Ijaq Johny, Chandra Deepika, Ray Malay Kumar, Jagannadham M V
Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India.
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
Front Genet. 2022 Mar 11;13:825269. doi: 10.3389/fgene.2022.825269. eCollection 2022.
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured workflow combining different bioinformatics tools and databases for functional annotation. sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of sp. Lz4W. Our approach emphasizes the importance of addressing the "hypothetical protein problem" for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier-PXD029741.
探索细菌适应极端温度背后的分子机制具有潜在的生物技术应用价值。在本研究中，我们选择了一种适应在南极洲生存的革兰氏阴性嗜冷菌Lz4W菌株，以解析其冷适应的分子机制。对在4°C下生长的分离株进行了蛋白质组分析，以确定负责适应的蛋白质和途径。然而，从表达的蛋白质组中发现许多蛋白质是功能未知的假设蛋白（HPs）。研究这些蛋白质的功能作用可能会为细菌冷适应的生物学理解提供更多信息。因此，我们的研究旨在为这些假设蛋白赋予功能，并在分子水平上理解它们的作用。我们使用了一种结构化的工作流程，结合不同的生物信息学工具和数据库进行功能注释。Lz4W菌株基因组（CP017432，版本1）包含4493个基因和4412个编码序列（CDS），其中743个CDS被注释为假设蛋白。其中，通过蛋白质组分析发现，有61个假设蛋白在蛋白质水平上持续表达。将这61个假设蛋白的氨基酸序列提交到我们的工作流程中，我们成功地为18个假设蛋白赋予了功能。这些蛋白质中的大多数被预测参与冷适应的生物学机制，如肽聚糖代谢、细胞壁组织、ATP水解、外膜流动性、催化作用等。本研究更好地理解了假设蛋白在Lz4W菌株冷适应中的功能意义。我们的方法强调了解决“假设蛋白问题”对于全面理解细胞水平机制的重要性，同时，也提供了将蛋白质组学方法与各种注释和整理方法相结合以表征假设或未表征蛋白质数据的评估。本研究产生的质谱蛋白质组学数据已通过PRIDE存入ProteomeXchange，数据集标识符为PXD029741。
