d-Alanine Metabolism via d-Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2

• Published in: Applied and environmental microbiology Vol. 88; no. 3; p. e0221921
• Main Authors: Yu, Yang, Yang, Jie, Teng, Zhao-Jie, Zheng, Li-Yuan, Sheng, Qi, Li, Ping-Yi, Fu, Hui-Hui, Li, Chun-Yang, Chen, Yin, Zhang, Yu-Zhong, Ding, Jun-Mei, Chen, Xiu-Lan
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 08.02.2022
• Subjects: Alanine; Alanine - metabolism; Amino acids; Antiviral Agents; Bacteria; Catabolism; Cell walls; Chemical analysis; D-Alanine; Food chains; Food webs; Gammaproteobacteria; Genomes; Metabolism; Microbial Genetics; Microorganisms; Mineralization; Peptidoglycans; Physiology; Pseudoalteromonas; Pseudoalteromonas - genetics; Pseudoalteromonas - metabolism; Seawater; Seawater - microbiology; Transaminases; Transaminases - genetics; Transcription; Water analysis; marine bacteria; d-Ala; d-alanine catabolism; d-alanine; alanine racemase; d-alanine aminotransferase
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.02219-21

As the most abundant d-amino acid (DAA) in the ocean, d-alanine (d-Ala) is a key component of peptidoglycan in the bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of d-Ala through the microbial food web remain largely unknown. In this study, the metabolism of d-Ala by marine bacterium sp. strain CF6-2 was investigated. Based on genomic, transcriptional, and biochemical analyses combined with gene knockout, d-Ala aminotransferase was found to be indispensable for the catabolism of d-Ala in strain CF6-2. Investigation on other marine bacteria also showed that d-Ala aminotransferase gene is a reliable indicator for their ability to utilize d-Ala. Bioinformatic investigation revealed that d-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and represents the predominant group containing d-Ala aminotransferase. Thus, is likely the dominant group to utilize d-Ala via d-Ala aminotransferase to drive the recycling and mineralization of d-Ala in the ocean. As the most abundant d-amino acid in the ocean, d-Ala is a component of the marine DON (dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of d-Ala to drive the recycling and mineralization of d-Ala in the ocean is still largely unknown. The results in this study showed that d-Ala aminotransferase is specific and indispensable for d-Ala catabolism in marine bacteria and that marine bacteria containing d-Ala aminotransferase genes are predominantly widely distributed in global oceans. This study reveals marine d-Ala-utilizing bacteria and the mechanism of their metabolization of d-Ala. The results shed light on the mechanisms of recycling and mineralization of d-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.