Nucleotide sequence alignment of hdcA from Gram-positive bacteria

Abstract

The decarboxylation of histidine -carried out mainly by some gram-positive bacteria- yields the toxic dietary biogenic amine histamine (Ladero et al. 2010 〈10.2174/157340110791233256〉 [1], Linares et al. 2016 〈http://dx.doi.org/10.1016/j.foodchem.2015.11.013〉〉 [2]). The reaction is catalyzed by a pyruvoyl-dependent histidine decarboxylase (Linares et al. 2011 〈10.1080/10408398.2011.582813〉 [3]), which is encoded by the gene hdcA. In order to locate conserved regions in the hdcA gene of Gram-positive bacteria, this article provides a nucleotide sequence alignment of all the hdcA sequences from Gram-positive bacteria present in databases. For further utility and discussion, see 〈http://dx.doi.org/ 10.1016/j.foodcont.2015.11.035〉〉 [4].

Specifications table

Subject area	Microbiology
More specific subject area	Food microbiology
Type of data	Figure
How data was acquired	Retrieved from databases
Data format	Analyzed
Experimental factors	The nucleotide sequences were retrieved from NCBI database shown below
Experimental features	Sequences were aligned using ClustalW software and visualized using Jalview v.2 programme.
Data source location	N/A
Data accessibility	Data with article

Value of the data

• •Identification of Gram-positive bacteria hdcA gene present at databases.
• •Sequence alignment defines conserved and variable regions within the hdcA sequence.
• •Obtained data allowed to design primers within hdcA conserved regions -flanking variable ones- that can be used to identify histamine-producing species in food matrices by PCR-DGGE.

1. Data

Full-length hdcA sequences of the histamine-producing Gram-positive bacteria strains present in Genbank database were aligned using ClustalW software [5]. Based on the alignment of these sequences Fig. 1 was made and primers used in Diaz et al. 2016 [4] were designed. For reasoning and further utility and discussion, see [1], [2], [3], [4].

Fig. 1.

hdcA sequences of Gram-positive bacteria strains, which are indicated in Table 1, were aligned using ClustalW software. The bacterial species are indicated at the left of each sequence. The gray tones correspond to the percentage of residues in each column that agree with a hypothetical consensus sequence: >80%, >60%, >40%, <40%. Selected regions for primer design are indicated with a box.

2. Experimental design, materials and methods

Sequence data were obtained from NCBI (http://www.ncbi.nlm.nih.gov/) database. Full-length hdcA sequences of representative histamine-producing Gram-positive bacteria strains present in database were selected for the alignment (Table 1). The sequences were aligned by DNA multiple sequence alignment ClustalW software using default parameters [5]. The visualization, which included the percentage of conservation of each residue was obtained using Jalview v.2 programme [6].

Table 1.

Accession numbers of the hdcA gene sequences of representative histamine-producing Gram-positive bacteria strains present in database used for the alignment.

hdc+species	Accession number
Staphylococcus epidermidis	GeneBank: AB583189
Lactobacillus fructivorans	GeneBank: NZ_JOJZ01000009
Lactobacillus reuteri IPLA11078	GeneBank: LN877767
L. reuteri DSM20016	GeneBank: NC009513
Streptococcus thermophilus	GeneBank: FN686789
Lactobacillus saerimneri 30a	GeneBank: NZ_ANAG0000000
Lactobacillus vaginalis	GeneBank: LN828720
Tetragenococcus halophilus	GeneBank: AB362339
Tetragenococcus muriaticus	GeneBank: DQ132889
Oenococcus oeni	GeneBank: DQ132887
Lactobacillus sakei	GeneBank: DQ132888
Lactobacillus hilgardii	GeneBank: AY651779
Lactobacillus parabuchneri	GeneBank: LN877764
Staphylococcus capitis	GeneBank: AM283479
Clostridium perfringens	GeneBank: BA000016

Appendix A. Supplementary material

Supplementary material