New developments in RiPP discovery, enzymology and engineering

Manuel Montalbán-López; Thomas A. Scott; Sangeetha Ramesh; Imran R. Rahman; Auke J. Van Heel; Jakob H. Viel; Vahe Bandarian; Elke Dittmann; Olga Genilloud; Yuki Goto; María José Grande Burgos; Colin Hill; Seokhee Kim; Jesko Koehnke; John A. Latham; A. James Link; Beatriz Martínez; Satish K. Nair; Yvain Nicolet; Sylvie Rebuffat; Hans Georg Sahl; Dipti Sareen; Eric W. Schmidt; Lutz Schmitt; Konstantin Severinov; Roderich D. Süssmuth; Andrew W. Truman; Huan Wang; Jing Ke Weng; Gilles P. Van Wezel; Qi Zhang; Jin Zhong; Jörn Piel; Douglas A. Mitchell; Oscar P. Kuipers; Wilfred A. Van Der Donk

doi:10.1039/d0np00027b

New developments in RiPP discovery, enzymology and engineering

Manuel Montalbán-López, Thomas A. Scott, Sangeetha Ramesh, Imran R. Rahman, Auke J. Van Heel, Jakob H. Viel, Vahe Bandarian, Elke Dittmann, Olga Genilloud, Yuki Goto, María José Grande Burgos, Colin Hill, Seokhee Kim, Jesko Koehnke, John A. Latham, A. James Link, Beatriz Martínez, Satish K. Nair, Yvain Nicolet, Sylvie RebuffatHans Georg Sahl, Dipti Sareen, Eric W. Schmidt, Lutz Schmitt, Konstantin Severinov, Roderich D. Süssmuth, Andrew W. Truman, Huan Wang, Jing Ke Weng, Gilles P. Van Wezel, Qi Zhang, Jin Zhong, Jörn Piel, Douglas A. Mitchell, Oscar P. Kuipers, Wilfred A. Van Der Donk

Research output: Contribution to journal › Review article › peer-review

261 Scopus citations

Abstract

Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.

Original language	English (US)
Pages (from-to)	130-239
Number of pages	110
Journal	Natural Product Reports
Volume	38
Issue number	1
DOIs	https://doi.org/10.1039/d0np00027b
State	Published - 2021

All Science Journal Classification (ASJC) codes

Biochemistry
Drug Discovery
Organic Chemistry

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10.1039/d0np00027b

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Montalbán-López, M., Scott, T. A., Ramesh, S., Rahman, I. R., Van Heel, A. J., Viel, J. H., Bandarian, V., Dittmann, E., Genilloud, O., Goto, Y., Grande Burgos, M. J., Hill, C., Kim, S., Koehnke, J., Latham, J. A., Link, A. J., Martínez, B., Nair, S. K., Nicolet, Y., ... Van Der Donk, W. A. (2021). New developments in RiPP discovery, enzymology and engineering. Natural Product Reports, 38(1), 130-239. https://doi.org/10.1039/d0np00027b

@article{904db97545734016a87964fe62d4690d,

title = "New developments in RiPP discovery, enzymology and engineering",

abstract = "Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.",

author = "Manuel Montalb{\'a}n-L{\'o}pez and Scott, {Thomas A.} and Sangeetha Ramesh and Rahman, {Imran R.} and {Van Heel}, {Auke J.} and Viel, {Jakob H.} and Vahe Bandarian and Elke Dittmann and Olga Genilloud and Yuki Goto and {Grande Burgos}, {Mar{\'i}a Jos{\'e}} and Colin Hill and Seokhee Kim and Jesko Koehnke and Latham, {John A.} and Link, {A. James} and Beatriz Mart{\'i}nez and Nair, {Satish K.} and Yvain Nicolet and Sylvie Rebuffat and Sahl, {Hans Georg} and Dipti Sareen and Schmidt, {Eric W.} and Lutz Schmitt and Konstantin Severinov and S{\"u}ssmuth, {Roderich D.} and Truman, {Andrew W.} and Huan Wang and Weng, {Jing Ke} and {Van Wezel}, {Gilles P.} and Qi Zhang and Jin Zhong and J{\"o}rn Piel and Mitchell, {Douglas A.} and Kuipers, {Oscar P.} and {Van Der Donk}, {Wilfred A.}",

