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Hu W, Huo X, Bai H, Chen Z, Zhang J, Yang H, Feng S. Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress. World J Microbiol Biotechnol 2024; 40:105. [PMID: 38386219 DOI: 10.1007/s11274-024-03924-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.
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Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingyu Huo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Haochen Bai
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Zongling Chen
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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2
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Heßling LD, Troost-Kind B, Weiß M. NAADP-binding proteins - Linking NAADP signaling to cancer and immunity. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119531. [PMID: 37394011 DOI: 10.1016/j.bbamcr.2023.119531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
NAADP is one of the most potent calcium mobilizing second messengers. Only recently, two NAADP-binding proteins have been identified: HN1L/JPT2 and LSM12. Further, ASPDH was suggested as a less selective binding partner. Apart from this newly uncovered link, little is known about the shared mechanisms between these proteins. The aim of this review is to assess potential functional connections between NAADP and its binding proteins. We here give a description of two major links. For one, HN1L/JPT2 and LSM12 both have potent oncogenic functions in several cancer types. Second, they are involved in similar cellular pathways in both cancer and immunity.
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Affiliation(s)
- Louisa D Heßling
- The Calcium Signaling Group, Dept. of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
| | - Berit Troost-Kind
- The Calcium Signaling Group, Dept. of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Mariella Weiß
- The Calcium Signaling Group, Dept. of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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Mikhaylina A, Lekontseva N, Marchenkov V, Kolesnikova V, Khairetdinova A, Nikonov O, Balobanov V. The New Functional Hybrid Chaperone Protein ADGroEL-SacSm. Molecules 2023; 28:6196. [PMID: 37687025 PMCID: PMC10488932 DOI: 10.3390/molecules28176196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The creation of new proteins by combining natural domains is a commonly used technique in protein engineering. In this work, we have tested the possibilities and limitations of using circular homo-oligomeric Sm-like proteins as a basis for attaching other domains. Attachment to such a stable base should bring target domains together and keep them in the correct mutual orientation. We chose a circular homoheptameric Sm-like protein from Sulfolobus acidocaldarius as a stable backbone and the apical domain of the GroEL chaperone protein as the domain of study. This domain by itself, separated from the rest of the GroEL molecule, does not form an oligomeric ring. In our design, the hyperstable SacSm held the seven ADGroELs together and forced them to oligomerize. The designed hybrid protein was obtained and studied with various physical and chemical methods. Stepwise assembly and self-organization of this protein have been shown. First, the SacSm base was assembled, and then ADGroEL was folded on it. Functional testing showed that the obtained fusion protein was able to bind the same non-native proteins as the full-length GroEL chaperone. It also reduced the aggregation of a number of proteins when they were heated, which confirms its chaperone activity. Thus, the engineering path we chose made it possible to create an efficient thermostable chaperone. The result obtained shows the productivity of the way we chose for the creation and stabilization of oligomeric proteins.
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Affiliation(s)
| | | | | | | | | | | | - Vitalii Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str. 4, 142290 Pushchino, Russia
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Qin P, Huang H, Wang J, Jiang T, Zeng N, Wang Q, He Y, Zhou Y. The mechanism of LSM2 in the progression of live hepatocellular carcinoma was analyzed based on bioinformatics. Med Oncol 2023; 40:276. [PMID: 37612479 DOI: 10.1007/s12032-023-02152-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
Comprehensive analysis of the expression and probable function of LSM2 in Live hepatocellular carcinoma (LIHC), and validation via in vitro experiments. Integrated use of database resources to examine the differential expression, survival prognosis, clinicopathological characteristics, and functional enrichment of LSM2 in LIHC. The expression level of LSM2 in LIHC tissues and adjacent tissues was proven via immunohistochemical staining. The biological function of LSM2 in LIHC was detected by cell proliferation, cell cloning, cell scratch, cell migration, and invasion experiments in vitro. TIMER 2.0 and GEPIA indicated that LSM2 was highly expressed in cancers and was strongly associated with survival rates in LIHC, cholangiocarcinoma, breast cancer, and renal clear cell carcinoma. LSM2 was highly expressed in LIHC, which was closely associated to the clinicopathological characteristics of patients, and the overall survival rate and disease-free survival rate of patients with high expression of LSM2 were lower than those with low expression of LSM2. Functional enrichment results revealed that LSM2 was involved to ribosome formation, DNA replication, cell cycle, metabolic processes, JAK-STAT signaling pathways, and FoxO signaling pathways. Knockdown of LSM2 inhibited the proliferation, migration, and invasion of LIHC cells in vitro experiments. LSM2 was highly expressed in LIHC and was related to a poor prognosis. Knockdown of LSM2 could inhibit the proliferation, migration, and invasion of LIHC cells.
