Characterization of Smith-Waterman sequence database search in X10

The aim of our study was to determine complete nucleotide sequence of mcr-1-carrying plasmids from Enterobacterales isolates recovered from domestic and imported raw retailed meat and compare them with plasmids available at the GenBank sequence database. A set of 16 plasmids originating from Escherichia coli (n = 13), Klebsiella pneumoniae (n = 2), and Citrobacter braakii (n = 1) were analyzed. In our previous study, data from whole genome sequencing showed that mcr-1 gene was located on plasmids of different incompatibility groups (IncHI2, IncI2, and IncX4). The IncI2 (n = 3) and IncX4 (n = 8) plasmids harbored mcr-1.1 gene only, whereas IncHI2 sequence type 4 plasmids (n = 5) carried large multidrug resistance (MDR) regions. MDR regions of IncHI2 plasmids included additional antimicrobial resistance genes conferring resistance to β-lactams (blaTEM−1), aminoglycosides [aadA1, aadA2, and aph(6)-Id], macrolides [mef (B)], tetracycline (tetA, tetR), and sulphonamides (sul1, sul2, and sul3). Likewise, IncHI2 plasmids carried several insertion sequences including IS1, IS3, IS26, IS1326, and ISApl1. In conclusion, our findings confirmed the involvement of IncX4, IncI2, and IncHI2 plasmids in the dissemination of mcr-1.1 gene in several environmental niches, as in samples of retail meat originating from different geographical regions. In contrast to IncX4 and IncI2, IncHI2 plasmids were more diverse and carried additional genes for resistance to heavy metals and multiple antimicrobials.

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Genetic Analysis, Expression and Molecular Characterization of BoGSL-ELONG, a Major Gene Involved in the Aliphatic Glucosinolate Pathway of Brassica Species

Genetics ◽

10.1093/genetics/162.4.1937 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1937-1943

Author(s):

Genyi Li ◽

Carlos F Quiros

Keyword(s):

Gene Expression ◽

Gene Expression Analysis ◽

Major Gene ◽

Brassica Species ◽

Sequence Database ◽

Rt Pcr ◽

Site Mutation ◽

Splicing Site ◽

Aliphatic Glucosinolate

Abstract We cloned a major aliphatic glucosinolate (GSL) gene, BoGSL-ELONG in Brassica oleracea, using the Arabidopsis sequence database. We based our work on an Arabidopsis candidate gene forming part of a gene family coding for isopropyl malate synthetase-like enzymes (IPMS). This gene is presumably responsible for synthesis of GSL possessing side chains consisting of four carbons (4C). The similarity of the Brassica homolog IPMS-Bo from broccoli to its Arabidopsis counterpart IPMS-At was on the order of 78%, both sharing the same number of exons. A nonfunctional allele of the BoGSL-ELONG gene from white cauliflower, based on the absence of 4C GSL in this crop, displayed a 30-bp deletion, which allowed us to develop a codominant marker for 4C-GSL. Gene expression analysis based on RT-PCR revealed a splicing site mutation in the white cauliflower allele. This resulted in a longer transcript containing intron 3, which failed to excise. Perfect cosegregation was observed for broccoli and cauliflower alleles at the IPMS-Bo gene and 4C-GSL content, strongly indicating that this gene indeed corresponds to BoGSL-ELONG. Cloning of two other major genes, BoGSL-ALK and BoGSL-PRO, is underway. The availability of these genes and BoGSL-ELONG is essential for the manipulation of the aliphatic GSL profile of B. oleracea.

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