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Nair ZJ, Gao IH, Firras A, Chong KKL, Hill ED, Choo PY, Colomer-Winter C, Chen Q, Manzano C, Pethe K, Kline KA. An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalis. Mol Microbiol 2024; 121:1021-1038. [PMID: 38527904 DOI: 10.1111/mmi.15253] [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: 07/31/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Daptomycin is a last-line antibiotic commonly used to treat vancomycin-resistant Enterococci, but resistance evolves rapidly and further restricts already limited treatment options. While genetic determinants associated with clinical daptomycin resistance (DAPR) have been described, information on factors affecting the speed of DAPR acquisition is limited. The multiple peptide resistance factor (MprF), a phosphatidylglycerol-modifying enzyme involved in cationic antimicrobial resistance, is linked to DAPR in pathogens such as methicillin-resistant Staphylococcus aureus. Since Enterococcus faecalis encodes two paralogs of mprF and clinical DAPR mutations do not map to mprF, we hypothesized that functional redundancy between the paralogs prevents mprF-mediated resistance and masks other evolutionary pathways to DAPR. Here, we performed in vitro evolution to DAPR in mprF mutant background. We discovered that the absence of mprF results in slowed DAPR evolution and is associated with inactivating mutations in ftsH, resulting in the depletion of the chaperone repressor HrcA. We also report that ftsH is essential in the parental, but not in the ΔmprF, strain where FtsH depletion results in growth impairment in the parental strain, a phenotype associated with reduced extracellular acidification and reduced ability for metabolic reduction. This presents FtsH and HrcA as enticing targets for developing anti-resistance strategies.
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Affiliation(s)
- Zeus Jaren Nair
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Iris Hanxing Gao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aslam Firras
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cristina Colomer-Winter
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Qingyan Chen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kevin Pethe
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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2
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Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2024; 121:e2321510121. [PMID: 38635633 PMCID: PMC11046580 DOI: 10.1073/pnas.2321510121] [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: 12/06/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. Escherichia coli adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain. Here, we describe a cryo-EM structure of the complex formed between LpxC and the cytoplasmic domain of LapB (LapBcyto). The structure reveals how LapB exploits both its tetratricopeptide repeat (TPR) motifs and rubredoxin domain to interact with LpxC. Through both in vitro and in vivo analysis, we show that mutations at the LapBcyto/LpxC interface prevent LpxC degradation. Unexpectedly, binding to LapBcyto also inhibits the enzymatic activity of LpxC through allosteric effects reminiscent of LpxC activation by MurA in Pseudomonas aeruginosa. Our findings argue that LapB regulates LPS synthesis in two steps: In the first step, LapB inhibits the activity of LpxC, and in the second step, it commits LpxC to degradation by FtsH.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Cancer Biology Institute, Yale University, West Haven, CT06516
| | - Rajkanwar Nathawat
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
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3
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Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024:e0209023. [PMID: 38534142 DOI: 10.1128/aem.02090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
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Affiliation(s)
- Zachary T Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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4
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Cui Y, Zhao H, Zhang C. Zinc oxide nanoparticles enhance plasmid transfer among growth-promoting endophytes in Arabidopsis thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169682. [PMID: 38163607 DOI: 10.1016/j.scitotenv.2023.169682] [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: 11/19/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Nanoparticles (NPs) hold great promise for agricultural applications, yet their potential impact on exogenous gene transfer within plant remains poorly understood. In this study, we utilized the non-conjugative plasmid pCAMBIA1300, harboring the bialaphos resistance (bar) gene expressed in plant and the kanamycin resistance (kanR) gene as selectable marker in bacteria. Our results revealed a significant increase in the transfer of plasmid (via carrier Escherichia coli DH5α), both intra- and inter-species within the endophyte, when Arabidopsis thaliana was exposed to environmentally relevant level of zinc oxide (ZnO) NPs at a concentration of 0.7 μg/mL throughout its lifespan. Intriguingly, the plasmid exhibited selective transfer to growth-promoting endophytes, such as Enterobacter, Serratia, and Achromobacter, with the presence of ZnO NPs expanding the pool of potential recipients. This result is due to the facilitation of an endophytic and mutualistic lifestyle of invasive E. coli DH5α and the enrichment of beneficial bacteria aided by ZnO NPs. The plant's descendant generations did not express the bar gene, and the endophytes carrying the exogenous plasmid did not transmit it to sub sequent generation. This research provides crucial insights for assessing the potential risks associated with gene contamination and ensuring the safe and sustainable use of NPs in agriculture.
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Affiliation(s)
- Yueting Cui
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Huiru Zhao
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100857, China.
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5
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Wellner SM, Alobaidallah MSA, Fei X, Herrero-Fresno A, Olsen JE. Genome-wide identification of fitness-genes in aminoglycoside-resistant Escherichia coli during antibiotic stress. Sci Rep 2024; 14:4163. [PMID: 38378700 PMCID: PMC10879529 DOI: 10.1038/s41598-024-54169-8] [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: 12/07/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Resistance against aminoglycosides is widespread in bacteria. This study aimed to identify genes that are important for growth of E. coli during aminoglycoside exposure, since such genes may be targeted to re-sensitize resistant E. coli to treatment. We constructed three transposon mutant libraries each containing > 230.000 mutants in E. coli MG1655 strains harboring streptomycin (aph(3″)-Ib/aph(6)-Id), gentamicin (aac(3)-IV), or neomycin (aph(3″)-Ia) resistance gene(s). Transposon Directed Insertion-site Sequencing (TraDIS), a combination of transposon mutagenesis and high-throughput sequencing, identified 56 genes which were deemed important for growth during streptomycin, 39 during gentamicin and 32 during neomycin exposure. Most of these fitness-genes were membrane-located (n = 55) and involved in either cell division, ATP-synthesis or stress response in the streptomycin and gentamicin exposed libraries, and enterobacterial common antigen biosynthesis or magnesium sensing/transport in the neomycin exposed library. For validation, eight selected fitness-genes/gene-clusters were deleted (minCDE, hflCK, clsA and cpxR associated with streptomycin and gentamicin resistance, and phoPQ, wecA, lpp and pal associated with neomycin resistance), and all mutants were shown to be growth attenuated upon exposure to the corresponding antibiotics. In summary, we identified genes that are advantageous in aminoglycoside-resistant E. coli during antibiotic stress. In addition, we increased the understanding of how aminoglycoside-resistant E. coli respond to antibiotic exposure.
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Affiliation(s)
- Sandra Marina Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Mosaed Saleh A Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, 21423, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, 22384, Jeddah, Saudi Arabia
| | - Xiao Fei
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Universidade da Santiago de Compostela (USC), Campus Terra, 27002, Lugo, Spain.
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark.
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6
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Douchant K, He SM, Noordhof C, Greenlaw J, Vancuren S, Schroeter K, Allen-Vercoe E, Sjaarda C, Vanner SJ, Petrof EO, Sheth PM, Guzman M. Defined microbial communities and their soluble products protect mice from Clostridioides difficile infection. Commun Biol 2024; 7:135. [PMID: 38280981 PMCID: PMC10821944 DOI: 10.1038/s42003-024-05778-6] [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] [Received: 08/09/2023] [Accepted: 01/03/2024] [Indexed: 01/29/2024] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated infectious diarrhea. The development of C.difficile infection is tied to perturbations of the bacterial community in the gastrointestinal tract, called the gastrointestinal microbiota. Repairing the gastrointestinal microbiota by introducing lab-designed bacterial communities, or defined microbial communities, has recently shown promise as therapeutics against C.difficile infection, however, the mechanisms of action of defined microbial communities remain unclear. Using an antibiotic- C.difficile mouse model, we report the ability of an 18-member community and a refined 4-member community to protect mice from two ribotypes of C.difficile (CD027, CD078; p < 0.05). Furthermore, bacteria-free supernatant delivered orally to mice from the 4-member community proteolyzed C.difficile toxins in vitro and protected mice from C.difficile infection in vivo (p < 0.05). This study demonstrates that bacteria-free supernatant is sufficient to protect mice from C.difficile; and could be further explored as a therapeutic strategy against C.difficile infection.
