101
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Bai B, Schiffthaler B, van der Horst S, Willems L, Vergara A, Karlström J, Mähler N, Delhomme N, Bentsink L, Hanson J. SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2416-2432. [PMID: 36208446 PMCID: PMC10082931 DOI: 10.1093/jxb/erac394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/06/2022] [Indexed: 06/06/2023]
Abstract
Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.
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Affiliation(s)
- Bing Bai
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Bastian Schiffthaler
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sjors van der Horst
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Leo Willems
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Alexander Vergara
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jacob Karlström
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Niklas Mähler
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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102
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Aksoy Z, Ersus S. The comparative studies on the physicochemical properties of mung bean protein isolate–polysaccharide conjugates prepared by ultrasonic or controlled heating treatment. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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103
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Mahley RW. Apolipoprotein E4 targets mitochondria and the mitochondria-associated membrane complex in neuropathology, including Alzheimer's disease. Curr Opin Neurobiol 2023; 79:102684. [PMID: 36753858 DOI: 10.1016/j.conb.2023.102684] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
Apolipoprotein (apo) E4 sets the stage for neuropathology in Alzheimer's disease (AD) by causing mitochondrial dysfunction and altering mitochondria-associated membranes. Contact and apposition of mitochondrial-endoplasmic reticulum membranes are enhanced in brain cells in AD and associated with increases in tethering and spacing proteins that modulate many cellular processes. Contact site protein levels are higher in apoE4 cells. In apoE4 neurons, the NAD+/NADH ratio is lowered, reactive oxygen species are increased, and NAD/NADH pathway components and redox proteins are decreased. Oxidative phosphorylation is impaired and reserve ATP generation capacity is lacking. ApoE4 neurons have ∼50% fewer respiratory complex subunits (e.g., ATP synthase) and may increase translocase levels of the outer and inner mitochondrial membranes to facilitate delivery of nucleus-encoded complex subunits. Respiratory complex assembly relies on mitochondrial cristae organizing system subunits that are altered in apoE4 cells, and apoE4 increases mitochondrial proteases that control respiratory subunit composition for complex assembly.
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Affiliation(s)
- Robert W Mahley
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Departments of Pathology and Medicine, University of California, San Francisco, CA 94143, USA.
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104
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Liu M, Chu B, Sun R, Ding J, Ye H, Yang Y, Wu Y, Shi H, Song B, He Y, Wang H, Hong J. Antisense Oligonucleotides Selectively Enter Human-Derived Antibiotic-Resistant Bacteria through Bacterial-Specific ATP-Binding Cassette Sugar Transporter. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300477. [PMID: 37002615 DOI: 10.1002/adma.202300477] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Current vehicles used to deliver antisense oligonucleotides (ASOs) cannot distinguish between bacterial and mammalian cells, greatly hindering the preclinical or clinical treatment of bacterial infections, especially those caused by antibiotic-resistant bacteria. Herein, bacteria-specific ATP-binding cassette (ABC) sugar transporters are leveraged to selectively internalize ASOs by hitchhiking them on α (1-4)-glucosidically linked glucose polymers. Compared with their cell-penetrating peptide counterparts, which are non-specifically engulfed by mammalian and bacterial cells, the presented therapeutics consisting of glucose polymer and antisense peptide nucleic-acid-modified nanoparticles are selectively internalized into the human-derived multidrug-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus, and they display a much higher uptake rate (i.e., 51.6%). The developed strategy allows specific and efficient killing of nearly 100% of the antibiotic-resistant bacteria. Its significant curative efficacy against bacterial keratitis and endophthalmitis is also shown. This strategy will expand the focus of antisense technology to include bacterial cells other than mammalian cells.
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Affiliation(s)
- Mingzhu Liu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Binbin Chu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Rong Sun
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiali Ding
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Han Ye
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
| | - Yunmin Yang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yuqi Wu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Haoliang Shi
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Bin Song
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yao He
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Houyu Wang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
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105
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McGuire BE, Nano FE. Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains. BMC Genomics 2023; 24:154. [PMID: 36973666 PMCID: PMC10044804 DOI: 10.1186/s12864-023-09266-9] [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: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND High temperatures cause a suite of problems for cells, including protein unfolding and aggregation; increased membrane fluidity; and changes in DNA supercoiling, RNA stability, transcription and translation. Consequently, enhanced thermotolerance can evolve through an unknown number of genetic mechanisms even in the simple model bacterium Escherichia coli. To date, each E. coli study exploring this question resulted in a different set of mutations. To understand the changes that can arise when an organism evolves to grow at higher temperatures, we sequenced and analyzed two previously described E. coli strains, BM28 and BM28 ΔlysU, that have been laboratory adapted to the highest E. coli growth temperature reported to date. RESULTS We found three large deletions in the BM28 and BM28 ΔlysU strains of 123, 15 and 8.5 kb in length and an expansion of IS10 elements. We found that BM28 and BM28 ΔlysU have considerably different genomes, suggesting that the BM28 culture that gave rise to BM28 and BM28 ΔlysU was a mixed population of genetically different cells. Consistent with published findings of high GroESL expression in BM28, we found that BM28 inexplicitly carries the groESL bearing plasmid pOF39 that was maintained simply by high-temperature selection pressure. We identified over 200 smaller insertions, deletions, single nucleotide polymorphisms and other mutations, including changes in master regulators such as the RNA polymerase and the transcriptional termination factor Rho. Importantly, this genome analysis demonstrates that the commonly cited findings that LysU plays a crucial role in thermotolerance and that GroESL hyper-expression is brought about by chromosomal mutations are based on a previous misinterpretation of the genotype of BM28. CONCLUSIONS This whole-genome sequencing study describes genetically distinct mechanisms of thermotolerance evolution from those found in other heat-evolved E. coli strains. Studying adaptive laboratory evolution to heat in simple model organisms is important in the context of climate change. It is important to better understand genetic mechanisms of enhancing thermotolerance in bacteria and other organisms, both in terms of optimizing laboratory evolution methods for various organisms and in terms of potential genetic engineering of organisms most at risk or most important to our societies and ecosystems.
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Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada.
| | - Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada
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106
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Shinn MK, Chaturvedi SK, Kozlov AG, Lohman T. Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA. Nucleic Acids Res 2023; 51:2284-2297. [PMID: 36808259 PMCID: PMC10018359 DOI: 10.1093/nar/gkad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
Escherichia coli single stranded (ss) DNA binding protein (SSB) plays essential roles in DNA maintenance. It binds ssDNA with high affinity through its N-terminal DNA binding core and recruits at least 17 different SSB interacting proteins (SIPs) that are involved in DNA replication, recombination, and repair via its nine amino acid acidic tip (SSB-Ct). E. coli RecO, a SIP, is an essential recombination mediator protein in the RecF pathway of DNA repair that binds ssDNA and forms a complex with E. coli RecR protein. Here, we report ssDNA binding studies of RecO and the effects of a 15 amino acid peptide containing the SSB-Ct monitored by light scattering, confocal microscope imaging, and analytical ultracentrifugation (AUC). We find that one RecO monomer can bind the oligodeoxythymidylate, (dT)15, while two RecO monomers can bind (dT)35 in the presence of the SSB-Ct peptide. When RecO is in molar excess over ssDNA, large RecO-ssDNA aggregates occur that form with higher propensity on ssDNA of increasing length. Binding of RecO to the SSB-Ct peptide inhibits RecO-ssDNA aggregation. RecOR complexes can bind ssDNA via RecO, but aggregation is suppressed even in the absence of the SSB-Ct peptide, demonstrating an allosteric effect of RecR on RecO binding to ssDNA. Under conditions where RecO binds ssDNA but does not form aggregates, SSB-Ct binding enhances the affinity of RecO for ssDNA. For RecOR complexes bound to ssDNA, we also observe a shift in RecOR complex equilibrium towards a RecR4O complex upon binding SSB-Ct. These results suggest a mechanism by which SSB recruits RecOR to facilitate loading of RecA onto ssDNA gaps.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sumit K Chaturvedi
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy M Lohman
- To whom correspondence should be addressed. Tel: +1 314 362 4393; Fax: +1 314 362 7183;
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107
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Qin C, Xiang Y, Liu J, Zhang R, Liu Z, Li T, Sun Z, Ouyang X, Zong Y, Zhang HM, Ouyang Q, Qian L, Lou C. Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system. Nat Commun 2023; 14:1500. [PMID: 36932109 PMCID: PMC10023750 DOI: 10.1038/s41467-023-37244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Context-dependency of mammalian transcriptional elements has hindered the quantitative investigation of multigene expression stoichiometry and its biological functions. Here, we describe a host- and local DNA context-independent transcription system to gradually fine-tune single and multiple gene expression with predictable stoichiometries. The mammalian transcription system is composed of a library of modular and programmable promoters from bacteriophage and its cognate RNA polymerase (RNAP) fused to a capping enzyme. The relative expression of single genes is quantitatively determined by the relative binding affinity of the RNAP to the promoters, while multigene expression stoichiometry is predicted by a simple biochemical model with resource competition. We use these programmable and modular promoters to predictably tune the expression of three components of an influenza A virus-like particle (VLP). Optimized stoichiometry leads to a 2-fold yield of intact VLP complexes. The host-independent orthogonal transcription system provides a platform for dose-dependent control of multiple protein expression which may be applied for advanced vaccine engineering, cell-fate programming and other therapeutic applications.
