Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation.

M V Jagannadham,Deepika Chandra,Johny Ijaq,Malay Kumar Ray

doi:10.3389/fgene.2022.825269

M V Jagannadham, Deepika Chandra + Show 2 more

Open Access

https://doi.org/10.3389/fgene.2022.825269

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Abstract

Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas 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 insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas 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 Pseudomonas 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.

Highlights

Bacterial adaptation to cold environments is a fascinating area of research and reveals a great potential for biotechnological applications
Lz4W during cold adaptation to check whether any of these coding sequences (CDS) labelled as hypothetical proteins (HPs) are expressed at the protein level
HPs constitute about 30–50% of the microbial genomes, and the HP data is rapidly accumulating due to the deluge of sequencing data from sequencing technologies like NGS and mass spectrometry

Summary

Introduction

Bacterial adaptation to cold environments is a fascinating area of research and reveals a great potential for biotechnological applications. Studies on cold adaptation of Antarctic bacteria revealed many of their survival strategies like the ability to control membrane fluidity, catalyze biochemical reactions at frozen temperatures, sense the temperature cues, regulate transcription and translation machinery, and modify protein conformation (Ray et al, 1994; Chintalapati, et al, 2004; Shivaji and Prakash, 2010; Prakash et al, 2010). Modifications in the cell envelop components such as peptidoglycan, lipopolysaccharides (LPS), and exopolysaccharides appear to be an important strategy for cold adaptation (Tribelli and Lopez, 2018). Changes in the catalytic activity of the enzymes, changes in central metabolic activities, post-translational modifications, synthesis of storage polymers, like polyhydroxyalkanoates (PHAs) were reported to be advantageous for bacterial adaptation to cold temperatures (Tribelli and Lopez, 2018; Bargiela et al, 2020)

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