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Affiliation(s)
- Katya Douchant
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Shu-Mei He
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Curtis Noordhof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Jill Greenlaw
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Sarah Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Calvin Sjaarda
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Stephen J Vanner
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Elaine O Petrof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Prameet M Sheth
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada.
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, ON, Canada.
| | - Mabel Guzman
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
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Li M, Zhu X, Yu Q, Yu A, Chen L, Kang J, Wang X, Yang T, Yang Q, Long R. FtsH proteases confer protection against salt and oxidative stress in Medicago sativa L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111915. [PMID: 37944702 DOI: 10.1016/j.plantsci.2023.111915] [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: 02/20/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Plant filamentation temperature-sensitive H (FtsH) proteins are ATP-dependent zinc proteases that play an important role in regulating abiotic stress adaptions. Here we explore their potential role in abiotic stress tolerance in alfalfa, an important legume crop. Genomic analysis revealed seventeen MsFtsH genes in five clusters, which generally featured conserved domains and gene structures. Furthermore, the expression of MsFtsHs was found to be tightly associated with abiotic stresses, including osmotic, salt and oxidative stress. In addition, numerous stress responsive cis-elements, including those related to ABA, auxin, and salicylic acid, were identified in their promoter regions. Moreover, MsFtsH8 overexpression was shown to confer tolerance to salt and oxidative stress which was associated with reduced levels of reactive oxygen species, and enhanced expression and activity of antioxidant enzymes. Our results highlight MsFtsHs as key factors in abiotic stress tolerance, and show their potential usefulness for breeding alfalfa and other crops with improved yield and stress tolerance.
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Affiliation(s)
- Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiaoxi Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Qianwen Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Andong Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xue Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Tianhui Yang
- Institute of Animal Sciences, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, PR China
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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8
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Dupuy P, Gutierrez C, Neyrolles O. Modulation of bacterial membrane proteins activity by clustering into plasma membrane nanodomains. Mol Microbiol 2023; 120:502-507. [PMID: 37303242 DOI: 10.1111/mmi.15105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Recent research has demonstrated specific protein clustering within membrane subdomains in bacteria, challenging the long-held belief that prokaryotes lack these subdomains. This mini review provides examples of bacterial membrane protein clustering, discussing the benefits of protein assembly in membranes and highlighting how clustering regulates protein activity.
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Affiliation(s)
- Pierre Dupuy
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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9
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Song H, Choi E, Lee EJ. Membrane-Bound Protease FtsH Protects PhoP from the Proteolysis by Cytoplasmic ClpAP Protease in Salmonella Typhimurium. J Microbiol Biotechnol 2023; 33:1130-1140. [PMID: 37330414 PMCID: PMC10580885 DOI: 10.4014/jmb.2306.06016] [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] [Received: 06/08/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
Among the AAA+ proteases in bacteria, FtsH is a membrane-bound ATP-dependent metalloprotease, which is known to degrade many membrane proteins as well as some cytoplasmic proteins. In the intracellular pathogen Salmonella enterica serovar Typhimurium, FtsH is responsible for the proteolysis of several proteins including MgtC virulence factor and MgtA/MgtB Mg2+ transporters, the transcription of which is controlled by the PhoP/PhoQ two-component regulatory system. Given that PhoP response regulator itself is a cytoplasmic protein and also degraded by the cytoplasmic ClpAP protease, it seems unlikely that FtsH affects PhoP protein levels. Here we report an unexpected role of the FtsH protease protecting PhoP proteolysis from cytoplasmic ClpAP protease. In FtsH-depleted condition, PhoP protein levels decrease by ClpAP proteolysis, lowering protein levels of PhoP-controlled genes. This suggests that FtsH is required for normal activation of PhoP transcription factor. FtsH does not degrade PhoP protein but directly binds to PhoP, thus sequestering PhoP from ClpAP-mediated proteolysis. FtsH's protective effect on PhoP can be overcome by providing excess ClpP. Because PhoP is required for Salmonella's survival inside macrophages and mouse virulence, these data implicate that FtsH's sequestration of PhoP from ClpAP-mediated proteolysis is a mechanism ensuring the amount of PhoP protein during Salmonella infection.
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Affiliation(s)
- Hyungkeun Song
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eunna Choi
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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10
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Lei Y, Li B, Wang X, Wei J, Wang P, Zhao J, Yu F, Qi Y. Chloroplast SRP54 and FtsH protease coordinate thylakoid membrane-associated proteostasis in Arabidopsis. PLANT PHYSIOLOGY 2023; 192:2318-2335. [PMID: 36994815 PMCID: PMC10315307 DOI: 10.1093/plphys/kiad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Thylakoid membrane protein quality control (PQC), which requires the coordination of membrane protein translocation and degradation of unassembled proteins, determines chloroplast development during de-etiolation. Despite numerous efforts, the regulation of this process in land plants is largely unknown. Here, we report the isolation and characterization of pale green Arabidopsis4 (pga4) mutants in Arabidopsis (Arabidopsis thaliana) with defects in chloroplast development during de-etiolation. Map-based cloning and complementation assays confirmed that PGA4 encodes the chloroplast Signal Recognition Particle 54 kDa (cpSRP54) protein. A heterogeneous Light-Harvesting Chlorophyll a/b Binding-Green Fluorescent Protein (LhcB2-GFP) fusion protein was generated as an indicative reporter for cpSRP54-mediated thylakoid translocation. LhcB2-GFP was dysfunctional and degraded to a short-form dLhcB2-GFP during de-etiolation through an N-terminal degradation initiated on thylakoid membranes. Further biochemical and genetic evidence demonstrated that the degradation of LhcB2-GFP to dLhcB2-GFP was disrupted in pga4 and yellow variegated2 (var2) mutants caused by mutations in the Filamentous Temperature-Sensitive H2 (VAR2/AtFtsH2) subunit of thylakoid FtsH. The yeast two-hybrid assay showed that the N-terminus of LhcB2-GFP interacts with the protease domain of VAR2/AtFtsH2. Moreover, the over-accumulated LhcB2-GFP in pga4 and var2 formed protein aggregates, which were insoluble in mild nonionic detergents. Genetically, cpSRP54 is a suppressor locus for the leaf variegation phenotype of var2. Together, these results demonstrate the coordination of cpSRP54 and thylakoid FtsH in maintaining thylakoid membrane PQC during the assembly of photosynthetic complexes and provide a trackable substrate and product for monitoring cpSRP54-dependent protein translocation and FtsH-dependent protein degradation.
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Affiliation(s)
- Yang Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Bilang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaomin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Junyou Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Peiyi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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11
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Guo K, Glatter T, Paczia N, Liesack W. Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress. Appl Environ Microbiol 2023; 89:e0011323. [PMID: 37184406 PMCID: PMC10305061 DOI: 10.1128/aem.00113-23] [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: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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12
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Garrett SC, Philippe C, Kim JG, Wei Y, Johnson KA, Olson S, Graveley BR, Terns MP. Investigation of CRISPR-Independent Phage Resistance Mechanisms Reveals a Role for FtsH in Phage Adsorption to Streptococcus thermophilus. J Bacteriol 2023; 205:e0048222. [PMID: 37255445 PMCID: PMC10294649 DOI: 10.1128/jb.00482-22] [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: 01/06/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Prokaryotes are under constant pressure from phage infection and thus have evolved multiple means of defense or evasion. While CRISPR-Cas constitutes a robust immune system and appears to be the predominant means of survival for Streptococcus thermophilus when facing lytic phage infection, other forms of phage resistance coexist in this species. Here, we show that S. thermophilus strains with deleted CRISPR-Cas loci can still give rise to phage-resistant clones following lytic phage challenge. Notably, non-CRISPR phage-resistant survivors had multiple mutations which would truncate or recode a membrane-anchored host protease, FtsH. Phage adsorption was dramatically reduced in FtsH mutants, implicating this protein in phage attachment. Phages were isolated which could bypass FtsH-based resistance through mutations predicted to alter tape measure protein translation. Together, these results identify key components in phage propagation that are subject to mutation in the molecular arms race between phage and host cell. IMPORTANCE Streptococcus thermophilus is an important organism for production of cultured dairy foods, but it is susceptible to lytic phages which can lead to failed products. Consequently, mechanisms for phage resistance are an active area of research. One such mechanism is CRISPR-Cas, and S. thermophilus is a model organism for the study of this form of adaptive immunity. Here, we expand on known mechanisms with our finding that spontaneous mutations in ftsH, a gene encoding a membrane-anchored protease, protected against phage infection by disrupting phage adsorption. In turn, mutations in phage tail protein genes allowed phages to overcome ftsH-based resistance. Our results identified components in phage propagation that are subject to mutation in the molecular arms race between phage and host.
