Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA

Cheung-Lee, Wai Ling; Chen, Maria Y.; Maksimov, Mikhail O.; Link, A. James

doi:10.1021/acscentsci.6b00184

Cited by 32 publications

(41 citation statements)

References 33 publications

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“…However, subsequent analysis revealed that only ∼4,000 of these sequences co-occur with the requisite leader peptidase and lasso cyclase. This number is more consistent with the most recent lasso peptide survey, which reported ∼3,000 lasso peptide BGCs ( 23 , 41 ). Proteins retrieved by the discrete lasso peptide model often co-occur with other common RiPP enzymes, such as rSAM enzymes which represent ∼300 of the false positives.…”

Section: Resultssupporting

confidence: 89%

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

et al. 2020

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Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain. IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.

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Section: Resultssupporting

confidence: 89%

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

et al. 2020

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“…This number is more consistent with the most recent bioinformatic survey of lasso peptides, which reported ~3,000 lasso peptide BGCs with discretely encoded RREs 24,42 . Proteins retrieved by this model often co-occur with other common RiPP enzymes, such as rSAM enzymes (which represent ~300 of the "false positive" BGCs).…”

Section: Defining the Scope Of Rre-dependent Ripp Bgcssupporting

confidence: 89%

RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery

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Shelton

Wezel

et al. 2020

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Nearly half of the classes of natural products known as ribosomally synthesized and post-translationally modified peptides (RiPPs) are reliant on a protein domain called the RiPP recognition element (RRE) for peptide maturation. The RRE binds specifically to a linear precursor peptide and directs the posttranslational modification enzymes to their substrate. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE:precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of the RRE domain across RiPP classes has precluded automated identification of RREs based solely on sequence similarity. Here, we introduce RRE-Finder, a novel tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in "precision" mode to confidently identify RREs in a class-specific manner or in "exploratory" mode, which was designed to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved over 30,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP, putatively novel gene cluster architectures that will require future experimental work. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich dataset of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.

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“…1–4 This fold is maintained by bulky side chains positioned above and below the ring sterically trapping the tail inside. Lasso peptide biosynthesis usually requires three to four gene products (Figure 1): 1–3, 5–10 the precursor peptide A consists of an N-terminal leader and a C-terminal core region. The leader region is required for enzymatic recognition, while the core region is converted into the mature lasso peptide.…”

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confidence: 99%