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Affiliation(s)
- Chenrui Qin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jie Liu
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Ruilin Zhang
- Yuanpei College, Peking University, 100871, Beijing, China
| | - Ziming Liu
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Tingting Li
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Zhi Sun
- College of Life Science, University of Chinese Academy of Science, 100149, Beijing, China
| | - Xiaoyi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | | | | | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- College of Life Science, University of Chinese Academy of Science, 100149, Beijing, China.
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108
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Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG. Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. Cell Syst 2023; 14:220-236.e3. [PMID: 36696901 PMCID: PMC10125799 DOI: 10.1016/j.cels.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023]
Abstract
How enhancers interpret morphogen gradients to generate gene expression patterns is a central question in developmental biology. Recent studies have proposed that enhancers can dictate whether, when, and at what rate promoters engage in transcription, but the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal promoter-proximal synthetic enhancer in embryos of Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal DNA binding site. Using live imaging to quantify transcriptional activity, we found that a single binding site can regulate whether promoters engage in transcription in a concentration-dependent manner. By modulating the binding-site affinity, we determined that a gene's decision to transcribe and its transcriptional onset time can be explained by a simple model where the promoter traverses multiple kinetic barriers before transcription can ensue.
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Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Clay Westrum
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Meghan A Turner
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Paul Talledo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Emma Luu
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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109
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Cho SH, Dekoninck K, Collet JF. Envelope-Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram-Negative Bacteria. J Microbiol 2023; 61:317-329. [PMID: 36892778 DOI: 10.1007/s12275-023-00030-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial two-component systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking results in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium. .,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.
| | - Kilian Dekoninck
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.,University of California, Berkeley, CA, 94720, USA
| | - Jean-Francois Collet
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium
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110
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Dupuy E, Van der Verren SE, Lin J, Wilson MA, Dachsbeck AV, Viela F, Latour E, Gennaris A, Vertommen D, Dufrêne YF, Iorga BI, Goemans CV, Remaut H, Collet JF. A molecular device for the redox quality control of GroEL/ES substrates. Cell 2023; 186:1039-1049.e17. [PMID: 36764293 PMCID: PMC10044410 DOI: 10.1016/j.cell.2023.01.013] [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: 04/04/2022] [Revised: 10/27/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these chaperonins promote folding remain unsolved. Here, we report that the bacterial Hsp60 chaperonin GroEL forms a stable, functionally relevant complex with the chaperedoxin CnoX, a protein combining a chaperone and a redox function. Binding of GroES (Hsp10 cofactor) to GroEL induces CnoX release. Cryoelectron microscopy provided crucial structural information on the GroEL-CnoX complex, showing that CnoX binds GroEL outside the substrate-binding site via a highly conserved C-terminal α-helix. Furthermore, we identified complexes in which CnoX, bound to GroEL, forms mixed disulfides with GroEL substrates, indicating that CnoX likely functions as a redox quality-control plugin for GroEL. Proteins sharing structural features with CnoX exist in eukaryotes, suggesting that Hsp60 molecular plugins have been conserved through evolution.
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Affiliation(s)
- Emile Dupuy
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Sander Egbert Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium
| | - Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Mark Alan Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Vincent Dachsbeck
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Felipe Viela
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Emmanuelle Latour
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Alexandra Gennaris
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Yves Frédéric Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Bogdan Iuliu Iorga
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, 91198 Gif-sur-Yvette, France
| | - Camille Véronique Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium.
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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111
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Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli. Int J Mol Sci 2023; 24:ijms24054806. [PMID: 36902235 PMCID: PMC10003070 DOI: 10.3390/ijms24054806] [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: 02/01/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Earlier studies aimed at investigating the metabolism of endogenous nucleoside triphosphates in synchronous cultures of E. coli cells revealed an auto-oscillatory mode of functioning of the pyrimidine and purine nucleotide biosynthesis system, which the authors associated with the dynamics of cell division. Theoretically, this system has an intrinsic oscillatory potential, since the dynamics of its functioning are controlled through feedback mechanisms. The question of whether the nucleotide biosynthesis system has its own oscillatory circuit is still open. To address this issue, an integral mathematical model of pyrimidine biosynthesis was developed, taking into account all experimentally verified negative feedback in the regulation of enzymatic reactions, the data of which were obtained under in vitro conditions. Analysis of the dynamic modes of the model functioning has shown that in the pyrimidine biosynthesis system, both the steady-state and oscillatory functioning modes can be realized under certain sets of kinetic parameters that fit in the physiological boundaries of the investigated metabolic system. It has been demonstrated that the occurrence of the oscillatory nature of metabolite synthesis depended on the ratio of two parameters: the Hill coefficient, hUMP1-the nonlinearity of the UMP effect on the activity of carbamoyl-phosphate synthetase, and the parameter r characterizing the contribution of the noncompetitive mechanism of UTP inhibition to the regulation of the enzymatic reaction of UMP phosphorylation. Thus, it has been theoretically shown that the E. coli pyrimidine biosynthesis system possesses its own oscillatory circuit whose oscillatory potential depends to a significant degree on the mechanism of regulation of UMP kinase activity.
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112
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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113
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Coppens L, Tschirhart T, Leary DH, Colston SM, Compton JR, Hervey WJ, Dana KL, Vora GJ, Bordel S, Ledesma-Amaro R. Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation. Mol Syst Biol 2023; 19:e10523. [PMID: 36847213 PMCID: PMC10090949 DOI: 10.15252/msb.202110523] [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: 06/22/2021] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
Vibrio natriegens is a Gram-negative bacterium with an exceptional growth rate that has the potential to become a standard biotechnological host for laboratory and industrial bioproduction. Despite this burgeoning interest, the current lack of organism-specific qualitative and quantitative computational tools has hampered the community's ability to rationally engineer this bacterium. In this study, we present the first genome-scale metabolic model (GSMM) of V. natriegens. The GSMM (iLC858) was developed using an automated draft assembly and extensive manual curation and was validated by comparing predicted yields, central metabolic fluxes, viable carbon substrates, and essential genes with empirical data. Mass spectrometry-based proteomics data confirmed the translation of at least 76% of the enzyme-encoding genes predicted to be expressed by the model during aerobic growth in a minimal medium. iLC858 was subsequently used to carry out a metabolic comparison between the model organism Escherichia coli and V. natriegens, leading to an analysis of the model architecture of V. natriegens' respiratory and ATP-generating system and the discovery of a role for a sodium-dependent oxaloacetate decarboxylase pump. The proteomics data were further used to investigate additional halophilic adaptations of V. natriegens. Finally, iLC858 was utilized to create a Resource Balance Analysis model to study the allocation of carbon resources. Taken together, the models presented provide useful computational tools to guide metabolic engineering efforts in V. natriegens.