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Affiliation(s)
- Sandra C. Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Cecile Philippe
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Jenny G. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Katie A. Johnson
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Michael P. Terns
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
- Department of Genetics, University of Georgia Athens, Athens, Georgia, USA
- Department of Microbiology, University of Georgia Athens, Athens, Georgia, USA
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13
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Sha Y, Yan Q, Liu J, Yu J, Xu S, He Z, Ren J, Qu J, Zheng S, Wang G, Dong W. Homologous genes shared between probiotics and pathogens affect the adhesion of probiotics and exclusion of pathogens in the gut mucus of shrimp. Front Microbiol 2023; 14:1195137. [PMID: 37389343 PMCID: PMC10301755 DOI: 10.3389/fmicb.2023.1195137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
Clarifying mechanisms underlying the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine is a central theme for shrimp health. Under experimental manipulation of probiotic strain (i.e., Lactiplantibacillus plantarum HC-2) adhesion to the shrimp mucus, this study tested the core hypothesis that homologous genes shared between probiotic and pathogen would affect the adhesion of probiotics and exclusion of pathogens by regulating the membrane proteins of probiotics. Results indicated that the reduction of FtsH protease activity, which significantly correlated with the increase of membrane proteins, could increase the adhesion ability of L. plantarum HC-2 to the mucus. These membrane proteins mainly involved in transport (glycine betaine/carnitine/choline ABC transporter choS, ABC transporter, ATP synthase subunit a atpB, amino acid permease) and regulation of cellular processes (histidine kinase). The genes encoding the membrane proteins were significantly (p < 0.05) up-regulated except those encoding ABC transporters and histidine kinases in L. plantarum HC-2 when co-cultured with Vibrio parahaemolyticus E1, indicating that these genes could help L. plantarum HC-2 to competitively exclude pathogens. Moreover, an arsenal of genes predicted to be involved in carbohydrate metabolism and bacteria-host interactions were identified in L. plantarum HC-2, indicating a clear strain adaption to host's gastrointestinal tract. This study advances our mechanistic understanding of the selective adhesion of probiotics and competitive exclusion of pathogens in the intestine, and has important implications for screening and applying new probiotics for maintaining gut stability and host health.
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Affiliation(s)
- Yujie Sha
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Jiafeng Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Shicai Xu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jing Ren
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Shiying Zheng
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Shandong Engineering Laboratory of Swine Health Big Data and Intelligent Monitoring, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Guomin Wang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Weiying Dong
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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14
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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15
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Linz B, Sharafutdinov I, Tegtmeyer N, Backert S. Evolution and Role of Proteases in Campylobacter jejuni Lifestyle and Pathogenesis. Biomolecules 2023; 13:biom13020323. [PMID: 36830692 PMCID: PMC9953165 DOI: 10.3390/biom13020323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/26/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Infection with the main human food-borne pathogen Campylobacter jejuni causes campylobacteriosis that accounts for a substantial percentage of gastrointestinal infections. The disease usually manifests as diarrhea that lasts for up to two weeks. C. jejuni possesses an array of peptidases and proteases that are critical for its lifestyle and pathogenesis. These include serine proteases Cj1365c, Cj0511 and HtrA; AAA+ group proteases ClpP, Lon and FtsH; and zinc-dependent protease PqqE, proline aminopeptidase PepP, oligopeptidase PepF and peptidase C26. Here, we review the numerous critical roles of these peptide bond-dissolving enzymes in cellular processes of C. jejuni that include protein quality control; protein transport across the inner and outer membranes into the periplasm, cell surface or extracellular space; acquisition of amino acids and biofilm formation and dispersal. In addition, we highlight their role as virulence factors that inflict intestinal tissue damage by promoting cell invasion and mediating cleavage of crucial host cell factors such as epithelial cell junction proteins. Furthermore, we reconstruct the evolution of these proteases in 34 species of the Campylobacter genus. Finally, we discuss to what extent C. jejuni proteases have initiated the search for inhibitor compounds as prospective novel anti-bacterial therapies.
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Affiliation(s)
- Bodo Linz
- Correspondence: ; Tel.: +49-(0)-9131-8528988
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16
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Hari SB, Morehouse JP, Baker TA, Sauer RT. FtsH degrades kinetically stable dimers of cyclopropane fatty acid synthase via an internal degron. Mol Microbiol 2023; 119:101-111. [PMID: 36456794 PMCID: PMC9851988 DOI: 10.1111/mmi.15009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022]
Abstract
Targeted protein degradation plays important roles in stress responses in all cells. In E. coli, the membrane-bound AAA+ FtsH protease degrades cytoplasmic and membrane proteins. Here, we demonstrate that FtsH degrades cyclopropane fatty acid (CFA) synthase, whose synthesis is induced upon nutrient deprivation and entry into stationary phase. We find that neither the disordered N-terminal residues nor the structured C-terminal residues of the kinetically stable CFA-synthase dimer are required for FtsH recognition and degradation. Experiments with fusion proteins support a model in which an internal degron mediates FtsH recognition as a prelude to unfolding and proteolysis. These findings elucidate the terminal step in the life cycle of CFA synthase and provide new insight into FtsH function.
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17
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Xu W, Gao W, Bu Q, Li Y. Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism. Biomolecules 2022; 12:biom12121848. [PMID: 36551276 PMCID: PMC9775585 DOI: 10.3390/biom12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Hundreds of proteins work together in microorganisms to coordinate and control normal activity in cells. Their degradation is not only the last step in the cell's lifespan but also the starting point for its recycling. In recent years, protein degradation has been extensively studied in both eukaryotic and prokaryotic organisms. Understanding the degradation process is essential for revealing the complex regulatory network in microorganisms, as well as further artificial reconstructions and applications. This review will discuss several studies on protein quality-control family members Lon, FtsH, ClpP, the proteasome in Streptomyces, and a few classical model organisms, mainly focusing on their structure, recognition mechanisms, and metabolic influences.
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Affiliation(s)
- Weifeng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wenli Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qingting Bu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
- Correspondence:
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18
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Zhang H, Chen C, Yang Z, Ye L, Miao J, Lan Y, Wang Q, Ye Z, Cao Y, Liu G. Combined transcriptomic and proteomic analysis of the antibacterial mechanisms of an antimicrobial substance produced by Lactobacillus paracasei FX-6 against colistin-resistant Escherichia coli. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
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Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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20
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An in silico reverse vaccinology study of Brachyspira pilosicoli, the causative organism of intestinal spirochaetosis, to identify putative vaccine candidates. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Mahmoud SA, Aldikacti B, Chien P. ATP hydrolysis tunes specificity of a AAA+ protease. Cell Rep 2022; 40:111405. [PMID: 36130509 DOI: 10.1016/j.celrep.2022.111405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
In bacteria, AAA+ proteases such as Lon and ClpXP degrade substrates with exquisite specificity. These machines capture the energy of ATP hydrolysis to power unfolding and degradation of target substrates. Here, we show that a mutation in the ATP binding site of ClpX shifts protease specificity to promote degradation of normally Lon-restricted substrates. However, this ClpX mutant is worse at degrading ClpXP targets, suggesting an optimal balance in substrate preference for a given protease that is easy to alter. In vitro, wild-type ClpXP also degrades Lon-restricted substrates more readily when ATP levels are reduced, similar to the shifted specificity of mutant ClpXP, which has altered ATP hydrolysis kinetics. Based on these results, we suggest that the rates of ATP hydrolysis not only power substrate unfolding and degradation, but also tune protease specificity. We consider various models for this effect based on emerging structures of AAA+ machines showing conformationally distinct states.
