Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120

• Published in: Microbiology spectrum 2021-10, Vol.9 (2), p.e0049021-e0049021
• Main Authors: Yu, Shengchao, Yang, Mingkun, Xiong, Jie, Zhang, Qi, Gao, Xinxin, Miao, Wei, Ge, Feng
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; cyanobacteria; genome annotation; Genome, Bacterial; Genomics and Proteomics; Mass Spectrometry; Nitrogen - metabolism; Nostoc - chemistry; Nostoc - genetics; Nostoc - metabolism; Nostoc sp. PCC 7120; Proteogenomics; Research Article
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/Spectrum.00490-21

Cyanobacteria, capable of oxygenic photosynthesis, play a vital role in nitrogen and carbon cycles. sp. PCC 7120 ( 7120) is a model cyanobacterium commonly used to study cell differentiation and nitrogen metabolism. Although its genome was released in 2002, a high-quality genome annotation remains unavailable for this model cyanobacterium. Therefore, in this study, we performed an in-depth proteogenomic analysis based on high-resolution mass spectrometry (MS) data to refine the genome annotation of 7120. We unambiguously identified 5,519 predicted protein-coding genes and revealed 26 novel genes, 75 revised genes, and 27 different kinds of posttranslational modifications in 7120. A subset of these novel proteins were further validated at both the mRNA and peptide levels. Functional analysis suggested that many newly annotated proteins may participate in nitrogen or cadmium/mercury metabolism in 7120. Moreover, we constructed an updated 7120 database based on our proteogenomic results and presented examples of how the updated database could be used to improve the annotation of proteomic data. Our study provides the most comprehensive annotation of the 7120 genome thus far and will serve as a valuable resource for the study of nitrogen metabolism in 7120. Cyanobacteria are a large group of prokaryotes capable of oxygenic photosynthesis and play a vital role in nitrogen and carbon cycles on Earth. 7120 is a commonly used model cyanobacterium for studying cell differentiation and nitrogen metabolism. In this study, we presented the first comprehensive draft map of the 7120 proteome and a wide range of posttranslational modifications. In addition, we constructed an updated database of 7120 based on our proteogenomic results and presented examples of how the updated database could be used for system-level studies of 7120. Our study provides the most comprehensive annotation of 7120 genome and a valuable resource for the study of nitrogen metabolism in this model cyanobacterium.