Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

­, Hindra; Elliot, Marie A.

doi:10.1128/msystems.01368-23

Title: Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

Journal Article · Mon Mar 11 00:00:00 UTC 2024 · mSystems

DOI: https://doi.org/10.1128/msystems.01368-23 · OSTI ID:2469707

^[1];

^[1]

McMaster Univ., Hamilton, ON (Canada)

Streptomyces bacteria are renowned both for their antibiotic production capabilities and for their cryptic metabolic potential. Their metabolic repertoire is subject to stringent genetic control, with many of the associated biosynthetic gene clusters being repressed by the conserved nucleoid-associated protein Lsr2. In an effort to stimulate new antibiotic production in wild Streptomyces isolates, we leveraged the activity of an Lsr2 knockdown construct and successfully enhanced antibiotic production in the wild Streptomyces isolate WAC07094. We determined that this new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media; its levels were greatest in low-density cultures. This density-dependent control was exerted at the level of the cluster-situated regulatory gene sqnR and was mediated in part through the activity of the PhoRP two-component regulatory system, where deleting phoRP led to both constitutive antibiotic production and sqnR expression. This suggests that PhoP functions to repress the expression of sqnR at high cell density. We further discovered that magnesium supplementation could alleviate this density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. Intriguingly, we found that this low density-dependent production of saquayamycin was not unique to WAC07094; saquayamycin production by another wild isolate also exhibited low-density activation, suggesting that this spatial control may serve an important ecological function in their native environments.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2469707