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Affiliation(s)
- Samar A Mahmoud
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Berent Aldikacti
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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22
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Chloroplast envelope ATPase PGA1/AtFtsH12 is required for chloroplast protein accumulation and cytosol-chloroplast protein homeostasis in Arabidopsis. J Biol Chem 2022; 298:102489. [PMID: 36113581 PMCID: PMC9574505 DOI: 10.1016/j.jbc.2022.102489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
The establishment of photosynthetic protein complexes during chloroplast development requires the influx of a large number of chloroplast proteins that are encoded by the nuclear genome, which is critical for cytosol and chloroplast protein homeostasis and chloroplast development. However, the mechanisms regulating this process are still not well understood in higher plants. Here, we report the isolation and characterization of the pale green Arabidopsis pga1-1 mutant, which is defective in chloroplast development and chloroplast protein accumulation. Using genetic and biochemical evidence, we reveal that PGA1 encodes AtFtsH12, a chloroplast envelope-localized protein of the FtsH family proteins. We determined a G703R mutation in the GAD motif of the conserved ATPase domain renders the pga1-1 a viable hypomorphic allele of the essential gene AtFtsH12. In de-etiolation assays, we showed that the accumulation of photosynthetic proteins and the expression of photosynthetic genes were impaired in pga1-1. Using the FNRctp-GFP and pTAC2-GFP reporters, we demonstrated that AtFtsH12 was required for the accumulation of chloroplast proteins in vivo. Interestingly, we identified an increase in expression of the mutant AtFtsH12 gene in pga1-1, suggesting a feedback regulation. Moreover, we found that cytosolic and chloroplast proteostasis responses were triggered in pga1-1. Together, taking advantage of the novel pga1-1 mutant, we demonstrate the function of AtFtsH12 in chloroplast protein homeostasis and chloroplast development.
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23
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Morehouse JP, Baker TA, Sauer RT. FtsH degrades dihydrofolate reductase by recognizing a partially folded species. Protein Sci 2022; 31:e4410. [PMID: 36630366 PMCID: PMC9601784 DOI: 10.1002/pro.4410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/14/2023]
Abstract
AAA+ proteolytic machines play essential roles in maintaining and rebalancing the cellular proteome in response to stress, developmental cues, and environmental changes. Of the five AAA+ proteases in Escherichia coli, FtsH is unique in its attachment to the inner membrane and its function in degrading both membrane and cytosolic proteins. E. coli dihydrofolate reductase (DHFR) is a stable and biophysically well-characterized protein, which a previous study found resisted FtsH degradation despite the presence of an ssrA degron. By contrast, we find that FtsH degrades DHFR fused to a long peptide linker and ssrA tag. Surprisingly, we also find that FtsH degrades DHFR with shorter linkers and ssrA tag, and without any linker or tag. Thus, FtsH must be able to recognize a sequence element or elements within DHFR. We find that FtsH degradation of DHFR is noncanonical in the sense that it does not rely upon recognition of an unstructured polypeptide at or near the N-terminus or C-terminus of the substrate. Results using peptide-array experiments, mutant DHFR proteins, and fusion proteins suggest that FtsH recognizes an internal sequence in a species of DHFR that is partially unfolded. Overall, our findings provide insight into substrate recognition by FtsH and indicate that its degradation capacity is broader than previously reported.
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Affiliation(s)
- Juhee P. Morehouse
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Tania A. Baker
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Robert T. Sauer
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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24
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Kudzhaev AM, Andrianova AG, Gustchina AE, Smirnov IV, Rotanova TV. ATP-Dependent Lon Proteases in the Cellular Protein Quality Control System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Pu T, Mo Z, Su L, Yang J, Wan K, Wang L, Liu R, Liu Y. Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L. BMC Genomics 2022; 23:503. [PMID: 35831784 PMCID: PMC9281163 DOI: 10.1186/s12864-022-08719-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key gene for plant chloroplast development and photosynthesis regulation. In addition, the ftsH gene is also involved in plant response to stress. At present, the research and analysis of the ftsH gene family are conducted in microorganisms such as Escherichia coli and Oenococcus and various plants such as Arabidopsis, pear, rice, and corn. However, analysis reports on ftsH genes from tobacco (Nicotiana tabacum L.), an important model plant, are still lacking. Since ftsH genes regulate plant growth and development, it has become necessary to systematically study this gene in an economically important plant like tobacco. RESULTS This is the first study to analyze the ftsH gene from Nicotiana tabacum L. K326 (NtftsH). We identified 20 ftsH genes from the whole genome sequence, renamed them according to their chromosomal locations, and divided them into eight subfamilies. These 20 NtftsH genes were unevenly distributed across the 24 chromosomes. We found four pairs of fragment duplications. We further investigated the collinearity between these genes and related genes in five other species. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified differential expression patterns of NtftsH in different tissues and under various abiotic stress conditions. CONCLUSIONS This study provides a comprehensive analysis of the NtftsH gene family. The exon-intron structure and motif composition are highly similar in NtftsH genes that belong to the same evolutionary tree branch. Homology analysis and phylogenetic comparison of ftsH genes from several different plants provide valuable clues for studying the evolutionary characteristics of NtftsH genes. The NtftsH genes play important roles in plant growth and development, revealed by their expression levels in different tissues as well as under different stress conditions. Gene expression and phylogenetic analyses will provide the basis for the functional analysis of NtftsH genes. These results provide a valuable resource for a better understanding of the biological role of the ftsH genes in the tobacco plant.
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Affiliation(s)
- Tianxiunan Pu
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Zejun Mo
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Long Su
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Jing Yang
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Ke Wan
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Linqi Wang
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Renxiang Liu
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China
| | - Yang Liu
- Guizhou Province, College of Tobacco Science of Guizhou University/ Guizhou Key Laboratory for Tobacco Quality, Huaxi District, Guiyang City, 550025, People's Republic of China.
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Li X, Guo R, Zou X, Yao Y, Lu L. The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus. Front Microbiol 2022; 13:861793. [PMID: 35620087 PMCID: PMC9127768 DOI: 10.3389/fmicb.2022.861793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus–host interactions and provide reference information for viral metagenomic analysis in the ocean.
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Affiliation(s)
- Xuejing Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, China
| | - Ruizhe Guo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Yanyan Yao
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
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27
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Atanaskovic I, Sharp C, Press C, Kaminska R, Kleanthous C. Bacterial Competition Systems Share a Domain Required for Inner Membrane Transport of the Bacteriocin Pyocin G from Pseudomonas aeruginosa. mBio 2022; 13:e0339621. [PMID: 35343790 PMCID: PMC9040868 DOI: 10.1128/mbio.03396-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/28/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria exploit a variety of attack strategies to gain dominance within ecological niches. Prominent among these are contact-dependent inhibition (CDI), type VI secretion (T6SS), and bacteriocins. The cytotoxic endpoint of these systems is often the delivery of a nuclease to the cytosol. How such nucleases translocate across the cytoplasmic membrane of Gram-negative bacteria is unknown. Here, we identify a small, conserved, 15-kDa domain, which we refer to as the inner membrane translocation (IMT) domain, that is common to T6SS and bacteriocins and linked to nuclease effector domains. Through fluorescence microscopy assays using intact and spheroplasted cells, we demonstrate that the IMT domain of the Pseudomonas aeruginosa-specific bacteriocin pyocin G (PyoG) is required for import of the toxin nuclease domain to the cytoplasm. We also show that translocation of PyoG into the cytosol is dependent on inner membrane proteins FtsH, a AAA+ATPase/protease, and TonB1, the latter more typically associated with transport of bacteriocins across the outer membrane. Our study reveals that the IMT domain directs the cytotoxic nuclease of PyoG to cross the cytoplasmic membrane and, more broadly, has been adapted for the transport of other toxic nucleases delivered into Gram-negative bacteria by both contact-dependent and contact-independent means. IMPORTANCE Nuclease bacteriocins are potential antimicrobials for the treatment of antibiotic-resistant bacterial infections. While the mechanism of outer membrane translocation is beginning to be understood, the mechanism of inner membrane transport is not known. This study uses PyoG as a model nuclease bacteriocin and defines a conserved domain that is essential for inner membrane translocation and is widespread in other bacterial competition systems. Additionally, the presented data link two membrane proteins, FtsH and TonB1, with inner membrane translocation of PyoG. These findings point to the general importance of this domain to the cellular uptake mechanisms of nucleases delivered by otherwise diverse and distinct bacterial competition systems. The work is also of importance for the design of new protein antibiotics.