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Affiliation(s)
- Lucas Coppens
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Tanya Tschirhart
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Dagmar H Leary
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Sophie M Colston
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Jaimee R Compton
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - William Judson Hervey
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | | | - Gary J Vora
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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114
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Abstract
The universally conserved protein elongation factor P (EF-P) facilitates translation at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Despite its wide conservation, it is not essential in most bacteria and its physiological role remains unclear. Here, we show that EF-P affects the process of sporulation initiation in the bacterium Bacillus subtilis. We observe that the lack of EF-P delays expression of sporulation-specific genes. Using ribosome profiling, we observe that expression of spo0A, encoding a transcription factor that functions as the master regulator of sporulation, is lower in a Δefp strain than the wild type. Ectopic expression of Spo0A rescues the sporulation initiation phenotype, indicating that reduced spo0A expression explains the sporulation defect in Δefp cells. Since Spo0A is the earliest sporulation transcription factor, these data suggest that sporulation initiation can be delayed when protein synthesis is impaired. IMPORTANCE Elongation factor P (EF-P) is a universally conserved translation factor that prevents ribosome stalling at amino acids that form peptide bonds with low efficiency, particularly polyproline tracts. Phenotypes associated with EF-P deletion are pleiotropic, and the mechanistic basis underlying many of these phenotypes is unclear. Here, we show that the absence of EF-P affects the ability of B. subtilis to initiate sporulation by preventing normal expression of Spo0A, the key transcriptional regulator of this process. These data illustrate a mechanism that accounts for the sporulation delay and further suggest that cells are capable of sensing translation stress before committing to sporulation.
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115
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Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529291. [PMID: 36865326 PMCID: PMC9980150 DOI: 10.1101/2023.02.20.529291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigated whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions could be modularized in the same way to reveal novel relationships between their compositions. We found that; 1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, 2) the modules in the proteome often represent combinations of modules from the transcriptome, 3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and 4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.
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Affiliation(s)
- Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Svetlana Maurya
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
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116
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Decoupling of mRNA and Protein Expression in Aging Brains Reveals the Age-Dependent Adaptation of Specific Gene Subsets. Cells 2023; 12:cells12040615. [PMID: 36831282 PMCID: PMC9954025 DOI: 10.3390/cells12040615] [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: 01/26/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.
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117
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [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: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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118
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Wu C, Mori M, Abele M, Banaei-Esfahani A, Zhang Z, Okano H, Aebersold R, Ludwig C, Hwa T. Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nat Microbiol 2023; 8:347-359. [PMID: 36737588 PMCID: PMC9994330 DOI: 10.1038/s41564-022-01310-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/15/2022] [Indexed: 02/05/2023]
Abstract
Bacterial fitness depends on adaptability to changing environments. In rich growth medium, which is replete with amino acids, Escherichia coli primarily expresses protein synthesis machineries, which comprise ~40% of cellular proteins and are required for rapid growth. Upon transition to minimal medium, which lacks amino acids, biosynthetic enzymes are synthesized, eventually reaching ~15% of cellular proteins when growth fully resumes. We applied quantitative proteomics to analyse the timing of enzyme expression during such transitions, and established a simple positive relation between the onset time of enzyme synthesis and the fractional enzyme 'reserve' maintained by E. coli while growing in rich media. We devised and validated a coarse-grained kinetic model that quantitatively captures the enzyme recovery kinetics in different pathways, solely on the basis of proteomes immediately preceding the transition and well after its completion. Our model enables us to infer regulatory strategies underlying the 'as-needed' gene expression programme adopted by E. coli.
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Affiliation(s)
- Chenhao Wu
- Department of Physics, U.C. San Diego, La Jolla, CA, USA.
| | - Matteo Mori
- Department of Physics, U.C. San Diego, La Jolla, CA, USA
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Zhongge Zhang
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, USA
| | - Hiroyuki Okano
- Department of Physics, U.C. San Diego, La Jolla, CA, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany.
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, USA.
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119
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Zhu M, Dai X. Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nat Commun 2023; 14:467. [PMID: 36709335 PMCID: PMC9884231 DOI: 10.1038/s41467-023-36254-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Timely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
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120
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Construction and Characterization of Functional FtsA Sandwich Fusions for Studies of FtsA Localization and Dynamics during Escherichia coli Cell Division. J Bacteriol 2023; 205:e0037322. [PMID: 36622232 PMCID: PMC9879108 DOI: 10.1128/jb.00373-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
FtsA, a homolog of actin, is essential for cell division of Escherichia coli and is widely conserved among many bacteria. FtsA helps to tether polymers of the bacterial tubulin homolog FtsZ to the cytoplasmic membrane as part of the cytokinetic Z ring. GFP fusions to FtsA have illuminated FtsA's localization in live E. coli, but these fusions have not been fully functional and required the presence of the native FtsA. Here, we characterize "sandwich" fusions of E. coli FtsA to either mCherry or msfGFP that are functional for cell division and exhibit fluorescent rings at midcell that persist throughout constriction until cell separation. FtsA within the Z ring moved circumferentially like FtsZ, and FtsA outside the rings formed highly dynamic patches at the membrane. Notably, both FtsA-mCherrysw and FtsA-msfGFPsw acted as mild hypermorphs, as they were not toxic when overproduced, bypassed the essential cell division protein ZipA, and suppressed several thermosensitive fts alleles, although not as effectively as the prototypical hypermorph FtsA*. Overall, our results indicate that fluorescent FtsA sandwich fusions can be used as the sole FtsA in E. coli and thus should shed new light on FtsA dynamics during the cell division cycle in this model system. IMPORTANCE FtsA is a key conserved cell division protein, and E. coli is the most well studied model system for bacterial cell division. One obstacle to full understanding of this process is the lack of a fully functional fluorescent reporter for FtsA in vivo. Here, we describe a fluorescent fusion to E. coli FtsA that promotes efficient cell division in the absence of the native FtsA and can be used to monitor FtsA dynamics during cell division.
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121
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Sheng Q, Zhang MY, Liu SM, Chen ZW, Yang PL, Zhang HS, Liu MY, Li K, Zhao LS, Liu NH, Liu LN, Chen XL, Hobbs JK, Foster SJ, Zhang YZ, Su HN. In situ visualization of Braun's lipoprotein on E. coli sacculi. SCIENCE ADVANCES 2023; 9:eadd8659. [PMID: 36662863 PMCID: PMC9858504 DOI: 10.1126/sciadv.add8659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Braun's lipoprotein (Lpp) plays a major role in stabilizing the integrity of the cell envelope in Escherichia coli, as it provides a covalent cross-link between the outer membrane and the peptidoglycan layer. An important challenge in elucidating the physiological role of Lpp lies in attaining a detailed understanding of its distribution on the peptidoglycan layer. Here, using atomic force microscopy, we visualized Lpp directly on peptidoglycan sacculi. Lpp is homogeneously distributed over the outer surface of the sacculus at a high density. However, it is absent at the constriction site during cell division, revealing its role in the cell division process with Pal, another cell envelope-associated protein. Collectively, we have established a framework to elucidate the distribution of Lpp and other peptidoglycan-bound proteins via a direct imaging modality.
