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. 2024 Mar;22(1):100349.
doi: 10.1016/j.jgeb.2023.100349. Epub 2024 Jan 22.

AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: Three putative genes in phenol catabolic pathway of Acinetobacter sp. Strain DF4

Desouky Abd-El-Haleem  1
Affiliations

AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: Three putative genes in phenol catabolic pathway of Acinetobacter sp. Strain DF4

Desouky Abd-El-Haleem. J Genet Eng Biotechnol. 2024 Mar.

Abstract

The objective of this study was to identify genes associated with the biodegradation of phenol by Acinetobacter sp. strain DF4 through the use of differential display (DD) methodology. The bacteria were grown in YEPG medium, and total RNA was extracted and analyzed using labeled primers to detect gene expression differences. Three distinctively expressed cDNA bands (ph1, ph2, and ph3) were identified, cloned, and sequenced. DNA analysis involved searching for open reading frames (ORFs), verifying results with the NCBI database, predicting promoter regions, and constructing phylogenetic trees using bioinformatics tools. The ph1 gene displayed a 97% identity with the AraC transcriptional regulator, suggesting its potential role in regulating the ortho-catabolic pathway of phenol. The ph2 gene showed a 98% identity with aspartate semialdehyde dehydrogenase, which is involved in phenol degradation. The ph3 gene had a 93% identity with acetyltransferase. Essential transcription factors, such as TATA, GTGTGT, CACA, and CTTTT, were detected, and the three genes promoter regions were predicted. This study successfully identified functional genes involved in the metabolism of cyclic chemicals, particularly phenol, using the DD technique. These findings provide insights into the biodegradation pathways of phenol by Acinetobacter sp. Strain DF4 and may contribute to the development of more efficient bioremediation strategies for phenol-contaminated environments.

Keywords: Acetyltransferase; AraC transcriptional regulator; Dehydrogenase; Differential Display- Random primers; Phenol catabolic pathway; Putative genes; Transcriptional factors.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Schematic Diagram of the Differential Display Approach from Culturing to DNA Sequence Analysis.
Fig. 2
Fig. 2
The phylogenetic tree of differentially expressed DNA segments in Acinetobacter sp. strain DF4 under phenol stress, utilizing the DD approach. The bands, Ph1, Ph2, and Ph3, correspond to A, B, and C, respectively. The N-BLAST tool facilitated sequence comparison against databases, and the resulting phylogenetic tree was crafted through the neighbor-joining method.
Fig. 3
Fig. 3
Putative DNA response elements and binding sites for transcription factors present in Ph1, Ph2 and Ph3 DNA segments, respectively. The promoter regions and their transcription factors and/or binding sites are presented below each one of them.
See this image and copyright information in PMC

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