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Affiliation(s)
- Iva Atanaskovic
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Connor Sharp
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Cara Press
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state. Commun Biol 2022; 5:257. [PMID: 35322207 PMCID: PMC8943139 DOI: 10.1038/s42003-022-03213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/08/2022] Open
Abstract
AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.
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29
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Ma C, Wang C, Luo D, Yan L, Yang W, Li N, Gao N. Structural insights into the membrane microdomain organization by SPFH family proteins. Cell Res 2022; 32:176-189. [PMID: 34975153 PMCID: PMC8807802 DOI: 10.1038/s41422-021-00598-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023] Open
Abstract
The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and eukaryotes. The widespread Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are enriched in functional membrane microdomains at various subcellular locations, and therefore were hypothesized to play a scaffolding role in microdomain formation. In addition, many SPFH proteins are also implicated in highly specific processes occurring on the membrane. However, none of these functions is understood at the molecular level. Here we report the structure of a supramolecular complex that is isolated from bacterial membrane microdomains and contains two SPFH proteins (HflK and HflC) and a membrane-anchored AAA+ protease FtsH. HflK and HflC form a circular 24-mer assembly, featuring a laterally segregated membrane microdomain (20 nm in diameter) bordered by transmembrane domains of HflK/C and a completely sealed periplasmic vault. Four FtsH hexamers are embedded inside this microdomain through interactions with the inner surface of the vault. These observations provide a mechanistic explanation for the role of HflK/C and their mitochondrial homologs prohibitins in regulating membrane-bound AAA+ proteases, and suggest a general model for the organization and functionalization of membrane microdomains by SPFH proteins.
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Affiliation(s)
- Chengying Ma
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Chengkun Wang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Dingyi Luo
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Lu Yan
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Wenxian Yang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ningning Li
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ning Gao
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China
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Avendaño-Herrera R, Saldivia P, Bethke J, Vargas C, Hernández M. Proteomic analysis reveals Renibacterium salmoninarum grown under iron-limited conditions induces iron uptake mechanisms and overproduction of the 57-kDa protein. JOURNAL OF FISH DISEASES 2022; 45:289-300. [PMID: 34791674 DOI: 10.1111/jfd.13554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Renibacterium salmoninarum, a slow-growing facultative intracellular pathogen, is the causative agent of bacterial kidney disease, a chronic, progressive and granulomatous infection that threatens farmed and wild salmonids worldwide. Pathogenic R. salmoninarum colonizes tissues and invades the host through cell surface-associated and secreted proteins. While correlations between iron acquisition genes and virulence have been demonstrated in vitro, these mechanisms have not undergone proteomic characterization. The present study applied a proteomic approach to elucidate the differences between the virulent Chilean R. salmoninarum H-2 strain and the type strain ATCC 33209T . Analyses were conducted under normal (control) and iron-limited conditions (DIP) emulating the host environment. Interestingly, strain H-2 apparently responded better to the iron-limited condition-for example, only this strain presented a significantly enriched iron ion homeostasis pathway. Furthermore, key virulence factors related to an iron-limited environment were more abundant in strain H-2. Importantly, the lack of iron favoured the expression of the 57-kDa protein in strain H-2, the principal virulence factor for R. salmoninarum. Our findings can be employed in the design and development of treatments targeted to iron uptake mechanisms (e.g. siderophore synthesis or haem uptake), which represents a promising therapeutic approach for treating this persistent fastidious bacterium.
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Affiliation(s)
- Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Pablo Saldivia
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
| | - Jorn Bethke
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Cristian Vargas
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
| | - Mauricio Hernández
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Concepción, Chile
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31
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Tsviklist V, Guest RL, Raivio TL. The Cpx Stress Response Regulates Turnover of Respiratory Chain Proteins at the Inner Membrane of Escherichia coli. Front Microbiol 2022; 12:732288. [PMID: 35154019 PMCID: PMC8831704 DOI: 10.3389/fmicb.2021.732288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/20/2021] [Indexed: 12/03/2022] Open
Abstract
The Cpx envelope stress response is a major signaling pathway monitoring bacterial envelope integrity, activated both internally by excessive synthesis of membrane proteins and externally by a variety of environmental cues. The Cpx regulon is enriched with genes coding for protein folding and degrading factors, virulence determinants, and large envelope-localized complexes. Transcriptional repression of the two electron transport chain complexes, NADH dehydrogenase I and cytochrome bo3, by the Cpx pathway has been demonstrated, however, there is evidence that additional regulatory mechanisms exist. In this study, we examine the interaction between Cpx-regulated protein folding and degrading factors and the respiratory complexes NADH dehydrogenase I and succinate dehydrogenase in Escherichia coli. Here we show that the cellular need for Cpx-mediated stress adaptation increases when respiratory complexes are more prevalent or active, which is demonstrated by the growth defect of Cpx-deficient strains on media that requires a functional electron transport chain. Interestingly, deletion of several Cpx-regulated proteolytic factors and chaperones results in similar growth-deficient phenotypes. Furthermore, we find that the stability of the NADH dehydrogenase I protein complex is lower in cells with a functional Cpx response, while in its absence, protein turnover is impaired. Finally, we demonstrated that the succinate dehydrogenase complex has reduced activity in E. coli lacking the Cpx pathway. Our results suggest that the Cpx two-component system serves as a sentry of inner membrane protein biogenesis, ensuring the function of large envelope protein complexes and maintaining the cellular energy status of the cell.
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Affiliation(s)
- Valeria Tsviklist
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Randi L. Guest
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Tracy L. Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Tracy L. Raivio,
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32
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Yadavalli SS, Yuan J. Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer. J Bacteriol 2022; 204:e0034421. [PMID: 34516282 PMCID: PMC8765417 DOI: 10.1128/jb.00344-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.
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Affiliation(s)
- Srujana S. Yadavalli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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Yi L, Liu B, Nixon PJ, Yu J, Chen F. Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases. FRONTIERS IN PLANT SCIENCE 2022; 13:837528. [PMID: 35463435 PMCID: PMC9020784 DOI: 10.3389/fpls.2022.837528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 05/18/2023]
Abstract
The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.
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Affiliation(s)
- Lanbo Yi
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Bin Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Peter J. Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter J. Nixon, ; orcid.org/0000-0003-1952-6937
| | - Jianfeng Yu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- Jianfeng Yu, ; orcid.org/0000-0001-7174-3803
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
- Feng Chen, ; orcid.org/0000-0002-9054-943X
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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36
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Powell M, Blaskovich MAT, Hansford KA. Targeted Protein Degradation: The New Frontier of Antimicrobial Discovery? ACS Infect Dis 2021; 7:2050-2067. [PMID: 34259518 DOI: 10.1021/acsinfecdis.1c00203] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeted protein degradation aims to hijack endogenous protein quality control systems to achieve direct knockdown of protein targets. This exciting technology utilizes event-based pharmacology to produce therapeutic outcomes, a feature that distinguishes it from classical occupancy-based inhibitor agents. Early degrader candidates display resilience to mutations while possessing potent nanomolar activity and high target specificity. Paired with the rapid advancement of our knowledge in the factors driving targeted degradation, the expansion of this style of therapeutic agent to a range of disease indications is eagerly awaited. In particular, the area of antibiotic discovery is sorely lacking in novel approaches, with the Antimicrobial Resistance (AMR) crisis looming as the next potential global health calamity. Here, the current advances in targeted protein degradation are highlighted, and potential approaches for designing novel antimicrobial protein degraders are proposed, ranging from adaptations of current strategies to completely novel approaches to targeted protein degradation.