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Affiliation(s)
- Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Meng-Yao Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Si-Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhuo-Wei Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Pei-Ling Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hong-Su Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Meng-Yun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Kang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Long-Sheng Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lu-Ning Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jamie K. Hobbs
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - Simon J. Foster
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, UK
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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122
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Dolgalev GV, Safonov TA, Arzumanian VA, Kiseleva OI, Poverennaya EV. Estimating Total Quantitative Protein Content in Escherichia coli, Saccharomyces cerevisiae, and HeLa Cells. Int J Mol Sci 2023; 24:ijms24032081. [PMID: 36768409 PMCID: PMC9916689 DOI: 10.3390/ijms24032081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes of many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers of total protein molecules per specific cell type. In this article, we explore the results of proteomic studies of Escherichia coli, Saccharomyces cerevisiae, and HeLa cells in terms of total protein copy numbers per cell. We observe up to a ten-fold difference between reported values. Investigating possible reasons for this discrepancy, we conclude that neither an unmeasured fraction of the proteome nor biases in the quantification of individual proteins can explain the observed discrepancy. We normalize protein copy numbers in each study using a total protein amount per cell as reported in the literature and create integrated proteome maps of the selected model organisms. Our results indicate that cells contain from one to three million protein molecules per µm3 and that protein copy density decreases with increasing organism complexity.
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Affiliation(s)
| | - Taras A. Safonov
- X-BIO Institute, University of Tyumen, 6 Volodarskogo St., Tyumen 625003, Russia
| | | | | | - Ekaterina V. Poverennaya
- Institute of Biomedical Chemistry, Moscow 119281, Russia
- X-BIO Institute, University of Tyumen, 6 Volodarskogo St., Tyumen 625003, Russia
- Correspondence:
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Hao P, Lv Z, Wu S, Zhang X, Gou C, Wang L, Zhu Y, Basang W, Gao Y. Transcriptome profiling of Microbacterium resistens MZT7 reveals mechanisms of 17β-estradiol response and biotransformation. ENVIRONMENTAL RESEARCH 2023; 217:114963. [PMID: 36471558 DOI: 10.1016/j.envres.2022.114963] [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: 10/05/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
17β-estradiol (E2) pollution has attracted much attention, and the existence of E2 poses certain risks to the environment and human health. However, the mechanism of microbial degradation of E2 remains unclear. In this study, the location of E2-degrading enzymes was investigated, and transcriptome analysis of Microbacterium resistens MZT7 (M. resistens MZT7) exposed to E2. The degradation of E2 by M. resistens MZT7 was via the biological action of E2-induced intracellular enzymes. With the RNA sequencing, we found 1109 differentially expressed genes (DEGs). Among them, 773 genes were up-regulated and 336 genes were down-regulated. The results of the RNA sequencing indicated the DEGs were related to transport, metabolism, and stress response. Genes for transport, transmembrane transport, oxidoreductase activity, ATPase activity, transporter activity and quorum sensing were up-regulated. Genes for the tricarboxylic acid cycle, ribosome, oxidative phosphorylation and carbon metabolism were down-regulated. In addition, heterologous expression of one enzymes efficiently degraded E2. These findings provide some new insights into the molecular mechanism of biotransformation of E2 by M. resistens MZT7.
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Affiliation(s)
- Peng Hao
- College of of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China.
| | - Zongshuo Lv
- College of of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China.
| | - Sicheng Wu
- College of of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China.
| | - Xiqing Zhang
- College of of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China.
| | - Changlong Gou
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China.
| | - Lixia Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China.
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Yunhang Gao
- College of of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China.
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Matilla MA, Genova R, Martín-Mora D, Maaβ S, Becher D, Krell T. The Cellular Abundance of Chemoreceptors, Chemosensory Signaling Proteins, Sensor Histidine Kinases, and Solute Binding Proteins of Pseudomonas aeruginosa Provides Insight into Sensory Preferences and Signaling Mechanisms. Int J Mol Sci 2023; 24:ijms24021363. [PMID: 36674894 PMCID: PMC9864684 DOI: 10.3390/ijms24021363] [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: 12/05/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/12/2023] Open
Abstract
Chemosensory pathways and two-component systems are important bacterial signal transduction systems. In the human pathogen Pseudomonas aeruginosa, these systems control many virulence traits. Previous studies showed that inorganic phosphate (Pi) deficiency induces virulence. We report here the abundance of chemosensory and two-component signaling proteins of P. aeruginosa grown in Pi deficient and sufficient media. The cellular abundance of chemoreceptors differed greatly, since a 2400-fold difference between the most and least abundant receptors was observed. For many chemoreceptors, their amount varied with the growth condition. The amount of chemoreceptors did not correlate with the magnitude of chemotaxis to their cognate chemoeffectors. Of the four chemosensory pathways, proteins of the Che chemotaxis pathway were most abundant and showed little variation in different growth conditions. The abundance of chemoreceptors and solute binding proteins indicates a sensing preference for amino acids and polyamines. There was an excess of response regulators over sensor histidine kinases in two-component systems. In contrast, ratios of the response regulators CheY and CheB to the histidine kinase CheA of the Che pathway were all below 1, indicative of different signaling mechanisms. This study will serve as a reference for exploring sensing preferences and signaling mechanisms of other bacteria.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Roberta Genova
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Sandra Maaβ
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
- Correspondence: ; Tel.: +34-958-526579
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Wu K, Tang S, Wu X, Zhu J, Song J, Zhong Y, Zhou J, Cai Z. Colony formation of Phaeocystis globosa: A case study of evolutionary strategy for competitive adaptation. MARINE POLLUTION BULLETIN 2023; 186:114453. [PMID: 36495614 DOI: 10.1016/j.marpolbul.2022.114453] [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: 08/15/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Some algae possess a multi-morphic life cycle, either in the form of free-living solitary cells or colonies which constantly occur in algal blooms. Though colony formation seems to consume extra energy and materials, many algae tend to outbreak in form of colonies. Here, we hypothesized that colony formation is a selected evolutionary strategy to improve population competitiveness and environmental adaptation. To test the hypothesis, different sizes of colonies and solitary cells in a natural bloom of Phaeocystis globosa were investigated. The large colony showed a relatively low oxidant stress level, a nutrient trap effect, and high nutrient use efficiency. The colonial nitrogen and phosphorus concentrations were about 5-10 times higher than solitary cell phycosphere and cellular nutrient allocation decreased with the enlargement of the colonial diameter following the economies of scale law. These features provide the colony with monopolistic competence and could function as an evolutionary strategy for competitive adaptation.
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Affiliation(s)
- Kebi Wu
- School of Life Sciences, Tsinghua University, Beijing 100086, China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Si Tang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Xiaotian Wu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Junting Song
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yanlin Zhong
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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Rettenbacher LA, von der Haar T. A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microb Cell Fact 2022; 21:268. [PMID: 36550495 PMCID: PMC9773447 DOI: 10.1186/s12934-022-01982-3] [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: 10/24/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Escherichia coli is of central interest to biotechnological research and a widely used organism for producing proteins at both lab and industrial scales. However, many proteins remain difficult to produce efficiently in E. coli. This is particularly true for proteins that require post translational modifications such as disulfide bonds. RESULTS In this study we develop a novel approach for quantitatively investigating the ability of E. coli to produce disulfide bonds in its own proteome. We summarise the existing knowledge of the E. coli disulfide proteome and use this information to investigate the demand on this organism's quantitative oxidative folding apparatus under different growth conditions. Furthermore, we built an ordinary differential equation-based model describing the cells oxidative folding capabilities. We use the model to infer the kinetic parameters required by the cell to achieve the observed oxidative folding requirements. We find that the cellular requirement for disulfide bonded proteins changes significantly between growth conditions. Fast growing cells require most of their oxidative folding capabilities to keep up their proteome while cells growing in chemostats appear limited by their disulfide bond isomerisation capacities. CONCLUSION This study establishes a novel approach for investigating the oxidative folding capacities of an organism. We show the capabilities and limitations of E. coli for producing disulfide bonds under different growth conditions and predict under what conditions excess capability is available for recombinant protein production.
