1
|
Xu J, Li Q, Zhang J, Li X, Sun T. In Silico Structural and Functional Analysis of Cold Shock Proteins in Pseudomonas fluorescens PF08 from Marine Fish. J Food Prot 2021; 84:1446-1454. [PMID: 33852731 DOI: 10.4315/jfp-21-044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022]
Abstract
ABSTRACT Pseudomonas fluorescens is a specific spoilage microorganism of refrigerated marine fish, and is highly adapted to low temperature. Cold shock proteins (CSPs) play an important role in cold adaptation of bacteria. In this study, CSP genes were identified from the genome of P. fluorescens PF08 by search of the conserved domain of CSPs with HMMER software, and the CSP physicochemical properties, structures, and functions were analyzed through bioinformatics. Five typical CSPs were identified in the P. fluorescens PF08 genome (PfCSPs). All five PfCSPs are small hydrophilic acidic proteins with a molecular mass of ca. 7.4 kDa. They are located in the cytoplasm and are nonsecretory and nontransmembrane proteins. Multiple sequence alignment analysis indicated that the CSPs are highly conserved between species, especially in DNA-binding sites and RNA-binding motifs that can bind to single-stranded DNA and RNA. The five PfCSPs clustered with CspD from Escherichia coli and Salmonella Typhimurium, which suggests a close homology and high functional similarity among the five PfCSPs and CspD. The secondary and tertiary structures of the PfCSPs are in accordance with the characteristics of the CSP family, and ligand binding sites with higher likelihood were found in PfCSPs. The five PfCSPs were predicted to interact with some of the same proteins that are involved in virulence, stress responses (including to low temperature), cell growth, ribosome assembly, and RNA degradation. The results provide further elucidation of the function of CSPs in adaptation to low temperatures by P. fluorescens. HIGHLIGHTS
Collapse
Affiliation(s)
- Jinxiu Xu
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Qiuying Li
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Jingyang Zhang
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Xuepeng Li
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| | - Tong Sun
- College of Food Science and Engineering, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, People's Republic of China
| |
Collapse
|
2
|
Goh KJ, Ero R, Yan XF, Park JE, Kundukad B, Zheng J, Sze SK, Gao YG. Translational GTPase BipA Is Involved in the Maturation of a Large Subunit of Bacterial Ribosome at Suboptimal Temperature. Front Microbiol 2021; 12:686049. [PMID: 34326822 PMCID: PMC8313970 DOI: 10.3389/fmicb.2021.686049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
BPI-inducible protein A (BipA), a highly conserved paralog of the well-known translational GTPases LepA and EF-G, has been implicated in bacterial motility, cold shock, stress response, biofilm formation, and virulence. BipA binds to the aminoacyl-(A) site of the bacterial ribosome and establishes contacts with the functionally important regions of both subunits, implying a specific role relevant to the ribosome, such as functioning in ribosome biogenesis and/or conditional protein translation. When cultured at suboptimal temperatures, the Escherichia coli bipA genomic deletion strain (ΔbipA) exhibits defects in growth, swimming motility, and ribosome assembly, which can be complemented by a plasmid-borne bipA supplementation or suppressed by the genomic rluC deletion. Based on the growth curve, soft agar swimming assay, and sucrose gradient sedimentation analysis, mutation of the catalytic residue His78 rendered plasmid-borne bipA unable to complement its deletion phenotypes. Interestingly, truncation of the C-terminal loop of BipA exacerbates the aforementioned phenotypes, demonstrating the involvement of BipA in ribosome assembly or its function. Furthermore, tandem mass tag-mass spectrometry analysis of the ΔbipA strain proteome revealed upregulations of a number of proteins (e.g., DeaD, RNase R, CspA, RpoS, and ObgE) implicated in ribosome biogenesis and RNA metabolism, and these proteins were restored to wild-type levels by plasmid-borne bipA supplementation or the genomic rluC deletion, implying BipA involvement in RNA metabolism and ribosome biogenesis. We have also determined that BipA interacts with ribosome 50S precursor (pre-50S), suggesting its role in 50S maturation and ribosome biogenesis. Taken together, BipA demonstrates the characteristics of a bona fide 50S assembly factor in ribosome biogenesis.
