Journal Article

Identification and examination of nitrogen metabolic genes in Lelliottia amnigena PTJIIT1005 for their ability to perform nitrate remediation

Thakur, Preeti, Gauba, Pammi

2023

Overview

Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media . The annotation was done related to nitrogen metabolic genes using the PATRIC, RAST tools, and PGAP from the genome sequence of this bacterium. Multiple sequence alignments and phylogenetic analysis of respiratory nitrate reductase, assimilatory nitrate reductase, nitrite reductase, glutamine synthetase, hydroxylamine reductase, nitric oxide reductase genes from PTJIIT1005 were done to find out sequence identities with the most similar species. The identification of operon arrangement in bacteria was also identified. The PATRIC KEGG feature mapped the N-metabolic pathway to identify the chemical process, and the 3D structure of representative enzymes was also elucidated. The putative protein 3D structure was analyzed using I-TASSER software. It gave good quality protein models of all nitrogen metabolism genes and showed good sequence identity with reference templates, approximately 81–99%, except for two genes; assimilatory nitrate reductase and nitrite reductase. This study suggested that PTJIIT1005 can remove N-nitrate from water because of having N-assimilation and denitrification genes.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Annotations / Assimilation / Bacteria / Bacteria - metabolism / Biomedical and Life Sciences / Bioremediation / Denitrification / E coli / Enterobacter / Enterobacteriaceae / Enzymes / Genes / Genetic aspects / Genetic engineering / Genome sequence / Genomes / Genomics / Glutamate-ammonia ligase / Glutamine / Hydroxylamine reductase / Lelliottia amnigena / Life Sciences / Metabolic pathways / Metabolism / Methods / Microarrays / Microbial Genetics and Genomics / N-metabolic pathway / Nitrate reductase / Nitrate Reductase - genetics / Nitrate Reductase - metabolism / Nitrates / Nitrates - metabolism / Nitric oxide / Nitric-oxide reductase / Nitrite reductase / Nitrite Reductases - genetics / Nitrite Reductases - metabolism / Nitrogen / Nitrogen - metabolism / Nucleotide sequence / Phylogenetics / Phylogeny / Plant Genetics and Genomics / Protein structure / Protein turnover / Proteins / Proteomics / Reductases / Respiration / Transfer RNA