalante¹, Margaret Alexander¹, Kai Trepka¹, Almut Heinken³, Yuanyuan Liu⁴, Dylan Dodd⁴, Ines Thiele³, Brian C DeFelice², Peter J Turnbaugh¹

Affiliations

Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
Chan Zuckerberg Biohub-San Francisco, San Francisco, California, United States of America
School of Medicine, National University of Ireland, Galway, Ireland
Department of Pathology, Stanford University, Stanford, California, United States of America

Interested in microbial interactions in the gut?

This resource paper provides an in-depth view of the
metabolic niche of gut microbiome keystone species E. lenta
@PTurnbaugh

2023-05-23

core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction

The New England journal of medicine

Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome.

2023-05-31

PubMed:37256972; DOI:10.1056/NEJMoa2202318

Hratch Baghdassarian¹, Sarah A Blackstone¹, Owen S Clay¹, Rachael Philips¹, Brynja Matthiasardottir¹, Michele Nehrebecky¹, Vivian K Hua¹, Rachael McVicar¹, Yang Liu¹, Suzanne M Tucker¹, Davide Randazzo¹, Natalie Deuitch¹, Sofia Rosenzweig¹, Adam Mark¹, Roman Sasik¹, Kathleen M Fisch¹, Pallavi Pimpale Chavan¹, Elif Eren¹, Norman R Watts¹, Chi A Ma¹, Massimo Gadina¹, Daniella M Schwartz¹, Anwesha Sanyal¹, Giffin Werner¹, David R Murdock¹, Nobuyuki Horita¹, Shimul Chowdhury¹, David Dimmock¹, Kristen Jepsen¹, Elaine F Remmers¹, Raphaela Goldbach-Mansky¹, William A Gahl¹, John J O’Shea¹, Joshua D Milner¹, Nathan E Lewis¹, Johanna Chang¹, Daniel L Kastner¹, Kathryn Torok¹, Hirotsugu Oda¹, Christopher D Putnam¹, Lori Broderick¹

Affiliations

From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children’s Institute for Genomic Medicine (S.C., D.D.), and Rady Children’s Hospital Foundation (J.C., L.B.), Rady Children’s Hospital, San Diego – all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) – all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) – all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)

Original Article: Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome https://nej.md/3N4ctBD

Photographs show waxy, erythematous nodular lesions on bilateral hands and feet before (Panel B) and after (Panel C) initiation of ruxolitinib therapy.

2023-06-20

Angewandte Chemie (International ed. in English)

Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production.

2023-05-07

PubMed:37151182; DOI:10.1002/anie.202304646

Devon Van Cura¹, Tai L Ng¹, Jing Huang², Harry Hager¹, John F Hartwig³, Jay D Keasling², Emily P Balskus⁴

Affiliations

Harvard University, Chemistry and Chemical Biology, UNITED STATES
Lawrence Berkeley Laboratory: E O Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, UNITED STATES
University of California Berkeley, Chemistry, UNITED STATES
Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford St., Mallinckrodt 303N, 2138, Cambridge, UNITED STATES

AMR

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bioRxiv

Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species

2023-05-28

DOI:10.1101/2023.05.26.542542

J. C. Hyun, J. M. Monk, R. Szubin, Y. Hefner, B. Palsson

Affiliations

University of California, San Diego

bioRxiv

Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection

2023-05-10

DOI:10.1101/2023.05.10.540184

H. Bajpe, K. Rychel, C. Lamoureux, A. V. Sastry, B. O. Palsson

Affiliations

UCSD

BØPosphere – May 2023

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