A compilation of histidine kinase genes in Enterobacter hormaechei strain HCF3 isolated from the North West Province of South Africa

Introduction

It is well recognized that E. hormaechei can adapt to various ecological niches, such as soil, water, plants, and clinical settings. The bacteria are receiving more attention because of their association with antimicrobial resistance (AMR) and their significance in hospital-acquired illnesses. In North West Province in South Africa, E. hormaechei strain HCF₃ was isolated from cow dung, providing an opportunity to investigate its genetic components, particularly those related to environmental sensing and adaptability.

Histidine kinases are essential components of bacterial two-component systems (TCS), that enable bacteria to detect environmental cues and modify gene expression in response. Cow dung and other manure-rich settings contain bacteria with competing microbial populations, fluctuating nutrient availability, and moisture fluctuations. Determining the histidine kinase genes in E. hormaechei HCF₃ might help us understand how the bacterium endures these circumstances and whether or not these genes are involved in its pathogenicity and antibiotic resistance.

Essential sensor proteins in prokaryotes, histidine kinases (HKs), serve as receptors for stimuli such as mechanical stress, quorum-sensing molecules, and signals unique to certain plants, allowing bacteria to react to changes in their environment (Kabbara et al., 2019; Wang and Qian, 2019).

Crop improvement efforts rely heavily on HKs since they are essential to plants’ two-component systems (TCS), controlling development and environmental responses (Kenney, 2021). HKs are also used in industrial settings, to improve the synthesis of polyunsaturated fatty acids using genetic engineering (Hoang et al., 2021). Lembke and Carlson (2022) indicated that they are attractive targets for the development of antivirulence and antibiotics. In particular, suppressing Enterobacter hormaechei HKs may lessen the effects of the pathogen on plants. E. hormaechei enhances plant growth and development in crops such as tomatoes and okra by solubilizing vital macronutrients, such as phosphate and potassium. This increases biomass and improves plant architecture (Ranawat et al., 2021a, b); Roslan et al., 2020). According to Bendaha and Belaouni (2019), treated plants exhibit an enhanced fruit output and quality. It also improves the soil fertility, plant productivity, and crop quality. Furthermore, according to Pan et al. (2019), E. hormaechei encourages development without impairing anti-herbivore defense.

Although histidine kinases are essential, little information is available regarding these genes in E. hormaechei HCF₃. Our work seeks to close this knowledge gap by assembling an extensive dataset of this HK genes in this strain. We discovered and annotated histidine kinase genes using genome sequencing and bioinformatics methods, offering information on their sequences and expected activities. Comparative investigations were carried out with different Enterobacter strains to further enhance our understanding of these genes and to identify commonalities and differences.

Therefore, this data provides the histidine kinase gene compilation of E. hormaechei HCF₃, a valuable tool for scientists studying bacterial signalling pathways. A list of histidine kinase genes of E. hormaechei strain HCF₃, whose complete genome sequence was published by Makhetha et al. (2023), was created. The dataset not only enhances our knowledge of E. hormaechei HCF₃ but also serves as a foundation for future studies exploring the applications of these genes in agriculture and biotechnology.

Methodology

The genome sequences of 12 Enterobacter hormaechei strains HCF3 from faeces isolated from Fresh cow dung rectums samples from Mogosane Village in North West Province, South Africa (25°45′30.6″S 25°33′43.9″E) yielded E. hormaechei strain HCF3. The genome sizes ranged from 4.43 to 5.02Mb, with G + C contents of 55.5–56%, and contained 16–262 contigs. After cultivating the bacterial isolate Enterobacter hormaechei. The extracted DNA concentration was measured using a NanoDrop (ThermoFisher Scientific, Carlsbad, CA, USA), while DNA quality was evaluated using 2% agarose gel electrophoresis. The Illumina TruSeq DNA Nano Preparation Kit (Illumina, San Diego, CA, USA) was utilized to construct paired-end libraries with 2 × 150 bp reads. These libraries were subsequently sequenced on an Illumina Hiseq X platform, adhering to standard protocols at the Agricultural Research Council-Biotechnology Platform in South Africa. This procedure generated between 4,676,625 and 6,656,610 paired-end reads, each 2 × 150 bp in length. After quality-checking, the readings were combined together using SPAdes, annotated, and deposited in NCBI, as reported by Makhetha et al. (2023).

Thus, the genome sequence of the HCF₃ strain of E. hormaechei, with BioProject number PRJNA991313 and raw reads under accession number JAUOLV000000000.1, BioSample number SAMN36292742, and GenBank assembly accession number GCA_022172285.1, were obtained. The genome sizes ranged from 4.43 to 5.02 Mb, and the G + C contents ranged from 55.5 to 56%. Conserved domains linked to HKs, specifically the HisKA (histidine kinase A) and HATPase domains, were used to identify histidine kinase genes. The histidine kinase gene catalogue was created by listing the genes with their characteristics, including locus tag, protein accession number, and annotation (shown in Table 1).

Dataset validation

The discovered histidine kinase genes discovered from strain BD163 were compared with other Enterobacter genomes accessible in the NCBI database to confirm the histidine kinase gene set of E. hormaechei. This study aimed to investigate the diversity and conservation of histidine kinase genes in the Enterobacter genus. The histidine kinase genes of three Enterobacter strains (Enterobacter hormaechei HCF₁, Enterobacter hormaechei HCF₂, and Enterobacter hormaechei HCF₄) were analyzed as part of a genome comparison study.

The methods described in the methodology section were followed to identify histidine kinase genes. Comparative analysis showed that, similar to strain HCF₃, E. hormaechei HCF₁ had 21 histidine kinase genes, and HCF₂ strains each had 25 histidine kinase genes; however, strain HCF₄ of E. hormaechei only had 19. These results show that different Enterobacter species have different frequencies of histidine kinase genes.

Authors contributions

Udeh EL: Data Curation, Methodology, Writing – Final Draft Preparation; Otun SO: Writing – Review & Editing and Makhetha L – Original Draft Preparation; Writing – Review & Editing; Ntushelo K: Conceptualization, Supervision, Writing – Review & Editing