Recent advances in lincosamide biosynthetic studies

The Journal of Antibiotics https://doi.org/10.1038/s41429-025-00884-x SPECIAL FEATURE: REVIEW ARTICLE Recent advances in lincosamide biosynthetic studies Yi Yang1 Takahiro Mori ● 1,2 Received: 19 September 2025 / Revised: 31 October 2025 / Accepted: 5 November 2025 © The Author(s) 2025. This article is published with open access 1234567890();,: 1234567890();,: Abstract Lincomycin A and celesticetin are representative members of the lincosamide class of clinically used antibiotics produced by Streptomyces species. Their distinctive chemical architectures arise from atypical biosynthetic gene clusters that lack well observed signature genes, and since the complete determination of the lincomycin A biosynthetic pathway, current research has focused on the genetic manipulation of regulatory elements and the protein engineering of biosynthetic enzymes. This review summarizes recent advances in elucidating the transcriptional regulation of lincosamide biosynthetic gene clusters and the structure–function relationships and engineering of their biosynthetic enzymes. Introduction Historically, natural products have been an important source of lead molecules for drug discovery. This is especially so for antibiotics, whereby the discovery and subsequent development of penicillin in the early 1940s heralded the golden age of antibiotics, spanning from the early 1940s to the late 1960s. However, since the 1970s, the dramatic reduction in the discovery rate of novel compound classes and the emergence of multi-drug resistance in pathogens have challenged scientists and clinicians to devise new strategies in the fight against infectious diseases [1, 2]. Accordingly, significant efforts have been made toward the chemical and enzymatic modification of naturally derived antibiotics, leading to a spectrum of semi-synthetic compounds with improved antimicrobial activities over their parent molecules. Additionally, facilitated by new technologies in the post-genomic era, explorations of novel biosynthetic gene clusters with unusual features and organizations promise to uncover new lead scaffolds that were previously overlooked and provide biocatalysts for the generation of unique analogs [3–5]. * Takahiro Mori 1 Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan 2 Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan An important class of antibiotics that has emerged from these approaches is the lincosamides. Lincomycin A (1) and its semisynthetic derivative, clindamycin (2), have been used for over five decades to treat infections caused by Gram-positive bacteria and mycoplasmas, particularly in patients with penicillin hypersensitivity [6, 7]. These compounds inhibit bacterial protein synthesis by binding to the peptidyltransferase domain of the 50S ribosomal subunit. Structurally, lincosamides consist of a thiooctose core conjugated at the C6 position to either proline or an alkylproline moiety, with an additional S-alkyl substitution at the C1 position [8]. Lincomycin A, produced by Streptomyces lincolnensis, incorporates N-methylated trans-4-propyl-Lproline (PPL) at C6 and carries a C1 S-methyl group. In contrast, celesticetin (3), isolated from Streptomyces caelestis, contains N-methylproline at C6, a C7 methoxy group, and a salicylic acid moiety tethered to the C1 sulfur atom via a two-carbon linker (Fig. 1) [9, 10]. The biosynthetic pathway of lincomycin A was confirmed in 2020, by the identification of the functions of LmbM, LmbL, CcbZ (an LmbZ homologue), and CcbS (an LmbS homologue) in catalyzing the conversion of GDP-octose (15) to GDP-D-α-D-lincosamide (16) (Fig. 2) [11]. Likewise, analyses of celesticetin biosynthesis have elucidated most of its pathway. Collectively, the biosynthesis and pharmacodynamics of lincomycin A, celesticetin, and their semisynthetic analogs are now well established and have been comprehensively reviewed in the literature [9, 11, 12]. Research on the regulatory mechanisms controlling the expression of lincosamide biosynthetic gene clusters (BGCs) has been ongoing for over a decade. More recently, advances in molecular biology and systems approaches have Y. Yang, T. Mori Fig. 1 Chemical structures of natural and semi-synthetic lincosamides deepened our understanding of these networks and facilitated their manipulation for strain improvement. In parallel, structure–function analyses of key biosynthetic enzymes have enabled protein engineering strategies to generate novel lincosamide analogs. This review highlights recent progress in the exploitation of lincosamide biosynthetic genes for enhanced antibiotic production. The lmb and ccb BGCs The 35-kb lincomycin biosynthetic gene cluster (BGC) was first cloned and characterized from the industrial strain Streptomyces lincolnensis 78-11 [13]. It comprises 26 biosynthetic and regulatory genes (lmb) and 3 resistance genes (lmr) (Fig. 3 and Table 1). Aside from lmrA and lmrC, which flank the cluster, the remaining 27 open reading frames are organized into 8 operons headed by lmbA, lmbC, lmbD, lmbJ, lmbK, lmbV, lmbW and lmbU, respectively. The genes in these operons are loosely grouped based on their biosynthetic functions: alkylproline formation, thiooctose formation, condensation coupling, and S-alkyl functionalization (Table 2) [14]. In the celesticetin (ccb) BGC from Streptomyces caelestis, the homologs of the lmb genes responsible for thiooctose generation and condensation are highly conserved. In contrast, this cluster contains only one resistance gene, ccr1, which is homologous to lmrB (Fig. 3 and Table 1) [14]. The lmb and ccb clusters are atypical BGCs in that they lack signature enzymes such as non-ribosomal peptide synthases (NRPSs) and polyketide synthases (PKSs). Instead, their core scaffold is assembled by unusual condensation enzymes that catalyze the amide bond formation between an amino acid and a thiooctose moiety (Fig. 2). Another distinctive feature of the lincomycin BGC is its reliance on three different self-resistance mechanisms. The lmrA, lmrB, and lmrC genes encode an MFS transporter, a 23S rRNA methyltransferase, and an ATP-binding cassette-F (ABCF) ATPase, respectively [13, 15]. Each of these mechanisms can individually provide a different degree of protection against lincosamide antibiotics. Regulation of lincosamide BGC expression Lincosamides are chemically complex and are therefore produced industrially through bacterial fermentation [16]. These natural products are further modified into semisynthetic analogs, such as clindamycin. Following the elucidation of the lincomycin biosynthetic pathway, research has increasingly shifted toward understanding and manipulating the transcriptional regulation of the cluster, with the practical goal of developing overproducing strains for improved antibiotic yields. Such regulation is typically mediated by transcription factors that bind to cis-regulatory e (...truncated)