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Affiliation(s)
- Lukas A. Rettenbacher
- grid.9759.20000 0001 2232 2818Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, UK
| | - Tobias von der Haar
- grid.9759.20000 0001 2232 2818Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, UK
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Bennett SP, Crack JC, Puglisi R, Pastore A, Le Brun NE. Native mass spectrometric studies of IscSU reveal a concerted, sulfur-initiated mechanism of iron-sulfur cluster assembly. Chem Sci 2022; 14:78-95. [PMID: 36605734 PMCID: PMC9769115 DOI: 10.1039/d2sc04169c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors essential for life. Though the proteins that function in the assembly of Fe-S clusters are well known, details of the molecular mechanism are less well established. The Isc (iron-sulfur cluster) biogenesis apparatus is widespread in bacteria and is the closest homologue to the human system. Mutations in certain components of the human system lead to disease, and so further studies of this system could be important for developing strategies for medical treatments. We have studied two core components of the Isc biogenesis system: IscS, a cysteine desulfurase; and IscU, a scaffold protein on which clusters are built before subsequent transfer onto recipient apo-proteins. Fe2+-binding, sulfur transfer, and formation of a [2Fe-2S] was followed by a range of techniques, including time-resolved mass spectrometry, and intermediate and product species were unambiguously identified through isotopic substitution experiments using 57Fe and 34S. Under cluster synthesis conditions, sulfur adducts and the [2Fe-2S] cluster product readily accumulated on IscU, but iron adducts (other than the cluster itself) were not observed at physiologically relevant Fe2+ concentrations. Our data indicate that either Fe2+ or sulfur transfer can occur first, but that the transfer of sulfane sulfur (S0) to IscU must occur first if Zn2+ is bound to IscU, suggesting that it is the key step that initiates cluster assembly. Following this, [2Fe-2S] cluster formation is a largely concerted reaction once Fe2+ is introduced.
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Affiliation(s)
- Sophie P. Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Rita Puglisi
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Annalisa Pastore
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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128
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Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli. mBio 2022; 13:e0237122. [PMID: 36226957 PMCID: PMC9765468 DOI: 10.1128/mbio.02371-22] [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] [Indexed: 11/20/2022] Open
Abstract
The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 3' portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate. Overproduction of the protein attenuators CspD and Rof resulted in more frequent readthrough at terminators of SgrS and two other sRNAs, and regulation by SgrS of target mRNAs was reduced. The effect of Rof, a known inhibitor of Rho, was mimicked by bicyclomycin or by a rho mutant, suggesting an unexpected role for Rho in sRNA termination. CspD, a member of the cold shock protein family, bound both terminated and readthrough transcripts, stabilizing them and attenuating termination. By RNA sequencing analysis of the CspD overexpression strain, we found global effects of CspD on gene expression across some termination sites. We further demonstrated effects of endogenous CspD under slow growth conditions where cspD is highly expressed. These findings provided evidence of changes in the efficiency of intrinsic termination, confirming this as an additional layer of the regulation of sRNA signaling. IMPORTANCE Growing evidence suggests that the modulation of intrinsic termination and readthrough of transcription is more widespread than previously appreciated. For small RNAs, proper termination plays a critical role in their regulatory function. Here, we present a multicopy screen approach to identify factors that attenuate small RNA termination and therefore abrogate signaling dependent on the small RNA. This study highlights a new aspect of regulation of small RNA signaling as well as the modulation of intrinsic termination.
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129
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Balakrishnan R, Mori M, Segota I, Zhang Z, Aebersold R, Ludwig C, Hwa T. Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science 2022; 378:eabk2066. [PMID: 36480614 PMCID: PMC9804519 DOI: 10.1126/science.abk2066] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.
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Affiliation(s)
- Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Matteo Mori
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Igor Segota
- Departments of Medicine and Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Zhongge Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
| | - Ruedi Aebersold
- Faculty of Science, University of Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
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130
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Schink S, Ammar C, Chang Y, Zimmer R, Basan M. Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival. Mol Syst Biol 2022; 18:e11160. [PMID: 36479616 PMCID: PMC9728487 DOI: 10.15252/msb.202211160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteria reorganize their physiology upon entry to stationary phase. What part of this reorganization improves starvation survival is a difficult question because the change in physiology includes a global reorganization of the proteome, envelope, and metabolism of the cell. In this work, we used several trade-offs between fast growth and long survival to statistically score over 2,000 Escherichia coli proteins for their global correlation with death rate. The combined ranking allowed us to narrow down the set of proteins that positively correlate with survival and validate the causal role of a subset of proteins. Remarkably, we found that important survival genes are related to the cell envelope, i.e., periplasm and outer membrane, because the maintenance of envelope integrity of E. coli plays a crucial role during starvation. Our results uncover a new protective feature of the outer membrane that adds to the growing evidence that the outer membrane is not only a barrier that prevents abiotic substances from reaching the cytoplasm but also essential for bacterial proliferation and survival.
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Affiliation(s)
- Severin Schink
- Systems Biology DepartmentHarvard Medical SchoolMABostonUSA
| | - Constantin Ammar
- Systems Biology DepartmentHarvard Medical SchoolMABostonUSA,Institute of InformaticsLudwig‐Maximilians‐Universität MünchenMunichGermany,Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Yu‐Fang Chang
- Systems Biology DepartmentHarvard Medical SchoolMABostonUSA
| | - Ralf Zimmer
- Institute of InformaticsLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Markus Basan
- Systems Biology DepartmentHarvard Medical SchoolMABostonUSA
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131
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Correspondence between gene expression and neurotransmitter receptor and transporter density in the human brain. Neuroimage 2022; 264:119671. [PMID: 36209794 DOI: 10.1016/j.neuroimage.2022.119671] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
Neurotransmitter receptors modulate signaling between neurons. Thus, neurotransmitter receptors and transporters play a key role in shaping brain function. Due to the lack of comprehensive neurotransmitter receptor/transporter density datasets, microarray gene expression measuring mRNA transcripts is often used as a proxy for receptor densities. In the present report, we comprehensively test the spatial correlation between gene expression and protein density for a total of 27 neurotransmitter receptors, receptor binding-sites, and transporters across 9 different neurotransmitter systems, using both PET and autoradiography radioligand-based imaging modalities. We find poor spatial correspondences between gene expression and density for all neurotransmitter receptors and transporters except four single-protein metabotropic receptors (5-HT1A, CB1, D2, and MOR). These expression-density associations are related to gene differential stability and can vary between cortical and subcortical structures. Altogether, we recommend using direct measures of receptor and transporter density when relating neurotransmitter systems to brain structure and function.
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132
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Wang T, Shen P, Chai R, He Y, Liu J. Profiling of bacterial transcriptome from ultra-low input with MiniBac-seq. Environ Microbiol 2022; 24:5774-5787. [PMID: 36053758 DOI: 10.1111/1462-2920.16169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/10/2022] [Indexed: 01/12/2023]
Abstract
There is a lack of appropriate methods for preparing bacterial RNA-seq library with ultra-low amount of RNA. To address this issue, we developed miniBac-seq, a strand-specific method for high-quality library construction from sub-nanogram of total RNA, which is 100-fold lower than the current benchmark kit and dramatically reduces preparation cost ($28 + $15 × samples). We further demonstrated the high sensitivity of miniBac-seq via detecting more than 500 genes from amount of total RNA equivalent to that of a single bacterial cell. Finally, we profiled the transcriptome of growth-arrested bacteria in isogenic culture of Escherichia coli. This subpopulation of bacteria is generally low in abundance but is a potent reservoir of antibiotic persistence, and their gene expression has been largely unknown due to technical limitations. Using miniBac-seq, we identified potential molecular driver towards arrested growth as well as antibiotic tolerance. Our method thus expands the capacity to quantify bacterial transcriptome in situ, which is useful to the understanding of bacterial physiology and regulation in their native contexts.
