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Nolte RJM, Elemans JAAW. Artificial Processive Catalytic Systems. Chemistry 2024; 30:e202304230. [PMID: 38314967 DOI: 10.1002/chem.202304230] [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: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).
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Affiliation(s)
- Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
| | - Johannes A A W Elemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
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2
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Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, Rotanova TV. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int J Mol Sci 2022; 23:11425. [PMID: 36232729 PMCID: PMC9569914 DOI: 10.3390/ijms231911425] [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: 08/19/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as Bacillus subtilis LonB, combined with the modeled structure of its ATPase domain. Several structural features present in both domains differ from their counterparts in either LonA or LonB subfamilies. We thus postulate that this enzyme is the founding member of a newly identified LonBA subfamily, so far found only in the gene sequences of firmicutes.
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Affiliation(s)
- Alla Gustchina
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna G Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Arsen M Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - George T Lountos
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bartosz Sekula
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Lodz, Poland
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Joseph E Tropea
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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3
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Zhang A, Lebrun R, Espinosa L, Galinier A, Pompeo F. PrkA is an ATP-dependent protease that regulates sporulation in Bacillus subtilis. J Biol Chem 2022; 298:102436. [PMID: 36041628 PMCID: PMC9512850 DOI: 10.1016/j.jbc.2022.102436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
In Bacillus subtilis, sporulation is a sequential and highly regulated process. Phosphorylation events by histidine kinases are key points in the phosphorelay that initiates sporulation, but serine/threonine protein kinases also play important auxiliary roles in this regulation. PrkA has been proposed to be a serine protein kinase expressed during the initiation of sporulation and involved in this differentiation process. Additionally, the role of PrkA in sporulation has been previously proposed to be mediated via the transition phase regulator ScoC, which in turn regulates the transcriptional factor σK and its regulon. However, the kinase activity of PrkA has not been clearly demonstrated, and neither its autophosphorylation nor phosphorylated substrates have been unambiguously established in B. subtilis. We demonstrated here that PrkA regulation of ScoC is likely indirect. Following bioinformatic homology searches, we revealed sequence similarities of PrkA with the ATPases associated with diverse cellular activities ATP-dependent Lon protease family. Here, we showed that PrkA is indeed able to hydrolyze α-casein, an exogenous substrate of Lon proteases, in an ATP-dependent manner. We also showed that this ATP-dependent protease activity is essential for PrkA function in sporulation since mutation in the Walker A motif leads to a sporulation defect. Furthermore, we found that PrkA protease activity is tightly regulated by phosphorylation events involving one of the Ser/Thr protein kinases of B. subtilis, PrkC. Taken together, our results clarify the key role of PrkA in the complex process of B. subtilis sporulation.
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Affiliation(s)
- Ao Zhang
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Régine Lebrun
- Plateforme Protéomique de l'IMM, Marseille Protéomique (MaP), CNRS FR 3479, Aix-Marseille Université, Marseille, France
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France
| | - Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, Marseille, France.
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4
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Wlodawer A, Sekula B, Gustchina A, Rotanova TV. Structure and the mode of activity of Lon proteases from diverse organisms. J Mol Biol 2022; 434:167504. [PMID: 35183556 PMCID: PMC9013511 DOI: 10.1016/j.jmb.2022.167504] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022]
Abstract
Lon proteases, members of the AAA+ superfamily of enzymes, are key components of the protein quality control system in bacterial cells, as well as in the mitochondria and other specialized organelles of higher organisms. These enzymes have been subject of extensive biochemical and structural investigations, resulting in 72 crystal and solution structures, including structures of the individual domains, multi-domain constructs, and full-length proteins. However, interpretation of the latter structures still leaves some questions unanswered. Based on their amino acid sequence and details of their structure, Lon proteases can be divided into at least three subfamilies, designated as LonA, LonB, and LonC. Protomers of all Lons are single-chain polypeptides and contain two functional domains, ATPase and protease. The LonA enzymes additionally include a large N-terminal region, and different Lons may also include non-conserved inserts in the principal domains. These ATP-dependent proteases function as homohexamers, in which unfolded substrates are translocated to a large central chamber where they undergo proteolysis by a processive mechanism. X-ray crystal structures provided high-resolution models which verified that Lons are hydrolases with the rare Ser-Lys catalytic dyad. Full-length LonA enzymes have been investigated by cryo-electron microscopy (cryo-EM), providing description of the functional enzyme at different stages of the catalytic cycle, indicating extensive flexibility of their N-terminal domains, and revealing insights into the substrate translocation mechanism. Structural studies of Lon proteases provide an interesting case for symbiosis of X-ray crystallography and cryo-EM, currently the two principal techniques for determination of macromolecular structures.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bartosz Sekula
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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5
