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. 2025 Apr 1:16:1548894.
doi: 10.3389/fmicb.2025.1548894. eCollection 2025.

Biosynthetic Pathway of psi, psi-Carotene from Streptomyces sp. VITGV38 (MCC 4869)

Veilumuthu Pattapulavar  1 , Sathiyabama Ramanujam  2 , Manoj Sekaran  3 , Rajasekaran Chandrasekaran  3 , Shweta Panchal  4 , John Godwin Christopher  1
Affiliations

Biosynthetic Pathway of psi, psi-Carotene from Streptomyces sp. VITGV38 (MCC 4869)

Veilumuthu Pattapulavar et al. Front Microbiol. .

Abstract

Introduction: Endophytic Streptomyces play a crucial role in plant-microbe interactions, often exhibiting beneficial biological activities, including the production of bioactive secondary metabolites. This study aimed to characterize the carotene biosynthetic pathway of a newly discovered Streptomyces sp. VITGV38, isolated from tomato (Lycopersicon esculentum).

Methods: The strain (Streptomyces sp. VITGV38, MCC4869) was cultured in starch casein broth, and its metabolite profile was analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). Whole-genome sequencing was performed using the Illumina platform, and the biosynthetic gene clusters (BGCs) were identified using antiSMASH.

Results: Metabolite analysis revealed the presence of pigmented compounds, including psi, psi-carotene, detected at a retention time of 25.094, constituting 1.26% of the crude extract. Whole-genome sequencing uncovered an 8.27 Mb genome encoding 26 distinct secondary metabolite biosynthetic gene clusters. Notably, scaffold 26.3 was identified as a terpene biosynthetic cluster, accounting for 62% of the total secondary metabolite content and associated with carotenoid and β-carotene production.

Discussion: These findings highlight the biotechnological potential of Streptomyces sp. VITGV38 for sustainable microbial production of carotenoids, offering an eco-friendly alternative to synthetic pigments. This study provides valuable insights into microbial carotenoid biosynthesis and its potential industrial applications.

Keywords: Streptomyces sp. VITGV38; antiSMASH; biosynthetic gene cluster; pigment; psi; psi-carotene; secondary metabolite.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Growth and pigment production of Streptomyces sp. VITGV38, grown for 7 days in starch casein agar.
Figure 2
Figure 2
Phylogeny of Streptomyes sp. VITGV38. A Neighbor-joining tree based on 16S rRNA gene sequence data, depicting the phylogenetic position of the strain VITGV156 among the recognized type strains of the genus Streptomyces. The minimum evolution tree based on genome sequence of recognized strains from the genus Streptomyces was constructed blastn database provided pair wise alignment. The strain used in this study was provided in yellow color highlighted.
Figure 3
Figure 3
Circular genome map of Streptomyces sp. VITGV38, generated using CG View (1.0). The following features are shown (moving from the outermost track to the innermost track); origin of replication positioned: ORF genes in green color, positive and negative GC content skew in green and purple, respectively. GC content (black) and the genome position in the center. The innermost ring displays the overall genome size of Streptomyces sp. VITGV38.
Figure 4
Figure 4
(A) GC-MS chromatogram of Streptomyces sp. VITGV38 ethyl acetate extract. (B) Mass spectrum of psi, psi-carotene. (C) Molecular structure of psi, psi-carotene.
Figure 5
Figure 5
A RP-HPLC separation of crude extract of 38. (A) 3D counter view. (B) Chromatogram of the crude extract. (C) UV spectrum at retention time (RT) 54.6 min. (D) Purity index of the peak at RT 54.6. (E) Peak profile of the targeted compound.
Figure 6
Figure 6
LC-MS/MS chromatogram of the secondary metabolite of Streptomyces sp. VITGV38. The peak corresponds to the bioactive molecule psi, psi-carotene (peak at 3.637, m/z = 546.5165).
Figure 7
Figure 7
LC-HRMS-ESI spectrum of the compound psi, psi-carotene retention times, names, molecular formulas, molecular masses, and obtained masses of analyzed compounds.
Figure 8
Figure 8
The overall genetic architecture of (isorenieratene) terpene gene cluster in Streptomyces sp. VITGV38. (A) Overall view of biosynthetic gene clusters. (B) Specific region for terpene clusters. (C) The comparison between the proposed hopene gene cluster (dark red gene) in strain Streptomyces sp. VITGV38 and the proposed identified cluster of isorenieratene in Streptomyces argillaceus with a similarity score of 0.30 on the MIBiG website. (D) The proposed terpene gene cluster in region 23.6 from strain Streptomyces sp. VITGV38 genome contains; 2Fe-2S ferredoxin, phytoene/squalene synthase, phytoene desaturase, geranylgeranyl pyrophosphase synthase, RNA polymerase Sigma-24 subunit, lycopene cyclase, methyltransferase and isorenieratene synthase. (E) Represents the predicted genes involved in isorenieratene biosynthesis based on the genes overview on the antiSMASH website.
Figure 9
Figure 9
Psi, psi-carotene biosynthetic pathway of Streptomyces sp. VITGV38 and functions of the carotenoid biosynthesis genes associate with the compound. Inferred crt biosynthetic pathway leading to the formation of isoneriatene in Streptomyces sp. VITGV38. The enzyme encoded by each of the genes is also specified.
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