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Affiliation(s)
- Tianmin Wang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ping Shen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Ruochen Chai
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yihui He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jintao Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
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133
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A proteome-wide map of chaperone-assisted protein refolding in a cytosol-like milieu. Proc Natl Acad Sci U S A 2022; 119:e2210536119. [PMID: 36417429 PMCID: PMC9860312 DOI: 10.1073/pnas.2210536119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain's intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting many proteins safe passage to their native states; however, it is challenging to interrogate the folding process for large numbers of proteins in a complex background with most biophysical techniques. Hence, most chaperone-assisted protein refolding studies are conducted in defined buffers on single purified clients. Here, we develop a limited proteolysis-mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding Escherichia coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. We suggest that these proteins may fold most efficiently cotranslationally, and then remain kinetically trapped in their native conformations.
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134
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Gao R, Brokaw SE, Li Z, Helfant LJ, Wu T, Malik M, Stock AM. Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites. PLoS Comput Biol 2022; 18:e1010738. [PMID: 36413575 PMCID: PMC9725139 DOI: 10.1371/journal.pcbi.1010738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/06/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Abstract
Binding of transcription factor (TF) proteins to regulatory DNA sites is key to accurate control of gene expression in response to environmental stimuli. Theoretical modeling of transcription regulation is often focused on a limited set of genes of interest, while binding of the TF to other genomic sites is seldom considered. The total number of TF binding sites (TFBSs) affects the availability of TF protein molecules and sequestration of a TF by TFBSs can promote bistability. For many signaling systems where a graded response is desirable for continuous control over the input range, biochemical parameters of the regulatory proteins need be tuned to avoid bistability. Here we analyze the mono-/bistable parameter range for positively autoregulated two-component systems (TCSs) in the presence of different numbers of competing TFBSs. TCS signaling, one of the major bacterial signaling strategies, couples signal perception with output responses via protein phosphorylation. For bistability, competition for TF proteins by TFBSs lowers the requirement for high fold change of the autoregulated transcription but demands high phosphorylation activities of TCS proteins. We show that bistability can be avoided with a low phosphorylation capacity of TCSs, a high TF affinity for the autoregulated promoter or a low fold change in signaling protein levels upon induction. These may represent general design rules for TCSs to ensure uniform graded responses. Examining the mono-/bistability parameter range allows qualitative prediction of steady-state responses, which are experimentally validated in the E. coli CusRS system.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Samantha E. Brokaw
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Zeyue Li
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Libby J. Helfant
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Ti Wu
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Muhammad Malik
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Ann M. Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University - Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- * E-mail:
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135
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Rosselli R, López-Pérez M, Martin-Cuadrado AB, Rodriguez-Valera F, Bolhuis H. Differences in gene expression patterns between cultured and natural Haloquadratum walsbyi ecotypes. Front Microbiol 2022; 13:1044446. [DOI: 10.3389/fmicb.2022.1044446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Solar crystallizer ponds are characterized by high population density with a relatively simple community structure in terms of species composition. The microbial community in the solar saltern of Santa Pola (Alicante, Spain), is largely dominated by the hyperhalophilic square archaeon Haloquadratum walsbyi. Here we studied metatranscriptomes retrieved from a crystallizer pond during the winter of 2012 and summer of 2014 and compared Hqr. walsbyi’s transcription patterns with that of the cultured strain Hqr. walsbyi HBSQ001. Significant differences were found between natural and the cultured grown strain in the distribution of transcript levels per gene. This likely reflects the adaptation of the cultured strain to the relative homogeneous growth conditions while the natural species, which is represented by multiple ecotypes, is adapted to heterogeneous environmental conditions and challenges of nutrient competition, viral attack, and other stressors. An important consequence of this study is that expression patterns obtained under artificial cultivation conditions cannot be directly extrapolated to gene expression under natural conditions. Moreover, we found 195 significantly differential expressed genes between the seasons, with 140 genes being higher expressed in winter and mainly encode proteins involved in energy and carbon source acquiring processes, and in stress responses.
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136
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Webby MN, Oluwole AO, Pedebos C, Inns PG, Olerinyova A, Prakaash D, Housden NG, Benn G, Sun D, Hoogenboom BW, Kukura P, Mohammed S, Robinson CV, Khalid S, Kleanthous C. Lipids mediate supramolecular outer membrane protein assembly in bacteria. SCIENCE ADVANCES 2022; 8:eadc9566. [PMID: 36322653 PMCID: PMC9629720 DOI: 10.1126/sciadv.adc9566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
β Barrel outer membrane proteins (OMPs) cluster into supramolecular assemblies that give function to the outer membrane (OM) of Gram-negative bacteria. How such assemblies form is unknown. Here, through photoactivatable cross-linking into the Escherichia coli OM, coupled with simulations, and biochemical and biophysical analysis, we uncover the basis for OMP clustering in vivo. OMPs are typically surrounded by an annular shell of asymmetric lipids that mediate higher-order complexes with neighboring OMPs. OMP assemblies center on the abundant porins OmpF and OmpC, against which low-abundance monomeric β barrels, such as TonB-dependent transporters, are packed. Our study reveals OMP-lipid-OMP complexes to be the basic unit of supramolecular OMP assembly that, by extending across the entire cell surface, couples the requisite multifunctionality of the OM to its stability and impermeability.
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Affiliation(s)
- Melissa N. Webby
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Abraham O. Oluwole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Conrado Pedebos
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick G. Inns
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Nicholas G. Housden
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Georgina Benn
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Dawei Sun
- Structural Biology, Genentech Inc., South San Francisco, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Physics and Astronomy, University College London, WC1E 6BT London, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Mechanistic Proteomics, Rosalind Franklin Institute, Harwell Campus, Didcot OX11 OFA, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Syma Khalid
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
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137
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Csibra E, Stan GB. Absolute protein quantification using fluorescence measurements with FPCountR. Nat Commun 2022; 13:6600. [PMID: 36329019 PMCID: PMC9633595 DOI: 10.1038/s41467-022-34232-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
This paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe an 'ECmax' assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It also reveals that mCherry absorption at 600 nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits.
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Affiliation(s)
- Eszter Csibra
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
| | - Guy-Bart Stan
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
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138
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Rohaun SK, Imlay JA. The vulnerability of radical SAM enzymes to oxidants and soft metals. Redox Biol 2022; 57:102495. [PMID: 36240621 PMCID: PMC9576991 DOI: 10.1016/j.redox.2022.102495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022] Open
Abstract
Radical S-adenosylmethionine enzymes (RSEs) drive diverse biological processes by catalyzing chemically difficult reactions. Each of these enzymes uses a solvent-exposed [4Fe-4S] cluster to coordinate and cleave its SAM co-reactant. This cluster is destroyed during oxic handling, forcing investigators to work with these enzymes under anoxic conditions. Analogous substrate-binding [4Fe-4S] clusters in dehydratases are similarly sensitive to oxygen in vitro; they are also extremely vulnerable to reactive oxygen species (ROS) in vitro and in vivo. These observations suggested that ROS might similarly poison RSEs. This conjecture received apparent support by the observation that when E. coli experiences hydrogen peroxide stress, it induces a cluster-free isozyme of the RSE HemN. In the present study, surprisingly, the purified RSEs viperin and HemN proved quite resistant to peroxide and superoxide in vitro. Furthermore, pathways that require RSEs remained active inside E. coli cells that were acutely stressed by hydrogen peroxide and superoxide. Viperin, but not HemN, was gradually poisoned by molecular oxygen in vitro, forming an apparent [3Fe-4S]+ form that was readily reactivated. The modest rate of damage, and the known ability of cells to repair [3Fe-4S]+ clusters, suggest why these RSEs remain functional inside fully aerated organisms. In contrast, copper(I) damaged HemN and viperin in vitro as readily as it did fumarase, a known target of copper toxicity inside E. coli. Excess intracellular copper also impaired RSE-dependent biosynthetic processes. These data indicate that RSEs may be targets of copper stress but not of reactive oxygen species.