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Affiliation(s)
- Matthew Powell
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Karl A. Hansford
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Ivanova A, Ghifari AS, Berkowitz O, Whelan J, Murcha MW. The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly. PLANT PHYSIOLOGY 2021; 186:599-610. [PMID: 33616659 PMCID: PMC8154063 DOI: 10.1093/plphys/kiab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 06/02/2023]
Abstract
ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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Zeng Y, Wang J, Yang C, Ding M, Hamilton PB, Zhang X, Yang C, Zhnag L, Dai X. A Streptomyces globisporus strain kills Microcystis aeruginosa via cell-to-cell contact. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144489. [PMID: 33465632 DOI: 10.1016/j.scitotenv.2020.144489] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) bring economic loss, damage aquatic ecosystems, and produce cyanobacterial toxins that threaten human health. Algicidal bacteria as pathogens can expediate the decline of CyanoHABs. In this study, a Streptomyces globisporus strain (designated G9), isolated from soil near a eutrophic pond, showed high algicidal activity against Microcystis aeruginosa. Experimental results show that G9 preyed on Microcystis through cell-to-cell contact: (1) the hyphae of G9 killed cyanobacterial cells by twining around them, while cells beyond the reach of G9 hyphae were in normal shapes; (2) No algicides were detectable in the supernatant of G9 cultures or G9-Microcystis cocultures. The algicidal ratio of G9 to M. aeruginosa reached 96.7% after 6 days. G9 selectively killed the tested cyanobacterial strains, while it had only minor impacts on the growth of tested Chlorophyceae. Differential gene expression studies show that G9 affected the expression of key genes of M. aeruginosa involved in photosynthesis, microcystin synthesis and cellular emergency responses. Further, the microcystin-LR content decreased gradually with G9 treatment. As the first reported Streptomyces sp. with algicidal (predation) activity requiring cell-to-cell contact with target prey, G9 is a good candidate for the exploration of additional cyanobacteria-bacteria interactions and the development of novel strategies to control CyanoHABs.
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Affiliation(s)
- Yudie Zeng
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Jiayu Wang
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chunyan Yang
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Mengyue Ding
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Paul B Hamilton
- Canadian Museum of Nature, 240 McLeod Street, Ottawa, Ontario K1P 6P4, Canada
| | - Xiaohui Zhang
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Caiyun Yang
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Lei Zhnag
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Xianzhu Dai
- Chongqing Key Laboratory of Bio-resource development for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, China.
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Wang Y, Cao W, Merritt J, Xie Z, Liu H. Characterization of FtsH Essentiality in Streptococcus mutans via Genetic Suppression. Front Genet 2021; 12:659220. [PMID: 33986772 PMCID: PMC8112672 DOI: 10.3389/fgene.2021.659220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
FtsH belongs to the AAA+ ATP-dependent family of proteases, which participate in diverse cellular processes and are ubiquitous among bacteria, chloroplasts, and mitochondria. FtsH is poorly characterized in most organisms, especially compared to other major housekeeping proteases. In the current study, we examined the source of FtsH essentiality in the human oral microbiome species Streptococcus mutans, one of the primary etiological agents of dental caries. By creating a conditionally lethal ftsH mutant, we were able to identify a secondary suppressor missense mutation in the vicR gene, encoding the response regulator of the essential VicRK two-component system (TCS). Transcriptomic analysis of the vicR (G195R) mutant revealed significantly reduced expression of 46 genes, many of which were located within the genomic island Tnsmu2, which harbors the mutanobactin biosynthetic gene cluster. In agreement with the transcriptomic data, deletion of the mutanobactin biosynthetic gene cluster suppressed ftsH essentiality in S. mutans. We also explored the role of FtsH in S. mutans physiology and demonstrated its critical role in stress tolerance, especially acid stress. The presented results reveal the first insights within S. mutans for the pleiotropic regulatory function of this poorly understood global regulator.
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Affiliation(s)
- Yaqi Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health & Science University, Portland, OR, United States.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, United States
| | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
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Ribonuclease J-Mediated mRNA Turnover Modulates Cell Shape, Metabolism and Virulence in Corynebacterium diphtheriae. Microorganisms 2021; 9:microorganisms9020389. [PMID: 33672886 PMCID: PMC7917786 DOI: 10.3390/microorganisms9020389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/16/2023] Open
Abstract
Controlled RNA degradation is a crucial process in bacterial cell biology for maintaining proper transcriptome homeostasis and adaptation to changing environments. mRNA turnover in many Gram-positive bacteria involves a specialized ribonuclease called RNase J (RnJ). To date, however, nothing is known about this process in the diphtheria-causative pathogen Corynebacterium diphtheriae, nor is known the identity of this ribonuclease in this organism. Here, we report that C. diphtheriae DIP1463 encodes a predicted RnJ homolog, comprised of a conserved N-terminal β-lactamase domain, followed by β-CASP and C-terminal domains. A recombinant protein encompassing the β-lactamase domain alone displays 5'-exoribonuclease activity, which is abolished by alanine-substitution of the conserved catalytic residues His186 and His188. Intriguingly, deletion of DIP1463/rnj in C. diphtheriae reduces bacterial growth and generates cell shape abnormality with markedly augmented cell width. Comparative RNA-seq analysis revealed that RnJ controls a large regulon encoding many factors predicted to be involved in biosynthesis, regulation, transport, and iron acquisition. One upregulated gene in the ∆rnj mutant is ftsH, coding for a membrane protease (FtsH) involved in cell division, whose overexpression in the wild-type strain also caused cell-width augmentation. Critically, the ∆rnj mutant is severely attenuated in virulence in a Caenorhabditis elegans model of infection, while the FtsH-overexpressing and toxin-less strains exhibit full virulence as the wild-type strain. Evidently, RNase J is a key ribonuclease in C. diphtheriae that post-transcriptionally influences the expression of numerous factors vital to corynebacterial cell physiology and virulence. Our findings have significant implications for basic biological processes and mechanisms of corynebacterial pathogenesis.
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Zhang G, Zhong F, Chen L, Qin P, Li J, Zhi F, Tian L, Zhou D, Lin P, Chen H, Tang K, Liu W, Jin Y, Wang A. Integrated Proteomic and Transcriptomic Analyses Reveal the Roles of Brucella Homolog of BAX Inhibitor 1 in Cell Division and Membrane Homeostasis of Brucella suis S2. Front Microbiol 2021; 12:632095. [PMID: 33584633 PMCID: PMC7876416 DOI: 10.3389/fmicb.2021.632095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022] Open
Abstract
BAX inhibitor 1 (BI-1) is an evolutionarily conserved transmembrane protein first identified in a screening process for human proteins that suppress BAX-induced apoptosis in yeast cells. Eukaryotic BI-1 is a cytoprotective protein that suppresses cell death induced by multiple stimuli in eukaryotes. Brucella, the causative agent of brucellosis that threatens public health and animal husbandry, contains a conserved gene that encodes BI-1-like protein. To explore the role of the Brucella homolog of BI-1, BrBI, in Brucella suis S2, we constructed the brbI deletion mutant strain and its complemented strain. brbI deletion altered the membrane properties of Brucella suis S2 and decreased its resistance to acidic pH, H2O2, polymyxin B, and lincomycin. Additionally, deleting brbI led to defective growth, cell division, and viability in Brucella suis S2. We then revealed the effect of brbI deletion on the physiological characteristics of Brucella suis S2 via integrated transcriptomic and proteomic analyses. The integrated analysis showed that brbI deletion significantly affected the expression of multiple genes at the mRNA and/or protein levels. Specifically, the affected divisome proteins, FtsB, FtsI, FtsL, and FtsQ, may be the molecular basis of the impaired cell division of the brbI mutant strain, and the extensively affected membrane proteins and transporter-associated proteins were consistent with the phenotype of the membrane properties’ alterations of the brbI mutant strain. In conclusion, our results revealed that BrBI is a bacterial cytoprotective protein involved in membrane homeostasis, cell division, and stress resistance in Brucella suis S2.