Collapse
Affiliation(s)
- Kwok Jian Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rya Ero
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jung-Eun Park
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
3
|
Choi E, Hwang J. The GTPase BipA expressed at low temperature in Escherichia coli assists ribosome assembly and has chaperone-like activity. J Biol Chem 2018; 293:18404-18419. [PMID: 30305394 DOI: 10.1074/jbc.ra118.002295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
BPI-inducible protein A (BipA) is a conserved ribosome-associated GTPase in bacteria that is structurally similar to other GTPases associated with protein translation, including IF2, EF-Tu, and EF-G. Its binding site on the ribosome appears to overlap those of these translational GTPases. Mutations in the bipA gene cause a variety of phenotypes, including cold and antibiotics sensitivities and decreased pathogenicity, implying that BipA may participate in diverse cellular processes by regulating translation. According to recent studies, a bipA-deletion strain of Escherichia coli displays a ribosome assembly defect at low temperature, suggesting that BipA might be involved in ribosome assembly. To further investigate BipA's role in ribosome biogenesis, here, we compared and analyzed the ribosomal protein compositions of MG1655 WT and bipA-deletion strains at 20 °C. Aberrant 50S ribosomal subunits (i.e. 44S particles) accumulated in the bipA-deletion strain at 20 °C, and the ribosomal protein L6 was absent in these 44S particles. Furthermore, bipA expression was significantly stimulated at 20 °C, suggesting that it encodes a cold shock-inducible GTPase. Moreover, the transcriptional regulator cAMP receptor protein (CRP) positively promoted bipA expression only at 20 °C. Importantly, GFP and α-glucosidase refolding assays revealed that BipA has chaperone activity. Our findings indicate that BipA is a cold shock-inducible GTPase that participates in 50S ribosomal subunit assembly by incorporating the L6 ribosomal protein into the 44S particle during the assembly.
Collapse
Affiliation(s)
- Eunsil Choi
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea
| | - Jihwan Hwang
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea.
| |
Collapse
|
4
|
Ng TW, Ip M, Chao CYH, Tang JW, Lai KP, Fu SC, Leung WT, Lai KM. Differential gene expression in Escherichia coli during aerosolization from liquid suspension. Appl Microbiol Biotechnol 2018; 102:6257-6267. [DOI: 10.1007/s00253-018-9083-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/29/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
|
5
|
Hücker SM, Simon S, Scherer S, Neuhaus K. Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation. FEMS Microbiol Lett 2016; 364:fnw262. [PMID: 27856567 DOI: 10.1093/femsle/fnw262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 12/24/2022] Open
Abstract
The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5'UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally.
Collapse
Affiliation(s)
- Sarah Maria Hücker
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Svenja Simon
- Chair for Data Analysis and Visualization, Department of Computer and Information Science, University of Konstanz, Box 78, 78457 Konstanz, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| |
Collapse
|
6
|
A novel role for Crp in controlling magnetosome biosynthesis in Magnetospirillum gryphiswaldense MSR-1. Sci Rep 2016; 6:21156. [PMID: 26879571 PMCID: PMC4754748 DOI: 10.1038/srep21156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/18/2016] [Indexed: 01/10/2023] Open
Abstract
Magnetotactic bacteria (MTB) are specialized microorganisms that synthesize intracellular magnetite particles called magnetosomes. Although many studies have focused on the mechanism of magnetosome synthesis, it remains unclear how these structures are formed. Recent reports have suggested that magnetosome formation is energy dependent. To investigate the relationship between magnetosome formation and energy metabolism, a global regulator, named Crp, which mainly controls energy and carbon metabolism in most microorganisms, was genetically disrupted in Magnetospirillum gryphiswaldense MSR-1. Compared with the wild-type or complemented strains, the growth, ferromagnetism and intracellular iron content of crp-deficient mutant cells were dramatically decreased. Transmission electron microscopy (TEM) showed that magnetosome synthesis was strongly impaired by the disruption of crp. Further gene expression profile analysis showed that the disruption of crp not only influenced genes related to energy and carbon metabolism, but a series of crucial magnetosome island (MAI) genes were also down regulated. These results indicate that Crp is essential for magnetosome formation in MSR-1. This is the first time to demonstrate that Crp plays an important role in controlling magnetosome biomineralization and provides reliable expression profile data that elucidate the mechanism of Crp regulation of magnetosome formation in MSR-1.
Collapse
|
7
|
Uppal S, Jawali N. The cyclic AMP receptor protein (CRP) regulates mqsRA, coding for the bacterial toxin-antitoxin gene pair, in Escherichia coli. Res Microbiol 2015; 167:58-62. [PMID: 26408451 DOI: 10.1016/j.resmic.2015.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/03/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022]
Abstract
Bacterial persisters represent a small number of slow-growing antibiotic-tolerant cells among populations of rapidly growing cells, and are the main cause of frequent recurrent infections. MqsR-MqsA, the toxin-antitoxin (TA) pair, is the most frequently induced TA system associated with antibiotic persistence in Escherichia coli. In this study, we show that the cyclic AMP receptor protein (CRP) indirectly upregulates mqsRA transcription. We also show that CRP plays an important role in antibiotic persistence, which seems to be partially mediated through MqsRA. Overall, this study highlights the role of CRP as an important regulator of antibiotic persistence in E. coli.
Collapse
Affiliation(s)
- Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - Narendra Jawali
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| |
Collapse
|