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 4 Vol. 9; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Cloning and Sequencing of the Biosynthetic Gene Cluster for Saquayamycin Z and Galtamycin B and the Elucidation of the Assembly of Their Saccharide Chains Erb, Annette; Luzhetskyy, Andriy; Hardter, Uwe ChemBioChem, Vol. 10, Issue 8 https://doi.org/10.1002/cbic.200900054	journal	May 2009
Impact of novel microbial secondary metabolites on the pharma industry Ramírez-Rendon, Dulce; Passari, Ajit Kumar; Ruiz-Villafán, Beatriz Applied Microbiology and Biotechnology, Vol. 106, Issue 5-6 https://doi.org/10.1007/s00253-022-11821-5	journal	February 2022
Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector MacNeil, Douglas J.; Gewain, Keith M.; Ruby, Carolyn L. Gene, Vol. 111, Issue 1 https://doi.org/10.1016/0378-1119(92)90603-m	journal	February 1992
N-Acyl Homoserinelactone-mediated Gene Regulation in Gram-negative Bacteria Eberl, Leo Systematic and Applied Microbiology, Vol. 22, Issue 4 https://doi.org/10.1016/S0723-2020(99)80001-0	journal	December 1999
Butyrolactone signalling circuits for synthetic biology Biarnes-Carrera, Marc; Breitling, Rainer; Takano, Eriko Current Opinion in Chemical Biology, Vol. 28 https://doi.org/10.1016/j.cbpa.2015.06.024	journal	October 2015
An RNA Sensor for Intracellular Mg2+ Cromie, Michael J.; Shi, Yixin; Latifi, Tammy Cell, Vol. 125, Issue 1 https://doi.org/10.1016/j.cell.2006.01.043	journal	April 2006
Structure and Mechanism of a Metal-Sensing Regulatory RNA Dann, Charles E.; Wakeman, Catherine A.; Sieling, Cecelia L. Cell, Vol. 130, Issue 5 https://doi.org/10.1016/j.cell.2007.06.051	journal	September 2007
Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019 Newman, David J.; Cragg, Gordon M. Journal of Natural Products, Vol. 83, Issue 3 https://doi.org/10.1021/acs.jnatprod.9b01285	journal	March 2020
An Engineered Allele of afsQ1 Facilitates the Discovery and Investigation of Cryptic Natural Products Daniel-Ivad, Martin; Hameed, Nabeela; Tan, Stephanie ACS Chemical Biology, Vol. 12, Issue 3 https://doi.org/10.1021/acschembio.6b01002	journal	January 2017
Two Cooperative Glycosyltransferases Are Responsible for the Sugar Diversity of Saquayamycins Isolated from Streptomyces sp. KY 40-1 Salem, Shaimaa M.; Weidenbach, Stevi; Rohr, Jürgen ACS Chemical Biology, Vol. 12, Issue 10 https://doi.org/10.1021/acschembio.7b00453	journal	September 2017
Nature Builds Macrocycles and Heterocycles into Its Antimicrobial Frameworks: Deciphering Biosynthetic Strategy Walsh, Christopher T. ACS Infectious Diseases, Vol. 4, Issue 9 https://doi.org/10.1021/acsinfecdis.8b00101	journal	July 2018
Temperature Regulates Stability, Ligand Binding (Mg²⁺ and ATP), and Stoichiometry of GroEL–GroES Complexes Walker, Thomas E.; Shirzadeh, Mehdi; Sun, He Mirabel Journal of the American Chemical Society, Vol. 144, Issue 6 https://doi.org/10.1021/jacs.1c11341	journal	February 2022
Mayamycin, a Cytotoxic Polyketide from a Streptomyces Strain Isolated from the Marine Sponge Halichondria panicea Schneemann, Imke; Kajahn, Inga; Ohlendorf, Birgit Journal of Natural Products, Vol. 73, Issue 7 https://doi.org/10.1021/np100135b	journal	June 2010
Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces Rigali, Sébastien; Titgemeyer, Fritz; Barends, Sharief EMBO reports, Vol. 9, Issue 7 https://doi.org/10.1038/embor.2008.83	journal	May 2008
Integrative genomics viewer Robinson, James T.; Thorvaldsdóttir, Helga; Winckler, Wendy Nature Biotechnology, Vol. 29, Issue 1 https://doi.org/10.1038/nbt.1754	journal	January 2011
A cell-cell communication signal integrates quorum sensing and stress response Lee, Jasmine; Wu, Jien; Deng, Yinyue Nature Chemical Biology, Vol. 9, Issue 5 https://doi.org/10.1038/nchembio.1225	journal	March 2013
Rethinking 'secondary' metabolism: physiological roles for phenazine antibiotics Price-Whelan, Alexa; Dietrich, Lars E. P.; Newman, Dianne K. Nature Chemical Biology, Vol. 2, Issue 2 https://doi.org/10.1038/nchembio764	journal	January 2006
NIH Image to ImageJ: 25 years of image analysis Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W. Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2089	journal	June 2012
Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance Waglechner, Nicholas; McArthur, Andrew G.; Wright, Gerard D. Nature Microbiology, Vol. 4, Issue 11 https://doi.org/10.1038/s41564-019-0531-5	journal	August 2019
