Apiaceae FNS I originated from F3H through tandem gene duplication

Pucker, Boas; Iorizzo, Massimo

doi:10.1371/journal.pone.0280155

Cited by 14 publications

(22 citation statements)

References 53 publications

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“…A combined set of the previously characterized bait sequences and their homologues identified in this search served as the basis for the construction of a global alignment with MUSCLE v5.1 using 16 iterations in the alignment process . The alignment was trimmed to remove columns with occupancy below 10% using a previously described Python script . A phylogenetic tree was constructed based on the trimmed alignment with IQ-TREE v1.6.12 using the parameters “-alrt 1000 -bb 1000”.…”

Section: Methodsmentioning

confidence: 99%

“…35 The alignment was trimmed to remove columns with occupancy below 10% using a previously described Python script. 33 A phylogenetic tree was constructed based on the trimmed alignment with IQ-TREE v1.6.12 36 using the parameters "-alrt 1000 -bb 1000".…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…A collection of previously characterized lycopene β-cyclase polypeptide sequences was generated by retrieving the respective sequences from the NCBI (additional file A on github). This FASTA file served as input for a previously developed Python script to identify the five closest homologues of each of these bait sequences based on sequence similarity via BLAST v2.8.1+ in a range of bacteria, archaea, fungi, and plant species (additional file B on Github). A combined set of the previously characterized bait sequences and their homologues identified in this search served as the basis for the construction of a global alignment with MUSCLE v5.1 using 16 iterations in the alignment process .…”

Section: Methodsmentioning

confidence: 99%

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Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum

Göttl

Pucker

Wendisch

et al. 2023

J. Agric. Food Chem.

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Lycopene β-cyclase (EC 5.5.1.19) is one of the key enzymes in the biosynthesis of β-carotene and derived carotenoids. It catalyzes isomerase reactions to form β-carotene from lycopene by β-cyclization of both of its ψ-ends. Lycopene β-cyclases are widespread in nature. We systematically analyzed the phylogeny of lycopene β-cyclases from all kingdoms of life and predicted their transmembrane structures. To this end, a collection of previously characterized lycopene β-cyclase polypeptide sequences served as bait sequences to identify their closest homologues in a range of bacteria, archaea, fungi, algae, and plant species. Furthermore, a DeepTMHMM scan was applied to search for the presence of transmembrane domains. A phylogenetic tree suggests at least five distinct clades, and the DeepTMHMM scan revealed that lycopene β-cyclases are a group of structurally different proteins: membrane-bound and cytosolic enzymes. Representative lycopene β-cyclases were screened in the lycopene-overproducing Corynebacterium glutamicum strain for β-carotene and astaxanthin production. This systematic screening facilitates the identification of new enzymes for carotenoid production. Higher astaxanthin production and less reduction of total carotenoids were achieved with the cytosolic lycopene β-cyclase CrtL from Synechococcus elongatus and the membrane-bound heterodimeric lycopene β-cyclase CrtYcd from Brevibacterium linens.

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Section: Methodsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum

Göttl

Pucker

Wendisch

et al. 2023

J. Agric. Food Chem.

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“…bHLHs with a high grade of sequence divergence were identified in the well studied species Arabidopsis thaliana [1, 9, 11] and Oryza sativa [11, 31] (see Additional file 1 for details). The BLASTp-based Python script “collect_best_BLAST_hits.py” in version v0.29 [69] was used to find the best BLAST hits in predicted polypeptide sequences of Brassica napus for the diverged sequences in A. thaliana and Zea mays in O. sativa. The obtained sequences were added to the bait sequence collection to represent the diverged sequences with a higher phylogenetic diversity.…”

Section: Methodsmentioning

confidence: 99%

“…Afterwards, the pipeline was deployed on polypeptide sequences of the A. thaliana accession Nd-1 [86], Dioscorea dumetorum [87] and Croton tiglium [88] with the complete bait collection. The identified candidates in the A. thaliana Nd-1 accession were assigned to the Col-0 candidates by using them as baits for the BLASTp-based Python script “collect_best_BLAST_hits.py” v0.29 [69] to compare the results of both accessions.…”

Section: Methodsmentioning

confidence: 99%

Automatic annotation of the bHLH gene family in plants

Thoben

Pucker

2023

Preprint

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Background: The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised. Results: A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator for the automated functional annotation of bHLHs was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified. Conclusions: The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.

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Bacterial biosynthesis of flavonoids: Overview, current biotechnology applications, challenges, and prospects

Jiang

et al. 2023

Journal Cellular Physiology

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Flavonoids are secondary metabolites present in plant organs and tissues. These natural metabolites are the most prevalent and display a wide range of beneficial physiological effects, making them usually intriguing in several scientific fields. Due to their safety for use and protective attributes, including antioxidant, anti‐inflammatory, anticancer, and antimicrobial functions, flavonoids are broadly utilized in foods, pharmaceuticals, and nutraceuticals. However, conventional methods for producing flavonoids, such as plant extraction and chemical synthesis, entailed dangerous substances, and laborious procedures, with low product yield. Recent studies have documented the ability of microorganisms, such as fungi and bacteria, to synthesize adequate amounts of flavonoids. Bacterial biosynthesis of flavonoids from plant biomass is a viable and environmentally friendly technique for producing flavonoids on a larger scale and has recently received much attention. Still, only a few bacteria species, particularly Escherichia coli, have been extensively studied. The most recent developments in bacterial biosynthesis of flavonoids are reviewed and discussed in this article, including their various applications as natural food biocontrol agents. In addition, the challenges currently faced in bacterial flavonoid biosynthesis and possible solutions, including the application of modern biotechnology approaches for developing bacterial strains that could successfully produce flavonoids on an industrial scale, were elucidated.

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Apiaceae FNS I originated from F3H through tandem gene duplication

Cited by 14 publications

References 53 publications

Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum

Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum

Automatic annotation of the bHLH gene family in plants

Bacterial biosynthesis of flavonoids: Overview, current biotechnology applications, challenges, and prospects

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