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Liu Y, Ge H, Lu D. Functional proteomics reveals that Slr0237 is a SigE-regulated glycogen debranching enzyme pivotal for glycogen breakdown. Proteomics 2024:e2300222. [PMID: 38581091 DOI: 10.1002/pmic.202300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The group 2 σ factor for RNA polymerase SigE plays important role in regulating central carbon metabolism in cyanobacteria. However, the regulation of SigE for these pathways at a proteome level remains unknown. Using a sigE-deficient strain (ΔsigE) of Synechocystis sp. PCC 6803 and quantitative proteomics, we found that SigE depletion induces differential protein expression for sugar catabolic pathways including glycolysis, oxidative pentose phosphate (OPP) pathway, and glycogen catabolism. Two glycogen debranching enzyme homologues Slr1857 and Slr0237 are found differentially expressed in ΔsigE. Glycogen determination indicated that Δslr0237 accumulated glycogen under photomixotrophic condition but was unable to utilize these reserves in the dark, whereas Δslr1857 accumulates and utilizes glycogen in a similar way as the WT strain does in the same condition. These results suggest that Slr0237 plays the major role as the glycogen debranching enzyme in Synechocystis.
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Affiliation(s)
- Ye Liu
- Science & Technology Department of Sichuan Province, Chengdu, Sichuan, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
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Collins KM, Evans NJ, Torpey JH, Harris JM, Haynes BA, Camp AH, Isaacson RL. Structural Analysis of Bacillus subtilis Sigma Factors. Microorganisms 2023; 11:microorganisms11041077. [PMID: 37110501 PMCID: PMC10141391 DOI: 10.3390/microorganisms11041077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Bacteria use an array of sigma factors to regulate gene expression during different stages of their life cycles. Full-length, atomic-level structures of sigma factors have been challenging to obtain experimentally as a result of their many regions of intrinsic disorder. AlphaFold has now supplied plausible full-length models for most sigma factors. Here we discuss the current understanding of the structures and functions of sigma factors in the model organism, Bacillus subtilis, and present an X-ray crystal structure of a region of B. subtilis SigE, a sigma factor that plays a critical role in the developmental process of spore formation.
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Affiliation(s)
- Katherine M Collins
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Nicola J Evans
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - James H Torpey
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jonathon M Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Bethany A Haynes
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Amy H Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
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Oh Y, Lee HN, Ko EM, Jeong JA, Park SW, Oh JI. Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions. J Microbiol 2023; 61:297-315. [PMID: 36847970 DOI: 10.1007/s12275-023-00026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eon-Min Ko
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Ji-A Jeong
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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Hernandez-Pando R, Shin SJ, Clark S, Casonato S, Becerril-Zambrano M, Kim H, Boldrin F, Mata-Espinoza D, Provvedi R, Arbues A, Marquina-Castillo B, Cioetto Mazzabò L, Barrios-Payan J, Martin C, Cho SN, Williams A, Manganelli R. Construction and Characterization of the Mycobacterium tuberculosis sigE fadD26 Unmarked Double Mutant as a Vaccine Candidate. Infect Immun 2019; 88:e00496-19. [PMID: 31591165 DOI: 10.1128/IAI.00496-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/30/2019] [Indexed: 01/17/2023] Open
Abstract
Despite the great increase in the understanding of the biology and pathogenesis of Mycobacterium tuberculosis achieved by the scientific community in recent decades, tuberculosis (TB) still represents one of the major threats to global human health. The only available vaccine (Mycobacterium bovis BCG) protects children from disseminated forms of TB but does not effectively protect adults from the respiratory form of the disease, making the development of new and more-efficacious vaccines against the pulmonary forms of TB a major goal for the improvement of global health. Among the different strategies being developed to reach this goal is the construction of attenuated strains more efficacious and safer than BCG. We recently showed that a sigE mutant of M. tuberculosis was more attenuated and more efficacious than BCG in a mouse model of infection. In this paper, we describe the construction and characterization of an M. tuberculosis sigE fadD26 unmarked double mutant fulfilling the criteria of the Geneva Consensus for entering human clinical trials. The data presented suggest that this mutant is even more attenuated and slightly more efficacious than the previous sigE mutant in different mouse models of infection and is equivalent to BCG in a guinea pig model of infection.
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