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Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan US, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim FY, Needelman H, Cusick RA, Mychaliska GB, Warner BW, Wagner AJ, Danko ME, Chung D, Potoka D, Kosiński P, McCulley DJ, Elfiky M, Azarow K, Fialkowski E, Schindel D, Soffer SZ, Lyon JB, Zalieckas JM, Vardarajan BN, Aspelund G, Duron VP, High FA, Sun X, Donahoe PK, Shen Y, Chung WK. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. Am J Hum Genet 2021; 108:1964-1980. [PMID: 34547244 PMCID: PMC8546037 DOI: 10.1016/j.ajhg.2021.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Le Xu
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annette Zygmunt
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | | | | | - David J McCulley
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 52726, USA
| | | | - Kenneth Azarow
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | | | | | - Jane B Lyon
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Badri N Vardarajan
- Department of Neurology, Taub Institute for Research on Alzheimer Disease and the Aging Brain and the Gertrude H. Sergievsky Center, Columbia University, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincent P Duron
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego Medical School, San Diego, CA 92093, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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6
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Li S, Hsieh KY, Su SC, Pintilie GD, Zhang K, Chang CI. Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. J Biol Chem 2021; 297:101239. [PMID: 34563541 PMCID: PMC8503904 DOI: 10.1016/j.jbc.2021.101239] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022] Open
Abstract
The Lon AAA+ (adenosine triphosphatases associated with diverse cellular activities) protease (LonA) converts ATP-fuelled conformational changes into sufficient mechanical force to drive translocation of a substrate into a hexameric proteolytic chamber. To understand the structural basis for the substrate translocation process, we determined the cryo-electron microscopy (cryo-EM) structure of Meiothermus taiwanensis LonA (MtaLonA) in a substrate-engaged state at 3.6 Å resolution. Our data indicate that substrate interactions are mediated by the dual pore loops of the ATPase domains, organized in spiral staircase arrangement from four consecutive protomers in different ATP-binding and hydrolysis states. However, a closed AAA+ ring is maintained by two disengaged ADP-bound protomers transiting between the lowest and highest position. This structure reveals a processive rotary translocation mechanism mediated by LonA-specific nucleotide-dependent allosteric coordination among the ATPase domains, which is induced by substrate binding.
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Affiliation(s)
- Shanshan Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Kan-Yen Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shih-Chieh Su
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Grigore D Pintilie
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, California, USA
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan.
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Gibellini L, De Gaetano A, Mandrioli M, Van Tongeren E, Bortolotti CA, Cossarizza A, Pinti M. The biology of Lonp1: More than a mitochondrial protease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 354:1-61. [PMID: 32475470 DOI: 10.1016/bs.ircmb.2020.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Initially discovered as a protease responsible for degradation of misfolded or damaged proteins, the mitochondrial Lon protease (Lonp1) turned out to be a multifaceted enzyme, that displays at least three different functions (proteolysis, chaperone activity, binding of mtDNA) and that finely regulates several cellular processes, within and without mitochondria. Indeed, LONP1 in humans is ubiquitously expressed, and is involved in regulation of response to oxidative stress and, heat shock, in the maintenance of mtDNA, in the regulation of mitophagy. Furthermore, its proteolytic activity can regulate several biochemical pathways occurring totally or partially within mitochondria, such as TCA cycle, oxidative phosphorylation, steroid and heme biosynthesis and glutamine production. Because of these multiple activities, Lon protease is highly conserved throughout evolution, and mutations occurring in its gene determines severe diseases in humans, including a rare syndrome characterized by Cerebral, Ocular, Dental, Auricular and Skeletal anomalies (CODAS). Finally, alterations of LONP1 regulation in humans can favor tumor progression and aggressiveness, further highlighting the crucial role of this enzyme in mitochondrial and cellular homeostasis.
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Affiliation(s)
- Lara Gibellini
- Department of Medical and Surgical Sciences of Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna De Gaetano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elia Van Tongeren
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Andrea Cossarizza
- Department of Medical and Surgical Sciences of Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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8
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Song S, Wood TK. Toxin/Antitoxin System Paradigms: Toxins Bound to Antitoxins Are Not Likely Activated by Preferential Antitoxin Degradation. ACTA ACUST UNITED AC 2020; 4:e1900290. [PMID: 32293143 DOI: 10.1002/adbi.201900290] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Indexed: 12/28/2022]
Abstract
Periodically, a scientific field should examine its early premises. For ubiquitous toxin/antitoxin (TA) systems, several initial paradigms require adjustment based on accumulated data. For example, it is now clear that under physiological conditions, there is little evidence that toxins of TA systems cause cell death and little evidence that TA systems cause persistence. Instead, TA systems are utilized to reduce metabolism during stress, inhibit phages, stabilize genetic elements, and influence biofilm formation (bacterial cells attached via an extracellular matrix). In this essay, it is argued that toxins bound to antitoxins are not likely to become activated by preferential antitoxin degradation but instead, de novo toxin synthesis in the absence of stoichiometric amounts of antitoxin activates toxins.
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Affiliation(s)
- Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
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Boël G, Danot O, de Lorenzo V, Danchin A. Omnipresent Maxwell's demons orchestrate information management in living cells. Microb Biotechnol 2019; 12:210-242. [PMID: 30806035 PMCID: PMC6389857 DOI: 10.1111/1751-7915.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.