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Affiliation(s)
- Guangdong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Fangli Zhong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Lei Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Peipei Qin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Junmei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Feijie Zhi
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Lulu Tian
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Dong Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Pengfei Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Huatao Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Keqiong Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Wei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
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42
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Li JY, Sun JL, Tian YY, Liu JX. The FtsH-Inactive Protein FtsHi5 Is Required for Chloroplast Development and Protein Accumulation in Chloroplasts at Low Ambient Temperature in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:830390. [PMID: 35185971 PMCID: PMC8850778 DOI: 10.3389/fpls.2021.830390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 05/03/2023]
Abstract
Chloroplasts are indispensable for higher plants. The growth and development of plants are very sensitive to environmental temperature changes, and chloroplast development is also regulated by adverse environmental temperatures. However, the molecular mechanism of how plants coordinate chloroplast development and environmental temperature changes remains largely unknown. Here, a temperature-conditioned chloroplast development defective mutant thermo-sensitive mutant in leaf color 2 (tsl2) of Arabidopsis was obtained through a forward genetic screening. The tsl2 mutant showed a weak yellowish phenotype at normal growth temperature (22°C), and the phenotype was more pronounced at low growth temperature (16°C) and largely rescued at high growth temperature (29°C). Bulk Segregant Analysis (BSA) revealed that TSL2 encodes FtsH-Inactive Protein 5 (FtsHi5). Genetic complementation analysis confirmed that complemented expression of FtsHi5 rescued the chlorophyll content and thylakoid development defects observed in tsl2 mutants at 16°C. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling revealed broad changes in the chloroplast proteome of tsl2 mutant plants at low temperature, which is agreed with the impaired chloroplast biogenesis and function in tsl2 plants. Together, our data demonstrates that FtsHi5/TSL2 plays an important role in chloroplast development and protein accumulation in chloroplasts, especially at low environmental temperatures in Arabidopsis.
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Affiliation(s)
- Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing-Liang Sun
- College of Environment and Resources, Dalian Nationalities University, Dalian, China
| | - Ying-Ying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Jian-Xiang Liu,
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Update on relevant trypanosome peptidases: Validated targets and future challenges. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140577. [PMID: 33271348 DOI: 10.1016/j.bbapap.2020.140577] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Trypanosoma cruzi, the agent of the American Trypanosomiasis, Chagas disease, and Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, the agents of Sleeping sickness (Human African Trypanosomiasis, HAT), as well as Trypanosoma brucei brucei, the agent of the cattle disease nagana, contain cysteine, serine, threonine, aspartyl and metallo peptidases. The most abundant among these enzymes are the cysteine proteases from the Clan CA, the Cathepsin L-like cruzipain and rhodesain, and the Cathepsin B-like enzymes, which have essential roles in the parasites and thus are potential targets for chemotherapy. In addition, several other proteases, present in one or both parasites, have been characterized, and some of them are also promising candidates for the developing of new drugs. Recently, new inhibitors, with good selectivity for the parasite proteasomes, have been described and are very promising as lead compounds for the development of new therapies for these neglected diseases. This article is part of a Special Issue entitled: "Play and interplay of proteases in health and disease".
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Lin HH, Filloux A, Lai EM. Role of Recipient Susceptibility Factors During Contact-Dependent Interbacterial Competition. Front Microbiol 2020; 11:603652. [PMID: 33281802 PMCID: PMC7690452 DOI: 10.3389/fmicb.2020.603652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved multiple strategies to survive and develop optimal fitness in their ecological niche. They deployed protein secretion systems for robust and efficient delivery of antibacterial toxins into their target cells, therefore inhibiting their growth or killing them. To maximize antagonism, recipient factors on target cells can be recognized or hijacked to enhance the entry or toxicity of these toxins. To date, knowledge regarding recipient susceptibility (RS) factors and their mode of action is mostly originating from studies on the type Vb secretion system that is also known as the contact-dependent inhibition (CDI) system. Yet, recent studies on the type VI secretion system (T6SS), and the CDI by glycine-zipper protein (Cdz) system, also reported the emerging roles of RS factors in interbacterial competition. Here, we review these RS factors and their mechanistic impact in increasing susceptibility of recipient cells in response to CDI, T6SS, and Cdz. Past and future strategies for identifying novel RS factors are also discussed, which will help in understanding the interplay between attacker and prey upon secretion system-dependent competition. Understanding these mechanisms would also provide insights for developing novel antibacterial strategies to antagonize aggressive bacteria-killing pathogens.
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Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Ozdemir O, Soyer F. Pseudomonas aeruginosa Presents Multiple Vital Changes in Its Proteome in the Presence of 3-Hydroxyphenylacetic Acid, a Promising Antimicrobial Agent. ACS OMEGA 2020; 5:19938-19951. [PMID: 32832748 PMCID: PMC7439270 DOI: 10.1021/acsomega.0c00703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/21/2020] [Indexed: 05/06/2023]
Abstract
Pseudomonas aeruginosa, a widely distributed opportunistic pathogen, is an important threat to human health for causing serious infections worldwide. Due to its antibiotic resistance and virulence factors, it is so difficult to combat this bacterium; thus, new antimicrobial agents are in search. 3-Hydroxyphenylacetic acid (3-HPAA), which is a phenolic acid mostly found in olive oil wastewater, can be a promising candidate with its dose-dependent antimicrobial properties. Elucidating the molecular mechanism of action is crucial for future examinations and the presentation of 3-HPAA as a new agent. In this study, the antimicrobial activity of 3-HPAA on P. aeruginosa and its action mechanism was investigated via shot-gun proteomics. The data, which are available via ProteomeXchange with identifier PXD016243, were examined by STRING analysis to determine the interaction networks of proteins. KEGG Pathway enrichment analysis via the DAVID bioinformatics tool was also performed to investigate the metabolic pathways that undetected and newly detected groups of the proteins. The results displayed remarkable changes after 3-HPAA exposure in the protein profile of P. aeruginosa related to DNA replication and repair, RNA modifications, ribosomes and proteins, cell envelope, oxidative stress, as well as nutrient availability. 3-HPAA showed its antimicrobial action on P. aeruginosa by affecting multiple bacterial processes; hence, it could be categorized as a multitarget antimicrobial agent.
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46
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Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter. Proc Natl Acad Sci U S A 2020; 117:20235-20243. [PMID: 32753384 DOI: 10.1073/pnas.2006116117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
All cells require Mg2+ to replicate and proliferate. The macrophage protein Slc11a1 is proposed to protect mice from invading microbes by causing Mg2+ starvation in host tissues. However, the Mg2+ transporter MgtB enables the facultative intracellular pathogen Salmonella enterica serovar Typhimurium to cause disease in mice harboring a functional Slc11a1 protein. Here, we report that, unexpectedly, the Salmonella small protein MgtR promotes MgtB degradation by the protease FtsH, which raises the question: How does Salmonella preserve MgtB to promote survival inside macrophages? We establish that the Salmonella small protein MgtU prevents MgtB proteolysis, even when MgtR is absent. Like MgtB, MgtU is necessary for survival in Slc11a1 +/+ macrophages, resistance to oxidative stress, and growth under Mg2+ limitation conditions. The Salmonella Mg2+ transporter MgtA is not protected by MgtU despite sharing 50% amino acid identity with MgtB and being degraded in an MgtR- and FtsH-dependent manner. Surprisingly, the mgtB, mgtR, and mgtU genes are part of the same transcript, providing a singular example of transcript-specifying proteins that promote and hinder degradation of the same target. Our findings demonstrate that small proteins can confer pathogen survival inside macrophages by altering the abundance of related transporters, thereby furthering homeostasis.