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Affiliation(s)
- Peifang Qin
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China
- Department of Clinical Laboratory, Guigang City People's Hospital, Guigang, Guangxi, 537100, China
- Guangxi Medical and Health Key Disciplines Infectious Diseases Key Disciplines, The Second Affiliated Hospital of Guilin Medical College, Guilin, 541004, China
| | - Haitao Huang
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China
| | - Jiahui Wang
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China
| | - Tingting Jiang
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China
| | - Nannan Zeng
- Department of Physiology, Guilin Medical University, Guilin, 541004, China
| | - Qi Wang
- Department of Physiology, Guilin Medical University, Guilin, 541004, China
| | - Yulin He
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China.
| | - Yali Zhou
- Institute of Pathogenic Biology, Guilin Medical University, Guilin, 541004, China.
- Guangxi Medical and Health Key Disciplines Infectious Diseases Key Disciplines, The Second Affiliated Hospital of Guilin Medical College, Guilin, 541004, China.
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Vosseberg J, Stolker D, von der Dunk SHA, Snel B. Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Mol Biol Evol 2023; 40:6985000. [PMID: 36631250 PMCID: PMC9887622 DOI: 10.1093/molbev/msad011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands,Laboratory of Microbiology, Wageningen University & Research, 6700 EH Wageningen, the Netherlands
| | - Daan Stolker
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
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Sun X, Zhang J, Xiao C, Ge Z. Expression profile and prognostic values of LSM family in skin cutaneous melanoma. BMC Med Genomics 2022; 15:238. [DOI: 10.1186/s12920-022-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
The like-Smith (LSM) family is a group of RNA-binding proteins involved in RNA metabolism. However, their involvement in tumors, particularly skin cutaneous melanoma (SKCM), is not fully understood. In this study, we focused on the expression profiles and prognostic values of the LSM family in SKCM.
Methods
Raw data were downloaded from The Cancer Genome Atlas. The expression profile and prognostic value of LSM genes in SKCM were explored using the GEPIA, cBioPortal, and HPA databases. Protein–protein and gene–gene interaction analyses were performed using STRING and GeneMANIA. Enrichment and Cox regression analysis were conducted using R software. The TISIDB database was used to explore the relationship between LSMs and immunomodulators. Receiver operating characteristic curves and nomogram models were constructed to validate prognostic values.
Results
mRNA and protein expression levels of LSM2, LSM4, and LSM12 were significantly elevated in SKCM. The upregulated mRNA expression of LSM2 (p = 0.0013) and LSM4 (p = 0.0043) was significantly correlated with poor overall survival in patients with SKCM, whereas only LSM2 (p = 0.049) overexpression was markedly associated with worse disease-free survival. LSM2 overexpression was an independent risk factor (p = 0.013) and was confirmed to have a high prognostic value in SKCM using the receiver operating characteristic curve (AUC = 0.942) and nomogram models. All LSM genes were identified as genomic mutations, whereas alteration of LSM2 (p = 0.0153) significantly affected the overall survival in patients with SKCM. Significant correlations were observed between LSM family expression, immune cell infiltration, and immunomodulator. Furthermore, function and pathway enrichment analysis showed that the LSM family was mainly RNA binding proteins and involved in RNA splicing and degradation.