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Affiliation(s)
- Grégory Boël
- UMR 8261 CNRS‐University Paris DiderotInstitut de Biologie Physico‐Chimique13 rue Pierre et Marie Curie75005ParisFrance
| | - Olivier Danot
- Institut Pasteur25‐28 rue du Docteur Roux75724Paris Cedex 15France
| | - Victor de Lorenzo
- Molecular Environmental Microbiology LaboratorySystems Biology ProgrammeCentro Nacional de BiotecnologiaC/Darwin n° 3, Campus de Cantoblanco28049MadridEspaña
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
- The School of Biomedical SciencesLi Kashing Faculty of MedicineHong Kong University21, Sassoon RoadPokfulamSAR Hong Kong
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10
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Lin CC, Su SC, Su MY, Liang PH, Feng CC, Wu SH, Chang CI. Structural Insights into the Allosteric Operation of the Lon AAA+ Protease. Structure 2016; 24:667-675. [PMID: 27041592 DOI: 10.1016/j.str.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/21/2016] [Accepted: 03/04/2016] [Indexed: 11/28/2022]
Abstract
The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine.
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Affiliation(s)
- Chien-Chu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
| | - Shih-Chieh Su
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC
| | - Ming-Yuan Su
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Pi-Hui Liang
- School of Pharmacy, National Taiwan University, Taipei, Taiwan 10051, ROC
| | - Chia-Cheng Feng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC.
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11
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Casjens SR, Hendrix RW. Bacteriophage lambda: Early pioneer and still relevant. Virology 2015; 479-480:310-30. [PMID: 25742714 PMCID: PMC4424060 DOI: 10.1016/j.virol.2015.02.010] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/13/2015] [Accepted: 02/05/2015] [Indexed: 12/14/2022]
Abstract
Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112, USA; Biology Department, University of Utah, Salt Lake City, UT 84112, USA.
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Exploiting the proteomics revolution in biotechnology: from disease and antibody targets to optimizing bioprocess development. Curr Opin Biotechnol 2014; 30:80-6. [PMID: 24997444 DOI: 10.1016/j.copbio.2014.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 06/02/2014] [Accepted: 06/08/2014] [Indexed: 11/24/2022]
Abstract
Recent advancements in proteomics have enabled the generation of high-quality data sets useful for applications ranging from target and monoclonal antibody (mAB) discovery to bioprocess optimization. Comparative proteomics approaches have recently been used to identify novel disease targets in oncology and other disease conditions. Proteomics has also been applied as a new avenue for mAb discovery. Finally, CHO and Escherichia coli cells represent the dominant production hosts for biopharmaceutical development, yet the physiology of these cells types has yet to be fully established. Proteomics approaches can provide new insights into these cell types, aiding in recombinant protein production, cell growth regulation, and medium formulation. Optimization of sample preparations and protein database developments are enhancing the quantity and accuracy of proteomic results. In these ways, innovations in proteomics are enriching biotechnology and bioprocessing research across a wide spectrum of applications.
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Ambro Ľ, Pevala V, Ondrovičová G, Bellová J, Kunová N, Kutejová E, Bauer J. Mutations to a glycine loop in the catalytic site of human Lon changes its protease, peptidase and ATPase activities. FEBS J 2014; 281:1784-97. [PMID: 24520911 DOI: 10.1111/febs.12740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 12/05/2013] [Accepted: 01/30/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Lon, also called protease La, is an ATP-dependent protease present in all kingdoms of life. It is involved in protein quality control and several regulatory processes. Eukaryotic Lon possesses three domains, an N-terminal domain, an ATPase domain and a proteolytic domain. It requires ATP hydrolysis to digest larger, intact proteins, but can cleave small, fluorogenic peptides such as Glu-Ala-Ala-Phe-MNA by only binding, but not hydrolyzing, ATP. Both ATPase and peptidase activities can be stimulated by the binding of a larger protein substrate, such as β-casein. To better understand its mechanism of action, we have prepared several point mutants of four conserved residues of human Lon (G893A, G893P, G894A, G894P, G894S, G893A-G894A, G893P-G894A, G893A-G894P, T880V, W770A, W770P) and studied their ATPase, protease and peptidase activities. Our results show that mutations to Gly894 enhance its basal ATPase activity but do not change its β-casein-stimulated activity. The loop containing Gly893 and Gly894, which flanks Lon's proteolytic active site, therefore appears to be involved in the conformational change that occurs upon substrate binding. Furthermore, mutations to Trp770 have the same general effects on the ATPase activity as mutations to Gly893, indicating that Trp770 is involved in ATPase stimulation. We have also established that this loop does not need to move in order to cleave small, fluorogenic peptides, but does move during the digestion of β-casein. Finally, we also noted that Lon's ability to digest small peptides can be inhibited by moderate ATP concentrations. DATABASE Lon (Endopeptidase La), EC 4.4.21.53 STRUCTURED DIGITAL ABSTRACT: • hLonP cleaves beta casein by protease assay (1, 2, 3, 4, 5, 6) • hLon and hLon bind by cross-linking study (View interaction).
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Affiliation(s)
- Ľuboš Ambro
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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