note = "Funding Information: RiPP research in the laboratories of the corresponding authors is supported by grants from the National Institutes of Health (GM123998 to DAM, AI144967 to WAV and DAM, GM058822 to WAV, and 5T32-GM070421 to IRR), the EU FW7 programme SynPeptide (to MML, OPK and JP), the EU Horizon 2020 programme Ras4Biotech (to AJvH), the Swiss National Science Foundation (407240_1167051 to JP), the Dutch Research Council (NWO-ALWOP-214 to JV), a European Molecular Biology Organization Long-Term Fellowship (ALTF 344-2018 to TAS), and the Howard Hughes Medical Institute (to WAV). Publisher Copyright: {\textcopyright} The Royal Society of Chemistry.",

year = "2021",

doi = "10.1039/d0np00027b",

language = "English (US)",

volume = "38",

pages = "130--239",

journal = "Natural Product Reports",

issn = "0265-0568",

publisher = "Royal Society of Chemistry",

number = "1",

}

Montalbán-López, M, Scott, TA, Ramesh, S, Rahman, IR, Van Heel, AJ, Viel, JH, Bandarian, V, Dittmann, E, Genilloud, O, Goto, Y, Grande Burgos, MJ, Hill, C, Kim, S, Koehnke, J, Latham, JA, Link, AJ, Martínez, B, Nair, SK, Nicolet, Y, Rebuffat, S, Sahl, HG, Sareen, D, Schmidt, EW, Schmitt, L, Severinov, K, Süssmuth, RD, Truman, AW, Wang, H, Weng, JK, Van Wezel, GP, Zhang, Q, Zhong, J, Piel, J, Mitchell, DA, Kuipers, OP & Van Der Donk, WA 2021, 'New developments in RiPP discovery, enzymology and engineering', Natural Product Reports, vol. 38, no. 1, pp. 130-239. https://doi.org/10.1039/d0np00027b

TY - JOUR

T1 - New developments in RiPP discovery, enzymology and engineering

AU - Montalbán-López, Manuel

AU - Scott, Thomas A.

AU - Ramesh, Sangeetha

AU - Rahman, Imran R.

AU - Van Heel, Auke J.

AU - Viel, Jakob H.

AU - Bandarian, Vahe

AU - Dittmann, Elke

AU - Genilloud, Olga

AU - Goto, Yuki

AU - Grande Burgos, María José

AU - Hill, Colin

AU - Kim, Seokhee

AU - Koehnke, Jesko

AU - Latham, John A.

AU - Link, A. James

AU - Martínez, Beatriz

AU - Nair, Satish K.

AU - Nicolet, Yvain

AU - Rebuffat, Sylvie

AU - Sahl, Hans Georg

AU - Sareen, Dipti

AU - Schmidt, Eric W.

AU - Schmitt, Lutz

AU - Severinov, Konstantin

AU - Süssmuth, Roderich D.

AU - Truman, Andrew W.

AU - Wang, Huan

AU - Weng, Jing Ke

AU - Van Wezel, Gilles P.

AU - Zhang, Qi

AU - Zhong, Jin

AU - Piel, Jörn

AU - Mitchell, Douglas A.

AU - Kuipers, Oscar P.

AU - Van Der Donk, Wilfred A.

N1 - Funding Information: RiPP research in the laboratories of the corresponding authors is supported by grants from the National Institutes of Health (GM123998 to DAM, AI144967 to WAV and DAM, GM058822 to WAV, and 5T32-GM070421 to IRR), the EU FW7 programme SynPeptide (to MML, OPK and JP), the EU Horizon 2020 programme Ras4Biotech (to AJvH), the Swiss National Science Foundation (407240_1167051 to JP), the Dutch Research Council (NWO-ALWOP-214 to JV), a European Molecular Biology Organization Long-Term Fellowship (ALTF 344-2018 to TAS), and the Howard Hughes Medical Institute (to WAV). Publisher Copyright: © The Royal Society of Chemistry.

PY - 2021

Y1 - 2021

N2 - Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.

AB - Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.

UR - http://www.scopus.com/inward/record.url?scp=85101053260&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85101053260&partnerID=8YFLogxK

U2 - 10.1039/d0np00027b

DO - 10.1039/d0np00027b

M3 - Review article

C2 - 32935693

AN - SCOPUS:85101053260

SN - 0265-0568

VL - 38

SP - 130

EP - 239

JO - Natural Product Reports

JF - Natural Product Reports

IS - 1

ER -

New developments in RiPP discovery, enzymology and engineering

Abstract

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