Assembly of long, error-prone reads using repeat graphs Kolmogorov, Mikhail; Yuan, Jeffrey; Lin, Yu Nature Biotechnology, Vol. 37, Issue 5 https://doi.org/10.1038/s41587-019-0072-8	journal	April 2019
Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides Caraballo-Rodríguez, Andrés M.; Dorrestein, Pieter C.; Pupo, Monica T. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-05532-5	journal	July 2017
Angucyclines: Biosynthesis, mode-of-action, new natural products, and synthesis Kharel, Madan K.; Pahari, Pallab; Shepherd, Micah D. Nat. Prod. Rep., Vol. 29, Issue 2 https://doi.org/10.1039/c1np00068c	journal	January 2012
Unusual relatives of the multisubunit RNA polymerase Forrest, David Biochemical Society Transactions, Vol. 47, Issue 1 https://doi.org/10.1042/BST20180505	journal	December 2018
PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin Gust, B.; Challis, G. L.; Fowler, K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 4 https://doi.org/10.1073/pnas.0337542100	journal	January 2003
The Role of the Novel Fem Protein VanK in Vancomycin Resistance in Streptomyces coelicolor Hong, Hee-Jeon; Hutchings, Matthew I.; Hill, Lionel M. Journal of Biological Chemistry, Vol. 280, Issue 13 https://doi.org/10.1074/jbc.M413801200	journal	January 2005
Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases Vashishtha, Ashwani Kumar; Wang, Jimin; Konigsberg, William H. Journal of Biological Chemistry, Vol. 291, Issue 40 https://doi.org/10.1074/jbc.R116.742494	journal	September 2016
Minimap2: pairwise alignment for nucleotide sequences Li, Heng Bioinformatics, Vol. 34, Issue 18 https://doi.org/10.1093/bioinformatics/bty191	journal	May 2018
Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory Cook, Michael A.; Pallant, Daniel; Ejim, Linda Journal of Industrial Microbiology and Biotechnology, Vol. 50, Issue 1 https://doi.org/10.1093/jimb/kuad042	journal	February 2023
Target genes and structure of the direct repeats in the DNA-binding sequences of the response regulator PhoP in Streptomyces coelicolor Sola-Landa, Alberto; Rodríguez-García, Antonio; Apel, Alexander Kristian Nucleic Acids Research, Vol. 36, Issue 4 https://doi.org/10.1093/nar/gkm1150	journal	January 2008
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1103	journal	November 2016
Modulation of H-NS transcriptional silencing by magnesium Will, W. Ryan; Whitham, Patrick J.; Reid, Philip J. Nucleic Acids Research, Vol. 46, Issue 11 https://doi.org/10.1093/nar/gky387	journal	May 2018
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential Alanjary, Mohammad; Steinke, Katharina; Ziemert, Nadine Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz282	journal	April 2019
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline Blin, Kai; Shaw, Simon; Steinke, Katharina Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz310	journal	April 2019
Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics Chater, Keith F. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1469 https://doi.org/10.1098/rstb.2005.1758	journal	February 2006
Methods for characterization of Streptomyces species Shirling, E. B.; Gottlieb, D. International Journal of Systematic Bacteriology, Vol. 16, Issue 3 https://doi.org/10.1099/00207713-16-3-313	journal	July 1966
Cell density influences antibiotic biosynthesis in Streptomyces clavuligerus Sánchez, L.; Braña, A. F. Microbiology, Vol. 142, Issue 5 https://doi.org/10.1099/13500872-142-5-1209	journal	May 1996
Protein synthesis controls phosphate homeostasis Pontes, Mauricio H.; Groisman, Eduardo A. Genes & Development, Vol. 32, Issue 1 https://doi.org/10.1101/gad.309245.117	journal	January 2018
Fast and accurate de novo genome assembly from long uncorrected reads Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.214270.116	journal	January 2017
Binding of PhoP to promoters of phosphate-regulated genes in Streptomyces coelicolor: identification of PHO boxes: Binding of PhoP to Streptomyces promoters Sola-Landa, Alberto; Rodríguez-García, Antonio; Franco-Domínguez, Etelvina Molecular Microbiology, Vol. 56, Issue 5 https://doi.org/10.1111/j.1365-2958.2005.04631.x	journal	March 2005
Cross‐talk between two global regulators in Streptomyces: PhoP and AfsR interact in the control of afsS, pstS and phoRP transcription Santos‐Beneit, Fernando; Rodríguez‐García, Antonio; Sola‐Landa, Alberto Molecular Microbiology, Vol. 72, Issue 1 https://doi.org/10.1111/j.1365-2958.2009.06624.x	journal	March 2009
Signals and regulators that govern Streptomyces development McCormick, Joseph R.; Flärdh, Klas FEMS Microbiology Reviews, Vol. 36, Issue 1 https://doi.org/10.1111/j.1574-6976.2011.00317.x	journal	January 2012