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47
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Kovalinka T, Pánek T, Kováčová B, Horváth A. Orientation of FtsH protease homologs in Trypanosoma brucei inner mitochondrial membrane and its evolutionary implications. Mol Biochem Parasitol 2020; 238:111282. [DOI: 10.1016/j.molbiopara.2020.111282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 12/18/2022]
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48
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Lon Protease Removes Excess Signal Recognition Particle Protein in Escherichia coli. J Bacteriol 2020; 202:JB.00161-20. [PMID: 32366590 DOI: 10.1128/jb.00161-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Correct targeting of membrane proteins is essential for membrane integrity, cell physiology, and viability. Cotranslational targeting depends on the universally conserved signal recognition particle (SRP), which is a ribonucleoprotein complex comprised of the protein component Ffh and the 4.5S RNA in Escherichia coli About 25 years ago it was reported that Ffh is an unstable protein, but the underlying mechanism has never been explored. Here, we show that Lon is the primary protease responsible for adjusting the cellular Ffh level. When overproduced, Ffh is particularly prone to degradation during transition from exponential to stationary growth and the cellular Ffh amount is lowest in stationary phase. The Ffh protein consists of two domains, the NG domain, responsible for GTP hydrolysis and docking to the membrane receptor FtsY, and the RNA-binding M domain. We find that the NG domain alone is stable, whereas the isolated M domain is degraded. Consistent with the importance of Lon in this process, the M domain confers synthetic lethality to the lon mutant. The Ffh homolog from the model plant Arabidopsis thaliana, which forms a protein-protein complex rather than a protein-RNA complex, is stable, suggesting that the RNA-binding ability residing in the M domain of E. coli Ffh is important for proteolysis. Our results support a model in which excess Ffh not bound to 4.5S RNA is subjected to proteolysis until an appropriate Ffh concentration is reached. The differential proteolysis adjusts Ffh levels to the cellular demand and maintains cotranslational protein transport and membrane integrity.IMPORTANCE Since one-third of all bacterial proteins reside outside the cytoplasm, protein targeting to the appropriate address is an essential process. Cotranslational targeting to the membrane relies on the signal recognition particle (SRP), which is a protein-RNA complex in bacteria. We report that the protein component Ffh is a substrate of the Lon protease. Regulated proteolysis of Ffh provides a simple mechanism to adjust the concentration of the essential protein to the cellular demand. This is important because elevated or depleted SRP levels negatively impact protein targeting and bacterial fitness.
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Andrade YMFS, Santos-Junior MN, Rezende IS, Barbosa MS, Amorim AT, Silva ÍBS, Queiroz EC, Bastos BL, Campos GB, Timenetsky J, Marques LM. Multilocus sequence typing characterizes diversity of Ureaplasma diversum strains, and intra-species variability induces different immune response profiles. BMC Vet Res 2020; 16:163. [PMID: 32456681 PMCID: PMC7249313 DOI: 10.1186/s12917-020-02380-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Background Ureaplasma diversum is a pathogen found in the genital tract of cattle and associated with genital disorders such as infertility, placentitis, abortion, birth of weak calves, low sperm motility, seminal vesiculitis and epididymitis. There are few studies evaluating the genetic diversity of U. diversum strains and their influence on the immune response in cattle. Therefore, to better understand genetic relationships of the pathogenicity of U. diversum, a multilocus sequence typing (MLST) scheme was performed to characterize the ATCC 49782 strain and another 40 isolates recovered from different Brazilian states. Results Primers were designed for housekeeping genes ftsH, polC, rpL22, rpoB, valS and ureA and for virulence genes, phospholipase D (pld), triacylglycerol lipase (tgl), hemolysin (hlyA), MIB-MIP system (mib,mip), MBA (mba), VsA (VsA) and ribose transporter (tABC). PCRs were performed and the targeted gene products were purified and sequenced. Sequence types (STs), and clonal complexes (CCs) were assigned and the phylogenetic relationship was also evaluated. Thus, a total of 19 STs and 4 CCs were studied. Following the molecular analysis, six isolates of U. diversum were selected, inoculated into bovine monocyte/macrophage culture and evaluated for gene expression of the cytokines TNF-α, IL-1, IL-6, IL-10 and IL-17. Differences were detected in the induction of cytokines, especially between isolates 198 and BA78, promoted inflammatory and anti-inflammatory profiles, respectively, and they also differed in virulence factors. Conclusion It was observed that intra-species variability between isolates of U. diversum can induce variations of virulent determinants and, consequently, modulate the expression of the triggered immune response.
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Affiliation(s)
- Yasmin M F S Andrade
- Universidade Estadual de Santa Cruz, Brazil, Jorge Amado Highway, Km 16, Salobrinho, Ilheus, Bahia, 45662-900, Brazil.,Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Brazil, Waldemar Falcao Street, 121, Candeal, Salvador, Bahia, 40296-710, Brazil
| | - Manoel N Santos-Junior
- Universidade Estadual de Santa Cruz, Brazil, Jorge Amado Highway, Km 16, Salobrinho, Ilheus, Bahia, 45662-900, Brazil
| | - Izadora S Rezende
- Instituto de Ciências Biomedicas, Universidade de Sao Paulo, Brazil, Professor Lineu Prestes Avenue, 2415, Butantã, São Paulo, 05508-900, Brazil
| | - Maysa S Barbosa
- Instituto de Ciências Biomedicas, Universidade de Sao Paulo, Brazil, Professor Lineu Prestes Avenue, 2415, Butantã, São Paulo, 05508-900, Brazil
| | - Aline T Amorim
- Instituto de Ciências Biomedicas, Universidade de Sao Paulo, Brazil, Professor Lineu Prestes Avenue, 2415, Butantã, São Paulo, 05508-900, Brazil
| | - Ícaro B S Silva
- Instituto Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Brazil, Waldemar Falcao Street, 121, Candeal, Salvador, Bahia, 40296-710, Brazil
| | - Ellunny C Queiroz
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Brazil, Hormindo Barros Street, 58, Candeias, Vitória da Conquista, Bahia, 45029-094, Brazil
| | - Bruno L Bastos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Brazil, Hormindo Barros Street, 58, Candeias, Vitória da Conquista, Bahia, 45029-094, Brazil
| | - Guilherme B Campos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Brazil, Hormindo Barros Street, 58, Candeias, Vitória da Conquista, Bahia, 45029-094, Brazil
| | - Jorge Timenetsky
- Instituto de Ciências Biomedicas, Universidade de Sao Paulo, Brazil, Professor Lineu Prestes Avenue, 2415, Butantã, São Paulo, 05508-900, Brazil
| | - Lucas M Marques
- Universidade Estadual de Santa Cruz, Brazil, Jorge Amado Highway, Km 16, Salobrinho, Ilheus, Bahia, 45662-900, Brazil. .,Instituto de Ciências Biomedicas, Universidade de Sao Paulo, Brazil, Professor Lineu Prestes Avenue, 2415, Butantã, São Paulo, 05508-900, Brazil. .,Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Brazil, Hormindo Barros Street, 58, Candeias, Vitória da Conquista, Bahia, 45029-094, Brazil.
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A Membrane-Bound Transcription Factor is Proteolytically Regulated by the AAA+ Protease FtsH in Staphylococcus aureus. J Bacteriol 2020; 202:JB.00019-20. [PMID: 32094161 DOI: 10.1128/jb.00019-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
In bacteria, chromosomal DNA resides in the cytoplasm, and most transcription factors are also found in the cytoplasm. However, some transcription factors, called membrane-bound transcription factors (MTFs), reside in the cytoplasmic membrane. Here, we report the identification of a new MTF in the Gram-positive pathogen Staphylococcus aureus and its regulation by the protease FtsH. The MTF, named MbtS (membrane-bound transcription factor of Staphylococcus aureus), is encoded by SAUSA300_2640 and predicted to have an N-terminal DNA binding domain and three transmembrane helices. The MbtS protein was degraded by membrane vesicles containing FtsH or by the purified FtsH. MbtS bound to an inverted repeat sequence in its promoter region, and the DNA binding was essential for its transcription. Transcriptional comparison between the ftsH deletion mutant and the ftsH mbtS double mutant showed that MbtS could alter the transcription of over 200 genes. Although the MbtS protein was not detected in wild-type (WT) cells grown in a liquid medium, the protein was detected in some isolated colonies on an agar plate. In a murine model of a skin infection, the disruption of mbtS increased the lesion size. Based on these results, we concluded that MbtS is a new S. aureus MTF whose activity is proteolytically regulated by FtsH.IMPORTANCE Staphylococcus aureus is an important pathogenic bacterium causing various diseases in humans. In the bacterium, transcription is typically regulated by the transcription factors located in the cytoplasm. In this study, we report an atypical transcription factor identified in S. aureus Unlike most other transcription factors, the newly identified transcription factor is located in the cytoplasmic membrane, and its activity is proteolytically controlled by the membrane-bound AAA+ protease FtsH. The newly identified MTF, named MbtS, has the potential to regulate the transcription of over 200 genes. This study provides a molecular mechanism by which a protease affects bacterial transcription and illustrates the diversity of the bacterial transcriptional regulation.
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