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Affiliation(s)
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA.
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139
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Schultz D, Stevanovic M, Tsimring LS. Optimal transcriptional regulation of dynamic bacterial responses to sudden drug exposures. Biophys J 2022; 121:4137-4152. [PMID: 36168291 PMCID: PMC9675034 DOI: 10.1016/j.bpj.2022.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Cellular responses to the presence of toxic compounds in their environment require prompt expression of the correct levels of the appropriate enzymes, which are typically regulated by transcription factors that control gene expression for the duration of the response. The characteristics of each response dictate the choice of regulatory parameters such as the affinity of the transcription factor to its binding sites and the strength of the promoters it regulates. Although much is known about the dynamics of cellular responses, we still lack a framework to understand how different regulatory strategies evolved in natural systems relate to the selective pressures acting in each particular case. Here, we analyze a dynamical model of a typical antibiotic response in bacteria, where a transcriptionally repressed enzyme is induced by a sudden exposure to the drug that it processes. We identify strategies of gene regulation that optimize this response for different types of selective pressures, which we define as a set of costs associated with the drug, enzyme, and repressor concentrations during the response. We find that regulation happens in a limited region of the regulatory parameter space. While responses to more costly (toxic) drugs favor the usage of strongly self-regulated repressors, responses where expression of enzyme is more costly favor the usage of constitutively expressed repressors. Only a very narrow range of selective pressures favor weakly self-regulated repressors. We use this framework to determine which costs and benefits are most critical for the evolution of a variety of natural cellular responses that satisfy the approximations in our model and to analyze how regulation is optimized in new environments with different demands.
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Affiliation(s)
- Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San Diego, La Jolla, California
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140
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Cai T, Zhao QH, Xiang WL, Zhu L, Rao Y, Tang J. HigBA toxin-antitoxin system of Weissella cibaria is involved in response to the bile salt stress. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6749-6756. [PMID: 35633128 DOI: 10.1002/jsfa.12042] [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: 01/27/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Toxin-antitoxin (TA) systems are prevalent adaptive genetic elements in bacterial genomes, which can respond to environmental stress. While, few studies have addressed TA systems in probiotics and their roles in the adaptation to gastrointestinal transit (GIT) environments. RESULTS The Weissella cibaria 018 could survive in pH 3.0-5.0 and 0.5-3.0 g L-1 bile salt, and its HigBA system responded to the bile salt stress, but not to acid stress. The toxin protein HigB and its cognate antitoxin protein HigA had 85.1% and 100% similarity with those of Lactobacillus plantarum, respectively, and they formed the stable tetramer HigB-(HigA)2 -HigB structure in W. cibaria 018. When exposed to 1.5-3.0 g L-1 bile salt, the transcriptions of higB and higA were up-regulated with 4.39-19.29 and 5.94-30.91 folds, respectively. Meanwhile, W. cibaria 018 gathered into a mass with 48.07% survival rate and its persister cells were found to increase 8.21% under 3.0 g L-1 bile salt. CONCLUSION The HigBA TA system of W. cibaria 018 responded to the bile salt stress, but not to acid stress, which might offer novel perspectives to understand the tolerant mechanism of probiotics to GIT environment. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Ting Cai
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Qiu-Huan Zhao
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Wen-Liang Xiang
- School of Food and Bioengineering, Xihua University, Chengdu, China
- Key Laboratory of Food Biotechnology of Sichuan, Xihua University, Chengdu, China
| | - Lin Zhu
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Yu Rao
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Jie Tang
- School of Food and Bioengineering, Xihua University, Chengdu, China
- Key Laboratory of Food Biotechnology of Sichuan, Xihua University, Chengdu, China
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141
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Cylke KC, Si F, Banerjee S. Effects of antibiotics on bacterial cell morphology and their physiological origins. Biochem Soc Trans 2022; 50:1269-1279. [PMID: 36093840 PMCID: PMC10152891 DOI: 10.1042/bst20210894] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
Abstract
Characterizing the physiological response of bacterial cells to antibiotic treatment is crucial for the design of antibacterial therapies and for understanding the mechanisms of antibiotic resistance. While the effects of antibiotics are commonly characterized by their minimum inhibitory concentrations or the minimum bactericidal concentrations, the effects of antibiotics on cell morphology and physiology are less well characterized. Recent technological advances in single-cell studies of bacterial physiology have revealed how different antibiotic drugs affect the physiological state of the cell, including growth rate, cell size and shape, and macromolecular composition. Here, we review recent quantitative studies on bacterial physiology that characterize the effects of antibiotics on bacterial cell morphology and physiological parameters. In particular, we present quantitative data on how different antibiotic targets modulate cellular shape metrics including surface area, volume, surface-to-volume ratio, and the aspect ratio. Using recently developed quantitative models, we relate cell shape changes to alterations in the physiological state of the cell, characterized by changes in the rates of cell growth, protein synthesis and proteome composition. Our analysis suggests that antibiotics induce distinct morphological changes depending on their cellular targets, which may have important implications for the regulation of cellular fitness under stress.
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Affiliation(s)
- K. Callaghan Cylke
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Fangwei Si
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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142
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Zhang D, Li SHJ, King CG, Wingreen NS, Gitai Z, Li Z. Global and gene-specific translational regulation in Escherichia coli across different conditions. PLoS Comput Biol 2022; 18:e1010641. [PMID: 36264977 PMCID: PMC9624429 DOI: 10.1371/journal.pcbi.1010641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/01/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a gene's cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for the control of translation in synthetic biology. In addition, our data offers a resource for future multi-omics studies.
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Affiliation(s)
- Di Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Sophia Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Christopher G. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (ZG); (ZL)
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail: (NSW); (ZG); (ZL)
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143
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Komarova ES, Slesarchuk AN, Rubtsova MP, Osterman IA, Tupikin AE, Pyshnyi DV, Dontsova OA, Kabilov MR, Sergiev PV. Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5'-UTR of Variable Length. Int J Mol Sci 2022; 23:ijms232012293. [PMID: 36293163 PMCID: PMC9604319 DOI: 10.3390/ijms232012293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. Here, we constructed a library of fluorescent protein-based reporters preceded by a set of 648 natural 5'-untranslated regions (5'-UTRs) of Escherichia coli genes. Usually, Flow-seq libraries are constructed using uniform-length sequence elements, in contrast to natural situations, where functional elements are of heterogenous lengths. Here, we demonstrated that a 5'-UTR library of variable length could be created and analyzed with Flow-seq. In line with previous Flow-seq experiments with randomized 5'-UTRs, we observed the influence of an RNA secondary structure and Shine-Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5'-UTRs in our library was smaller in comparison with randomized libraries. In line with this, we only observed a 30-fold difference in translation efficiency between the best and worst bins sorted with this factor. The results correlated with those obtained with ribosome profiling.
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Affiliation(s)
- Ekaterina S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anna N. Slesarchuk
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maria P. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitry V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Correspondence: (M.R.K.); (P.V.S.)
| | - Petr V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (M.R.K.); (P.V.S.)
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144
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Hör J, Jung J, Ðurica-Mitić S, Barquist L, Vogel J. INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors. Nucleic Acids Res 2022; 50:e128. [PMID: 36229039 PMCID: PMC9825163 DOI: 10.1093/nar/gkac838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 01/29/2023] Open
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with the analysis of translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro Ribo-seq (INRI-seq), a cell-free method to analyze the translational landscape of a fully customizable synthetic transcriptome. Using Escherichia coli as an example, we show how INRI-seq can be used to analyze the translation initiation sites of a transcriptome of interest. We also study the global impact of direct translation inhibition by antisense peptide nucleic acid (PNA) to analyze PNA off-target effects. Overall, INRI-seq presents a scalable, sensitive method to study translation initiation in a transcriptome-wide manner without the potentially confounding effects of extracting ribosomes from living cells.