Intertwining nutrient-sensory networks and the control of antibiotic production in Streptomyces: Intertwining nutrient-sensory networks Urem, Mia; Świątek-Połatyńska, Magdalena A.; Rigali, Sébastien Molecular Microbiology, Vol. 102, Issue 2 https://doi.org/10.1111/mmi.13464	journal	August 2016
New Blue Pigment Produced by Pantoea agglomerans and Its Production Characteristics at Various Temperatures Fujikawa, Hiroshi; Akimoto, Ryo Applied and Environmental Microbiology, Vol. 77, Issue 1 https://doi.org/10.1128/AEM.00264-10	journal	January 2011
Lsr2 of Mycobacterium Represents a Novel Class of H-NS-Like Proteins Gordon, Blair R. G.; Imperial, Robin; Wang, Linru Journal of Bacteriology, Vol. 190, Issue 21 https://doi.org/10.1128/JB.00733-08	journal	November 2008
Integration Site for Streptomyces Phage φBT1 and Development of Site-Specific Integrating Vectors Gregory, Matthew A.; Till, Rob; Smith, Margaret C. M. Journal of Bacteriology, Vol. 185, Issue 17 https://doi.org/10.1128/JB.185.17.5320-5323.2003	journal	September 2003
Transcriptional Studies and Regulatory Interactions between thephoR-phoPOperon and thephoU,mtpA, andppkGenes ofStreptomyces lividansTK24 Ghorbel, Sofiane; Kormanec, Jan; Artus, Alexandra Journal of Bacteriology, Vol. 188, Issue 2 https://doi.org/10.1128/JB.188.2.677-686.2006	journal	January 2006
Molecular Regulation of Antibiotic Biosynthesis in Streptomyces Liu, G.; Chater, K. F.; Chandra, G. Microbiology and Molecular Biology Reviews, Vol. 77, Issue 1 https://doi.org/10.1128/MMBR.00054-12	journal	March 2013
Interplay between Nucleoid-Associated Proteins and Transcription Factors in Controlling Specialized Metabolism in Streptomyces Zhang, Xiafei; Andres, Sara N.; Elliot, Marie A. mBio, Vol. 12, Issue 4 https://doi.org/10.1128/mBio.01077-21	journal	August 2021
Cellular Adaptations to Cytoplasmic Mg²⁺ Limitation Groisman, Eduardo A.; Chan, Carissa Annual Review of Microbiology, Vol. 75, Issue 1 https://doi.org/10.1146/annurev-micro-020518-115606	journal	October 2021
Nitrogen Metabolism in Streptomyces coelicolor: Transcriptional and Post-Translational Regulation Reuther, Jens; Wohlleben, Wolfgang Microbial Physiology, Vol. 12, Issue 1-2 https://doi.org/10.1159/000096469	journal	December 2006
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads Jiang, Hongshan; Lei, Rong; Ding, Shou-Wei BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-182	journal	June 2014
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben; Trapnell, Cole; Pop, Mihai Genome Biology, Vol. 10, Issue 3 https://doi.org/10.1186/gb-2009-10-3-r25	journal	January 2009
The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in Streptomyces and Related Actinobacteria Martín, Juan F.; Liras, Paloma Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03120	journal	January 2020
Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria Martín, Juan Francisco; Liras, Paloma International Journal of Molecular Sciences, Vol. 22, Issue 3 https://doi.org/10.3390/ijms22031129	journal	January 2021
Saquaymycins, new aquayamycin-group antibiotics. Uchida, Takeshi; Imoto, Masaya; Watanabe, Yoshinowri The Journal of Antibiotics, Vol. 38, Issue 9 https://doi.org/10.7164/antibiotics.38.1171	journal	January 1985
Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2 Gehrke, Emma J.; Zhang, Xiafei; Pimentel-Elardo, Sheila M. eLife, Vol. 8 https://doi.org/10.7554/eLife.47691	journal	June 2019

Similar Records

Identification of an unusual type II thioesterase in the dithiolopyrrolone antibiotics biosynthetic pathway

Journal Article · Fri Apr 22 04:00:00 UTC 2016 · Biochemical and Biophysical Research Communications · OSTI ID:22596352

Zhai, Ying; Bai, Silei; Liu, Jingjing; +4 more

Comparison of beta-glucosidase activities in different Streptomyces strains. [S flavogriseus and S. strain CB-12]

Journal Article · Fri Jul 01 04:00:00 UTC 1983 · Appl. Environ. Microbiol.; (United States) · OSTI ID:5147453

Moldoveanu, N; Kluepfel, D

Rational design of small molecules that modulate the transcriptional function of the response regulator PhoP

Journal Article · Mon Jan 15 04:00:00 UTC 2018 · Biochemical and Biophysical Research Communications · OSTI ID:23100627

Qing, Xiaoyu; De Weerdt, Ami; De Maeyer, Marc; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Streptomyces
antibiotic
cell density
magnesium
phosphate
regulation

Title: Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

Citation Formats

References (56)

Similar Records

Related Subjects