Conclusion
Expression profiles and prognostic values of LSM in SKCM were inconsistent. Among the LSM family, only LSM2 may serve as a potential poor prognosticator and immunotherapeutic target of SKCM.
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Marchant JS, Gunaratne GS, Cai X, Slama JT, Patel S. NAADP-binding proteins find their identity. Trends Biochem Sci 2022; 47:235-249. [PMID: 34810081 PMCID: PMC8840967 DOI: 10.1016/j.tibs.2021.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger that releases Ca2+ from endosomes and lysosomes by activating ion channels called two-pore channels (TPCs). However, no NAADP-binding site has been identified on TPCs. Rather, NAADP activates TPCs indirectly by engaging NAADP-binding proteins (NAADP-BPs) that form part of the TPC complex. After a decade of searching, two different NAADP-BPs were recently identified: Jupiter microtubule associated homolog 2 (JPT2) and like-Sm protein 12 (LSM12). These discoveries bridge the gap between NAADP generation and NAADP activation of TPCs, providing new opportunity to understand and manipulate the NAADP-signaling pathway. The unmasking of these NAADP-BPs will catalyze future studies to define the molecular choreography of NAADP action.
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Affiliation(s)
- Jonathan S. Marchant
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA,Correspondence: (J.S. Marchant) and (S. Patel)
| | - Gihan S. Gunaratne
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Xinjiang Cai
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - James T. Slama
- Department of Medicinal and Biological Chemistry, University of Toledo College of Pharmacy and Pharmaceutical Sciences, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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Activation of endo-lysosomal two-pore channels by NAADP and PI(3,5)P2. Five things to know. Cell Calcium 2022; 103:102543. [PMID: 35123238 PMCID: PMC9552313 DOI: 10.1016/j.ceca.2022.102543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/31/2022]
Abstract
Two-pore channels are ancient members of the voltage-gated ion channel superfamily that are expressed predominantly on acidic organelles such as endosomes and lysosomes. Here we review recent advances in understanding how TPCs are activated by their ligands and identify five salient features: (1) TPCs are Ca2+-permeable non-selective cation channels gated by NAADP. (2) NAADP activation is indirect through associated NAADP receptors. (3) TPCs are also Na+-selective channels gated by PI(3,5)P2. (4) PI(3,5)P2 activation is direct through a structurally-resolved binding site. (5) TPCs switch their ion selectivity in an agonist-dependent manner.
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Fando MS, Mikhaylina AO, Lekontseva NV, Tishchenko SV, Nikulin AD. Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum. BIOCHEMISTRY (MOSCOW) 2021; 86:833-842. [PMID: 34284708 DOI: 10.1134/s000629792107004x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure and the RNA-binding properties of the Lsm protein from Halobacterium salinarum have been determined. A distinctive feature of this protein is the presence of a short L4 loop connecting the β3 and β4 strands. Since bacterial Lsm proteins (also called Hfq proteins) have a short L4 loop and form hexamers, whereas archaeal Lsm proteins (SmAP) have a long L4 loop and form heptamers, it has been suggested that the length of the L4 loop may affect the quaternary structure of Lsm proteins. Moreover, the L4 loop covers the region of SmAP corresponding to one of the RNA-binding sites in Hfq, and thus can affect the RNA-binding properties of the protein. Our results show that the SmAP from H. salinarum forms heptamers and possesses the same RNA-binding properties as homologous proteins with the long L4 loop. Therefore, the length of the L4 does not govern the number of monomers in the protein particles and does not affect the RNA-binding properties of Lsm proteins.
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Affiliation(s)
- Maria S Fando
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alisa O Mikhaylina
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nataliya V Lekontseva
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Svetlana V Tishchenko
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey D Nikulin
- Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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