1
|
Nabi B, Kumawat M, Ahlawat N, Ahlawat S. Molecular, Structural, and Functional Diversity of Universal Stress Proteins (USPs) in Bacteria, Plants, and Their Biotechnological Applications. Protein J 2024; 43:437-446. [PMID: 38492187 DOI: 10.1007/s10930-024-10192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival. We discussed the different types Of USPs and their role, aiming to carry out fundamental research in this field to identify significant constraints for better understanding of USP functions at molecular level. Additionally, we discussed concepts and research techniques that could help overcome these hurdles and facilitate new molecular approaches to better understand and target USPs as important stress adaptation and survival regulators. Although the precise characteristics of USPs are still unclear, numerous innovative uses have already been developed, tested, and implemented. Complementary approaches to basic research and applications, as well as new technology and analytical techniques, may offer insights into the cryptic but crucial activities of USPs in various living systems.
Collapse
Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India.
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Allahabad, 211007, India
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India.
| |
Collapse
|
2
|
Luo D, Wu Z, Bai Q, Zhang Y, Huang M, Huang Y, Li X. Universal Stress Proteins: From Gene to Function. Int J Mol Sci 2023; 24:ijms24054725. [PMID: 36902153 PMCID: PMC10003552 DOI: 10.3390/ijms24054725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Universal stress proteins (USPs) exist across a wide range of species and are vital for survival under stressful conditions. Due to the increasingly harsh global environmental conditions, it is increasingly important to study the role of USPs in achieving stress tolerance. This review discusses the role of USPs in organisms from three aspects: (1) organisms generally have multiple USP genes that play specific roles at different developmental periods of the organism, and, due to their ubiquity, USPs can be used as an important indicator to study species evolution; (2) a comparison of the structures of USPs reveals that they generally bind ATP or its analogs at similar sequence positions, which may underlie the regulatory role of USPs; and (3) the functions of USPs in species are diverse, and are generally directly related to the stress tolerance. In microorganisms, USPs are associated with cell membrane formation, whereas in plants they may act as protein chaperones or RNA chaperones to help plants withstand stress at the molecular level and may also interact with other proteins to regulate normal plant activities. This review will provide directions for future research, focusing on USPs to provide clues for the development of stress-tolerant crop varieties and for the generation of novel green pesticide formulations in agriculture, and to better understand the evolution of drug resistance in pathogenic microorganisms in medicine.
Collapse
|
3
|
de Souza CS, Torres AG, Caravelli A, Silva A, Polatto JM, Piazza RMF. Characterization of the universal stress protein F from atypical enteropathogenic Escherichia coli and its prevalence in Enterobacteriaceae. Protein Sci 2016; 25:2142-2151. [PMID: 27616205 PMCID: PMC5119564 DOI: 10.1002/pro.3038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/25/2016] [Accepted: 09/06/2016] [Indexed: 01/06/2023]
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) are heterogeneous strains in terms of serotypes, adherence patterns and the presence of novel virulence factors. This heterogeneity is intriguing, promoting studies trying to characterize these novel proteins and to better comprehend this pathotype group. In a previous study analyzing low-molecular mass proteomes of four representative aEPEC strains of three different adhesion phenotypes, we classified proteins according to their annotated function, with most of them being involved in metabolism and transport; while some of them were classified as hypothetical proteins. The majority of the hypothetical proteins were homologue products of genes identified in the genome of enterohemorrhagic E. coli. One of the hypothetical proteins was annotated as Z2335, with orthologue in EPEC, and by bioinformatics analysis, this protein was revealed to be the universal stress protein F (UspF). Thus, herein we successfully obtained a recombinant UspF protein from aEPEC, which is a α/β, ATP-binding protein involved in stress response, with comparable protein production among the four studied strains, but showing noteworthy differences when cultivated in different stress conditions, also present in other enterobacterial species, such as Shigella sonnei and Citrobacter freundii. Furthermore, our results confirm that the Usp protein superfamily encompasses a conserved group of proteins involved in stress resistance in aEPEC and other Enterobacteriaceae.
Collapse
Affiliation(s)
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | | | - Anderson Silva
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Juliana M Polatto
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Roxane M F Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| |
Collapse
|
4
|
Xu Y, Guo J, Jin X, Kim JS, Ji Y, Fan S, Ha NC, Quan CS. Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli. BMC STRUCTURAL BIOLOGY 2016; 16:3. [PMID: 26865045 PMCID: PMC4750201 DOI: 10.1186/s12900-016-0053-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022]
Abstract
Background The universal stress proteins (USP) family member UspE is a tandem-type USP that consists of two Usp domains. The UspE expression levels of the Escherichia coli (E. coli) become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. It has been shown that UspA family members are survival factors during cellular growth arrest. The structures and functions of the UspA family members control the growth of E. coli in animal hosts. While several UspA family members have known structures, the structure of E. coli UspE remains to be elucidated. Results To understand the biochemical function of UspE, we have determined the crystal structure of E. coli UspE at 3.2 Å resolution. The asymmetric unit contains two protomers related by a non-crystallographic symmetry, and each protomer contains two tandem Usp domains. The crystal structure shows that UspE is folded into a fan-shaped structure similar to that of the tandem-type Usp protein PMI1202 from Proteus mirabilis, and it has a hydrophobic cavity that binds its ligand. Structural analysis revealed that E. coli UspE has two metal ion binding sites, and isothermal titration calorimetry suggested the presence of two Cd2+ binding sites with a Kd value of 38.3–242.7 μM. Structural analysis suggested that E. coli UspE has two Cd2+ binding sites (Site I: His117, His 119; Site II: His193, His244). Conclusion The results show that the UspE structure has a hydrophobic pocket. This pocket is strongly bound to an unidentified ligand. Combined with a previous study, the ligand is probably related to an intermediate in lipid A biosynthesis. Subsequently, sequence analysis found that UspE has an ATP binding motif (Gly269- X2-Gly272-X9-Gly282-Asn) in its C-terminal domain, which was confirmed by in vitro ATPase activity monitored using Kinase-Glo® Luminescent Kinase Assay. However, the residues constituting this motif were disordered in the crystal structure, reflecting their intrinsic flexibility. ITC experiments revealed that the UspE probably has two Cd2+ binding sites. The His117, His 119, His193, and His244 residues within the β-barrel domain are necessary for Cd2+ binding to UspE protein. As mentioned above, USPs are associated with several functions, such as cadmium binding, ATPase function, and involvement in lipid A biosynthesis by some unknown way.
Collapse
Affiliation(s)
- Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. .,Laboratory of Biomedical Material Engineering, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.
| | - Jianyun Guo
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
| | - Xiaoling Jin
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
| | - Jin-Sik Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Ying Ji
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
| | - Shengdi Fan
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Chun-Shan Quan
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China.
| |
Collapse
|