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Affiliation(s)
- Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- To whom correspondence should be addressed. Tel: +49 931 3182576;
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145
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Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. The landscape of transcriptional and translational changes over 22 years of bacterial adaptation. eLife 2022; 11:e81979. [PMID: 36214449 PMCID: PMC9645810 DOI: 10.7554/elife.81979] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022] Open
Abstract
Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.
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Affiliation(s)
- John S Favate
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Shun Liang
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Alexander L Cope
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Robert Wood Johnson Medical School, Rutgers UniversityNew BrunswickUnited States
| | - Srujana S Yadavalli
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Premal Shah
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New Jersey, Rutgers UniversityPiscatawayUnited States
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146
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Loughran G, Fedorova AD, Khan YA, Atkins JF, Baranov PV. Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding. Mol Cell 2022; 82:3745-3749.e2. [PMID: 36115342 PMCID: PMC9548414 DOI: 10.1016/j.molcel.2022.08.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/03/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
The research article describing the discovery of ribosomal frameshifting in the bacterial CopA gene also reported the occurrence of frameshifting in the expression of the human ortholog ATP7B based on assays using dual luciferase reporters. An examination of the publicly available ribosome profiling data and the phylogenetic analysis of the proposed frameshifting site cast doubt on the validity of this claim and prompted us to reexamine the evidence. We observed similar apparent frameshifting efficiencies as the original authors using the same type of vector that synthesizes both luciferases as a single polyprotein. However, we noticed anomalously low absolute luciferase activities from the N-terminal reporter that suggests interference of reporter activity or levels by the ATP7B test cassette. When we tested the same proposed ATP7B frameshifting cassette in a more recently developed reporter system in which the reporters are released without being included in a polyprotein, no frameshifting was detected above background levels.
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Affiliation(s)
- Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Science Foundation Center for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
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147
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Lyu Z, Yahashiri A, Yang X, McCausland JW, Kaus GM, McQuillen R, Weiss DS, Xiao J. FtsN maintains active septal cell wall synthesis by forming a processive complex with the septum-specific peptidoglycan synthases in E. coli. Nat Commun 2022; 13:5751. [PMID: 36180460 PMCID: PMC9525312 DOI: 10.1038/s41467-022-33404-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/16/2022] [Indexed: 01/06/2023] Open
Abstract
FtsN plays an essential role in promoting the inward synthesis of septal peptidoglycan (sPG) by the FtsWI complex during bacterial cell division. How it achieves this role is unclear. Here we use single-molecule tracking to investigate FtsN's dynamics during sPG synthesis in E. coli. We show that septal FtsN molecules move processively at ~9 nm s-1, the same as FtsWI molecules engaged in sPG synthesis (termed sPG-track), but much slower than the ~30 nm s-1 speed of inactive FtsWI molecules coupled to FtsZ's treadmilling dynamics (termed FtsZ-track). Importantly, processive movement of FtsN is exclusively coupled to sPG synthesis and is required to maintain active sPG synthesis by FtsWI. Our findings indicate that FtsN is part of the FtsWI sPG synthesis complex, and that while FtsN is often described as a "trigger" for the initiation for cell wall constriction, it must remain part of the processive FtsWI complex to maintain sPG synthesis activity.
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Affiliation(s)
- Zhixin Lyu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Atsushi Yahashiri
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Joshua W McCausland
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Gabriela M Kaus
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - David S Weiss
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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148
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Comparative Study of Bacterial SPOR Domains Identifies Functionally Important Differences in Glycan Binding Affinity. J Bacteriol 2022; 204:e0025222. [PMID: 36005810 PMCID: PMC9487507 DOI: 10.1128/jb.00252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial SPOR domains target proteins to the divisome by binding septal peptidoglycan (PG) at sites where cell wall amidases have removed stem peptides. These PG structures are referred to as denuded glycans. Although all characterized SPOR domains bind denuded glycans, whether there are differences in affinity is not known. Here, we use isothermal titration calorimetry (ITC) to determine the relative PG glycan binding affinity (<i>K</i><sub>d</sub>) of four Escherichia coli SPOR domains and one Cytophaga hutchinsonii SPOR domain. We found that the <i>K</i><sub>d</sub> values ranged from approximately 1 μM for E. coli DamX<sup>SPOR</sup> and <i>C. hutchinsonii</i> CHU2221<sup>SPOR</sup> to about 10 μM for E. coli FtsN<sup>SPOR</sup>. To investigate whether these differences in PG binding affinity are important for SPOR domain protein function, we constructed and characterized a set of DamX and FtsN "swap" proteins. As expected, all SPOR domain swap proteins localized to the division site, and, in the case of FtsN, all of the heterologous SPOR domains supported cell division. However, for DamX, only the high-affinity SPOR domain from CHU2221 supported normal function in cell division. In summary, different SPOR domains bind denuded PG glycans with different affinities, which appears to be important for the functions of some SPOR domain proteins (e.g., DamX) but not for the functions of others (e.g., FtsN). <b>IMPORTANCE</b> SPOR domain proteins are prominent components of the cell division apparatus in a wide variety of bacteria. The primary function of SPOR domains is targeting proteins to the division site, which they accomplish by binding to septal peptidoglycan. However, whether SPOR domains have any functions beyond septal targeting is unknown. Here, we show that SPOR domains vary in their PG binding affinities and that, at least in the case of the E. coli cell division protein DamX, having a high-affinity SPOR domain contributes to proper function.
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149
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Abstract
Since Jacques Monod's foundational work in the 1940s, investigators studying bacterial physiology have largely (but not exclusively) focused on the exponential phase of bacterial cultures, which is characterized by rapid growth and high biosynthesis activity in the presence of excess nutrients. However, this is not the predominant state of bacterial life. In nature, most bacteria experience nutrient limitation most of the time. In fact, investigators even prior to Monod had identified other aspects of bacterial growth, including what is now known as the stationary phase, when nutrients become limiting. This review will discuss how bacteria transition to growth arrest in response to nutrient limitation through changes in transcription, translation, and metabolism. We will then examine how these changes facilitate survival during potentially extended periods of nutrient limitation, with particular attention to the metabolic strategies that underpin bacterial longevity in this state.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA;
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150
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Chang S, Thrall ES, Laureti L, Piatt SC, Pagès V, Loparo JJ. Compartmentalization of the replication fork by single-stranded DNA-binding protein regulates translesion synthesis. Nat Struct Mol Biol 2022; 29:932-941. [PMID: 36127468 PMCID: PMC9509481 DOI: 10.1038/s41594-022-00827-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
Processivity clamps tether DNA polymerases to DNA, allowing their access to the primer-template junction. In addition to DNA replication, DNA polymerases also participate in various genome maintenance activities, including translesion synthesis (TLS). However, owing to the error-prone nature of TLS polymerases, their association with clamps must be tightly regulated. Here we show that fork-associated ssDNA-binding protein (SSB) selectively enriches the bacterial TLS polymerase Pol IV at stalled replication forks. This enrichment enables Pol IV to associate with the processivity clamp and is required for TLS on both the leading and lagging strands. In contrast, clamp-interacting proteins (CLIPs) lacking SSB binding are spatially segregated from the replication fork, minimally interfering with Pol IV-mediated TLS. We propose that stalling-dependent structural changes within clusters of fork-associated SSB establish hierarchical access to the processivity clamp. This mechanism prioritizes a subset of CLIPs with SSB-binding activity and facilitates their exchange at the replication fork.
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Affiliation(s)
- Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Fordham University, New York City, NY, USA
| | - Luisa Laureti
- CRCM (Cancer Research Center of Marseille): Team DNA Damage and Genome Instability, Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Sadie C Piatt
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Harvard Graduate Program in Biophysics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Vincent Pagès
- CRCM (Cancer Research Center of Marseille): Team DNA Damage and Genome Instability, Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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